diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index a67298e7770a1445c38221ac4996499ef083d879..0fafefeb2176fcd3a2dbdbf69b3be02562079a65 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -18,27 +18,27 @@ test:centos7.3:
- yum -y -q -e 0 install make
- yum -y -q -e 0 install libicu
- yum -y -q -e 0 install libjpeg-turbo
- - yum -y -q -e 0 install mesa-libGL-devel
- - yum -y -q -e 0 install mesa-libGLU-devel
- yum -y -q -e 0 install freetype
- - yum -y -q -e 0 install libpng
+ - yum -y -q -e 0 install openssl
- mkdir -p /scicore/soft/modules
- ln -s /export/soft/apps/centos7/generic /scicore/soft/apps
- ln -s /export/soft/modules/centos7/generic/all /scicore/soft/modules
- source /export/soft/lua_lmod/centos7/lmod/lmod/init/bash
- module use /scicore/soft/modules/all
- - module load CMake/3.4.3-goolf-1.7.20
- - module load Python/2.7.11-goolf-1.7.20
- - module load OpenBLAS/0.2.13-GCC-4.8.4-LAPACK-3.5.0
- - module load Eigen/3.2.8-goolf-1.7.20
- - module load numpy/1.10.1-goolf-1.7.20-Python-2.7.11
- - module load Boost/1.53.0-goolf-1.7.20-Python-2.7.11
- - module load Qt5/5.9.3-goolf-1.7.20
- - module load LibTIFF/.4.0.4-goolf-1.7.20
- - module load Perl/5.22.2-goolf-1.7.20
- - module load HH-suite/2.0.16-goolf-1.7.20-Boost-1.53.0-Python-2.7.11
- - module load OpenMM/6.1-goolf-1.7.20-Python-2.7.11
- - module load SQLite/3.9.2-goolf-1.7.20
+ - module load foss/2018b
+ - module load CMake/3.12.1-GCCcore-7.3.0
+ - module load Python/3.6.6-foss-2018b
+ - module load Eigen/3.3.1
+ - module load Boost/1.68.0-foss-2018b-Python-3.6.6
+ - module load LibTIFF/.4.0.9-GCCcore-7.3.0
+ - module load libpng/.1.6.34-GCCcore-7.3.0
+ - module load HH-suite/2.0.16-foss-2018b
+ - module load Perl/5.28.0-GCCcore-7.3.0
+ - module load OpenMM/7.1.1-foss-2018b-Python-3.6.6
+ - module load SQLite/3.24.0-GCCcore-7.3.0
+ - module load dssp/2.2.1-foss-2018b-Boost-1.68.0-Python-3.6.6
+ - module load msms/2.6.1-linux-x86_64
+ - module load ClustalW2/2.1-foss-2018b
- echo "... done running centos7.3 'before_script'."
script:
- echo "Testing on CentOS 7..."
@@ -50,7 +50,8 @@ test:centos7.3:
-DOPEN_MM_PLUGIN_DIR=$EBROOTOPENMM/lib/plugins
-DOPEN_MM_INCLUDE_DIR=$EBROOTOPENMM/include
-DCOMPILE_TMTOOLS=1
- -DENABLE_GFX=ON
+ -DENABLE_INFO=OFF
+ -DENABLE_GFX=OFF
-DENABLE_GUI=OFF
-DUSE_NUMPY=1
-DUSE_RPATH=1
@@ -61,17 +62,18 @@ test:centos7.3:
-DSQLITE3_LIBRARY=$EBROOTSQLITE/lib/libsqlite3.so
-DSQLITE3_INCLUDE_DIR=$EBROOTSQLITE/include
-DBOOST_ROOT=$EBROOTBOOST
- -DQT_QMAKE_EXECUTABLE=$EBROOTQT5/bin/qmake
-DPNG_LIBRARY=$EBROOTLIBPNG/lib/libpng.so
- -DPNG_INCLUDE_DIR=$EBROOTLIBPNG/include
-DPNG_PNG_INCLUDE_DIR=$EBROOTLIBPNG/include
-DZLIB_LIBRARY=$EBROOTZLIB/lib/libz.so
-DZLIB_INCLUDE_DIR=$EBROOTZLIB/include
-DTIFF_INCLUDE_DIR=$EBROOTLIBTIFF/include
-DTIFF_LIBRARY=$EBROOTLIBTIFF/lib/libtiff.so
+ -DZLIB_INCLUDE_DIR=$EBROOTZLIB/include
+ -DZLIB_LIBRARY=$EBROOTZLIB/lib/libz.so
-DOPTIMIZE=1
- -DCMAKE_C_FLAGS='-L/scicore/soft/apps/LibTIFF/4.0.4-goolf-1.7.20/lib/ -L/scicore/soft/apps/libpng/1.6.18-goolf-1.7.20/lib/ -L/scicore/soft/apps/Boost/1.53.0-goolf-1.7.20-Python-2.7.11/lib/ -L/scicore/soft/apps/Qt5/5.9.3-goolf-1.7.20/lib/ -Wno-unused-local-typedefs'
- -DCMAKE_CXX_FLAGS='-L/scicore/soft/apps/LibTIFF/4.0.4-goolf-1.7.20/lib/ -L/scicore/soft/apps/libpng/1.6.18-goolf-1.7.20/lib/ -L/scicore/soft/apps/Boost/1.53.0-goolf-1.7.20-Python-2.7.11/lib/ -L/scicore/soft/apps/Qt5/5.9.3-goolf-1.7.20/lib/ -Wno-unused-local-typedefs'
+ -DCMAKE_C_FLAGS='-L${EBROOTLIBPNG}/lib/ -L${EBROOTLIBTIFF}/lib/ -L${EBROOTZLIB}/lib/ -isystem ${EBROOTBOOST}/include -isystem ${EBROOTOPENMM}/include'
+ -DCMAKE_CXX_FLAGS='-L${EBROOTLIBPNG}/lib/ -L${EBROOTLIBTIFF}/lib/ -L${EBROOTZLIB}/lib/ -isystem ${EBROOTBOOST}/include -isystem ${EBROOTOPENMM}/include'
+ -DCMAKE_EXE_LINKER_FLAGS=" -pthread"
- make -j 2
- echo " ... done building OST."
- echo " Running unit tests for OST..."
diff --git a/CHANGELOG.txt b/CHANGELOG.txt
index ea3c60e1ad55bdae6936eb6677b188327f6f2bb1..1fbce23648212c90ee0f65b8674d4fdfccbac73c 100644
--- a/CHANGELOG.txt
+++ b/CHANGELOG.txt
@@ -1,3 +1,12 @@
+Changes in Release 2.0.0
+--------------------------------------------------------------------------------
+
+ * Port OpenStructure to Python 3 (3.6).
+ * Updated versions of dependencies
+ * Reduced amount of warnings during compilation.
+ * Removed OpenMM density plugin and out-dated bindings (3dcomb, MMalign).
+ * Several minor bug fixes and improvements.
+
Changes in Release 1.11.0
--------------------------------------------------------------------------------
diff --git a/CMakeLists.txt b/CMakeLists.txt
index c7b1c5ceeafa4fafc9863670a718cdac505261f9..91af96562fbee8cccd2d9e6c0ae957bdbfddd485 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -2,11 +2,19 @@
# Author: Marco Biasini
#-------------------------------------------------------------------------------
-cmake_minimum_required(VERSION 2.6.4 FATAL_ERROR)
+cmake_minimum_required(VERSION 3.10.2 FATAL_ERROR)
+
+# Set CMake policies
+# Behaviour of target_link_libraries, always link by full path. CMP0060 can
+# disable this to stay compatible with old projects. We want the new behaviour
+# since before we needed to provide the full path ourselves, that is: we
+# manually forced CMake to the new scheme.
+cmake_policy(SET CMP0060 NEW)
+
project(OpenStructure CXX C)
set (CMAKE_EXPORT_COMPILE_COMMANDS 1)
-set (OST_VERSION_MAJOR 1)
-set (OST_VERSION_MINOR 11)
+set (OST_VERSION_MAJOR 2)
+set (OST_VERSION_MINOR 0)
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)
@@ -23,7 +31,9 @@ option(PROFILE "whether to compile with profiling support"
option(ENABLE_GUI "whether the graphical user interface should be enabled"
ON)
option(ENABLE_GFX "whether graphics support should be enabled"
- ON)
+ ON)
+option(OPENGLPREFERENCE_LEGACY "whether to use the OpenGL Legacy GL implementation"
+ OFF)
option(ENABLE_IMG "whether the image processing module should be compiled"
ON)
option(ENABLE_INFO "whether openstructure should be compiled with support for the info library"
@@ -177,7 +187,7 @@ if (ENABLE_STATIC AND UNIX AND NOT APPLE)
endif()
# Python needed before Boost
-find_package(Python 2.4 REQUIRED)
+find_package(Python 3.6 REQUIRED)
# Split version string
string(REPLACE "." ";" _python_version_list ${PYTHON_VERSION})
list(GET _python_version_list 0 PYTHON_VERSION_MAJOR)
@@ -213,6 +223,11 @@ else()
endif()
endif()
if (ENABLE_GFX)
+ if (OPENGLPREFERENCE_LEGACY)
+ set(OpenGL_GL_PREFERENCE LEGACY)
+ else()
+ set(OpenGL_GL_PREFERENCE GLVND)
+ endif(OPENGLPREFERENCE_LEGACY)
find_package(OpenGL REQUIRED)
endif()
@@ -262,8 +277,8 @@ if (ENABLE_GUI)
find_package(Qt5Widgets REQUIRED)
find_package(Qt5OpenGL REQUIRED)
set(QT_LIBRARIES ${QT_LIBRARIES} Qt5::Gui Qt5::Widgets Qt5::Core)
- ost_find_python_module(sip)
ost_find_python_module(PyQt5)
+ ost_find_python_module_alt("PyQt5.sip;sip")
endif()
if (ENABLE_SPNAV)
@@ -289,6 +304,13 @@ if (CMAKE_COMPILER_IS_GNUCXX)
endif(HIDDEN_VISIBILITY)
endif()
+if(CMAKE_CXX_COMPILER_ID MATCHES "Clang")
+ set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-unknown-warning-option")
+endif(CMAKE_CXX_COMPILER_ID MATCHES "Clang")
+if(CMAKE_C_COMPILER_ID MATCHES "Clang")
+ set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wno-unknown-warning-option")
+endif(CMAKE_C_COMPILER_ID MATCHES "Clang")
+
# basic environment
include_directories(${Boost_INCLUDE_DIRS}
${FFTW_INCLUDE_DIRS}
@@ -362,3 +384,5 @@ message(STATUS
" Debian/Ubuntu directory layout (-DUBUNTU_LAYOUT) : ${_UBUNTU_LAYOUT}"
${HIDDEN_VIS_MSG})
+
+# LocalWords: CMake CMP
diff --git a/actions/ost-compare-structures b/actions/ost-compare-structures
index 8ae9ff19e36718f38b319b40e79fea337d883a1f..0ae1dad2d0dc692b544d05b8f0d8d8408a7b0d01 100644
--- a/actions/ost-compare-structures
+++ b/actions/ost-compare-structures
@@ -513,7 +513,7 @@ def _RevertChainNames(ent):
used_names[original_name] += 1
for chain in ent.chains:
editor.RenameChain(chain, reverted_chains[chain.name[:-len(suffix)]])
- rev_out = ["%s -> %s" % (on, nn) for on, nn in reverted_chains.iteritems()]
+ rev_out = ["%s -> %s" % (on, nn) for on, nn in list(reverted_chains.items())]
ost.LogInfo("Reverted chains: %s" % ", ".join(rev_out))
@@ -522,7 +522,7 @@ def _CheckConsistency(alignments, log_error):
for alignment in alignments:
ref_chain = Renumber(alignment.GetSequence(0)).CreateFullView()
mdl_chain = Renumber(alignment.GetSequence(1)).CreateFullView()
- new_is_cons = ResidueNamesMatch(ref_chain, mdl_chain, log_error)
+ new_is_cons = ResidueNamesMatch(mdl_chain, ref_chain, log_error)
is_cons = is_cons and new_is_cons
return is_cons
@@ -989,9 +989,6 @@ def _Main():
with open(opts.output, "w") as outfile:
json.dump(result, outfile, indent=4, sort_keys=True)
-
if __name__ == '__main__':
- # make script 'hot'
- unbuffered = os.fdopen(sys.stdout.fileno(), 'w', 0)
- sys.stdout = unbuffered
_Main()
+
diff --git a/build_configs/buildconfig_bc2 b/build_configs/buildconfig_bc2
index ae7aa9384f42215d685e16c9c8eda6389243fd08..5c8dccf19548f179ea581798867d4ebbcb557f1c 100644
--- a/build_configs/buildconfig_bc2
+++ b/build_configs/buildconfig_bc2
@@ -1,8 +1,8 @@
-set(FFTW_INCLUDE_PATH "/scicore/soft/apps/FFTW/3.3.3-gompi-1.4.10/include/" CACHE PATH "")
-set(FFTW_LIBRARY "/scicore/soft/apps/FFTW/3.3.3-gompi-1.4.10/lib/libfftw3f.a" CACHE PATH "")
-set(PYTHON_ROOT "/scicore/soft/apps/Python/2.7.5-goolf-1.4.10" CACHE PATH "")
-set(EIGEN3_INCLUDE_DIR "/scicore/soft/apps/Eigen/3.2.1-goolf-1.4.10/include/Eigen" CACHE PATH "")
-set(BOOST_ROOT "/import/bc2/apps/Boost/1.53.0-goolf-1.4.10-Python-2.7.5" CACHE PATH "")
-set(QT_QMAKE_EXECUTABLE "/usr/bin/qmake-qt4" CACHE PATH "")
-set(COMPOUND_LIB "/import/bc2/home/schwede/GROUP/OpenStructure/ChemLib/compounds.chemlib" CACHE PATH "")
+set(FFTW_INCLUDE_PATH "/scicore/soft/apps/FFTW/3.3.8-gompi-2018b/include/" CACHE PATH "")
+set(FFTW_LIBRARY "/scicore/soft/apps/FFTW/3.3.8-gompi-2018b/lib/libfftw3f.a" CACHE PATH "")
+set(PYTHON_ROOT "/scicore/soft/apps/Python/3.6.6-foss-2018" CACHE PATH "")
+set(EIGEN3_INCLUDE_DIR "/scicore/soft/apps/Eigen/3.3.1/include/Eigen" CACHE PATH "")
+set(BOOST_ROOT "/scicore/soft/apps/Boost/1.68.0-foss-2018b-Python-3.6.6" CACHE PATH "")
+set(QT_QMAKE_EXECUTABLE "/usr/bin/qmake-qt5" CACHE PATH "")
+set(COMPOUND_LIB "/scicore/home/schwede/GROUP/OpenStructure/ChemLib/1.8/compounds.chemlib" CACHE PATH "")
set (CMAKE_BUILD_TYPE "Release" CACHE PATH "")
diff --git a/build_configs/buildconfig_bc2_static b/build_configs/buildconfig_bc2_static
index d25730b349840c25abf398a9b7d981d13bab5c2d..bf27f7e8f959a9a0aec244240bd839b6784427e0 100644
--- a/build_configs/buildconfig_bc2_static
+++ b/build_configs/buildconfig_bc2_static
@@ -1,10 +1,10 @@
-set(FFTW_INCLUDE_PATH "/scicore/soft/apps/FFTW/3.3.3-gompi-1.4.10/include/" CACHE PATH "")
-set(FFTW_LIBRARY "/scicore/soft/apps/FFTW/3.3.3-gompi-1.4.10/lib/libfftw3f.a" CACHE PATH "")
+set(FFTW_INCLUDE_PATH "/scicore/soft/apps/FFTW/3.3.8-gompi-2018b/include/" CACHE PATH "")
+set(FFTW_LIBRARY "/scicore/soft/apps/FFTW/3.3.8-gompi-2018b/lib/libfftw3f.a" CACHE PATH "")
set(DL_LIBRARIES "/usr/lib64/libdl.a" CACHE PATH "")
set(PTHREAD_LIBRARIES "/usr/lib64/libpthread.a" CACHE PATH "")
-set(ZLIB_LIBRARY "/scicore/soft/apps/zlib/1.2.8-goolf-1.4.10/lib/libz.a" CACHE PATH "")
-set(PYTHON_ROOT "/scicore/soft/apps/Python/2.7.5-goolf-1.4.10" CACHE PATH "")
-set(EIGEN3_INCLUDE_DIR "/scicore/soft/apps/Eigen/3.2.1-goolf-1.4.10/include/Eigen" CACHE PATH "")
-set(QT_QMAKE_EXECUTABLE "/usr/bin/qmake-qt4" CACHE PATH "")
-set(COMPOUND_LIB "/import/bc2/home/schwede/GROUP/OpenStructure/ChemLib/compounds.chemlib" CACHE PATH "")
+set(ZLIB_LIBRARY "/scicore/soft/apps/zlib/1.2.11-GCCcore-7.3.0/lib/libz.a" CACHE PATH "")
+set(PYTHON_ROOT "/scicore/soft/apps/Python/3.6.6-foss-2018" CACHE PATH "")
+set(EIGEN3_INCLUDE_DIR "/scicore/soft/apps/Eigen/3.3.1/include/Eigen" CACHE PATH "")
+set(QT_QMAKE_EXECUTABLE "/usr/bin/qmake-qt5" CACHE PATH "")
+set(COMPOUND_LIB "/scicore/home/schwede/GROUP/OpenStructure/ChemLib/1.8/compounds.chemlib" CACHE PATH "")
set (CMAKE_BUILD_TYPE "Release" CACHE PATH "")
diff --git a/cmake_support/FindNumpy.cmake b/cmake_support/FindNumpy.cmake
index 6348b9c91a934e4c01edac011cc861adc9fd059a..e5bd944544c090fbde843c25fb561228cd8f36ca 100644
