Merge branch 'develop' into mmcifparser

.gitignore

@@ -12,6 +12,7 @@ CTestTestfile.cmake
 .*
 !.gitignore
 CMakeCache.txt
+version.hh
 config.hh
 *.pyc
 index.txt

CMakeLists.txt

@@ -4,13 +4,17 @@
 
 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 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)
 
 
 option(USE_SHADER "whether to compile with shader support"
        OFF)
-option(SET_RPATH "embed rpath upon make install"
+option(USE_RPATH "embed rpath upon make install"
        OFF)
 option(COMPILE_TMTOOLS "whether to compile the tmalign and tmscore programs"
        OFF)
@@ -30,8 +34,10 @@ option(ENABLE_SPNAV "whether 3DConnexion devices should be supported"
       OFF)
 option(STATIC_PROPERTY_WORKAROUND "workaround for static property bug with some boost/boost_python combinations" OFF)
 option(DEPLOYMENT "switch on deployment settings" OFF)
-option(COMPILE_TESTS "wheter unit tests should be compiled by default" OFF)
+option(COMPILE_TESTS "whether unit tests should be compiled by default" OFF)
 option(ENABLE_STATIC "whether static libraries should be compiled" OFF)
+option(DEBIAN_STYLE_LIBEXEC "whether 'libexec' should be put under 'lib/openstructure" OFF)
+
 if (CXX)
   set(CMAKE_CXX_COMPILER ${CXX})
 endif()
@@ -110,6 +116,12 @@ else()
   set(_PROFILE OFF)
 endif()
 
+if (DEBIAN_STYLE_LIBEXEC)
+  set(_DEBIAN_STYLE_LIBEXEC ON)
+else()
+  set(_DEBIAN_STYLE_LIBEXEC OFF)
+endif()
+
 add_definitions(-DEIGEN2_SUPPORT)
 
 if (COMPOUND_LIB)
@@ -218,16 +230,17 @@ set_directory_properties(PROPERTIES ADDITIONAL_MAKE_CLEAN_FILES
 
 message(STATUS 
         "OpenStructure will be built with the following options:\n"
-        "   Install Prefix                 (-DPREFIX) : ${CMAKE_INSTALL_PREFIX}\n"
-        "   RPath in install            (-DUSE_RPATH) : ${_USE_RPATH}\n"
-        "   Graphical interface        (-DENABLE_GUI) : ${_UI}\n"
-        "   OpenGL support             (-DENABLE_GFX) : ${_OPENGL}\n"
-        "   Image Processing support   (-DENABLE_IMG) : ${_IMG}\n"
-        "   Shader support             (-DUSE_SHADER) : ${_SHADER}\n"
-        "   Numpy support               (-DUSE_NUMPY) : ${_NUMPY}\n"
-        "   Optimize                     (-DOPTIMIZE) : ${_OPT}\n"
-        "   Profiling support             (-DPROFILE) : ${_PROFILE}\n"
-        "   Double Precision (-DUSE_DOUBLE_PRECISION) : ${_DOUBLE_PREC}\n"
-        "   Compound Lib             (-DCOMPOUND_LIB) : ${_COMP_LIB}\n"
-        "   TMAlign and TMScore   (-DCOMPILE_TMTOOLS) : ${_TM_TOOLS}\n"
-        "   Static Libraries        (-DENABLE_STATIC) : ${ENABLE_STATIC}")
+        "   Install Prefix                       (-DPREFIX) : ${CMAKE_INSTALL_PREFIX}\n"
+        "   RPath in install                  (-DUSE_RPATH) : ${_USE_RPATH}\n"
+        "   Graphical interface              (-DENABLE_GUI) : ${_UI}\n"
+        "   OpenGL support                   (-DENABLE_GFX) : ${_OPENGL}\n"
+        "   Image Processing support         (-DENABLE_IMG) : ${_IMG}\n"
+        "   Shader support                   (-DUSE_SHADER) : ${_SHADER}\n"
+        "   Numpy support                     (-DUSE_NUMPY) : ${_NUMPY}\n"
+        "   Optimize                           (-DOPTIMIZE) : ${_OPT}\n"
+        "   Profiling support                   (-DPROFILE) : ${_PROFILE}\n"
+        "   Double Precision       (-DUSE_DOUBLE_PRECISION) : ${_DOUBLE_PREC}\n"
+        "   Compound Lib                   (-DCOMPOUND_LIB) : ${_COMP_LIB}\n"
+        "   TMAlign and TMScore         (-DCOMPILE_TMTOOLS) : ${_TM_TOOLS}\n"
+        "   Static Libraries              (-DENABLE_STATIC) : ${ENABLE_STATIC}\n"
+        "   Debian-style 'libexec' (-DDEBIAN_STYLE_LIBEXEC) : ${_DEBIAN_STYLE_LIBEXEC}")
\ No newline at end of file

cmake_support/OST.cmake

@@ -187,6 +187,9 @@ macro(module)
     get_target_property(_DEFS ${_LIB_NAME} COMPILE_DEFINITIONS)
     set_target_properties(${_LIB_NAME} PROPERTIES
                           COMPILE_DEFINITIONS OST_MODULE_${_UPPER_LIB_NAME})
+    set_target_properties(${_LIB_NAME} PROPERTIES
+                          VERSION ${OST_VERSION_STRING}
+                          SOVERSION ${OST_VERSION_MAJOR}.${OST_VERSION_MINOR})    
     set_target_properties(${_LIB_NAME} PROPERTIES
                           LIBRARY_OUTPUT_DIRECTORY ${LIB_STAGE_PATH}
                           ARCHIVE_OUTPUT_DIRECTORY ${LIB_STAGE_PATH}
@@ -310,6 +313,40 @@ macro(executable)
 endmacro()
 
