Merge branch 'master' into develop

CHANGELOG.txt

-Changes in Release 1.x.x
+Changes in Release 1.10.0
 --------------------------------------------------------------------------------
 
  * Use system provided SQLite3 library.
@@ -9,6 +9,7 @@ Changes in Release 1.x.x
    for further details.
  * Improved support for recent compilers and libraries.
  * Removed support for USE_MESA.
+ * Bugfix of string representation of ResNum which now includes insertion code.
  * Several minor bug fixes and improvements.
 
 Changes in Release 1.9.0

CMakeLists.txt

@@ -6,22 +6,12 @@ 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 9)
+set (OST_VERSION_MINOR 10)
 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)
 include(OST)
 
-
-if (CMAKE_COMPILER_IS_GNUCXX)  
-  exec_program(gcc ARGS --version OUTPUT_VARIABLE CMAKE_C_COMPILER_VERSION)
-  if(CMAKE_C_COMPILER_VERSION MATCHES ".*4\\.[5-9].*")
-    set(OST_GCC_45 true)
-  else()   
-    set(OST_GCC_45 false)  
-  endif()
-endif()
-
 option(USE_SHADER "whether to compile with shader support"
        OFF)
 option(USE_RPATH "embed rpath upon make install"

actions/ost-compare-structures

@@ -31,7 +31,7 @@ Only model structures are "Molck-ed" in CAMEO. The call to molck is as follows:
 
   molck \\
       --complib=<COMPOUND LIB> \\
-      --rm=hyd,oxt,unk \\
+      --rm=hyd,oxt,unk,nonstd \\
       --fix-ele \\
       --map-nonstd \\
       --out=<OUTPUT> \\
@@ -45,7 +45,7 @@ compare-structures as follows:
       --reference <REF> \\
       --output output.json \\
       --molck \\
-      --remove oxt hyd unk \\
+      --remove oxt hyd unk nonstd \\
       --clean-element-column \\
       --map-nonstandard-residues \\
       --structural-checks \\
@@ -243,7 +243,7 @@ def _ParseArgs():
               " * hyd - remove hydrogen atoms\n"
               " * oxt - remove terminal oxygens\n"
               " * nonstd - remove all residues not one of the 20\n"
-              " * standard amino acids\n"
+              "            standard amino acids\n"
               " * unk - Remove unknown and atoms not following the\n"
               "         nomenclature\n"
               "Defaults to hyd."))

cmake_support/OST.cmake

@@ -321,15 +321,15 @@ macro(executable)
   if (ENABLE_STATIC AND _ARG_STATIC)
     target_link_libraries(${_ARG_NAME} ${STATIC_LIBRARIES})
     if (UNIX AND NOT APPLE)
-      if (OST_GCC_45)    
-        set_target_properties(${_ARG_NAME}
-                              PROPERTIES LINK_SEARCH_END_STATIC TRUE  
-                              LINK_FLAGS "-static-libgcc -static-libstdc++ -static -pthread")
+      set_target_properties(${_ARG_NAME} PROPERTIES LINK_SEARCH_START_STATIC TRUE)
+      set_target_properties(${_ARG_NAME} PROPERTIES LINK_SEARCH_END_STATIC TRUE)
+      if (OST_GCC_LESS_45)
+        set_target_properties(${_ARG_NAME} PROPERTIES LINK_FLAGS
+                              "-static-libgcc -static -pthread")
       else()
-        set_target_properties(${_ARG_NAME}
-                              PROPERTIES LINK_SEARCH_END_STATIC TRUE  
-                              LINK_FLAGS "-static-libgcc -static -pthread")
-      endif()        
+        set_target_properties(${_ARG_NAME} PROPERTIES LINK_FLAGS
+                              "-static-libgcc -static-libstdc++ -static -pthread")
+      endif()
     endif()
   endif()
   install(TARGETS ${_ARG_NAME} DESTINATION bin)
@@ -859,7 +859,7 @@ endmacro()
 #-------------------------------------------------------------------------------
 function(get_compiler_version _OUTPUT_VERSION)
   exec_program(${CMAKE_CXX_COMPILER}
-               ARGS ${CMAKE_CXX_COMPILER_ARG1} -dumpversion
+               ARGS ${CMAKE_CXX_COMPILER_ARG1} -dumpfullversion -dumpversion
                OUTPUT_VARIABLE _COMPILER_VERSION
   )
   string(REGEX REPLACE "([0-9])\\.([0-9])(\\.[0-9])?" "\\1\\2"
@@ -899,9 +899,13 @@ macro(setup_compiler_flags)
     #message(STATUS "GCC VERSION " ${_GCC_VERSION})
     if ((ENABLE_INFO OR ENABLE_GUI) AND _GCC_VERSION LESS "60")
       # for older compilers we need to enable C++11 for Qt5
-      #message(STATUS "ADDING C++11 FLAG")
       set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
     endif()
+    if (_GCC_VERSION LESS "45")
+      set(OST_GCC_LESS_45 true)
+    else()
+      set(OST_GCC_LESS_45 false)
+    endif()
   endif()
 endmacro()
 set(_BOOST_MIN_VERSION 1.31)