--- a/cmake_support/FindNumpy.cmake
+++ b/cmake_support/FindNumpy.cmake
@@ -7,16 +7,15 @@ endif (PYTHON_NUMPY_INCLUDE_DIR)
IF(PYTHON_BINARY)
EXEC_PROGRAM ("${PYTHON_BINARY}"
- ARGS "-c 'import numpy; print numpy.get_include()'"
+ ARGS "-c 'import numpy; print(numpy.get_include())'"
OUTPUT_VARIABLE PYTHON_NUMPY_INCLUDE_DIR
RETURN_VALUE PYTHON_NUMPY_NOT_FOUND)
-
- if (PYTHON_NUMPY_INCLUDE_DIR)
+ if (PYTHON_NUMPY_NOT_FOUND)
+ set(PYTHON_NUMPY_FOUND FALSE)
+ else (PYTHON_NUMPY_NOT_FOUND)
set (PYTHON_NUMPY_FOUND TRUE)
set (PYTHON_NUMPY_INCLUDE_DIR ${PYTHON_NUMPY_INCLUDE_DIR} CACHE STRING "Numpy include path")
- else (PYTHON_NUMPY_INCLUDE_DIR)
- set(PYTHON_NUMPY_FOUND FALSE)
- endif (PYTHON_NUMPY_INCLUDE_DIR)
+ endif (PYTHON_NUMPY_NOT_FOUND)
ENDIF(PYTHON_BINARY)
if (PYTHON_NUMPY_FOUND)
@@ -24,9 +23,9 @@ if (PYTHON_NUMPY_FOUND)
message (STATUS "Numpy headers found")
endif (NOT PYTHON_NUMPY_FIND_QUIETLY)
else (PYTHON_NUMPY_FOUND)
- if (PYTHON_NUMPY_FIND_REQUIRED)
+ if (Numpy_FIND_REQUIRED)
message (FATAL_ERROR "Numpy headers missing")
- endif (PYTHON_NUMPY_FIND_REQUIRED)
+ endif (Numpy_FIND_REQUIRED)
endif (PYTHON_NUMPY_FOUND)
-MARK_AS_ADVANCED (PYTHON_NUMPY_INCLUDE_DIR)
\ No newline at end of file
+MARK_AS_ADVANCED (PYTHON_NUMPY_INCLUDE_DIR)
diff --git a/cmake_support/FindPython.cmake b/cmake_support/FindPython.cmake
index 673a802199b94de7b43a08b38a549eec275ae85e..852c91d44dbc345a305aa08633d66b4f0a5d56e6 100644
--- a/cmake_support/FindPython.cmake
+++ b/cmake_support/FindPython.cmake
@@ -17,8 +17,8 @@
# Author: Marco Biasini
#-------------------------------------------------------------------------------
-set(PYTHON_VERSIONS 2.7 2.6 2.5 2.4 2.3 2.2 )
-set(PYTHON_MIN_VERSION 2.2.1)
+set(PYTHON_VERSIONS 3.8 3.7 3.6 )
+set(PYTHON_MIN_VERSION 3.6.0)
#-------------------------------------------------------------------------------
# check for python framework
@@ -45,7 +45,8 @@ macro(_find_python PYTHON_ROOT VERSION)
string(REPLACE "." "" _VERSION_NO_DOTS "${VERSION}")
if(PYTHON_ROOT)
find_library(PYTHON_LIBRARIES
- NAMES "python${_VERSION_NO_DOTS}" "python${VERSION}"
+ NAMES "python${_VERSION_NO_DOTS}" "python${VERSION}"
+ "python${_VERSION_NO_DOTS}m" "python${VERSION}m"
HINTS "${PYTHON_ROOT}"
PATH_SUFFIXES lib libs
NO_SYSTEM_ENVIRONMENT_PATH NO_DEFAULT_PATH
@@ -53,17 +54,20 @@ macro(_find_python PYTHON_ROOT VERSION)
find_path(PYTHON_INCLUDE_PATH
NAMES Python.h
HINTS "${PYTHON_ROOT}/include"
- PATH_SUFFIXES include "python${_VERSION_NO_DOTS}" "python${VERSION}"
+ PATH_SUFFIXES include "python${_VERSION_NO_DOTS}" "python${VERSION}"
+ "python${_VERSION_NO_DOTS}m" "python${VERSION}m"
NO_SYSTEM_ENVIRONMENT_PATH NO_DEFAULT_PATH
)
else()
find_library(PYTHON_LIBRARIES
- NAMES "python${_VERSION_NO_DOTS}" "python${VERSION}"
+ NAMES "python${_VERSION_NO_DOTS}" "python${VERSION}"
+ "python${_VERSION_NO_DOTS}m" "python${VERSION}m"
PATH_SUFFIXES lib
)
find_path(PYTHON_INCLUDE_PATH
NAMES Python.h
- PATH_SUFFIXES include "python${_VERSION_NO_DOTS}" "python${VERSION}"
+ PATH_SUFFIXES include "python${_VERSION_NO_DOTS}" "python${VERSION}"
+ "python${_VERSION_NO_DOTS}m" "python${VERSION}m"
)
endif()
endmacro()
diff --git a/cmake_support/OST.cmake b/cmake_support/OST.cmake
index 31c304804c033fc6f4cb142c726c618a45db1138..3b6821210f742eefd36ca60cef70bc4674c6a41f 100644
--- a/cmake_support/OST.cmake
+++ b/cmake_support/OST.cmake
@@ -759,6 +759,34 @@ macro(ost_find_python_module MODULE)
endif()
endmacro()
+#-------------------------------------------------------------------------------
+# make sure the previously detected Python interpreter has the given module
+# while allowing alternative module names
+#-------------------------------------------------------------------------------
+macro(ost_find_python_module_alt MODULES)
+ set(_PY_MODS "")
+ foreach(py_mod ${MODULES})
+ if (NOT PYTHON_MODULE_${py_mod})
+ set(_PY_MODS "${_PY_MODS} ${py_mod}")
+ message(STATUS "Searching for python module ${py_mod} for ${PYTHON_BINARY}")
+ execute_process(COMMAND ${PYTHON_BINARY} -c "import ${py_mod}"
+ OUTPUT_QUIET ERROR_QUIET
+ RESULT_VARIABLE _IMPORT_ERROR)
+ if (NOT _IMPORT_ERROR)
+ message(STATUS "Found python module ${py_mod}")
+ set("PYTHON_MODULE_${py_mod}" FOUND CACHE STRING "" FORCE)
+ break()
+ endif (NOT _IMPORT_ERROR)
+ else ()
+ message(STATUS "Already found python module ${py_mod}")
+ unset(_IMPORT_ERROR)
+ break()
+ endif (NOT PYTHON_MODULE_${py_mod})
+ endforeach(py_mod ${MODULES})
+ if (_IMPORT_ERROR)
+ message(FATAL_ERROR "Could not find one of python modules ${_PY_MODS}. Please install one of them.")
+ endif ()
+endmacro()
#-------------------------------------------------------------------------------
# this macro tries to detect a very common problem during configuration stage:
@@ -897,7 +925,7 @@ macro(setup_compiler_flags)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fno-strict-aliasing" )
endif()
#message(STATUS "GCC VERSION " ${_GCC_VERSION})
- if ((ENABLE_INFO OR ENABLE_GUI) AND _GCC_VERSION LESS "60")
+ if (_GCC_VERSION LESS "60")
# for older compilers we need to enable C++11 for Qt5
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
endif()
@@ -917,10 +945,10 @@ macro(setup_boost)
# python${PYTHON_VERSION_MAJOR}${PYTHON_VERSION_MINOR} REQUIRED)
# set(BOOST_PYTHON_LIBRARIES ${Boost_LIBRARIES})
# see https://cmake.org/cmake/help/v3.11/module/FindBoost.html
- foreach(_python_lib_name python
- python${PYTHON_VERSION_MAJOR}${PYTHON_VERSION_MINOR}
+ foreach(_python_lib_name python${PYTHON_VERSION_MAJOR}${PYTHON_VERSION_MINOR}
python${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}
- python${PYTHON_VERSION_MAJOR})
+ python${PYTHON_VERSION_MAJOR}
+ python)
find_package(Boost ${_BOOST_MIN_VERSION} COMPONENTS ${_python_lib_name} QUIET)
if(Boost_FOUND)
message(STATUS "Found Boost package: " ${_python_lib_name})
@@ -1004,4 +1032,4 @@ macro(ost_action ACTION TARGET)
set(_ACTION_NAMES "${stripped_action}")
endif()
set(OST_ACTION_NAMES "${_ACTION_NAMES}" CACHE INTERNAL "" FORCE)
-endmacro(ost_action)
\ No newline at end of file
+endmacro(ost_action)
diff --git a/deployment/CMakeLists.txt b/deployment/CMakeLists.txt
index 7f455981bfe56bf0d5b0f3f20f2221e9fd13aa64..59e6f0867bfaff0755dca3b45941884aebe5ec8e 100644
--- a/deployment/CMakeLists.txt
+++ b/deployment/CMakeLists.txt
@@ -11,7 +11,7 @@ if(${PROJECT_SOURCE_DIR} STREQUAL ${CMAKE_SOURCE_DIR})
INCLUDE(InstallRequiredSystemLibraries)
set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "OpenStructure Framework")
- set(CPACK_PACKAGE_VENDOR "2008-2010 -- The OpenStructure Team")
+ set(CPACK_PACKAGE_VENDOR "2008-2020 -- The OpenStructure Team")
set(CPACK_PACKAGE_DESCRIPTION_FILE "${PROJECT_SOURCE_DIR}/ReadMe.txt")
set(CPACK_RESOURCE_FILE_LICENSE "${PROJECT_SOURCE_DIR}/LICENSE.txt")
set(CPACK_PACKAGE_VERSION_MAJOR ${OST_VERSION_MAJOR})
diff --git a/deployment/README.html.in b/deployment/README.html.in
index 2201c8d3ddb15b268dfa16c6e2580a65304218fa..23893a86ce8b8b856d1afad9019a44cf9877bf05 100644
--- a/deployment/README.html.in
+++ b/deployment/README.html.in
@@ -18,7 +18,7 @@
-----------------------------README----------------------------------------<br/>
This file is part of the OpenStructure project <www.openstructure.org><br/>
<br/>
- Copyright (C) 2008-2011 by the OpenStructure authors<br/>
+ Copyright (C) 2008-2020 by the OpenStructure authors<br/>
<br/>
This library is free software; you can redistribute it and/or modify it under<br/>
the terms of the GNU Lesser General Public License as published by the Free<br/>
diff --git a/deployment/macos/deps.py b/deployment/macos/deps.py
index 91ef55c9ada53c569dcf76fde350f57f8161f9e6..63fb51cf797d082f90433e535f6255fec6ae4501 100644
--- a/deployment/macos/deps.py
+++ b/deployment/macos/deps.py
@@ -37,7 +37,7 @@ def collect_deps(stage_dir, components, binaries, libexec_binaries,
lib_name=os.path.abspath(os.path.join(stage_dir, 'lib',
_lib_name(component)))
if not os.path.exists(lib_name):
- print 'WARNING:', lib_name, 'does not exist'
+ print('WARNING:', lib_name, 'does not exist')
if lib_name not in pool:
_deps_for_lib(lib_name, pool)
pool.add(lib_name)
@@ -45,7 +45,7 @@ def collect_deps(stage_dir, components, binaries, libexec_binaries,
bin_name=os.path.abspath(os.path.join(stage_dir, 'bin',
bin))
if not os.path.exists(bin_name):
- print 'WARNING:', bin_name, 'does not exist'
+ print('WARNING:', bin_name, 'does not exist')
continue
if bin_name not in pool:
_deps_for_lib(bin_name, pool)
@@ -53,15 +53,15 @@ def collect_deps(stage_dir, components, binaries, libexec_binaries,
bin_name=os.path.abspath(os.path.join(stage_dir, 'libexec/openstructure',
bin))
if not os.path.exists(bin_name):
- print 'WARNING:', bin_name, 'does not exist'
+ print('WARNING:', bin_name, 'does not exist')
continue
if bin_name not in pool:
_deps_for_lib(bin_name, pool)
for site_package in site_packages:
full_path=get_python_module_path(site_package)
- print full_path
+ print(full_path)
if not os.path.exists(full_path):
- print 'WARNING:', site_package, 'does not exists'
+ print('WARNING:', site_package, 'does not exists')
continue
if os.path.isdir(full_path):
for so_file in glob.glob(os.path.join(full_path, '*.so')):
@@ -99,7 +99,7 @@ def copy_binaries(stage_dir, outdir, binary_names, scripts, bin_dir,
else:
bin_name=os.path.join(stage_dir, binary_name)
if not os.path.exists(bin_name):
- print 'WARNING:', binary_name, 'does not exist'
+ print('WARNING:', binary_name, 'does not exist')
continue
dst_name=os.path.join(outdir, bin_dir, os.path.basename(bin_name))
shutil.copy(bin_name, dst_name)
@@ -123,14 +123,14 @@ def split_framework_components(abs_path):
return lead, trail
def change_id(id, lib):
- os.chmod(lib, 0666)
+ os.chmod(lib, 0o666)
os.system(CHANGE_ID_RPATH % (id,lib))
- os.chmod(lib, 0444)
+ os.chmod(lib, 0o444)
def update_load_commands(lib, exe, exe_path):
direct_deps=set()
_deps_for_lib(lib, direct_deps, recursive=False)
- os.chmod(lib, 0666)
+ os.chmod(lib, 0o666)
for direct_dep in direct_deps:
if direct_dep.endswith('.dylib'):
new_name=os.path.basename(direct_dep)
@@ -142,9 +142,9 @@ def update_load_commands(lib, exe, exe_path):
new_name=os.path.join(framework_name, rel_path)
os.system(CHANGE_LOAD_CMD_RPATH % (direct_dep, new_name, lib))
if exe:
- os.chmod(lib, 0555)
+ os.chmod(lib, 0o555)
else:
- os.chmod(lib, 0444)
+ os.chmod(lib, 0o444)
def copy_deps(dependencies, outdir):
exe_path=os.path.join(outdir, 'bin')
@@ -218,7 +218,7 @@ def make_standalone(stage_dir, outdir, no_includes, force_no_rpath=False,
os.system('mkdir -p "%s/lib"' % outdir)
os.system('mkdir -p "%s/bin"' % outdir)
os.system('mkdir -p "%s/libexec/openstructure"' % outdir)
- print 'copying shared datafiles'
+ print('copying shared datafiles')
shutil.copytree(os.path.join(stage_dir, 'share'),
os.path.join(outdir, 'share'))
scripts=SCRIPTS
@@ -233,7 +233,7 @@ def make_standalone(stage_dir, outdir, no_includes, force_no_rpath=False,
components+=GUI_COMPONENTS
libexec_binaries+=GUI_LIBEXEC_BINARIES
site_packages+=GUI_SITE_PACKAGES
- print 'collecting dependencies'
+ print('collecting dependencies')
deps=collect_deps(stage_dir, components, binaries, libexec_binaries,
site_packages, site_packages_dir)
# when running in non-gui mode, we are most likely missing the boost
@@ -242,14 +242,14 @@ def make_standalone(stage_dir, outdir, no_includes, force_no_rpath=False,
pymod_dir='lib/python%d.%d/site-packages' % sys.version_info[0:2]
_deps_for_lib(os.path.join(stage_dir, pymod_dir, 'ost/_ost_base.so'),
deps, recursive=False)
- print 'copying dependencies'
+ print('copying dependencies')
copy_deps(deps, outdir)
- print 'copying libexec binaries'
+ print('copying libexec binaries')
copy_binaries(stage_dir, outdir, libexec_binaries, libexec_scripts,
'libexec/openstructure')
- print 'copying binaries'
+ print('copying binaries')
copy_binaries(stage_dir, outdir, binaries, scripts, 'bin')
- print 'copying pymod'
+ print('copying pymod')
shutil.copytree(os.path.join(stage_dir,pymod_dir),
os.path.join(outdir, pymod_dir))
copied_py_framework=False
@@ -261,10 +261,10 @@ def make_standalone(stage_dir, outdir, no_includes, force_no_rpath=False,
if len(glob.glob(os.path.join(outdir, 'lib', 'libpython*')))>0:
non_std_python=True
if non_std_python:
- print 'looks like we are using a non-standard python.'