 
+#-------------------------------------------------------------------------------
+# Synopsis
+#   executable_libexec(NAME exe_name SOURCES source1 source2 LINK link1 link2)
+#
+# Description:
+#  Compile, link and stage a C++ executable into the libexec directory
+#-------------------------------------------------------------------------------
+macro(executable_libexec)
+  parse_argument_list(_ARG 
+                      "NAME;SOURCES;LINK;DEPENDS_ON" "NO_RPATH;STATIC" ${ARGN})
+  if (NOT _ARG_NAME)
+    message(FATAL_ERROR "invalid use of executable(): a name must be provided")
+  endif()   
+  add_executable(${_ARG_NAME} ${_ARG_SOURCES})
+  set_target_properties(${_ARG_NAME}
+                        PROPERTIES RUNTIME_OUTPUT_DIRECTORY
+                       "${LIBEXEC_STAGE_PATH}")  
+  if (APPLE AND NOT _ARG_NO_RPATH AND NOT _ARG_STATIC)
+    set_target_properties(${_ARG_NAME} PROPERTIES
+                          LINK_FLAGS "-Wl,-rpath,@loader_path/../lib")
+  endif()
+  if (_ARG_LINK)
+    target_link_libraries(${_ARG_NAME} ${_ARG_LINK})
+  endif()
+  if (ENABLE_STATIC AND _ARG_STATIC)
+    set(TARGET_SUFFIX _static)
+    target_link_libraries(${_ARG_NAME} ${STATIC_LIBRARIES})
+  endif()
+  foreach(_DEP ${_ARG_DEPENDS_ON})
+    target_link_libraries(${_ARG_NAME} ${_DEP}${TARGET_SUFFIX})
+  endforeach()
+  install(TARGETS ${_ARG_NAME} DESTINATION ${LIBEXEC_PATH})
+endmacro()
+
 #-------------------------------------------------------------------------------
 # Synopsis:
 #   substitute(IN_FILE in_file OUT_FILE out_file DICT a=b c=d)
@@ -583,7 +620,7 @@ macro(ost_unittest)
       endif()
       if (WIN32)
         target_link_libraries(${_test_name} ${BOOST_UNIT_TEST_LIBRARIES} "${_ARG_PREFIX}_${_ARG_MODULE}")  
-        add_custom_target("${_test_name}_run"
+        add_custom_target("${_test_name}_run":
                         COMMAND ${CMAKE_CURRENT_BINARY_DIR}/${CMAKE_BUILD_TYPE}/${_test_name}.exe || echo
                         WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/${CMAKE_BUILD_TYPE}/..
                         COMMENT "running checks for module ${_ARG_MODULE}"
@@ -722,7 +759,6 @@ macro(setup_stage)
   set(STAGE_DIR "${CMAKE_BINARY_DIR}/stage")
   set(EXECUTABLE_OUTPUT_PATH ${STAGE_DIR}/bin  )
   set(HEADER_STAGE_PATH ${STAGE_DIR}/include )
-  set(LIBEXEC_STAGE_PATH ${STAGE_DIR}/libexec/openstructure  )
   set(SHARED_DATA_PATH ${STAGE_DIR}/share/openstructure  )
 
   if (UNIX AND NOT APPLE)
@@ -736,6 +772,16 @@ macro(setup_stage)
     set(LIB_DIR lib  )
     set(LIB_STAGE_PATH "${STAGE_DIR}/lib"  )
   endif()
+  if (_DEBIAN_STYLE_LIBEXEC)
+    set(LIBEXEC_PATH ${LIB_DIR}/openstructure/libexec  )
+  else()
+    set(LIBEXEC_PATH libexec/openstructure  )
+  endif()
+  if (_DEBIAN_STYLE_LIBEXEC)
+    set(LIBEXEC_STAGE_PATH ${LIB_STAGE_PATH}/openstructure/libexec  )
+  else()
+    set(LIBEXEC_STAGE_PATH ${STAGE_DIR}/libexec/openstructure  )
+  endif()
 
   include_directories("${HEADER_STAGE_PATH}")
   link_directories(${LIB_STAGE_PATH})

deployment/linux/README.txt

@@ -4,13 +4,3 @@ HOW TO USE THE BUNDLE SCRIPTS:
 2. Move to the <OpenStructure folder>/deployment/linux folder and start the create_bundle.py script using python
 3. In <OpenStructure> you'll find a tar.gz file. That's the bundle!
 4. If the process stops without completing, run the reset_repository.py script or delete the <OpenStructure Folder> and restart from scratch
-
-
-HOW TO USE THE QMEAN BUNDLE SCRIPTS:
-
-1. Checkout a copy of the OpenStructure repository.
-2. Check out a copy of the scratch repository in modules/scratch
-3. Create a folder called ChemLib in the <OpenStructure Folder> and copy the compunds.chemlib file into it.
-4. Move to the <OpenStructure folder>/deployment/linux folder and start the create_qmeqn_bundle.py script using python
-3. In <OpenStructure> you'll find a tar.gz file. That's the bundle!
-4. If the process stops without completing, run the reset_qmean_repository.py script or delete the <OpenStructure Folder> and restart from scratch
\ No newline at end of file

deployment/linux/create_bundle.py

@@ -12,7 +12,7 @@ if len(sys.argv) < 3:
   print 'usage: create_bundle.py  additional_label system_python_version'
   sys.exit()
 
