Merge branch 'master' into develop

CMakeLists.txt

@@ -6,7 +6,7 @@ cmake_minimum_required(VERSION 2.6.4 FATAL_ERROR)
 project(OpenStructure CXX C)
 set (OST_VERSION_MAJOR 1)
 set (OST_VERSION_MINOR 2)
-set (OST_VERSION_PATCH 1)
+set (OST_VERSION_PATCH 2)
 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)

build_configs/buildconfig_arch_clang

+set(PYTHON_BINARY "/usr/bin/python2"  CACHE PATH "")
+set(CMAKE_C_COMPILER "/usr/bin/clang" CACHE PATH "")
+set(CMAKE_CXX_COMPILER "/usr/bin/clang++" CACHE PATH "")
+set(CMAKE_AR "/usr/bin/llvm-ar" CACHE PATH "")
+set(CMAKE_LINKER "/usr/bin/llvm-ld" CACHE PATH "")
+set(CMAKE_NM "/usr/bin/llvm-inm" CACHE PATH "")
+set(CMAKE_OBJDUMP "/usr/bin/llvm-objdump" CACHE PATH "")
+set(CMAKE_RANLIB "/usr/bin/llvm-ranlib" CACHE PATH "")
+set(CMAKE_CXX_FLAGS_RELEASE "-Wno-array-bounds -pthread -O3 -DNDEBUG -Wno-parentheses -Wno-constant-logical-operand -fcolor-diagnostics" CACHE STRING "")
+set(CMAKE_CXX_FLAGS_DEBUG "-Wno-array-bounds -g -pthread -Wno-parentheses -Wno-constant-logical-operand -fcolor-diagnostics" CACHE STRING "")

deployment/linux/ldd-rec.pl

@@ -16,7 +16,7 @@ push @check_queue, @ARGV;
 
 while (@check_queue) {
   my $to_check = pop @check_queue;
-  if (exists $checked_libs{$to_check}) {
+  if (exists $checked_libs{$to_check} or $to_check =~ /ld-linux.so.2/) {
     next;
   } else {
     $checked_libs{$to_check} = 1;

modules/io/doc/mmcif.rst

@@ -782,6 +782,7 @@ of the annotation available.
   .. attribute:: align_id
     
     Uniquely identifies every struct_ref_seq item in the mmCIF file.
+
     :type: :class:`str`
 
   .. attribute:: seq_begin

modules/mol/alg/src/lddt.cc

@@ -111,8 +111,8 @@ int main (int argc, char **argv)
 {
   // sets some default values for parameters
   String version = "1.2";
-  Real bond_tolerance = 15.0;
-  Real angle_tolerance = 15.0;
+  Real bond_tolerance = 12.0;
+  Real angle_tolerance = 12.0;
   Real radius=15.0; 
   int sequence_separation = 0;