+ print('looks like we are using a non-standard python.')
python_home=get_python_home()
if not copied_py_framework:
- print 'also copying python modules from %s' % python_home
+ print('also copying python modules from %s' % python_home)
modules_dst=os.path.join(outdir, 'lib', os.path.basename(python_home))
shutil.copytree(python_home, modules_dst)
if os.path.exists(os.path.join(modules_dst, 'site-packages')):
@@ -298,23 +298,23 @@ def make_standalone(stage_dir, outdir, no_includes, force_no_rpath=False,
shutil.rmtree(directory)
# replace the python executable
ost_script=os.path.join(outdir, 'libexec', 'openstructure', 'ost_config')
- os.chmod(ost_script, 0666)
+ os.chmod(ost_script, 0o666)
script=''.join(open(ost_script, 'r').readlines())
script=script.replace(python_bin, '$BIN_DIR/python')
open(ost_script, 'w').write(script)
- os.chmod(ost_script, 0555)
+ os.chmod(ost_script, 0o555)
if no_includes:
os.system(REMOVE_HEADERS % outdir)
os.system(REMOVE_CURRENT % outdir)
- print 'copying site-packages'
+ print('copying site-packages')
for sp in SITE_PACKAGES:
src=get_python_module_path(sp)
if os.path.isdir(src):
shutil.copytree(src, os.path.join(outdir, pymod_dir, sp))
else:
shutil.copy(src, os.path.join(outdir, pymod_dir, sp))
- print 'updating link commands of python shared objects'
+ print('updating link commands of python shared objects')
os.path.walk(os.path.join(outdir, 'lib'),
update_pymod_shared_objects,
os.path.join(outdir, 'lib'))
diff --git a/deployment/macos/pack.py b/deployment/macos/pack.py
index beb7d7d74932339475945cee35ccc59048e9f5e1..16b5165778c57433f3fdb505443f697827d7e470 100644
--- a/deployment/macos/pack.py
+++ b/deployment/macos/pack.py
@@ -42,7 +42,7 @@ def collect_deps(stage_dir, components, binaries, libexec_binaries,
lib_name=os.path.abspath(os.path.join(stage_dir, 'lib',
_lib_name(component)))
if not os.path.exists(lib_name):
- print 'WARNING:', lib_name, 'does not exist'
+ print('WARNING:', lib_name, 'does not exist')
if lib_name not in pool:
_deps_for_lib(lib_name, pool)
pool.add(lib_name)
@@ -50,7 +50,7 @@ def collect_deps(stage_dir, components, binaries, libexec_binaries,
bin_name=os.path.abspath(os.path.join(stage_dir, 'bin',
bin))
if not os.path.exists(bin_name):
- print 'WARNING:', bin_name, 'does not exist'
+ print('WARNING:', bin_name, 'does not exist')
continue
if bin_name not in pool:
_deps_for_lib(bin_name, pool)
@@ -58,15 +58,15 @@ def collect_deps(stage_dir, components, binaries, libexec_binaries,
bin_name=os.path.abspath(os.path.join(stage_dir, 'libexec', libexec_path,
bin))
if not os.path.exists(bin_name):
- print 'WARNING:', bin_name, 'does not exist'
+ print('WARNING:', bin_name, 'does not exist')
continue
if bin_name not in pool:
_deps_for_lib(bin_name, pool)
for site_package in site_packages:
full_path=get_python_module_path(site_package)
- print full_path
+ print(full_path)
if not os.path.exists(full_path):
- print 'WARNING:', site_package, 'does not exists'
+ print('WARNING:', site_package, 'does not exists')
continue
if os.path.isdir(full_path):
for so_file in glob.glob(os.path.join(full_path, '*.so')):
@@ -104,7 +104,7 @@ def copy_binaries(stage_dir, outdir, binary_names, scripts, bin_dir,
else:
bin_name=os.path.join(stage_dir, binary_name)
if not os.path.exists(bin_name):
- print 'WARNING:', binary_name, 'does not exist'
+ print('WARNING:', binary_name, 'does not exist')
continue
dst_name=os.path.join(outdir, bin_dir, os.path.basename(bin_name))
shutil.copy(bin_name, dst_name)
@@ -128,14 +128,14 @@ def split_framework_components(abs_path):
return lead, trail
def change_id(id, lib):
- os.chmod(lib, 0666)
+ os.chmod(lib, 0o666)
os.system(CHANGE_ID_RPATH % (id,lib))
- os.chmod(lib, 0444)
+ os.chmod(lib, 0o444)
def update_load_commands(lib, exe, exe_path):
direct_deps=set()
_deps_for_lib(lib, direct_deps, recursive=False)
- os.chmod(lib, 0666)
+ os.chmod(lib, 0o666)
for direct_dep in direct_deps:
if direct_dep.endswith('.dylib'):
new_name=os.path.basename(direct_dep)
@@ -147,9 +147,9 @@ def update_load_commands(lib, exe, exe_path):
new_name=os.path.join(framework_name, rel_path)
os.system(CHANGE_LOAD_CMD_RPATH % (direct_dep, new_name, lib))
if exe:
- os.chmod(lib, 0555)
+ os.chmod(lib, 0o555)
else:
- os.chmod(lib, 0444)
+ os.chmod(lib, 0o444)
def copy_deps(dependencies, outdir):
exe_path=os.path.join(outdir, 'bin')
@@ -209,20 +209,20 @@ def merge_tree(src, dst):
merge_tree(srcname, dstname)
else:
shutil.copy2(srcname, dstname)
- except (IOError, os.error), why:
+ except (IOError, os.error) as why:
errors.append((srcname, dstname, str(why)))
- except shutil.Error, err:
+ except shutil.Error as err:
errors.extend(err.args[0])
try:
shutil.copystat(src, dst)
- except OSError, why:
+ except OSError as why:
if WindowsError is not None and isinstance(why, WindowsError):
# Copying file access times may fail on Windows
pass
else:
errors.extend((src, dst, str(why)))
if errors:
- raise shutil.Error, errors
+ raise shutil.Error(errors)
def get_site_package_dir():
"""
@@ -269,7 +269,7 @@ class Package(object):
self.site_packages=[]
self.site_packages_dir=''
def status(self, message):
- print '%s: %s' % (self.name, message)
+ print('%s: %s' % (self.name, message))
def _prepare_output_dir(self, output_dir):
"""
@@ -287,7 +287,7 @@ class Package(object):
if self.libexec_dir:
out_exec_dir=os.path.join(output_dir, 'libexec', self.libexec_dir)
if not os.path.exists(out_exec_dir):
- print 'making...', out_exec_dir
+ print('making...', out_exec_dir)
os.makedirs(out_exec_dir)
def _copy_site_packages(self, output_dir):
for sp in SITE_PACKAGES:
@@ -296,7 +296,7 @@ class Package(object):
merge_tree(src, os.path.joini(output_dir, self.pymod_dir, sp))
else:
shutil.copy(src, os.path.join(output_dir, self.pymod_dir, sp))
- print 'updating link commands of python shared objects'
+ print('updating link commands of python shared objects')
os.path.walk(os.path.join(output_dir, 'lib'),
update_pymod_shared_objects,
os.path.join(output_dir, 'lib'))
diff --git a/deployment/win/dng.bat b/deployment/win/dng.bat
index f16b3c4bd3652a48a13b43829a03e5cf45b23610..366d4b07d82d9dc38c3d568170a1178688eaaf8a 100644
--- a/deployment/win/dng.bat
+++ b/deployment/win/dng.bat
@@ -2,7 +2,7 @@
REM ------------------------------------------------------------------------------
REM This file is part of the OpenStructure project <www.openstructure.org>
REM
-REM Copyright (C) 2008-2011 by the OpenStructure authors
+REM Copyright (C) 2008-2020 by the OpenStructure authors
REM
REM This library is free software; you can redistribute it and/or modify it under
REM the terms of the GNU Lesser General Public License as published by the Free
diff --git a/doc/conf/conf.py b/doc/conf/conf.py
index d1b395a9222cfa2feb2d1823e6986f3cb49afce0..cb5290b6daa1e635e84c6f577730acfac581941f 100644
--- a/doc/conf/conf.py
+++ b/doc/conf/conf.py
@@ -189,8 +189,8 @@ htmlhelp_basename = 'openstructure-doc'
# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title, author, documentclass [howto/manual]).
latex_documents = [
- ('index', 'OpenStructure.tex', u'OpenStructure Documentation',
- u'OpenStructure authors', 'manual'),
+ ('index', 'OpenStructure.tex', 'OpenStructure Documentation',
+ 'OpenStructure authors', 'manual'),
]
# The name of an image file (relative to this directory) to place at the top of
diff --git a/doc/make.py b/doc/make.py
index 57da9479e30ff0c1d89adef2723f3c843177486b..5d088e7981c3c5844b7e7a0fd876ece97647ab68 100644
--- a/doc/make.py
+++ b/doc/make.py
@@ -5,18 +5,13 @@ import shutil
from ost import settings
from optparse import OptionParser
import subprocess
+from sphinx.application import Sphinx
if len(sys.argv)==2:
root_dir=sys.argv[1]
else:
root_dir='.'
-def _CheckCall(cmd, shell):
- r = subprocess.call(cmd, shell=True)
- if r != 0:
- sys.stderr.write("Command '%s' returned non-zero exit status %d\n"%(cmd, r))
- sys.exit(-1)
-
def _OutputPath(inpath, outdir):
parts=inpath.split(os.path.sep)
filtered_parts=[outdir]
@@ -48,7 +43,7 @@ def _CreateAndCopy(in_name, outdir):
if not os.path.exists(out_dir):
_MkDir(out_dir)
if _RequireCopy(in_name, out_name):
- print 'cp %s %s' % (in_name, out_name)
+ print('cp %s %s' % (in_name, out_name))
os.system('cp %s %s' % (in_name, out_name))
def _MkDir(dirname):
@@ -71,7 +66,6 @@ def _CollectRstDocs(outdir, dirname, fnames):
img_name = os.path.join(dirname,img)
_CreateAndCopy(img_name, outdir)
-
def ParseArgs():
parser = OptionParser("usage: ost make.py [options] ")
parser.add_option("-l","--linkcheck", action="store_true", default=False, dest="linkcheck", help="validate all external links")
@@ -82,36 +76,44 @@ def ParseArgs():
parser.add_option("-q", "--quiet", action="store_true", default=False, dest="quiet", help="run all test")
return parser.parse_args()
+def _SelectBuilders(opts):
+ builders = []
+ if opts.html:
+ builders.append('html')
+
+ if opts.doctest:
+ builders.append('doctest')
+
+ if opts.build_json:
+ builders.append('json')
+
+ if opts.linkcheck:
+ builders.append('linkcheck')
+ return builders
+
+
opts, args=ParseArgs()
if not opts.html and\
not opts.linkcheck and\
not opts.doctest:
opts.html=True
-opt_str=''
+extra_args = {}
if opts.quiet:
- opt_str=' -Q '
+ extra_args['warning'] = None
+ extra_args['status'] = None
for sub_dir in ('modules',):
- os.path.walk(sub_dir, _CollectRstDocs, 'doc/source')
-sphinx_bin=settings.Locate(['sphinx-build', 'sphinx-build-2.6','sphinx-build-2.7'])
-
-if opts.html:
- cmd='%s %s -b html -c %s %s %s' % (sphinx_bin, opt_str,
- 'doc/conf', 'doc/source', 'doc/build/html')
- print cmd
- _CheckCall(cmd, shell=True)
-
-if opts.doctest:
- cmd='%s %s -b doctest -c %s %s %s' % (sphinx_bin, opt_str,
- 'doc/conf', 'doc/source',
- 'doc/build/doctest')
- _CheckCall(cmd, shell=True)
-if opts.build_json:
- cmd='%s %s -b json -c %s %s %s' % (sphinx_bin, opt_str, 'doc/conf',
- 'doc/source', 'doc/build/json')
- _CheckCall(cmd, shell=True)
-if opts.linkcheck:
- cmd='%s %s -b linkcheck -c %s %s %s' % (sphinx_bin, opt_str, 'doc/conf',
- 'doc/source', 'doc/build/check')
- _CheckCall(cmd, shell=True)
+ for directory, dirnames, filenames in os.walk(sub_dir):
+ _CollectRstDocs('doc/source', directory, filenames)
+
+builders = _SelectBuilders(opts)
+
+for builder in builders:
+ Sphinx(
+ srcdir='doc/source',
+ confdir='doc/conf',
+ outdir='doc/build/html',
+ doctreedir='doc/build/html/.doctrees',
+ buildername=builder,
+ **extra_args).build(True)
diff --git a/doc/to_sphinx.py b/doc/to_sphinx.py
index 09809d2351170a195c26aeada9f2c28b6d4a62fa..eab09effc055f273d7b2a89cafddd34ad999542d 100644
--- a/doc/to_sphinx.py
+++ b/doc/to_sphinx.py
@@ -6,9 +6,9 @@ class_name=parts[-1]
__import__(module, globals(), locals())
mod=sys.modules[module]
the_class=getattr(mod, class_name)
-print '.. currentmodule:: %s' % module
-print ''
-print '.. class:: %s' % class_name
+print('.. currentmodule:: %s' % module)
+print('')
+print('.. class:: %s' % class_name)
def _arg_type(arg_type):
if arg_type not in ('str', 'int', 'bool', 'float', 'None'):
@@ -63,10 +63,10 @@ def parse_signature(signature):
return Method(method_match.groupdict()['name'],
_arg_type(method_match.groupdict()['rtype']),
args[1:], opt_args)
- print signature, 'not matched'
+ print(signature, 'not matched')
if '--no-derived' in sys.argv:
- members=the_class.__dict__.keys()
+ members=list(the_class.__dict__.keys())
else:
members=dir(the_class)
for m in members:
@@ -75,4 +75,4 @@ for m in members:
member_doc=getattr(the_class, m).__doc__
if member_doc:
method=parse_signature(member_doc.split('\n')[1])
- print method.to_sphinx()
\ No newline at end of file
+ print(method.to_sphinx())
\ No newline at end of file
diff --git a/docker/Dockerfile b/docker/Dockerfile
index 552fa6b4f46ec6a6818e5ab3cc35d210e75d386a..63df3f9e4267df1c596a16410463708a6463792c 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -2,67 +2,46 @@ FROM ubuntu:18.04
# ARGUMENTS
###########
-
-ARG OPENSTRUCTURE_VERSION="1.11.0"
+ARG OPENSTRUCTURE_VERSION="2.0.0"
ARG SRC_FOLDER="/usr/local/src"
-ARG CPUS_FOR_MAKE=8
-ARG PYTHONPATH="/usr/local/lib64/python2.7/site-packages:${PYTHONPATH}"
-ARG OPENSTRUCTURE_SHARE="/usr/local/share/ost"
+ARG CPUS_FOR_MAKE=2
ARG MSMS_VERSION="2.6.1"
ARG OPENMM_VERSION="7.1.1"
-ARG DSSP_VERSION="2.2.1"
ARG OPENMM_INCLUDE_PATH="/usr/local/openmm/include/"