-system_python_version=sys.argv[2]
+system_python_version='python'+sys.argv[2]
 system_python_bin='/usr/bin/'+system_python_version
 system_python_libs='/usr/lib/'+system_python_version
 second_system_python_libs_flag=True
@@ -43,28 +43,21 @@ date_pattern='%Y-%b-%d'
 build=datetime.date.today()
 directory_name='openstructure-linux-'+archstring+'-'+additional_label+'-'+str(build)
 print 'Hardcoding package python binary path in openstructure executables'
-subprocess.call('mv scripts/ost.in scripts/ost.in.backup',shell=True,cwd='../../')
-subprocess.call('sed "s/@PYTHON_BINARY@/\$DNG_ROOT\/bin\/'+python_bin_in_bundle+'/g" scripts/ost.in.backup > scripts/ost.in.prepreprepre',shell=True,cwd='../../')
-subprocess.call('sed "s/\#export LD_LIBRARY_PATH/ export LD_LIBRARY_PATH/g" scripts/ost.in.prepreprepre > scripts/ost.in.preprepre',shell=True,cwd='../../')
-subprocess.call('sed "s/\#export PYTHONHOME/ export PYTHONHOME/g" scripts/ost.in.preprepre > scripts/ost.in.prepre',shell=True,cwd='../../')
-subprocess.call('sed "s/\#export PYTHONPATH/ export PYTHONPATH/g" scripts/ost.in.prepre > scripts/ost.in.pre',shell=True,cwd='../../')
-subprocess.call('sed "s/\#export QT_PLUGIN_PATH/ export QT_PLUGIN_PATH/g" scripts/ost.in.pre > scripts/ost.in',shell=True,cwd='../../')
-subprocess.call('mv scripts/dng.in scripts/dng.in.backup',shell=True,cwd='../../')
-subprocess.call('sed "s/\#export LD_LIBRARY_PATH/ export LD_LIBRARY_PATH/g" scripts/dng.in.backup > scripts/dng.in.preprepre',shell=True,cwd='../../')
-subprocess.call('sed "s/\#export PYTHONHOME/ export PYTHONHOME/g" scripts/dng.in.preprepre > scripts/dng.in.prepre',shell=True,cwd='../../')
-subprocess.call('sed "s/\#export PYTHONPATH/ export PYTHONPATH/g" scripts/dng.in.prepre > scripts/dng.in.pre',shell=True,cwd='../../')
-subprocess.call('sed "s/\#export QT_PLUGIN_PATH/ export QT_PLUGIN_PATH/g" scripts/dng.in.pre > scripts/dng.in',shell=True,cwd='../../')
+subprocess.call('mv scripts/ost_config.in scripts/ost_config.in.backup',shell=True,cwd='../../')
+subprocess.call('sed "s/@PYTHON_BINARY@/\$DNG_ROOT\/bin\/'+python_bin_in_bundle+'/g" scripts/ost_config.in.backup > scripts/ost_config.in.preprepre',shell=True,cwd='../../')
+subprocess.call('sed "s/\#export PYTHONHOME/ export PYTHONHOME/g" scripts/ost_config.in.preprepre > scripts/ost_config.in.prepre',shell=True,cwd='../../')
+subprocess.call('sed "s/\#export PYTHONPATH/ export PYTHONPATH/g" scripts/ost_config.in.prepre > scripts/ost_config.in.pre',shell=True,cwd='../../')
+subprocess.call('sed "s/\#export QT_PLUGIN_PATH/ export QT_PLUGIN_PATH/g" scripts/ost_config.in.pre > scripts/ost_config.in',shell=True,cwd='../../')
 #print 'Downloading Chemlib dictionary'
 #subprocess.call('wget ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif', shell=True, cwd='../../')
 #print 'Compiling Openstructure'
 #subprocess.call('cmake ./ -DCMAKE_BUILD_TYPE=Release -DPREFIX='+directory_name+' -DBoost_COMPILER='+boost_string+'-DENABLE_IMG=OFF -DENABLE_UI=OFF -DENABLE_GFX=OFF', shell=True,cwd='../../')
 #subprocess.call('cmake ./ -DCMAKE_BUILD_TYPE=Release -DPREFIX='+directory_name+' s-DENABLE_IMG=OFF -DENABLE_UI=OFF -DENABLE_GFX=OFF', shell=True,cwd='../../')
 #subprocess.call('make -j5',shell=True,cwd='../../')
-#print 'Converting Chemlib dictionary'
-#subprocess.call('stage/bin/chemdict_tool create components.cif compounds.chemlib', shell=True, cwd='../../')
-#print '\nStaging Chemlib dictionary'
+##print 'Converting Chemlib dictionary'
+##subprocess.call('stage/bin/chemdict_tool create components.cif compounds.chemlib', shell=True, cwd='../../')
+print '\nStaging Chemlib dictionary'
 print 'Compiling Openstructure'
-#subprocess.call('cmake ./ -DCMAKE_BUILD_TYPE=Release -DPREFIX='+directory_name+' -DBoost_COMPILER='+boost_string+' -DCOMPOUND_LIB=ChemLib/compounds.chemlib -DENABLE_IMG=ON -DENABLE_UI=ON -DENABLE_GFX=ON -DOPTIMIZE=ON',shell=True,cwd='../../')
 subprocess.call('cmake ./ -DCMAKE_BUILD_TYPE=Release -DPREFIX='+directory_name+' -DCOMPOUND_LIB=ChemLib/compounds.chemlib -DENABLE_IMG=ON -DENABLE_UI=ON -DENABLE_GFX=ON -DOPTIMIZE=ON',shell=True,cwd='../../')
 subprocess.call('make -j2',shell=True,cwd='../../')
 print 'Removing obsolete packages and package directory'
@@ -73,13 +66,14 @@ print 'Creating new package directory'
 subprocess.call('mkdir '+directory_name,shell=True,cwd='../../')
 subprocess.call('mkdir '+directory_name+'/bin',shell=True,cwd='../../')
 print 'Copy python executable into stage for dependency detection'
+print system_python_bin