modules/db/src/CMakeLists.txt

@@ -23,4 +23,6 @@ if(WIN32)
 else(WIN32)
   add_definitions(-DSQLITE_OMIT_LOAD_EXTENSION)
 endif(WIN32)
-
+if (ENABLE_STATIC AND UNIX AND NOT APPLE)
+  target_link_libraries(ost_db ${CMAKE_DL_LIBS})
+endif()

modules/doc/install.rst

@@ -234,7 +234,9 @@ Build Options
 
 * `ENABLE_STATIC` allows some parts of OpenStructure to be statically linked 
   and thus can be used more easily across a heterogeneous setup, e.g. older 
-  systems and newer systems. By default, this is switched off.
+  systems and newer systems. Note that enabling this flag will not compile the
+  full OpenStructure package and it is not guaranteed to lead to fully portable
+  binaries. By default, this is switched off.
 
 * For deployment of OpenStructure with `make install` there are two relevant
   settings to consider:

modules/index.rst

@@ -37,7 +37,7 @@ OpenStructure documentation
 For Starters
 --------------------------------------------------------------------------------
 
-**Installation**: `install from binary <http://www.openstructure.org/download/>`_ | :doc:`install from source <install>`
+**Installation**: :doc:`install from source <install>`
 
 **Tutorial Style**: :doc:`introduction <intro>` | :doc:`molecules intro <intro-01>` | :doc:`images intro <intro-02>` | :doc:`graphics intro <intro-03>` 
 

modules/mol/alg/doc/molck.rst

+..  Note on large code blocks: keep max. width to 100 or it will look bad
+                               on webpage!
+
 =========================
 Molecular Checker (Molck)
 =========================
@@ -37,23 +40,23 @@ please find them following:
 .. code-block:: bash 
 
     usage: molck [options] file1.pdb [file2.pdb [...]]
-    options 
-      --complib=path       location of the compound library file. If not provided, the 
-                           following locations are searched in this order: 
-                               1. Working directory,
-                               2. OpenStructure standard library location (if the 
-                                  executable is part of a standard OpenStructure installation) 
+    options
+      --complib=path       location of the compound library file. If not provided, the
+                           following locations are searched in this order:
+                           1. Working directory,
+                           2. OpenStructure standard library location (if the
+                              executable is part of a standard OpenStructure installation)
       --rm=<a>,<b>         remove atoms and residues matching some criteria:
-                                - zeroocc - Remove atoms with zero occupancy 
-                                - hyd - Remove hydrogen atoms 
-                                - oxt - Remove terminal oxygens 
-                                - nonstd - Remove all residues not one of the 20 standard amino acids 
-                                - unk - Remove unknown and atoms not following the nomenclature
+                           - zeroocc - Remove atoms with zero occupancy
+                           - hyd - Remove hydrogen atoms
+                           - oxt - Remove terminal oxygens
+                           - nonstd - Remove all residues not one of the 20 standard amino acids
+                           - unk - Remove unknown and atoms not following the nomenclature
       --fix-ele            clean up element column
-      --stdout             write cleaned file(s) to stdout 
-      --out=filename       write cleaned file(s) to disk. % characters in the filename are 
-                           replaced with the basename of the input file without extension. 
-                           Default: %-molcked.pdb 
+      --stdout             write cleaned file(s) to stdout
+      --out=filename       write cleaned file(s) to disk. % characters in the filename are
+                           replaced with the basename of the input file without extension.
+                           Default: %-molcked.pdb
       --color=auto|on|off  whether output should be colored
       --map-nonstd         maps modified residues back to the parent amino acid, for example
                            MSE -> MET, SEP -> SER.

singularity/Singularity

@@ -214,7 +214,7 @@ cd /home
 # ENVIRONMENT
 ##############################################################################
 export OST_ROOT="/usr/local"
-export OPENSTRUCTURE_VERSION="1.9.0"
+export OPENSTRUCTURE_VERSION="1.10.0"
 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}"