ARG OPENMM_LIB_PATH="/usr/local/openmm/lib/"
+ARG DEBIAN_FRONTEND=noninteractive
# INSTALL SYSTEM DEPS
#####################
RUN apt-get update -y && apt-get install -y cmake \
g++ \
+ gfortran \
+ wget \
+ tar \
+ libsqlite3-dev \
sip-dev \
libtiff-dev \
libfftw3-dev \
libeigen3-dev \
libboost-all-dev \
libpng-dev \
- python-all \
- python2.7 \
- python-pyqt5 \
qt5-qmake \
qtbase5-dev \
- wget \
- git \
- gfortran \
- python-pip \
- tar \
- libbz2-dev \
+ python3-all \
+ python3-pyqt5 \
+ python3-numpy \
+ python3-scipy \
+ python3-pandas \
doxygen \
swig \
clustalw \
- python-virtualenv \
- libsqlite3-dev \
dssp \
- python-enum34 \
locales && \
# CLEANUP
rm -rf /var/lib/apt/lists/*
-# INSTALL SOME PYTHON PACKAGES GLOBALY
-######################################
-RUN pip install -U pip==9.0.3 && \
- pip install -U setuptools==39.0.1 && \
- pip install --no-cache-dir numpy==1.10.4 \
- scipy==1.0.0 \
- pandas==0.22.0
-
-# SET LOCALE
-############
-# RUN echo "LC_ALL=en_US.UTF-8" >> /etc/environment
-# RUN echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen
-# RUN echo "LANG=en_US.UTF-8" > /etc/locale.conf
-# RUN locale-gen en_US.UTF-8
-
-# DOWNLOAD AND INSTALL MSMS
-###########################
+# INSTALL MSMS
+##############
RUN cd ${SRC_FOLDER} && \
mkdir -p msms && \
cd ${SRC_FOLDER}/msms && \
@@ -73,8 +52,8 @@ RUN cd ${SRC_FOLDER} && \
cp -v ${SRC_FOLDER}/msms/pdb_to_xyzrn /usr/local/bin/pdb_to_xyzrn && \
rm -rf ${SRC_FOLDER}/msms
-# COMPILE OPENMM FROM SOURCES. INSTALL TO /usr/local
-####################################################
+# INSTALL OPENMM
+################
RUN cd ${SRC_FOLDER} && \
wget -O openmm-${OPENMM_VERSION}.tar.gz -nc https://github.com/pandegroup/openmm/archive/${OPENMM_VERSION}.tar.gz && \
mkdir ${SRC_FOLDER}/openmm-${OPENMM_VERSION} && \
@@ -83,42 +62,20 @@ RUN cd ${SRC_FOLDER} && \
cd ${SRC_FOLDER}/openmm-${OPENMM_VERSION}/build && \
cmake .. && make -j $CPUS_FOR_MAKE && make install && \
cd ${SRC_FOLDER}/openmm-${OPENMM_VERSION}/build/python && \
- python setup.py build && python setup.py install && \
- rm -rf ${SRC_FOLDER}/openmm-${OPENMM_VERSION}.tar.gz && \
+ python3 setup.py build && python3 setup.py install && \
+ rm ${SRC_FOLDER}/openmm-${OPENMM_VERSION}.tar.gz && \
rm -rf ${SRC_FOLDER}/openmm-${OPENMM_VERSION}
# INSTALL OST
#############
RUN cd ${SRC_FOLDER} && \
-# copy ost release
+ # copy ost release
wget -O openstructure-${OPENSTRUCTURE_VERSION}.tar.gz -nc https://git.scicore.unibas.ch/schwede/openstructure/repository/${OPENSTRUCTURE_VERSION}/archive.tar.gz && \
mkdir openstructure-${OPENSTRUCTURE_VERSION} && \
tar xf openstructure-${OPENSTRUCTURE_VERSION}.tar.gz -C ${SRC_FOLDER}/openstructure-${OPENSTRUCTURE_VERSION} --strip-components=1 && \
- mkdir -p ${SRC_FOLDER}/openstructure-${OPENSTRUCTURE_VERSION}/build
-
-WORKDIR ${SRC_FOLDER}/openstructure-${OPENSTRUCTURE_VERSION}/build
-
-# cmake ost
-RUN cmake .. -DPYTHON_LIBRARIES=/usr/lib/x86_64-linux-gnu/libpython2.7.so \
- -DOPTIMIZE=ON \
- -DENABLE_MM=ON \
- -DCOMPILE_TMTOOLS=1 \
- -DUSE_NUMPY=1 \
- -DOPEN_MM_LIBRARY=$OPENMM_LIB_PATH/libOpenMM.so \
- -DOPEN_MM_INCLUDE_DIR=$OPENMM_INCLUDE_PATH \
- -DOPEN_MM_PLUGIN_DIR=$OPENMM_LIB_PATH/plugins \
- -DENABLE_GFX=ON \
- -DENABLE_GUI=ON && \
- # Build chemdict_tool
- make -j ${CPUS_FOR_MAKE} chemdict_tool
-
-# get the compound library
-RUN wget ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif.gz
-RUN stage/bin/chemdict_tool create components.cif.gz compounds.chemlib pdb && stage/bin/chemdict_tool update ../modules/conop/data/charmm.cif compounds.chemlib charmm
-RUN mkdir -p $OPENSTRUCTURE_SHARE && chmod a+rw -R $OPENSTRUCTURE_SHARE && mv compounds.chemlib $OPENSTRUCTURE_SHARE
-
-# Build and install OST
-RUN cmake .. -DPYTHON_LIBRARIES=/usr/lib/x86_64-linux-gnu/libpython2.7.so \
+ mkdir -p ${SRC_FOLDER}/openstructure-${OPENSTRUCTURE_VERSION}/build && \
+ cd ${SRC_FOLDER}/openstructure-${OPENSTRUCTURE_VERSION}/build && \
+ cmake .. -DPYTHON_LIBRARIES=/usr/lib/x86_64-linux-gnu/libpython3.6m.so \
-DOPTIMIZE=ON \
-DENABLE_MM=ON \
-DCOMPILE_TMTOOLS=1 \
@@ -128,34 +85,25 @@ RUN cmake .. -DPYTHON_LIBRARIES=/usr/lib/x86_64-linux-gnu/libpython2.7.so \
-DOPEN_MM_PLUGIN_DIR=$OPENMM_LIB_PATH/plugins \
-DENABLE_GFX=ON \
-DENABLE_GUI=ON \
- -DCOMPOUND_LIB=$OPENSTRUCTURE_SHARE/compounds.chemlib && \
- # Build OST with compound library
- make -j ${CPUS_FOR_MAKE} && make check && make install
-
-# GO HOME AND CLEANUP
-#####################
-# RUN apt-get purge -y cmake \
-# wget \
-# git \
-# gfortran \
-# python-pip \
-# libbz2-dev \
-# doxygen \
-# swig
-# RUN apt-get clean
-# RUN apt-get autoremove -y
-#
-# WORKDIR $SRC_FOLDER
-# RUN rm -rf $SRC_FOLDER/*
-
-WORKDIR /home
+ -DCMAKE_C_FLAGS="-isystem /usr/include/boost/ -isystem ${OPENMM_INCLUDE_PATH}/include" \
+ -DCMAKE_CXX_FLAGS="-isystem /usr/include/boost/ -isystem ${OPENMM_INCLUDE_PATH}/include" && \
+ make -j ${CPUS_FOR_MAKE} && \
+ wget ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif.gz && \
+ stage/bin/chemdict_tool create components.cif.gz compounds.chemlib pdb && stage/bin/chemdict_tool update ../modules/conop/data/charmm.cif compounds.chemlib charmm && \
+ cmake .. -DCOMPOUND_LIB=${SRC_FOLDER}/openstructure-${OPENSTRUCTURE_VERSION}/build/compounds.chemlib && \
+ make -j ${CPUS_FOR_MAKE} && make check && make install && \
+ rm ${SRC_FOLDER}/openstructure-${OPENSTRUCTURE_VERSION}.tar.gz && \
+ rm -rf ${SRC_FOLDER}/openstructure-${OPENSTRUCTURE_VERSION}
# ENVIRONMENT
-##############################################################################
+#############
+WORKDIR /home
ENV OST_ROOT="/usr/local"
-ENV PYTHONPATH="/usr/local/lib64/python2.7/site-packages:${PYTHONPATH}"
-ENV LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/local/lib64"
+ENV PYTHONPATH="/usr/local/lib64/python3.6/site-packages"
+ENV LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/local/lib64:/usr/local/openmm/lib/"
ENV QT_X11_NO_MITSHM=1
+ENV OPENSTRUCTURE_VERSION=$OPENSTRUCTURE_VERSION
ENTRYPOINT ["ost"]
CMD ["-i"]
+
diff --git a/docker/README.rst b/docker/README.rst
index bc6efa1ae0f062bcf78f78a6f426d1acff8bb7ae..974c4807bf59ac504fb800ae89f5286a093ab314 100644
--- a/docker/README.rst
+++ b/docker/README.rst
@@ -6,10 +6,22 @@ OST Docker
For many docker installations it is required to run docker commands as root. As
this depends on set up, we skip the ``sudo`` in all commands.
+Obtain Docker image from the OST registry
+-----------------------------------------
+
+OST has its own container registry inside GitLab. There we try to keep one
+image for the latest stable version of OST. You can import it by
+
+.. code-block:: bash
+
+ docker pull registry.scicore.unibas.ch/schwede/openstructure:<TAG>
+
+and just start using it without the overhead to build it yourself.
+
+
Build Docker image
------------------
-
In order to build OST image:
.. code-block:: bash
@@ -155,7 +167,9 @@ To see the help for compare-structures action run:
Run GUI
-------
-In order to run GUI do (tested on linux machine):
+The container is built with GUI support, but this is still to be considered an
+experimental feature as it is known to depend on some properties of the host
+where Docker is run. What works on some Linux machines is the following:
.. code-block:: bash
diff --git a/docker/test_docker.py b/docker/test_docker.py
index e191217e63f9f8de3ff979e54c787a422428394f..38fae4a6093ba8b437d1ca91e63992a6f12a068b 100644
--- a/docker/test_docker.py
+++ b/docker/test_docker.py
@@ -16,4 +16,4 @@ except qsscoring.QSscoreError as ex:
ost.LogError('QSscore failed:', str(ex))
qs_score = 0
-print "OST is working!"
+print("OST is working!")
diff --git a/doxygen/Doxyfile b/doxygen/Doxyfile
index d44e235b5f4b0830b6192bf3a849dd8956b63f5b..1c694fd733c8f4f6a3cebe188166b1146a9e469a 100644
--- a/doxygen/Doxyfile
+++ b/doxygen/Doxyfile
@@ -1,5 +1,8 @@
# Doxyfile 1.5.7
+# RUN in OST_ROOT with "doxygen doxygen/Doxyfile" (assumes compiled in build)
+# -> outout in doc/html
+
#---------------------------------------------------------------------------
# Project related configuration options
#---------------------------------------------------------------------------
@@ -91,7 +94,7 @@ WARN_LOGFILE =
#---------------------------------------------------------------------------
# configuration options related to the input files
#---------------------------------------------------------------------------
-INPUT = ./modules ./stage
+INPUT = ./modules ./build/stage
INPUT_ENCODING = UTF-8
FILE_PATTERNS = *.hh \
*.dox \
diff --git a/examples/code_fragments/ui/board.py b/examples/code_fragments/ui/board.py
deleted file mode 100644
index 6717d72911f1c3fba5490fc5dfb2738324157e4b..0000000000000000000000000000000000000000
--- a/examples/code_fragments/ui/board.py
+++ /dev/null
@@ -1,345 +0,0 @@
-#!/usr/bin/python
-
-# tetris.py
-
-import sys
-import random
-from PyQt5 import QtCore, QtGui, QtWidgets
-
-class Board(QtWidgets.QFrame):
- BoardWidth = 10
- BoardHeight = 22
- Speed = 300
- messageToStatusBar = QtCore.pyqtSignal(str)
-
- def __init__(self, parent=None):
- QtWidgets.QFrame.__init__(self, parent)
- self.resize(180, 380)
- self.setMinimumHeight(380)
- self.setMinimumWidth(180)
- self.timer = QtCore.QBasicTimer()
- self.isWaitingAfterLine = False
- self.curPiece = Shape()
- self.nextPiece = Shape()
- self.curX = 0
- self.curY = 0
- self.numLinesRemoved = 0
- self.board = []
-
- self.setFocusPolicy(QtCore.Qt.StrongFocus)
- self.isStarted = False
- self.isPaused = False
- self.clearBoard()
-
- self.nextPiece.setRandomShape()
-
-
- def shapeAt(self, x, y):
- return self.board[(y * Board.BoardWidth) + x]
-
- def setShapeAt(self, x, y, shape):
- self.board[(y * Board.BoardWidth) + x] = shape
-
- def squareWidth(self):
- return self.contentsRect().width() / Board.BoardWidth
-
- def squareHeight(self):
- return self.contentsRect().height() / Board.BoardHeight
-
- def start(self):
- if self.isPaused:
- return
-
- self.isStarted = True
- self.isWaitingAfterLine = False
- self.numLinesRemoved = 0
- self.clearBoard()
-
- self.messageToStatusBar.emit(str(self.numLinesRemoved))
-
- self.newPiece()
- self.timer.start(Board.Speed, self)
-
- def pause(self):
- if not self.isStarted:
- return
-
- self.isPaused = not self.isPaused
- if self.isPaused:
- self.timer.stop()
- self.messageToStatusBar.emit("paused")
- else:
- self.timer.start(Board.Speed, self)
- self.messageToStatusBar.emit(str(self.numLinesRemoved))
- self.update()
-
- def paintEvent(self, event):
- painter = QtGui.QPainter(self)
- rect = self.contentsRect()
-
- boardTop = rect.bottom() - Board.BoardHeight * self.squareHeight()
-
- for i in range(Board.BoardHeight):
- for j in range(Board.BoardWidth):
- shape = self.shapeAt(j, Board.BoardHeight - i - 1)
- if shape != Tetrominoes.NoShape:
- self.drawSquare(painter,
- rect.left() + j * self.squareWidth(),
- boardTop + i * self.squareHeight(), shape)
-
- if self.curPiece.shape() != Tetrominoes.NoShape:
- for i in range(4):
- x = self.curX + self.curPiece.x(i)
- y = self.curY - self.curPiece.y(i)
- self.drawSquare(painter, rect.left() + x * self.squareWidth(),
- boardTop + (Board.BoardHeight - y - 1) * self.squareHeight(),
- self.curPiece.shape())
-
- def keyPressEvent(self, event):
- if not self.isStarted or self.curPiece.shape() == Tetrominoes.NoShape:
- QtWidgets.QWidget.keyPressEvent(self, event)
- return
-
- key = event.key()
- if key == QtCore.Qt.Key_P:
- self.pause()
- return
- if self.isPaused:
- return
- elif key == QtCore.Qt.Key_Left:
- self.tryMove(self.curPiece, self.curX - 1, self.curY)
- elif key == QtCore.Qt.Key_Right:
- self.tryMove(self.curPiece, self.curX + 1, self.curY)
- elif key == QtCore.Qt.Key_Down:
- self.tryMove(self.curPiece.rotatedRight(), self.curX, self.curY)
- elif key == QtCore.Qt.Key_Up:
- self.tryMove(self.curPiece.rotatedLeft(), self.curX, self.curY)
- elif key == QtCore.Qt.Key_Space:
- self.dropDown()
- elif key == QtCore.Qt.Key_D:
- self.oneLineDown()
- else:
- QtWidgets.QWidget.keyPressEvent(self, event)
-
- def timerEvent(self, event):
- if event.timerId() == self.timer.timerId():
- if self.isWaitingAfterLine:
- self.isWaitingAfterLine = False
- self.newPiece()
- else:
- self.oneLineDown()
- else:
- QtGui.QFrame.timerEvent(self, event)
-
- def clearBoard(self):