 subprocess.call('cp '+system_python_bin+ ' stage/bin/python',shell=True,cwd='../../')
 print 'Copy python libraries into the stage for dependency detection'
-subprocess.call('cp -pRL '+system_python_libs+' stage/'+libdir,shell=True,cwd='../../')
-subprocess.call('rm -fr stage/'+libdir+'/'+system_python_version+'/dist-packages',shell=True,cwd='../../')
+subprocess.call('cp -pRL '+system_python_libs+' stage/'+libdir+'/python',shell=True,cwd='../../')
+subprocess.call('rm -fr stage/'+libdir+'/python/dist-packages',shell=True,cwd='../../')
 if second_system_python_libs_flag==True:
-  subprocess.call('cp -pRL '+second_system_python_libs+'/sip* stage/'+libdir+'/'+system_python_version,shell=True,cwd='../../')
-  subprocess.call('cp -pRL '+second_system_python_libs+'/PyQt* stage/'+libdir+'/'+system_python_version,shell=True,cwd='../../')
+  subprocess.call('cp -pRL '+second_system_python_libs+'/sip* stage/'+libdir+'/python/',shell=True,cwd='../../')
+  subprocess.call('cp -pRL '+second_system_python_libs+'/PyQt* stage/'+libdir+'/python/',shell=True,cwd='../../')
 print 'Creating new dependency list'
 so_list=[]
 walk_list=os.walk('../../stage')
@@ -104,22 +98,21 @@ for entry in sorted_dep_list:
        exclude=True
    if exclude==False: 
      filtered_dep_list.append(entry)
+print 'Installing OpenStructure into package directory structure'
+subprocess.call('make install',shell=True,cwd='../../')
 print 'Copy libraries in the package directory structure'
-subprocess.call('mkdir '+directory_name+'/'+libdir,shell=True,cwd='../../')
 for entry in filtered_dep_list:
   subprocess.call('cp '+entry+' '+directory_name+'/'+libdir,shell=True,cwd='../../')
 print 'Copy python executable into package directory structure'
 subprocess.call('cp '+system_python_bin+ ' '+directory_name+'/bin/python',shell=True,cwd='../../')
 print 'Copy python libraries into package directory structure'
-subprocess.call('cp -pRL '+system_python_libs+' '+directory_name+'/'+libdir,shell=True,cwd='../../')
-subprocess.call('rm -fr '+directory_name+'/'+libdir+'/'+system_python_version+'/dist-packages',shell=True,cwd='../../')
+subprocess.call('cp -pRL '+system_python_libs+' '+directory_name+'/'+libdir+'/python',shell=True,cwd='../../')
+subprocess.call('rm -fr '+directory_name+'/'+libdir+'/python/dist-packages',shell=True,cwd='../../')
 if second_system_python_libs_flag==True:
-  subprocess.call('cp -pRL '+second_system_python_libs+'/sip* '+directory_name+'/'+libdir+'/'+system_python_version,shell=True,cwd='../../')
-  subprocess.call('cp -pRL '+second_system_python_libs+'/PyQt* '+directory_name+'/'+libdir+'/'+system_python_version,shell=True,cwd='../../')
+  subprocess.call('cp -pRL '+second_system_python_libs+'/sip* '+directory_name+'/'+libdir+'/python/',shell=True,cwd='../../')
+  subprocess.call('cp -pRL '+second_system_python_libs+'/PyQt* '+directory_name+'/'+libdir+'/python/',shell=True,cwd='../../')
 print 'Copy Qt 4 plugins into package directory structure'
 subprocess.call('cp -pRL '+qt4_plugins+' '+directory_name+'/bin/',shell=True,cwd='../../')
-print 'Installing OpenStructure into package directory structure'
-subprocess.call('make install',shell=True,cwd='../../')
 print 'Copying supplementary material into package directory structure'
 subprocess.call('cp -pRL  stage/share/openstructure  '+directory_name+'/share/',shell=True,cwd='../../')
 print 'Copying examples into package directory structure'
@@ -140,11 +133,8 @@ print 'removing dokk and harmony examples from bundle'
 subprocess.call('rm -rf '+directory_name+'/share/openstructure/examples/code_fragments/dokk',shell=True,cwd='../../')
 subprocess.call('rm -rf '+directory_name+'/share/openstructure/examples/code_fragments/harmony',shell=True,cwd='../../')
 print 'De-hardcoding package python binary path from openstructure executables'
-subprocess.call('rm scripts/ost.in',shell=True,cwd='../../')
-subprocess.call('rm scripts/ost.in.pre*',shell=True,cwd='../../')
-subprocess.call('rm scripts/dng.in',shell=True,cwd='../../')
-subprocess.call('rm scripts/dng.in.pre*',shell=True,cwd='../../')
-subprocess.call('mv scripts/ost.in.backup scripts/ost.in',shell=True,cwd='../../')
-subprocess.call('mv scripts/dng.in.backup scripts/dng.in',shell=True,cwd='../../')
+subprocess.call('rm scripts/ost_config.in',shell=True,cwd='../../')
+subprocess.call('rm scripts/ost_config.in.pre*',shell=True,cwd='../../')
+subprocess.call('mv scripts/ost_config.in.backup scripts/ost_config.in',shell=True,cwd='../../')
 subprocess.call('tar cfz '+directory_name+'.tgz '+directory_name,shell=True,cwd='../../')
 