- for i in range(Board.BoardHeight * Board.BoardWidth):
- self.board.append(Tetrominoes.NoShape)
-
- def dropDown(self):
- newY = self.curY
- while newY > 0:
- if not self.tryMove(self.curPiece, self.curX, newY - 1):
- break
- newY -= 1
-
- self.pieceDropped()
-
- def oneLineDown(self):
- if not self.tryMove(self.curPiece, self.curX, self.curY - 1):
- self.pieceDropped()
-
- def pieceDropped(self):
- for i in range(4):
- x = self.curX + self.curPiece.x(i)
- y = self.curY - self.curPiece.y(i)
- self.setShapeAt(x, y, self.curPiece.shape())
-
- self.removeFullLines()
-
- if not self.isWaitingAfterLine:
- self.newPiece()
-
- def removeFullLines(self):
- numFullLines = 0
-
- rowsToRemove = []
-
- for i in range(Board.BoardHeight):
- n = 0
- for j in range(Board.BoardWidth):
- if not self.shapeAt(j, i) == Tetrominoes.NoShape:
- n = n + 1
-
- if n == 10:
- rowsToRemove.append(i)
-
- rowsToRemove.reverse()
-
- for m in rowsToRemove:
- for k in range(m, Board.BoardHeight):
- for l in range(Board.BoardWidth):
- self.setShapeAt(l, k, self.shapeAt(l, k + 1))
-
- numFullLines = numFullLines + len(rowsToRemove)
-
- if numFullLines > 0:
- self.numLinesRemoved = self.numLinesRemoved + numFullLines
- self.messageToStatusBar.emit(str(self.LinesRemoved))
- self.isWaitingAfterLine = True
- self.curPiece.setShape(Tetrominoes.NoShape)
- self.update()
-
- def newPiece(self):
- self.curPiece = self.nextPiece
- self.nextPiece.setRandomShape()
- self.curX = Board.BoardWidth / 2 + 1
- self.curY = Board.BoardHeight - 1 + self.curPiece.minY()
-
- if not self.tryMove(self.curPiece, self.curX, self.curY):
- self.curPiece.setShape(Tetrominoes.NoShape)
- self.timer.stop()
- self.isStarted = False
- self.messageToStatusBar.emit("Game over")
-
- def tryMove(self, newPiece, newX, newY):
- for i in range(4):
- x = newX + newPiece.x(i)
- y = newY - newPiece.y(i)
- if x < 0 or x >= Board.BoardWidth or y < 0 or y >= Board.BoardHeight:
- return False
- if self.shapeAt(x, y) != Tetrominoes.NoShape:
- return False
-
- self.curPiece = newPiece
- self.curX = newX
- self.curY = newY
- self.update()
- return True
-
- def drawSquare(self, painter, x, y, shape):
- colorTable = [0x000000, 0xCC6666, 0x66CC66, 0x6666CC,
- 0xCCCC66, 0xCC66CC, 0x66CCCC, 0xDAAA00]
-
- color = QtGui.QColor(colorTable[shape])
- painter.fillRect(x + 1, y + 1, self.squareWidth() - 2,
- self.squareHeight() - 2, color)
-
- painter.setPen(color.lighter())
- painter.drawLine(x, y + self.squareHeight() - 1, x, y)
- painter.drawLine(x, y, x + self.squareWidth() - 1, y)
-
- painter.setPen(color.darker())
- painter.drawLine(x + 1, y + self.squareHeight() - 1,
- x + self.squareWidth() - 1, y + self.squareHeight() - 1)
- painter.drawLine(x + self.squareWidth() - 1,
- y + self.squareHeight() - 1, x + self.squareWidth() - 1, y + 1)
-
-
-class Tetrominoes(object):
- NoShape = 0
- ZShape = 1
- SShape = 2
- LineShape = 3
- TShape = 4
- SquareShape = 5
- LShape = 6
- MirroredLShape = 7
-
-
-class Shape(object):
- coordsTable = (
- ((0, 0), (0, 0), (0, 0), (0, 0)),
- ((0, -1), (0, 0), (-1, 0), (-1, 1)),
- ((0, -1), (0, 0), (1, 0), (1, 1)),
- ((0, -1), (0, 0), (0, 1), (0, 2)),
- ((-1, 0), (0, 0), (1, 0), (0, 1)),
- ((0, 0), (1, 0), (0, 1), (1, 1)),
- ((-1, -1), (0, -1), (0, 0), (0, 1)),
- ((1, -1), (0, -1), (0, 0), (0, 1))
- )
-
- def __init__(self):
- self.coords = [[0,0] for i in range(4)]
- self.pieceShape = Tetrominoes.NoShape
-
- self.setShape(Tetrominoes.NoShape)
-
- def shape(self):
- return self.pieceShape
-
- def setShape(self, shape):
- table = Shape.coordsTable[shape]
- for i in range(4):
- for j in range(2):
- self.coords[i][j] = table[i][j]
-
- self.pieceShape = shape
-
- def setRandomShape(self):
- self.setShape(random.randint(1, 7))
-
- def x(self, index):
- return self.coords[index][0]
-
- def y(self, index):
- return self.coords[index][1]
-
- def setX(self, index, x):
- self.coords[index][0] = x
-
- def setY(self, index, y):
- self.coords[index][1] = y
-
- def minX(self):
- m = self.coords[0][0]
- for i in range(4):
- m = min(m, self.coords[i][0])
-
- return m
-
- def maxX(self):
- m = self.coords[0][0]
- for i in range(4):
- m = max(m, self.coords[i][0])
-
- return m
-
- def minY(self):
- m = self.coords[0][1]
- for i in range(4):
- m = min(m, self.coords[i][1])
-
- return m
-
- def maxY(self):
- m = self.coords[0][1]
- for i in range(4):
- m = max(m, self.coords[i][1])
-
- return m
-
- def rotatedLeft(self):
- if self.pieceShape == Tetrominoes.SquareShape:
- return self
-
- result = Shape()
- result.pieceShape = self.pieceShape
- for i in range(4):
- result.setX(i, self.y(i))
- result.setY(i, -self.x(i))
-
- return result
-
- def rotatedRight(self):
- if self.pieceShape == Tetrominoes.SquareShape:
- return self
-
- result = Shape()
- result.pieceShape = self.pieceShape
- for i in range(4):
- result.setX(i, -self.y(i))
- result.setY(i, self.x(i))
-
- return result
-
-
diff --git a/examples/code_fragments/ui/mdi_example.py b/examples/code_fragments/ui/mdi_example.py
index d6cd2abe2ebe3a9ad3498cd35e0f1bf650c89efe..4309979a0427c53b8740c56316e1b768608095cf 100644
--- a/examples/code_fragments/ui/mdi_example.py
+++ b/examples/code_fragments/ui/mdi_example.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
diff --git a/examples/code_fragments/ui/menubar_example.py b/examples/code_fragments/ui/menubar_example.py
index 52000903c445c972388c30bc11922e0304bb670a..e46db7c827a1b911dd62d878ba6e527a1552d7d6 100644
--- a/examples/code_fragments/ui/menubar_example.py
+++ b/examples/code_fragments/ui/menubar_example.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
diff --git a/examples/code_fragments/ui/widget_example.py b/examples/code_fragments/ui/widget_example.py
index ced1d02fa6b3422b41016a8fd8487c3f6479810b..94c0ff2d1d7b700141634fb652cb5ee8febeee87 100644
--- a/examples/code_fragments/ui/widget_example.py
+++ b/examples/code_fragments/ui/widget_example.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
@@ -19,23 +19,24 @@
from ost import gui
-from PyQt5 import QtCore, QtGui
-from board import Board
+from PyQt5 import QtCore, QtGui, QtWidgets
#Get Panels (Class which manages widgets)
panels=gui.GostyApp.Instance().perspective.panels
#Create Widget
-tetris=Board()
+my_awesome_widget = QtWidgets.QWidget()
+layout = QtWidgets.QVBoxLayout()
+layout.addWidget(QtWidgets.QPushButton('I dont do anything'))
+layout.addWidget(QtWidgets.QPushButton('I do even less'))
+my_awesome_widget.setLayout(layout)
#Wrap widget to Qt Widget
-wid=gui.Widget(tetris)
+wid=gui.Widget(my_awesome_widget)
#Add Widget to widget pool
-panels.AddWidgetToPool("Break Widget",wid)
+panels.AddWidgetToPool("Widget that doesnt do a thing", wid)
#Add Widget to right panel
panels.AddWidget(gui.PanelPosition.RIGHT_PANEL,wid,False)
-#Fun can start..
-tetris.start()
diff --git a/examples/demos/charmm_trj_blur.py b/examples/demos/charmm_trj_blur.py
index f65d0dbccb9f7fb51c4329b5668ec35fd66be378..b6f848ffb6607c9e1772fb42a7a85f9f916753fd 100644
--- a/examples/demos/charmm_trj_blur.py
+++ b/examples/demos/charmm_trj_blur.py
@@ -41,5 +41,5 @@ scene.AutoAutoslab(True)
# create an animation timer and start it
anim=Anim(cg,go)
-print 'Demo 6: Import of a CHARMM trajectory. Type anim.stop() to halt animation, anim.start(100) to start it again with stepsize 100!Starting animation now....'
+print('Demo 6: Import of a CHARMM trajectory. Type anim.stop() to halt animation, anim.start(100) to start it again with stepsize 100!Starting animation now....')
anim.start(50)
diff --git a/examples/demos/correlate.py b/examples/demos/correlate.py
index 55bb4d068002e6de2d4f38ece15a8236fa467b37..f7ff13f29253aaea04d7b2ae6983db1adcc89e0f 100644
--- a/examples/demos/correlate.py
+++ b/examples/demos/correlate.py
@@ -6,7 +6,7 @@
# tabula rasa first
scene.RemoveAll()
-
+import functools
import ost.img.alg as img_alg
from ost.mol.alg import EntityToDensityRosetta, HIGH_RESOLUTION
sdh=io.LoadPDB('data/sdh-complete.pdb')
@@ -42,7 +42,7 @@ scene.CenterOn(map_go)
candidates=io.LoadPDB('data/loop-candidates.pdb',
load_multi=True)
-print len(candidates)
+print(len(candidates))
#-------------------------------------------------------------------------------
def Correlate(candidates):
# this function converts the candidate loop into a density and calculates the
@@ -77,7 +77,7 @@ def Visualize(candidates):
return 0
else:
return 1
- candidates=sorted(candidates, cmp_correl)
+ candidates=sorted(candidates, key=functools.cmp_to_key(cmp_correl))
# create render objects and add to scene
for index, candidate in enumerate(candidates):
diff --git a/examples/demos/gfx_mapslab.py b/examples/demos/gfx_mapslab.py
index 8cc8ca334d2abf5f4dd7911bcb0b77f422da70b1..d7ca61c30dbbb9ea4ae2672a99075b186b3729af 100644
--- a/examples/demos/gfx_mapslab.py
+++ b/examples/demos/gfx_mapslab.py
@@ -12,7 +12,7 @@ for p in img.ExtentIterator(mh.GetExtent()):
mh.SetReal(p,val)
vmin=min(vmin,val)
vmax=max(vmax,val)
-print vmin, vmax
+print(vmin, vmax)
for p in img.ExtentIterator(mh.GetExtent()):
mh.SetReal(p,(mh.GetReal(p)-vmin)/(vmax-vmin))
@@ -55,4 +55,4 @@ scene.Add(go2)
go2.ColorBy('HEAT_MAP',0.2,0.8)
-print 'Demo 4: Projecting the density of a map onto a plane...'
+print('Demo 4: Projecting the density of a map onto a plane...')
diff --git a/examples/demos/load_and_display.py b/examples/demos/load_and_display.py
index 6ce59673c3918dcf0b4bc933af7b98b46541a1d6..b4e140520b5942cb4613ae65d692b5d369894155 100644
--- a/examples/demos/load_and_display.py
+++ b/examples/demos/load_and_display.py
@@ -18,4 +18,4 @@ scene.Add(go)
# center the scene on the geometric center of the SDH
scene.CenterOn(go)
-print 'Demo 1: loading and displaying a pdb file'
+print('Demo 1: loading and displaying a pdb file')
diff --git a/examples/demos/the_hammer.py b/examples/demos/the_hammer.py
index 1c308b2d7ae8ad20d3b0413d783e07b2db3dfd43..114e2baa21e7207e28b1daa2af1141f1fb2335e0 100644
--- a/examples/demos/the_hammer.py
+++ b/examples/demos/the_hammer.py
@@ -82,4 +82,4 @@ grad.SetColorAt(0.5, gfx.Color(1.0, 0.0, 1.0))
grad.SetColorAt(1.0, gfx.Color(1.0, 0.0, 0.0))
b_go.ColorBy('clash', gfx.Color(0,1,0), gfx.Color(1,0,0), 0.0, 10.0, mol.Prop.Level.ATOM)
scene.CenterOn(b_go)
-print 'Demo 7: Illustrating a clash score'
+print('Demo 7: Illustrating a clash score')
diff --git a/modules/base/doc/generic.rst b/modules/base/doc/generic.rst
index 919497f390775a68deee2fcc973a22f29beace75..2d71160dae7dd0640fa506bbea95976e2bea0d2d 100644
--- a/modules/base/doc/generic.rst
+++ b/modules/base/doc/generic.rst
@@ -54,7 +54,7 @@ already exists, it will be overwritten. To check if it exists, use:
.. code-block:: python
exists=atom.HasProp("myfloatprop")
- print exists
+ print(exists)
To access the value of a generic property, we first check if the property exists
and then access it, using the method suitable for the data type of the property.
@@ -65,7 +65,7 @@ level:
for atom in entity.GetAtomList():
if atom.HasProp("myfloatprop"):
- print atom.GetFloatProp("myfloatprop")
+ print(atom.GetFloatProp("myfloatprop"))
When trying to access a property that has not been set, or one that has been
set, but at a different level, an error is thrown. The same is true when trying
@@ -75,13 +75,13 @@ to access a property of a different data type, e.g.:
# all of the following lines will throw errors
# error because the property does not exist
- print atom.GetFloatProp("unknownprop")
+ print(atom.GetFloatProp("unknownprop"))
# error because the property was set at another level
- print entity.GetFloatProp("myfloatprop")
+ print(entity.GetFloatProp("myfloatprop"))
# error because the data type of the property is different
- print atom.GetStringProp("myfloatprop")
+ print(atom.GetStringProp("myfloatprop"))
Use of Generic Properties in Queries
diff --git a/modules/base/doc/logging.rst b/modules/base/doc/logging.rst
index adb5a57682981fec8c588b7bb9aa04d9839c3b15..e9cff1360835ef23e9880f3c5949a5d810e3d41b 100644
--- a/modules/base/doc/logging.rst
+++ b/modules/base/doc/logging.rst
@@ -106,7 +106,7 @@ You can change the verbosity level with the following two methods:
ost.LogLevel.Info
# Outputs: ost._ost_base.LogLevel.Info
- print ost.LogLevel.Info
+ print(ost.LogLevel.Info)
# Outputs: Info
int(ost.LogLevel.Info)
@@ -267,7 +267,7 @@ terminal (or the python shell in DNG). The logger also prints the current time.
levels=['ERROR', 'WARNING', 'SCRIPT', 'INFO',
'VERBOSE', 'DEBUG', 'TRACE']
level=levels[severity]
- print '%s[%s]: %s' % (level, str(datetime.datetime.now()), message),
+ print('%s[%s]: %s' % (level, str(datetime.datetime.now()), message))
py_logger=PyLogger()
ost.PushLogSink(py_logger)
diff --git a/modules/base/pymod/__init__.py.in b/modules/base/pymod/__init__.py.in
index 89316b83115438dfacae9a19500b388369187001..7b39730af57d4ba86e47dabb940dce9030360902 100644
--- a/modules/base/pymod/__init__.py.in
+++ b/modules/base/pymod/__init__.py.in
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
@@ -20,8 +20,8 @@
__all__=['CharList','Correl', 'FileLogSink', 'FloatList', 'FloatMatrix', 'FloatMatrix3', 'FloatMatrix4', 'GetCurrentLogSink', 'GetPrefixPath', 'GetSharedDataPath', 'GetVerbosityLevel', 'Histogram', 'IntList', 'LogDebug', 'LogError', 'LogInfo', 'LogScript', 'LogSink', 'LogTrace', 'LogVerbose', 'LogWarning', 'Max', 'Mean', 'Median', 'Min', 'MultiLogSink', 'PopLogSink', 'PopVerbosityLevel', 'PushLogSink', 'PushVerbosityLevel', 'Range', 'SetPrefixPath', 'StdDev', 'StreamLogSink', 'StringList', 'StringLogSink', 'Units', 'VERSION', 'VERSION_MAJOR', 'VERSION_MINOR', 'VERSION_PATCH', 'WITH_NUMPY', 'conop', 'geom', 'io', 'mol', 'seq', 'stutil' @ALL_ADDITIONAL_MODULES@]
-from _ost_base import *
-from stutil import *
+from ._ost_base import *
+from .stutil import *
class StreamLogSink(LogSink):
def __init__(self, stream):
diff --git a/modules/base/pymod/export_generic_property.cc b/modules/base/pymod/export_generic_property.cc
index b5fab8c7a1291ed4b56715a077e28ca7dac59831..0102ba6b013168bc09e700a132919fdc6739601a 100644
--- a/modules/base/pymod/export_generic_property.cc
+++ b/modules/base/pymod/export_generic_property.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/base/pymod/export_logger.cc b/modules/base/pymod/export_logger.cc
index 1434b4f6721113600427e205a18c85f2e4e754e6..61b5d3f2a60276f9d6b28a81ab26b9f552ae39f0 100644
--- a/modules/base/pymod/export_logger.cc
+++ b/modules/base/pymod/export_logger.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/base/pymod/export_range.cc b/modules/base/pymod/export_range.cc
index 6aea1e0c12d61a935c10a95889ed2f54924e6f69..aa9294b5b8dacdda4a18eae915eddc03bd4dbb7e 100644
--- a/modules/base/pymod/export_range.cc
+++ b/modules/base/pymod/export_range.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/base/pymod/export_units.cc b/modules/base/pymod/export_units.cc
index 80fa61862bd49513f2dfcc69013477479d07c59a..83016d6436587826af0f8912046c0b8f2f85092b 100644
--- a/modules/base/pymod/export_units.cc
+++ b/modules/base/pymod/export_units.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/base/pymod/stutil.py b/modules/base/pymod/stutil.py
index 506675f1213db243103f4a9ecd4a8b2c5502beec..705b56f8d125facef3adbdaa322809a128ff4df2 100644
--- a/modules/base/pymod/stutil.py
+++ b/modules/base/pymod/stutil.py
@@ -15,10 +15,11 @@ def Median(xs):
if len(xs)==0:
raise RuntimeError("Can't calculate median of empty sequence")
sorted_xs=sorted(xs)
+ central_idx = int((len(xs)-1)/2)
if (len(xs) % 2)==0:
- return (sorted_xs[(len(xs)-1)/2]+sorted_xs[(len(xs)-1)/2+1])/2.0
+ return (sorted_xs[central_idx]+sorted_xs[central_idx+1])/2.0
else:
- return sorted_xs[(len(xs)-1)/2]
+ return sorted_xs[central_idx]
def StdDev(xs):
"""
diff --git a/modules/base/pymod/table.py b/modules/base/pymod/table.py
index 994f01000658969c6cffe5291ffe9d67a374a16b..6c9a039f91430512bd800a3c82a51d9d02b047cd 100644
--- a/modules/base/pymod/table.py
+++ b/modules/base/pymod/table.py
@@ -4,7 +4,7 @@ import math
from ost import stutil
import itertools
import operator
-import cPickle
+import pickle
import weakref
from ost import LogError, LogWarning, LogInfo, LogVerbose
@@ -228,7 +228,7 @@ class Table(object):
self.rows=[]
if len(kwargs)>=0:
if not col_names:
- self.col_names=[v for v in kwargs.keys()]
+ self.col_names=[v for v in list(kwargs.keys())]
if not self.col_types:
self.col_types=['string' for u in range(len(self.col_names))]
if len(kwargs)>0:
@@ -249,8 +249,8 @@ class Table(object):
return None
short2long = {'s' : 'string', 'i': 'int', 'b' : 'bool', 'f' : 'float'}
- allowed_short = short2long.keys()
- allowed_long = short2long.values()
+ allowed_short = list(short2long.keys())
+ allowed_long = list(short2long.values())
type_list = []
@@ -359,7 +359,7 @@ class Table(object):
if ty=='string':
return str(value)
if ty=='bool':
- if isinstance(value, str) or isinstance(value, unicode):
+ if isinstance(value, str) or isinstance(value, str):
if value.upper() in ('FALSE', 'NO',):
return False
return True
@@ -525,11 +525,11 @@ Statistics for column %(col)s
data items is different for different columns.
'''
# get column indices
- idxs = [self.GetColIndex(k) for k in d.keys()]
+ idxs = [self.GetColIndex(k) for k in list(d.keys())]
# convert scalar values to list
old_len = None
- for k,v in d.iteritems():
+ for k,v in d.items():
if IsScalar(v):
v = [v]
d[k] = v
@@ -540,7 +540,7 @@ Statistics for column %(col)s
"for all columns in %s"%str(d))
# convert column based dict to row based dict and create row and add data
- for i,data in enumerate(zip(*d.values())):
+ for i,data in enumerate(zip(*list(d.values()))):
new_row = [None for a in range(len(self.col_names))]
for idx,v in zip(idxs,data):
new_row[idx] = self._Coerce(v, self.col_types[idx])
@@ -815,7 +815,7 @@ Statistics for column %(col)s
if not func(row):
matches=False
break
- for key, val in kwargs.iteritems():
+ for key, val in kwargs.items():
if row[self.GetColIndex(key)]!=val:
matches=False
break
@@ -835,7 +835,7 @@ Statistics for column %(col)s
Operands have to be the name of a column or an expression that can be
parsed to float, int, bool or string.
- Valid operators are: and, or, !=, !, <=, >=, ==, =, <, >, +, -, \*, /
+ Valid operators are: and, or, !=, !, <=, >=, ==, =, <, >, +, -, \\*, /
.. code-block:: python
@@ -861,7 +861,7 @@ Statistics for column %(col)s
"""
try:
- from table_selector import TableSelector
+ from .table_selector import TableSelector
except:
raise ImportError("Tried to import from the file table_selector.py, but could not find it!")
@@ -880,8 +880,10 @@ Statistics for column %(col)s
def _LoadOST(stream_or_filename):
fieldname_pattern=re.compile(r'(?P<name>[^[]+)(\[(?P<type>\w+)\])?')
values_pattern=re.compile("([^\" ]+|\"[^\"]*\")+")
+ file_opened=False
if not hasattr(stream_or_filename, 'read'):
stream=open(stream_or_filename, 'r')
+ file_opened=True
else:
stream=stream_or_filename
header=False
@@ -904,10 +906,18 @@ Statistics for column %(col)s
else:
fieldtypes.append('string')
fieldnames.append(match.group('name'))
- tab=Table(fieldnames, fieldtypes)
+ try:
+ tab=Table(fieldnames, fieldtypes)
+ except Exception as e:
+ # potentially fails if we read in crap... clean up and pass on error
+ if file_opened:
+ stream.close()
+ raise e
header=True
continue
tab.AddRow([x.strip('"') for x in values_pattern.findall(line)])
+ if file_opened:
+ stream.close()
if num_lines==0:
raise IOError("Cannot read table from empty stream")
return tab
@@ -921,8 +931,10 @@ Statistics for column %(col)s
@staticmethod
def _LoadCSV(stream_or_filename, sep):
+ file_opened=False
if not hasattr(stream_or_filename, 'read'):
stream=open(stream_or_filename, 'r')
+ file_opened=True
else:
stream=stream_or_filename
reader=csv.reader(stream, delimiter=sep)
@@ -935,6 +947,8 @@ Statistics for column %(col)s
first=False
else:
tab.AddRow(row)
+ if file_opened:
+ stream.close()
if first:
raise IOError('trying to load table from empty CSV stream/file')
@@ -943,17 +957,22 @@ Statistics for column %(col)s
@staticmethod
def _LoadPickle(stream_or_filename):
+ file_opened=False
if not hasattr(stream_or_filename, 'read'):
stream=open(stream_or_filename, 'rb')
+ file_opened=True
else:
stream=stream_or_filename
- return cPickle.load(stream)
+ tab = pickle.load(stream)
+ if file_opened:
+ stream.close()
+ return tab
@staticmethod
def _GuessFormat(filename):
try:
filename = filename.name
- except AttributeError, e:
+ except AttributeError as e:
pass
if filename.endswith('.csv'):
return 'csv'
@@ -1043,8 +1062,20 @@ Statistics for column %(col)s
sign=1
key_index=self.GetColIndex(by)
def _key_cmp(lhs, rhs):
- return sign*cmp(lhs[key_index], rhs[key_index])
- self.rows=sorted(self.rows, _key_cmp)
+ a = lhs[key_index]
+ b = rhs[key_index]
+ # mimic behaviour of the cmp function from Python2 that happily
+ # compared None values
+ if a is None or b is None:
+ if a is None and b is not None:
+ return -1 * sign
+ if b is None and a is not None:
+ return 1 * sign
+ return 0
+ return sign*((a > b) - (a < b))
+
+ import functools
+ self.rows=sorted(self.rows, key=functools.cmp_to_key(_key_cmp))
def GetUnique(self, col, ignore_nan=True):
"""
@@ -1085,7 +1116,7 @@ Statistics for column %(col)s
for col1, col2 in zip(tab['col1'], tab['col2']):
print col1, col2
"""
- return zip(*[self[arg] for arg in args])
+ return list(zip(*[self[arg] for arg in args]))
def Plot(self, x, y=None, z=None, style='.', x_title=None, y_title=None,
z_title=None, x_range=None, y_range=None, z_range=None,
@@ -1106,7 +1137,7 @@ Statistics for column %(col)s
:param z: column name for third dimension
:type z: :class:`str`
- :param style: symbol style (e.g. *.*, *-*, *x*, *o*, *+*, *\**). For a
+ :param style: symbol style (e.g. *.*, *-*, *x*, *o*, *+*, *\\**). For a
complete list check (`matplotlib docu <http://matplotlib.sourceforge.net/api/pyplot_api.html#matplotlib.pyplot.plot>`__).
:type style: :class:`str`
@@ -1172,7 +1203,7 @@ Statistics for column %(col)s
'linear')
:type z_interpol: :class:`str`
- :param \*\*kwargs: additional arguments passed to matplotlib
+ :param \\*\\*kwargs: additional arguments passed to matplotlib
:returns: the ``matplotlib.pyplot`` module
@@ -1468,7 +1499,8 @@ Statistics for column %(col)s
max_val = chr(0)
max_idx = None
for i in range(0, len(self.rows)):
- if self.rows[i][idx]>max_val:
+ val = self.rows[i][idx]
+ if val and val > max_val:
max_val = self.rows[i][idx]
max_idx = i
return max_val, max_idx
@@ -1561,7 +1593,7 @@ Statistics for column %(col)s
'specify the parameter rows with a list of row indices '\
'(max 7)')
else:
- rows=range(len(self.rows))
+ rows=list(range(len(self.rows)))
else:
if not isinstance(rows,list):
rows=[rows]
@@ -1989,7 +2021,7 @@ Statistics for column %(col)s
.. code-block:: python
- values[min(len(values), int(round(len(values)*nth/100+0.5)-1))]
+ values[min(len(values)-1, int(math.floor(len(values)*nth/100.0)))]
where values are the sorted values of *col* not equal to ''None''
@@ -2020,7 +2052,9 @@ Statistics for column %(col)s
percentiles=[]
for nth in nths:
- p=vals[min(len(vals)-1, int(round(len(vals)*nth/100.0+0.5)-1))]
+ # rounding behaviour between Python2 and Python3 changed....
+ # p=vals[min(len(vals)-1, int(round(len(vals)*nth/100.0+0.5)-1))]
+ p=vals[min(len(vals)-1, int(math.floor(len(vals)*nth/100.0)))]
percentiles.append(p)
return percentiles
@@ -2195,9 +2229,13 @@ Statistics for column %(col)s
raise ValueError('unknown format "%s"' % format)
def _SavePickle(self, stream):
+ file_opened=False
if not hasattr(stream, 'write'):
stream=open(stream, 'wb')
- cPickle.dump(self, stream, cPickle.HIGHEST_PROTOCOL)
+ file_opened=True
+ pickle.dump(self, stream, pickle.HIGHEST_PROTOCOL)
+ if file_opened:
+ stream.close()
def _SaveHTML(self, stream_or_filename):
def _escape(s):
@@ -2273,8 +2311,10 @@ Statistics for column %(col)s
stream.close()
def _SaveCSV(self, stream, sep):
+ file_opened=False
if not hasattr(stream, 'write'):
- stream=open(stream, 'wb')
+ stream=open(stream, 'w')
+ file_opened=True
writer=csv.writer(stream, delimiter=sep)
writer.writerow(['%s' % n for n in self.col_names])
@@ -2284,13 +2324,18 @@ Statistics for column %(col)s
if c==None:
row[i]='NA'
writer.writerow(row)
+ if file_opened:
+ stream.close()
+
def _SaveOST(self, stream):
+ file_opened=False
if hasattr(stream, 'write'):
writer=csv.writer(stream, delimiter=' ')
else:
stream=open(stream, 'w')
writer=csv.writer(stream, delimiter=' ')
+ file_opened=True
if self.comment:
stream.write(''.join(['# %s\n' % l for l in self.comment.split('\n')]))
writer.writerow(['%s[%s]' % t for t in zip(self.col_names, self.col_types)])
@@ -2300,17 +2345,22 @@ Statistics for column %(col)s
if c==None:
row[i]='NA'
writer.writerow(row)
-
-
- def GetNumpyMatrix(self, *args):
+ if file_opened:
+ stream.close()
+
+ def GetNumpyMatrixAsArray(self, *args):
'''
- Returns a numpy matrix containing the selected columns from the table as
- columns in the matrix.
+ Returns a numpy array containing the selected columns from the table as
+ columns as a matrix.
Only columns of type *int* or *float* are supported. *NA* values in the
table will be converted to *None* values.
- :param \*args: column names to include in numpy matrix
+ Originally the function used the numpy matrix class but that is going to be
+ deprecated in the future. Numpy itself suggests replacing numpy matrix by
+ numpy array.
+
+ :param \\*args: column names to include in numpy array
:warning: The function depends on *numpy*
'''
@@ -2325,16 +2375,40 @@ Statistics for column %(col)s
idx = self.GetColIndex(arg)
col_type = self.col_types[idx]
if col_type!='int' and col_type!='float':
- raise TypeError("Numpy matrix can only be generated from numeric column types")
+ raise TypeError("Numpy matrix can only be generated from numeric "+\
+ "column types")
idxs.append(idx)
- m = np.matrix([list(self[i]) for i in idxs])
- return m.T
+
+ a = np.array([list(self[i]) for i in idxs])
+ return a.T
except ImportError:
LogError("Function needs numpy, but I could not import it.")
raise
-
+ def GetNumpyMatrix(self, *args):
+ '''
+ *Caution*: Numpy is deprecating the use of the numpy matrix class.
+
+ Returns a numpy matrix containing the selected columns from the table as
+ columns in the matrix.
+
+ Only columns of type *int* or *float* are supported. *NA* values in the
+ table will be converted to *None* values.
+
+ :param \\*args: column names to include in numpy matrix
+
+ :warning: The function depends on *numpy*
+ '''
+ LogWarning("table.GetNumpyMatrix is deprecated, please use "+
+ "table.GetNumpyMatrixAsArray instead")
+ try:
+ import numpy as np
+ m = self.GetNumpyMatrixAsArray(*args)
+ return np.matrix(m)
+ except ImportError:
+ LogError("Function needs numpy, but I could not import it.")
+ raise
def GaussianSmooth(self, col, std=1.0, na_value=0.0, padding='reflect', c=0.0):
@@ -2413,7 +2487,7 @@ Statistics for column %(col)s
:math:`p` are the prefactors to optimize :math:`(a,b,c,...)` and :math:`z`
is the vector containing the result of equation :eq:`op1`.