deployment/linux/create_qmean_bundle.py

-import os
-import shutil
-import subprocess
-import string
-import sys
-
-
-# custom parameters
-
-boost_string='\".so.1.40.0\"'
-system_python_bin='/usr/bin/python2.6'
-name_python_bin='python2.6'
-system_python_libs='/usr/lib/python2.6'
-second_system_python_libs_flag=True
-second_system_python_libs='/usr/lib/pymodules/python2.6'
-qt4_plugins='/usr/lib/qt4/plugins'
-additional_label='ubuntu'
-list_of_excluded_libraries=['ld-linux','libexpat','libgcc_s','libglib','cmov','libice','libSM','libX','libg','libGL.so','libfontconfig','libfreetype','libdrm','libxcb','libICE']
-
-currdir=os.getcwd()
-if currdir.find('deployment')==-1 or currdir.find('linux')==-1:
-  print '\n'
-  print 'ERROR: Please run this script from the deployment/linux directory'
-  print '\n'
-  sys.exit()
-print '\n'
-print 'WARNING: If this script does not run to completion, please run the reset_repository_qmean.py script before restarting'
-print '\n'
-print 'Detecting architecture and revision'
-uname_output=subprocess.Popen('uname -a', shell=True, cwd='../../',stdout=subprocess.PIPE).stdout
-uname_line=uname_output.readlines()
-if uname_line[0].find('x86_64') !=-1:
-  libdir='lib64'
-  archstring='64bit'
-else: 
-  libdir='lib'
-  archstring='32bit'
-svninfo_output=subprocess.Popen('svn info', shell=True, cwd='../../',stdout=subprocess.PIPE).stdout
-svninfo_lines=svninfo_output.readlines()
-svninfo_split=string.split(svninfo_lines[4])
-revstring=svninfo_split[1]
-directory_name='qmean-'+archstring+'-'+additional_label+'-rev'+revstring
-print 'Stripping subversion information to avoid accidental commit'
-subprocess.call('rm -rf $(find . -name .svn)',shell=True,cwd='../../')
-print 'Tweaking scripts for bundle use'
-subprocess.call('mv scripts/ost.in scripts/ost.in.backup',shell=True,cwd='../../')
-subprocess.call('sed "s/@PYTHON_BINARY@/\$DNG_ROOT\/bin\/'+name_python_bin+'/g" scripts/ost.in.backup > scripts/ost.in.preprepre',shell=True,cwd='../../')
-subprocess.call('sed "s/\#export LD_LIBRARY_PATH/ export LD_LIBRARY_PATH/g" scripts/ost.in.prepreprepre > scripts/ost.in.preprepre',shell=True,cwd='../../')
-subprocess.call('sed "s/\#export PYTHONHOME/ export PYTHONHOME/g" scripts/ost.in.preprepre > scripts/ost.in.prepre',shell=True,cwd='../../')
-subprocess.call('sed "s/\#export PYTHONPATH/ export PYTHONPATH/g" scripts/ost.in.prepre > scripts/ost.in.pre',shell=True,cwd='../../')
-subprocess.call('sed "s/\#export QT_PLUGIN_PATH/ export QT_PLUGIN_PATH/g" scripts/ost.in.pre > scripts/ost.in',shell=True,cwd='../../')
-subprocess.call('mv modules/scratch/qmean/scripts/qmean.in modules/scratch/qmean/scripts/qmean.in.backup',shell=True,cwd='../../')
-subprocess.call('sed "s/@PYTHON_BINARY@/\$DNG_ROOT\/bin\/'+name_python_bin+'/g" modules/scratch/qmean/scripts/qmean.in.backup > modules/scratch/qmean/scripts/qmean.in.prepreprepre',shell=True,cwd='../../')
-subprocess.call('sed "s/\#export LD_LIBRARY_PATH/ export LD_LIBRARY_PATH/g" modules/scratch/qmean/scripts/qmean.in.prepreprepre > modules/scratch/qmean/scripts/qmean.in.preprepre',shell=True,cwd='../../')
-subprocess.call('sed "s/\#export PYTHONHOME/ export PYTHONHOME/g" modules/scratch/qmean/scripts/qmean.in.preprepre > modules/scratch/qmean/scripts/qmean.in.prepre',shell=True,cwd='../../')
-subprocess.call('sed "s/\#export PYTHONPATH/ export PYTHONPATH/g" modules/scratch/qmean/scripts/qmean.in.prepre > modules/scratch/qmean/scripts/qmean.in.pre',shell=True,cwd='../../')
-subprocess.call('sed "s/\#export QT_PLUGIN_PATH/ export QT_PLUGIN_PATH/g" modules/scratch/qmean/scripts/qmean.in.pre > modules/scratch/qmean/scripts/qmean.in',shell=True,cwd='../../')
-subprocess.call('mv scripts/dng.in scripts/dng.in.backup',shell=True,cwd='../../')
-subprocess.call('sed "s/\#export LD_LIBRARY_PATH/ export LD_LIBRARY_PATH/g" scripts/dng.in.backup > scripts/dng.in.preprepre',shell=True,cwd='../../')
-subprocess.call('sed "s/\#export PYTHONHOME/ export PYTHONHOME/g" scripts/dng.in.preprepre > scripts/dng.in.prepre',shell=True,cwd='../../')
-subprocess.call('sed "s/\#export PYTHONPATH/ export PYTHONPATH/g" scripts/ost.in.prepre > scripts/ost.in.pre',shell=True,cwd='../../')
-subprocess.call('sed "s/\#export QT_PLUGIN_PATH/ export QT_PLUGIN_PATH/g" scripts/dng.in.pre > scripts/dng.in',shell=True,cwd='../../')
-print 'Downloading Chemlib dictionary'
-subprocess.call('wget ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif', shell=True, cwd='../../')
-print 'Compiling Openstructure/Qmean'
-subprocess.call('cmake ./ -DCMAKE_BUILD_TYPE=Release -DPREFIX='+directory_name+' -DBoost_COMPILER='+boost_string+' -DONLY_QMEAN=ON -DENABLE_IMG=OFF -DENABLE_UI=OFF -DENABLE_GFX=OFF -DCOMPOUND_LIB=ChemLib/compounds.chemlib', shell=True,cwd='../../')
-subprocess.call('make',shell=True,cwd='../../')
-print 'Converting Chemlib dictionary'
-subprocess.call('stage/bin/chemdict_tool create components.cif compounds.chemlib', shell=True, cwd='../../')
-print '\nStaging Chemlib dictionary'
-subprocess.call('cmake ./ -DCOMPOUND_LIB=compounds.chemlib',shell=True,cwd='../../')
-subprocess.call('make',shell=True,cwd='../../')
-print 'Removing obsolete packages and package directory'
-subprocess.call('rm -fr qmean-*',shell=True,cwd='../../')
-print 'Creating new package directory'
-subprocess.call('mkdir '+directory_name,shell=True,cwd='../../')
-subprocess.call('mkdir '+directory_name+'/bin',shell=True,cwd='../../')
-so_list=[]
-print 'Creating new dependency list'
-walk_list=os.walk('../../stage')
-for dir_entry in walk_list:
-  for file_entry in dir_entry[2]:
-    if file_entry.find('.so')==len(file_entry)-3 or file_entry=='gosty':
-      filepath=os.path.join(dir_entry[0],file_entry)
-      so_list.append(filepath)  
-dep_list=[]
-for so_entry in so_list:
-   dep=subprocess.Popen('perl ./ldd-rec.pl '+so_entry,shell=True,stdout=subprocess.PIPE,cwd='./').stdout
-   dep_so_entry=dep.readlines()
-   for dep_entry in dep_so_entry:
-     dep_list.append(dep_entry[:-1]) 
-sorted_dep_list=sorted(list(set(dep_list)))
-print 'Filtering system libraries from depenedency list'
-filtered_dep_list=[]
-for entry in sorted_dep_list:
-   exclude=False
-   for exclusion in list_of_excluded_libraries:
-     if entry.find(exclusion)!=-1:
-       exclude=True
-   if exclude==False: 
-     filtered_dep_list.append(entry)
-print 'Copy libraries in the package directory structure'
-subprocess.call('mkdir '+directory_name+'/'+libdir,shell=True,cwd='../../')
-for entry in filtered_dep_list:
-  subprocess.call('cp '+entry+' '+directory_name+'/'+libdir,shell=True,cwd='../../')
-print 'Copy python executable into package directory structure'
-subprocess.call('cp '+system_python_bin+ ' '+directory_name+'/bin',shell=True,cwd='../../')
-print 'Copy python libraries into package directory structure'
-subprocess.call('cp -pRL '+system_python_libs+' '+directory_name+'/'+libdir,shell=True,cwd='../../')
-if second_system_python_libs_flag==True:
-  subprocess.call('cp -pRL '+second_system_python_libs+'/* '+directory_name+'/'+libdir+'/'+name_python_bin,shell=True,cwd='../../')
-print 'Copy Qt 4 plugins into package directory structure'
-subprocess.call('cp -pRL '+qt4_plugins+' '+directory_name+'/bin/',shell=True,cwd='../../')
-print 'Installing OpenStructure into package directory structure'
-subprocess.call('make install',shell=True,cwd='../../')
-print 'Copy examples into package directory structure'
-subprocess.call('cp -pRL  examples  '+directory_name+'/share/openstructure/',shell=True,cwd='../../')
-print 'Removing headers from package directory structure'
-subprocess.call('rm -fr   '+directory_name+'/include',shell=True,cwd='../../')
-print 'Copying supplementary material into package directory structure'
-subprocess.call('cp -pRL  stage/share/openstructure  '+directory_name+'/share/',shell=True,cwd='../../')
-print 'Copy qmean examples into package directory structure'
-subprocess.call('cp -pRL  modules/scratch/qmean/examples '+directory_name+'',shell=True,cwd='../../')
-print 'Copy readme and license files into package directory structure'
-subprocess.call('cp -pRL  modules/scratch/qmean/LICENSE.txt '+directory_name+'',shell=True,cwd='../../')
-subprocess.call('cp -pRL  modules/scratch/qmean/README.txt '+directory_name+'',shell=True,cwd='../../')
-print 'Resetting script to non-bundle versions'
-subprocess.call('rm scripts/ost.in',shell=True,cwd='../../')
-subprocess.call('rm scripts/ost.in.pre*',shell=True,cwd='../../')
-subprocess.call('rm scripts/dng.in',shell=True,cwd='../../')
-subprocess.call('rm modules/scratch/qmean/scripts/qmean.in',shell=True,cwd='../../')
-subprocess.call('rm modules/scratch/qmean/scripts/qmean.in.pre*',shell=True,cwd='../../')
-subprocess.call('rm scripts/dng.in.pre*',shell=True,cwd='../../')
-subprocess.call('mv scripts/ost.in.backup scripts/ost.in',shell=True,cwd='../../')
-subprocess.call('mv scripts/dng.in.backup scripts/dng.in',shell=True,cwd='../../')
-subprocess.call('mv modules/scratch/qmean/scripts/qmean.in.backup modules/scratch/qmean/scripts/qmean.in',shell=True,cwd='../../')
-subprocess.call('tar cfz '+directory_name+'.tgz '+directory_name,shell=True,cwd='../../')
-