- The parameter ref_col equals to :math:`z` in both equations, and \*args
+ The parameter ref_col equals to :math:`z` in both equations, and \\*args
are columns :math:`u`, :math:`v` and :math:`w` (or :math:`A` in :eq:`op2`).
All columns must be specified by their names.
@@ -2425,7 +2499,7 @@ Statistics for column %(col)s
The function returns a list containing the prefactors
:math:`a, b, c, ...` in the correct order (i.e. same as columns were
- specified in \*args).
+ specified in \\*args).
Weighting:
If the kwarg weights="columX" is specified, the equations are weighted by
@@ -2455,20 +2529,20 @@ Statistics for column %(col)s
if len(args)==0:
raise RuntimeError("At least one column must be specified.")
- b = self.GetNumpyMatrix(ref_col)
- a = self.GetNumpyMatrix(*args)
-
+ b = self.GetNumpyMatrixAsArray(ref_col)
+ a = self.GetNumpyMatrixAsArray(*args)
+
if len(kwargs)!=0:
- if kwargs.has_key('weights'):
- w = self.GetNumpyMatrix(kwargs['weights'])
+ if 'weights' in kwargs:
+ w = self.GetNumpyMatrixAsArray(kwargs['weights'])
b = np.multiply(b,w)
a = np.multiply(a,w)
else:
raise RuntimeError("specified unrecognized kwargs, use weights as key")
- k = (a.T*a).I*a.T*b
- return list(np.array(k.T).reshape(-1))
+ k = np.linalg.inv(a.T@a)@a.T@b
+ return list(k.T.reshape(-1))
except ImportError:
LogError("Function needs numpy, but I could not import it.")
@@ -3048,7 +3122,7 @@ Statistics for column %(col)s
num_rows = len(tab.rows)
for i in range(0,num_rows):
row = tab.rows[i]
- data = dict(zip(tab.col_names,row))
+ data = dict(list(zip(tab.col_names,row)))
self.AddRow(data, overwrite)
@@ -3133,7 +3207,7 @@ def Merge(table1, table2, by, only_matching=False):
raise ValueError('duplicate key "%s" in second table' % (str(key)))
common2[key]=row
new_tab=Table(table1.col_names+col_names, table1.col_types+col_types)
- for k, v in common1.iteritems():
+ for k, v in common1.items():
row=v+[None for i in range(len(table2.col_names)-len(common2_indices))]
matched=False
if k in common2:
@@ -3146,7 +3220,7 @@ def Merge(table1, table2, by, only_matching=False):
new_tab.AddRow(row)
if only_matching:
return new_tab
- for k, v in common2.iteritems():
+ for k, v in common2.items():
if not k in common1:
v2=[v[i] for i in new_index]
row=[None for i in range(len(table1.col_names))]+v2
@@ -3155,3 +3229,5 @@ def Merge(table1, table2, by, only_matching=False):
new_tab.AddRow(row)
return new_tab
+
+# LocalWords: numpy Numpy
diff --git a/modules/base/pymod/testutils.py b/modules/base/pymod/testutils.py
index 5dd8762e2dc31ccc6cdee9ef5af34631e4d7cfd8..4b701fe08fa6ae71e1648bd1330a2a907c777bb9 100644
--- a/modules/base/pymod/testutils.py
+++ b/modules/base/pymod/testutils.py
@@ -41,7 +41,7 @@ def RunTests():
import __main__
from ost import xmlrunner
for name, obj in inspect.getmembers(__main__):
- if (isinstance(obj, (type, types.ClassType)) and
+ if (isinstance(obj, type) and
issubclass(obj, unittest.TestCase)):
suite = unittest.TestLoader().loadTestsFromTestCase(obj)
stream = open('PYTEST-%s.xml'%name, 'w')
@@ -50,8 +50,8 @@ def RunTests():
else:
unittest.main()
- except Exception, e:
- print e
+ except Exception as e:
+ print(e)
def SetDefaultCompoundLib():
@@ -92,7 +92,7 @@ def SetDefaultCompoundLib():
# try to get the shared data path?
try:
shared_data_path = GetSharedDataPath()
- except Exception, e:
+ except Exception as e:
SetPrefixPath(os.path.abspath(os.path.join(conop.__path__[0], os.pardir,
os.pardir, os.pardir,
os.pardir, os.pardir)))
diff --git a/modules/base/pymod/wrap_base.cc b/modules/base/pymod/wrap_base.cc
index b0cfa84655e8574cad01d64f370d8e4ab5001163..2c4877911aced587eb5d5ae0f930beb5eab67cea 100644
--- a/modules/base/pymod/wrap_base.cc
+++ b/modules/base/pymod/wrap_base.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
@@ -58,15 +58,21 @@ struct stringref_from_python_string
static void* convertible(PyObject* obj_ptr)
{
- if (!PyString_Check(obj_ptr)) return 0;
+ if (!PyUnicode_Check(obj_ptr)) return 0;
return obj_ptr;
}
static void construct(PyObject* obj_ptr,
boost::python::converter::rvalue_from_python_stage1_data* data)
{
- const char* value = PyString_AsString(obj_ptr);
- if (value == 0) boost::python::throw_error_already_set();
+ PyObject* temp_bytes = PyUnicode_AsEncodedString(obj_ptr, "UTF-8", "strict");
+ char* value = NULL;
+ if (temp_bytes != NULL) {
+ value = PyBytes_AS_STRING(temp_bytes);
+ value = strdup(value);
+ Py_DECREF(temp_bytes);
+ }
+ if (value == NULL) boost::python::throw_error_already_set();
void* storage = (
(boost::python::converter::rvalue_from_python_storage<ost::StringRef>*)
data)->storage.bytes;
diff --git a/modules/base/pymod/xmlrunner.py b/modules/base/pymod/xmlrunner.py
index e2bcae76df26efef15363d6775dca6b8bbd0bc34..0ea3332628d3a85f26a55d140fcb5172dc379f5d 100644
--- a/modules/base/pymod/xmlrunner.py
+++ b/modules/base/pymod/xmlrunner.py
@@ -16,7 +16,7 @@ import unittest
from xml.sax.saxutils import escape
try:
- from StringIO import StringIO
+ from io import StringIO
except ImportError:
from io import StringIO
@@ -297,7 +297,7 @@ class XMLTestRunnerTest(unittest.TestCase):
"""
class TestTest(unittest.TestCase):
def test_foo(self):
- self.assert_(False)
+ self.assertTrue(False)
self._try_test_run(TestTest, """<testsuite errors="0" failures="1" name="unittest.TestSuite" tests="1" time="0.000">
<testcase classname="__main__.TestTest" name="test_foo" time="0.000">
<failure type="exceptions.AssertionError">Foobar</failure>
diff --git a/modules/base/src/boost_filesystem_helper.cc b/modules/base/src/boost_filesystem_helper.cc
index b235b0498dbb26fee19814e41692d254c2304f87..0bd4af2e7edc720da54b42b002bafde8a4fb841b 100644
--- a/modules/base/src/boost_filesystem_helper.cc
+++ b/modules/base/src/boost_filesystem_helper.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/base/src/boost_filesystem_helper.hh b/modules/base/src/boost_filesystem_helper.hh
index 03a9786e75d838d97fbee3694a59fb79dd177132..1e58965c4d0fda99f803f76a806abe99cbe4fc04 100644
--- a/modules/base/src/boost_filesystem_helper.hh
+++ b/modules/base/src/boost_filesystem_helper.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/base/src/dyn_cast.hh b/modules/base/src/dyn_cast.hh
index c5c5c6253138bb20a0bba21cbcdc379bb629f10c..683157ae1504b822662d06affff1701a6278b9c1 100644
--- a/modules/base/src/dyn_cast.hh
+++ b/modules/base/src/dyn_cast.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/base/src/export_helper/generic_property_def.hh b/modules/base/src/export_helper/generic_property_def.hh
index ff02641c5a1e436a590aa8f23e0529f7dda88031..0311ec2ad88bf469beb38c6d1bfebcf9ae559666 100644
--- a/modules/base/src/export_helper/generic_property_def.hh
+++ b/modules/base/src/export_helper/generic_property_def.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/base/src/export_helper/pair_to_tuple_conv.hh b/modules/base/src/export_helper/pair_to_tuple_conv.hh
index 887a8056733296689c5e2f4478211c05389afbb0..cacc8d8f87297f0d3e93c84fa9a52ebe7f7d7aa3 100644
--- a/modules/base/src/export_helper/pair_to_tuple_conv.hh
+++ b/modules/base/src/export_helper/pair_to_tuple_conv.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/base/src/export_helper/vec_to_list_conv.hh b/modules/base/src/export_helper/vec_to_list_conv.hh
index 0220885ae0d690447db23e8885350b7d2ef6dcb2..f8900bf476b02994521dccbea8420e0efd48c30b 100644
--- a/modules/base/src/export_helper/vec_to_list_conv.hh
+++ b/modules/base/src/export_helper/vec_to_list_conv.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/base/src/generic_property.cc b/modules/base/src/generic_property.cc
index d537009e5cca0ef75a3dea89a1814fe8dc0c4a6a..fb71af0f9c41e16cf10c74717951baad4d71e515 100644
--- a/modules/base/src/generic_property.cc
+++ b/modules/base/src/generic_property.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/base/src/generic_property.hh b/modules/base/src/generic_property.hh
index 7c0ba516ae6068b079028e940aa5708019cfbf5e..ff479e27bbffd04f3029eeab96cb99eaf6fa2c9f 100644
--- a/modules/base/src/generic_property.hh
+++ b/modules/base/src/generic_property.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/base/src/integrity_error.hh b/modules/base/src/integrity_error.hh
index ca6b01616d295475ddc5dc4868cf6b995d49893a..3a7acf14f8a9a20c5c2639da6fc1ec036355b1c5 100644
--- a/modules/base/src/integrity_error.hh
+++ b/modules/base/src/integrity_error.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/base/src/invalid_handle.hh b/modules/base/src/invalid_handle.hh
index 314d23cd4ae767bbf8a0905d3d939ba9a70c905c..bd3cf2cfb61116a22f13acf8e1ac26f70b95fef4 100644
--- a/modules/base/src/invalid_handle.hh
+++ b/modules/base/src/invalid_handle.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/base/src/log.cc b/modules/base/src/log.cc
index ff752c24f392d20d96c088e89eeb0d7fc46dbe92..3e06335827bf9a1ace4063fd4bbea8b14017acfe 100644
--- a/modules/base/src/log.cc
+++ b/modules/base/src/log.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/base/src/log.hh b/modules/base/src/log.hh
index 934ee37bb18b9d5806b42a8109078867258f1204..c75256de1bcd20f725b26b04e64d307b447ee55d 100644
--- a/modules/base/src/log.hh
+++ b/modules/base/src/log.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/base/src/log_sink.cc b/modules/base/src/log_sink.cc
index 4521e74a3398480327b98f44f318b20ab0886740..4b2a0fa77c4e040c3ecd4347c157b5eeef0ebb93 100644
--- a/modules/base/src/log_sink.cc
+++ b/modules/base/src/log_sink.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/base/src/log_sink.hh b/modules/base/src/log_sink.hh
index f06d4ae1c6221c0691a5715cc60bc355b4344431..1bb25e5ed26eb107090d3ed268c9b32e6c5e60ad 100644
--- a/modules/base/src/log_sink.hh
+++ b/modules/base/src/log_sink.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/base/src/message.cc b/modules/base/src/message.cc
index 572480206588eaf96cbe29e7f748d8c68c8952d2..7519c1e01ea9cfc38e82c4d20e0ccaed6e623b84 100644
--- a/modules/base/src/message.cc
+++ b/modules/base/src/message.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/base/src/message.hh b/modules/base/src/message.hh
index 5dd148264d3f6a867be593fcd0a5725dde377b31..1f6d24ab0be92b48905dffd48813a9360572b2c9 100644
--- a/modules/base/src/message.hh
+++ b/modules/base/src/message.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/base/src/module_config.hh b/modules/base/src/module_config.hh
index 6a4c6adf4fc740ffb994db67b2526011b13d4cf4..4b40fc211ffabbecf93d5d9e9242ab448902af8b 100644
--- a/modules/base/src/module_config.hh
+++ b/modules/base/src/module_config.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/base/src/platform.cc b/modules/base/src/platform.cc
index 66f96b82793ba061940963304a06f52ed2545597..48605adb4c348f4a2409b0ceeb1223709e3d6004 100644
--- a/modules/base/src/platform.cc
+++ b/modules/base/src/platform.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/base/src/platform.hh b/modules/base/src/platform.hh
index 57af6e9b5b73998915ced690fec3e1f99fd6c4d2..07ad202f72f86e5718ca209fe4ac8b96971716bc 100644
--- a/modules/base/src/platform.hh
+++ b/modules/base/src/platform.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/base/src/pod_vector.hh b/modules/base/src/pod_vector.hh
index 5e45bd2f88f3727b43ac81dc343b297c687c6f49..e299a265f68a53b97d965aef5dbd283b9d630a58 100644
--- a/modules/base/src/pod_vector.hh
+++ b/modules/base/src/pod_vector.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/base/src/profile.cc b/modules/base/src/profile.cc
index 1a3bae89c6d2c1486606294105fa2a8a31fd437a..4162bf79b176cd6f9e87ee0c57d871e6c24c01fc 100644
--- a/modules/base/src/profile.cc
+++ b/modules/base/src/profile.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/base/src/profile.hh b/modules/base/src/profile.hh
index a255bfce26a9a3a86edf515b89e37c7715674d05..d9854c471ae9ca814624eacb39d6b6b3df786fef 100644
--- a/modules/base/src/profile.hh
+++ b/modules/base/src/profile.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/base/src/ptr_observer.hh b/modules/base/src/ptr_observer.hh
index 4b98e1fd52b972deea02b6207dcb0f1bfedb48bc..f04dad9f1768662ad552d09addc247d3d046d0b6 100644
--- a/modules/base/src/ptr_observer.hh
+++ b/modules/base/src/ptr_observer.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/base/src/range.hh b/modules/base/src/range.hh
index 64f78a183a4f40ebca2fbdf42c0d1e3d7dea2f37..bed05bf308c778d9840dab2c82b8439adb8f9f8c 100644
--- a/modules/base/src/range.hh
+++ b/modules/base/src/range.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/base/src/string_ref.cc b/modules/base/src/string_ref.cc
index 03209b11fabacadbff82daae3f36c80b1140f898..a46245a274e864bb28eeaad9852fc1c584059133 100644
--- a/modules/base/src/string_ref.cc
+++ b/modules/base/src/string_ref.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/base/src/string_ref.hh b/modules/base/src/string_ref.hh
index 38ab290bfa7e97e5aac93b09180dc9b89e0f0af5..f7dfe59e4529ba53e97b9fbe7dfda4fee735b497 100644
--- a/modules/base/src/string_ref.hh
+++ b/modules/base/src/string_ref.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/base/src/test_utils/compare_files.cc b/modules/base/src/test_utils/compare_files.cc
index 13dac63adcd4a2f8244303f66d187cadade08ba3..265914ca1036d08e45c9b957656da7b184206e6c 100644
--- a/modules/base/src/test_utils/compare_files.cc
+++ b/modules/base/src/test_utils/compare_files.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/base/src/test_utils/compare_files.hh b/modules/base/src/test_utils/compare_files.hh
index 15edfa7c6aff8b51e794c52685a19dd5b7a830f2..57ab1f6c21e02d5c9b4c9df91663c84425c4f7e9 100644
--- a/modules/base/src/test_utils/compare_files.hh
+++ b/modules/base/src/test_utils/compare_files.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/base/src/units.cc b/modules/base/src/units.cc
index cb0f7dc554f31f5ddcd6955d5820d55897203e9f..28648bb0207601e64ff57b778574edd7f2edaed5 100644
--- a/modules/base/src/units.cc
+++ b/modules/base/src/units.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/base/src/units.hh b/modules/base/src/units.hh
index 65dcd8004754c1e87731fa6f3c5c202a47e9cff8..2b1cb7d0cb204c3b1789a402e443dbbd5c64b35e 100644
--- a/modules/base/src/units.hh
+++ b/modules/base/src/units.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/base/tests/test_generic_property.cc b/modules/base/tests/test_generic_property.cc
index c30c1fc6ffd83058a386b6afc4f6855d5db6244d..8846978a383566254a0ea90bc2617378b8261b64 100644
--- a/modules/base/tests/test_generic_property.cc
+++ b/modules/base/tests/test_generic_property.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/base/tests/test_pod_vector.cc b/modules/base/tests/test_pod_vector.cc
index 3cf34fc4c511f06619bea27f09e78b3ab70fe292..e500db5876cec214839e7ad37d662c5644548e6e 100644
--- a/modules/base/tests/test_pod_vector.cc
+++ b/modules/base/tests/test_pod_vector.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/base/tests/test_string_ref.cc b/modules/base/tests/test_string_ref.cc
index 7ef5b67768347822693f6d75918e7954a109e716..6b75fd0f6b9ec4f303d10df3d7a5ef1df197d1a7 100644
--- a/modules/base/tests/test_string_ref.cc
+++ b/modules/base/tests/test_string_ref.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
@@ -80,7 +80,7 @@ BOOST_AUTO_TEST_CASE(test_string_ref)
// to_int
std::pair<bool, int> r=sr.to_int();
BOOST_CHECK(r.first==true);
- BOOST_CHECK(r.second=12345);
+ BOOST_CHECK(r.second==12345);
r=StringRef("x", 1).to_int();
BOOST_CHECK(r.first==false);
r=StringRef("12.34", 5).to_int();
@@ -89,10 +89,10 @@ BOOST_AUTO_TEST_CASE(test_string_ref)
// to_float
std::pair<bool, Real> r2=StringRef("1", 1).to_float();
BOOST_CHECK(r2.first==true);
- BOOST_CHECK(r2.second=1.0);
+ BOOST_CHECK(r2.second==1.0);
r2=StringRef("1.5", 3).to_float();
BOOST_CHECK(r2.first==true);
- BOOST_CHECK(r2.second=1.5);
+ BOOST_CHECK(r2.second==1.5);
r2=StringRef("x", 1).to_float();
BOOST_CHECK(r2.first==false);
r2=StringRef("12.3.4", 6).to_float();
@@ -103,10 +103,10 @@ BOOST_AUTO_TEST_CASE(test_string_ref)
// to_float_with_exp
std::pair<bool, Real> r3=StringRef("1", 1).to_float();
BOOST_CHECK(r3.first==true);
- BOOST_CHECK(r3.second=1.0);
+ BOOST_CHECK(r3.second==1.0);
r3=StringRef("1.5", 3).to_float();
BOOST_CHECK(r3.first==true);
- BOOST_CHECK(r3.second=1.5);
+ BOOST_CHECK(r3.second==1.5);
r3=StringRef("x", 1).to_float();
BOOST_CHECK(r3.first==false);
r3=StringRef("12.3.4", 6).to_float();
diff --git a/modules/base/tests/test_table.py b/modules/base/tests/test_table.py
index 347183262b12b7881631d952da072652c5407996..52dee4de4d2dea7aba14fea4f299047156c7f0d6 100644
--- a/modules/base/tests/test_table.py
+++ b/modules/base/tests/test_table.py
@@ -19,19 +19,19 @@ try:
import numpy as np
except ImportError:
HAS_NUMPY=False
- print "Could not find numpy: ignoring some table class unit tests"
+ print("Could not find numpy: ignoring some table class unit tests")
try:
import scipy.stats.mstats
except ImportError:
HAS_SCIPY_STATS=False
- print "Could not find scipy.stats.mstats: ignoring some table class unit tests"
+ print("Could not find scipy.stats.mstats: ignoring some table class unit tests")
try:
import scipy.ndimage
except ImportError:
HAS_SCIPY_NDIMG=False
- print "Could not find scipy.ndimage: ignoring some table class unit tests"
+ print("Could not find scipy.ndimage: ignoring some table class unit tests")
try:
@@ -39,14 +39,14 @@ try:
matplotlib.use('Agg')
except ImportError:
HAS_MPL=False
- print "Could not find matplotlib: ignoring some table class unit tests"
+ print("Could not find matplotlib: ignoring some table class unit tests")
try:
from PIL import Image
from PIL import ImageChops
except ImportError:
HAS_PIL=False
- print "Could not find python imagine library: ignoring some table class unit tests"
+ print("Could not find python imagine library: ignoring some table class unit tests")
# setting up an OST LogSink to capture error messages
class _FetchLog(ost.LogSink):
@@ -57,7 +57,7 @@ class _FetchLog(ost.LogSink):
def LogMessage(self, message, severity):
levels=['ERROR', 'WARNING', 'INFO', 'VERBOSE', 'DEBUG', 'TRACE']
level=levels[severity]
- if not level in self.messages.keys():
+ if not level in list(self.messages.keys()):
self.messages[level] = list()
self.messages[level].append(message.strip())
@@ -128,7 +128,7 @@ class TestTable(unittest.TestCase):
dictionary containing a list of values for each column.