deployment/linux/debian/README

+1. Checkout OpenStructure into a directory called strictly:'openstructure-<version>' (currently is 1.1d - 1.1 develop)
+2. Remove all the .git* files and directories from the source
+3. Create a compressed file with the source directory called strictly 'openstructure_<version>.orig.tar.gz' 
+   (At the same level as the source directory)
+4. Copy the 'debian' directory into the top level of the source directory
+5. Go into the top level of the source directory
+6. Build package with 'debuilder -uc -us'
+7. You can find the built package at the same level as the source directory and the source zipped file

deployment/linux/debian/debian/README.source

+===============OPENSTRUCTURE molecular modelling framework ===============
+
+
+OpenStructure is the next generation molecular modelling tailored at anybody
+ using 3D Structures or electron density maps.
+
+Please refer to www.openstructure.org for more information or try out
+ directly one of the binary packages available for download.
+
+Thank you for you interest and enjoy the straightforward way of handling 
+protein structure data!
+
+Please do not hesitate to contact us for feedback or troubleshooting:
+
+ost-users@maillist.unibas.ch 
+
+
+=============== The OpenStructure Team ===================================

deployment/linux/debian/debian/changelog

+openstructure (1.1d-0ubuntu1) natty; urgency=low
+
+  * Initial release 
+
+ -- Valerio Mariani <valerio.mariani@unibas.ch>  Wed, 13 Jul 2011 15:41:35 +0200

deployment/linux/debian/debian/chemdict_tool.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.38.4.
+.TH CHEMDICT_TOOL: "1" "July 2011" "User Commands"
+.SH NAME
+chemdict_tool \- compound libary creation tool for OpenStructure
+.SH SYNOPSIS
+chemdict_tool action <compound\-dict> <db> (pdb|charmm|amber|opls)
+.SH OPTIONS
+Supported actions are:
+.TP
+create
+\- creates a new db
+.TP
+update
+\- update existing db
+.SS "supported actions are:"
+.TP
+create
+\- creates a new db
+.TP
+update
+\- update existing db
+.SH "SEE ALSO"
+The full documentation for
+.B usage:
+is maintained as a Texinfo manual.  If the
+.B info
+and
+.B usage:
+programs are properly installed at your site, the command
+.IP
+.B info usage:
+.PP
+should give you access to the complete manual.

deployment/linux/debian/debian/compat

+7

deployment/linux/debian/debian/control

+Source: openstructure
+Section: science
+Priority: extra
+Maintainer: Valerio Mariani <valerio.mariani@unibas.ch>
+Build-Depends: debhelper (>= 7.0.50~),cmake,desktop-file-utils,libboost-all-dev,libeigen2-dev,qt4-dev-tools,libqt4-dev,libqt4-opengl-dev,python-qt4-dev,pyqt4-dev-tools,libfftw3-dev,libpng12-dev,libtiff4-dev,python-dev
+Standards-Version: 3.9.1
+Homepage: http://www.openstructure.org
+          
+Package: openstructure
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, python-sip, python-qt4
+Description: Open-source computational structural biology framework
+ The Openstructure  project aims to provide an open-source, modular, flexible, 
+ molecular modelling and visualization environment. It is targeted at 
+ interested method developers in the field of structural bioinformatics.
+
+Package: openstructure-dev
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, openstructure
+Description: Open-source computational structural biology framework
+ The Openstructure  project aims to provide an open-source, modular, flexible, 
+ molecular modelling and visualization environment. It is targeted at 
+ interested method developers in the field of structural bioinformatics.

deployment/linux/debian/debian/copyright

+Format: http://dep.debian.net/deps/dep5
+Upstream-Name: openstructure
+Source: http://www.openstructure.org
+
+Files: *
+Copyright: 2008-2011 Torsten Schwede <torsten.schwede@unibas.ch>
+License: LGPL-3.0
+
+Files: debian/*
+Copyright: 2011 Valerio Mariani <valerio.mariani@unibas.ch>
+License: LGPL-3.0
+
+License: LGPL-3.0
+ This package is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ Lesser General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+ .
+ On Debian systems, the complete text of the GNU Lesser General
+ Public License can be found in "/usr/share/common-licenses/LGPL-3".
+
+Files: modules/db/src/sqlite3.h, modules/db/src/sqlite.c
+Copyright: 2011 Valerio Mariani <valerio.mariani@unibas.ch>
+License: None
+ 2001 September 15
+ .
+ The author disclaims copyright to this source code.  In place of
+ a legal notice, here is a blessing:
+ .
+    May you do good and not evil.
+    May you find forgiveness for yourself and forgive others.
+    May you share freely, never taking more than you give.

deployment/linux/debian/debian/dng.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.38.4.
+.TH DNG "1" "July 2011" "User Commands"
+.SH NAME
+dng \- GUI for OpenStructure
+.SH SYNOPSIS
+.B dng
+[\fIoptions\fR] [\fIfiles to load\fR]
+.SH OPTIONS
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-v\fR VLEVEL, \fB\-\-verbosity_level\fR=\fIVLEVEL\fR
+sets the verbosity level [default: 2]
+.TP
+\fB\-s\fR SCRIPT, \fB\-\-script\fR=\fISCRIPT\fR
+executes a script (syntax: \fB\-s\fR SCRIPT [options] [args])
+Anything that follows this option is passed to the
+script
+.TP
+\fB\-p\fR PDB_IDS, \fB\-\-pdb_id\fR=\fIPDB_IDS\fR
+PDB file ID. The file will be retrieved from PDB
+.TP
+\fB\-b\fR BUILDER, \fB\-\-builder\fR=\fIBUILDER\fR
+Type of builder used by the progam (either RULE_BASED
+or HEURISTIC) [default: HEURISTIC]
+.TP
+\fB\-c\fR COMPLIB, \fB\-\-compound_library\fR=\fICOMPLIB\fR
+Compound library for the RULE_BASED builder (only used
+if \fB\-\-builder\fR option is set to RULE_BASED, otherwise
+ignored [default: compounds.chemlib]
+.TP
+\fB\-q\fR QUERY, \fB\-\-query\fR=\fIQUERY\fR
+Selection query to be highlighted automatically upon
+loading (only used together with \fB\-p\fR option or when a
+PDB file is loaded, otherwise ignored [default: None]
+.TP
+\fB\-S\fR, \fB\-\-stereo\fR
+try to get a quad\-buffer stereo visual

deployment/linux/debian/debian/openstructure.desktop

+[Desktop Entry]
+Name=OpenStructure
+GenericName=Open-Source Computational Structural Biology Framework
+Exec=dng
+Icon=openstructure
+Terminal=false
+Type=Application
+Categories=Education;Science;

deployment/linux/debian/debian/openstructure.manpages

+debian/ost.1
+debian/dng.1
+debian/chemdict_tool.1

deployment/linux/debian/debian/ost.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.38.4.
+.TH OST "1" "July 2011" "User Commands"
+.SH NAME
+ost: \- command-line console for OpenStructure
+.SH SYNOPSIS
+.B ost
+[\fIost options\fR] [\fIscript to execute\fR] [\fIscript parameters\fR]
+.SH OPTIONS
+.TP
+\fB\-i\fR, \fB\-\-interactive\fR
+start interpreter interactively (must be first
+parameter, ignored otherwise)
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-v\fR VLEVEL, \fB\-\-verbosity_level\fR=\fIVLEVEL\fR
+sets the verbosity level [default: 2]

deployment/linux/debian/debian/postinst

+#!/bin/sh
+# postinst script for openstructure
+#
+# see: dh_installdeb(1)
+
+set -e
+
+# summary of how this script can be called:
+#        * <postinst> `configure' <most-recently-configured-version>
+#        * <old-postinst> `abort-upgrade' <new version>
+#        * <conflictor's-postinst> `abort-remove' `in-favour' <package>
+#          <new-version>
+#        * <postinst> `abort-remove'
+#        * <deconfigured's-postinst> `abort-deconfigure' `in-favour'
+#          <failed-install-package> <version> `removing'
+#          <conflicting-package> <version>
+# for details, see http://www.debian.org/doc/debian-policy/ or
+# the debian-policy package
+
+
+case "$1" in
+    configure)
+    ldconfig
+    ;;
+
+    abort-upgrade|abort-remove|abort-deconfigure)
+    ;;
+
+    *)
+        echo "postinst called with unknown argument \`$1'" >&2
+        exit 1
+    ;;
+esac
+
+# dh_installdeb will replace this with shell code automatically
+# generated by other debhelper scripts.
+
+#DEBHELPER#
+
+exit 0

deployment/linux/debian/debian/rules

+#!/usr/bin/make -f
+# -*- makefile -*-
+# Sample debian/rules that uses debhelper.
+# This file was originally written by Joey Hess and Craig Small.
+# As a special exception, when this file is copied by dh-make into a
+# dh-make output file, you may use that output file without restriction.
+# This special exception was added by Craig Small in version 0.37 of dh-make.
+
+# Uncomment this to turn on verbose mode.
+export DH_VERBOSE=1
+
+%:
+	dh $@ --buildsystem cmake 
+override_dh_auto_configure:
+	cmake ./ -DPREFIX=debian/openstructure/usr -DOPTIMIZE=ON -DCOMPOUND_LIB=compounds.chemlib
+override_dh_auto_build:
+	make -j6
+override_dh_auto_install:
+	make install
+	rm debian/openstructure/usr/bin/ldt
+	mkdir -p debian/openstructure-dev/usr
+	mv debian/openstructure/usr/include debian/openstructure-dev/usr/
+	mkdir -p debian/openstructure/usr/share/pixmaps/
+	cp modules/gui/share/images/logo-small.png debian/openstructure/usr/share/pixmaps/openstructure.png
+	mkdir -p debian/openstructure/usr/share/applications/
+	cp debian/openstructure.desktop debian/openstructure/usr/share/applications/
+	desktop-file-validate debian/openstructure/usr/share/applications/openstructure.desktop

deployment/linux/debian/debian/source/format

+3.0 (quilt)
+