'''
self.CompareColCount(t, len(data_dict))
- for k, v in data_dict.iteritems():
+ for k, v in data_dict.items():
self.CompareDataForCol(t, k, v)
def CompareDataForCol(self, t, col_name, ref_data):
@@ -186,8 +186,8 @@ class TestTable(unittest.TestCase):
def testAllowsToSearchColNames(self):
tab = self.CreateTestTable()
- self.assertEquals(tab.SearchColNames('d$'), ['second', 'third'])
- self.assertEquals(tab.SearchColNames('(first|third)'), ['first','third'])
+ self.assertEqual(tab.SearchColNames('d$'), ['second', 'third'])
+ self.assertEqual(tab.SearchColNames('(first|third)'), ['first','third'])
def testProvidesDirectAccessToColumns(self):
tab = Table(['x', 'two'], 'ii')
@@ -218,10 +218,10 @@ class TestTable(unittest.TestCase):
self.assertEqual(z[1][0], 'x')
self.assertEqual(z[1][1], 'x')
z=tab.Zip('col1', 'col4')
- self.assertEquals(type(z[0][0]),str)
- self.assertEquals(type(z[1][0]),str)
- self.assertEquals(type(z[0][1]),int)
- self.assertEquals(type(z[1][1]),int)
+ self.assertEqual(type(z[0][0]),str)
+ self.assertEqual(type(z[1][0]),str)
+ self.assertEqual(type(z[0][1]),int)
+ self.assertEqual(type(z[1][1]),int)
self.assertRaises(ValueError, tab.Zip, 'col5', 'col3')
def testPercentiles(self):
tab = Table(['nums'], 'i')
@@ -340,7 +340,7 @@ class TestTable(unittest.TestCase):
4.000
'''
- tab = Table(['x'], 'f', x=range(5))
+ tab = Table(['x'], 'f', x=list(range(5)))
self.CompareColCount(tab, 1)
self.CompareRowCount(tab, 5)
self.CompareColNames(tab, ['x'])
@@ -377,7 +377,7 @@ class TestTable(unittest.TestCase):
'''
- tab = Table(['foo', 'bar'], 'si', bar=range(10,14), foo=['i','love','unit','tests'])
+ tab = Table(['foo', 'bar'], 'si', bar=list(range(10,14)), foo=['i','love','unit','tests'])
self.CompareColCount(tab, 2)
self.CompareRowCount(tab, 4)
self.CompareColNames(tab, ['foo','bar'])
@@ -390,7 +390,7 @@ class TestTable(unittest.TestCase):
'''
self.assertRaises(ValueError, Table, ['foo', 'bar'], 'si',
- bar=range(10,14), foo=['i','love','tests'])
+ bar=list(range(10,14)), foo=['i','love','tests'])
def testTableInitMultiColMultiValueAndNoneNonEmpty(self):
@@ -672,40 +672,40 @@ class TestTable(unittest.TestCase):
def testParseColumnTypes(self):
types = Table._ParseColTypes(['i','f','s','b'])
- self.assertEquals(types, ['int','float','string','bool'])
+ self.assertEqual(types, ['int','float','string','bool'])
types = Table._ParseColTypes(['int','float','string','bool'])
- self.assertEquals(types, ['int','float','string','bool'])
+ self.assertEqual(types, ['int','float','string','bool'])
types = Table._ParseColTypes(['i','float','s','bool'])
- self.assertEquals(types, ['int','float','string','bool'])
+ self.assertEqual(types, ['int','float','string','bool'])
types = Table._ParseColTypes(['i','fLOAT','S','bool'])
- self.assertEquals(types, ['int','float','string','bool'])
+ self.assertEqual(types, ['int','float','string','bool'])
types = Table._ParseColTypes('ifsb')
- self.assertEquals(types, ['int','float','string','bool'])
+ self.assertEqual(types, ['int','float','string','bool'])
types = Table._ParseColTypes('int,float,string,bool')
- self.assertEquals(types, ['int','float','string','bool'])
+ self.assertEqual(types, ['int','float','string','bool'])
types = Table._ParseColTypes('int,f,s,bool')
- self.assertEquals(types, ['int','float','string','bool'])
+ self.assertEqual(types, ['int','float','string','bool'])
types = Table._ParseColTypes('INT,F,s,bOOL')
- self.assertEquals(types, ['int','float','string','bool'])
+ self.assertEqual(types, ['int','float','string','bool'])
types = Table._ParseColTypes('boOl')
- self.assertEquals(types, ['bool'])
+ self.assertEqual(types, ['bool'])
types = Table._ParseColTypes('S')
- self.assertEquals(types, ['string'])
+ self.assertEqual(types, ['string'])
types = Table._ParseColTypes(['i'])
- self.assertEquals(types, ['int'])
+ self.assertEqual(types, ['int'])
types = Table._ParseColTypes(['FLOAT'])
- self.assertEquals(types, ['float'])
+ self.assertEqual(types, ['float'])
self.assertRaises(ValueError, Table._ParseColTypes, 'bfstring')
self.assertRaises(ValueError, Table._ParseColTypes, ['b,f,string'])
@@ -765,23 +765,23 @@ class TestTable(unittest.TestCase):
tab = Table()
# None values
- self.assertEquals(tab._Coerce('NA', 'x'), None)
- self.assertEquals(tab._Coerce(None, 'x'), None)
+ self.assertEqual(tab._Coerce('NA', 'x'), None)
+ self.assertEqual(tab._Coerce(None, 'x'), None)
# int type
self.assertTrue(isinstance(tab._Coerce(2 ,'int'), int))
- self.assertEquals(tab._Coerce(2 ,'int'), 2)
+ self.assertEqual(tab._Coerce(2 ,'int'), 2)
self.assertTrue(isinstance(tab._Coerce(2.2 ,'int'), int))
- self.assertEquals(tab._Coerce(2.2 ,'int'), 2)
- self.assertEquals(tab._Coerce(True ,'int'), 1)
- self.assertEquals(tab._Coerce(False ,'int'), 0)
+ self.assertEqual(tab._Coerce(2.2 ,'int'), 2)
+ self.assertEqual(tab._Coerce(True ,'int'), 1)
+ self.assertEqual(tab._Coerce(False ,'int'), 0)
self.assertRaises(ValueError, tab._Coerce, "foo" , 'int')
# float type
self.assertTrue(isinstance(tab._Coerce(2 ,'float'), float))
- self.assertEquals(tab._Coerce(2 ,'float'), 2.000)
+ self.assertEqual(tab._Coerce(2 ,'float'), 2.000)
self.assertTrue(isinstance(tab._Coerce(3.141 ,'float'), float))
- self.assertEquals(tab._Coerce(3.141 ,'float'), 3.141)
+ self.assertEqual(tab._Coerce(3.141 ,'float'), 3.141)
self.assertRaises(ValueError, tab._Coerce, "foo" , 'float')
# string type
@@ -793,13 +793,13 @@ class TestTable(unittest.TestCase):
self.assertTrue(isinstance(tab._Coerce(False ,'string'), str))
# bool type
- self.assertEquals(tab._Coerce(True ,'bool'), True)
- self.assertEquals(tab._Coerce(False ,'bool'), False)
- self.assertEquals(tab._Coerce('falSE' ,'bool'), False)
- self.assertEquals(tab._Coerce('no' ,'bool'), False)
- self.assertEquals(tab._Coerce('not false and not no','bool'), True)
- self.assertEquals(tab._Coerce(0, 'bool'), False)
- self.assertEquals(tab._Coerce(1, 'bool'), True)
+ self.assertEqual(tab._Coerce(True ,'bool'), True)
+ self.assertEqual(tab._Coerce(False ,'bool'), False)
+ self.assertEqual(tab._Coerce('falSE' ,'bool'), False)
+ self.assertEqual(tab._Coerce('no' ,'bool'), False)
+ self.assertEqual(tab._Coerce('not false and not no','bool'), True)
+ self.assertEqual(tab._Coerce(0, 'bool'), False)
+ self.assertEqual(tab._Coerce(1, 'bool'), True)
# unknown type
self.assertRaises(ValueError, tab._Coerce, 'bla', 'abc')
@@ -861,7 +861,7 @@ class TestTable(unittest.TestCase):
self.CompareDataFromDict(tab_loaded_fname_pickle, {'first': ['x','foo',None], 'second': [3,None,9], 'third': [None,2.2,3.3]})
# read from disc: ost
- in_stream_ost = open("saveloadtable_filename_out.tab", 'rb')
+ in_stream_ost = open("saveloadtable_filename_out.tab", 'r')
tab_loaded_stream_ost = Table.Load(in_stream_ost)
in_stream_ost.close()
tab_loaded_fname_ost = Table.Load('saveloadtable_filename_out.tab')
@@ -880,7 +880,7 @@ class TestTable(unittest.TestCase):
def testLoadOSTDifficultHeaders(self):
tab = Table.Load(os.path.join('testfiles','ost-table-difficult-headers.tab'))
- self.assertEquals(tab.col_types, ['float','float','float','float','float'])
+ self.assertEqual(tab.col_types, ['float','float','float','float','float'])
def testSaveLoadTableOST(self):
tab = self.CreateTestTable()
@@ -907,6 +907,7 @@ class TestTable(unittest.TestCase):
self.assertRaises(IOError, Table.Load, os.path.join('testfiles','emptytable.tab'))
in_stream = open(os.path.join('testfiles','emptytable.csv'), 'r')
self.assertRaises(IOError, Table.Load, in_stream)
+ in_stream.close()
def testSaveLoadTableOSTWithSpaces(self):
tab = self.CreateTestTable()
@@ -920,18 +921,18 @@ class TestTable(unittest.TestCase):
tab_loaded_fname = Table.Load('saveloadtable_withspaces_filename_out.tab')
self.CompareDataFromDict(tab_loaded_fname, {'first': ['x','foo',None,'hello spaces'], 'second': [3,None,9,10], 'third': [None,2.2,3.3,10.1]})
def testSaveTableHTML(self):
- import StringIO
+ import io
tab = self.CreateTestTable()
- stream = StringIO.StringIO()
+ stream = io.StringIO()
tab.Save(stream, format='html')
self.assertEqual(stream.getvalue(), '<table><tr><th>first</th><th>second</th><th>third</th></tr><tr><td>x</td><td>3</td><td></td></tr><tr><td>foo</td><td></td><td>2.200</td></tr><tr><td></td><td>9</td><td>3.300</td></tr></table>')
def testSaveTableContext(self):
- import StringIO
+ import io
tab = self.CreateTestTable()
- stream = StringIO.StringIO()
+ stream = io.StringIO()
tab.Save(stream, format='context')
self.assertEqual(stream.getvalue(),
- '\\starttable[l|r|i3r|]\n\\HL\n\\NC \\bf first\\NC \\bf second\\NC \\bf third \\AR\\HL\n\\NC x\\NC 3\\NC --- \\AR\n\\NC foo\NC ---\NC 2.200 \\AR\n\\NC ---\\NC 9\\NC 3.300 \\AR\n\\HL\n\\stoptable')
+ '\\starttable[l|r|i3r|]\n\\HL\n\\NC \\bf first\\NC \\bf second\\NC \\bf third \\AR\\HL\n\\NC x\\NC 3\\NC --- \\AR\n\\NC foo\\NC ---\\NC 2.200 \\AR\n\\NC ---\\NC 9\\NC 3.300 \\AR\n\\HL\n\\stoptable')
def testSaveLoadTableCSV(self):
tab = self.CreateTestTable()
@@ -1042,44 +1043,44 @@ class TestTable(unittest.TestCase):
tab = self.CreateTestTable()
tab.AddCol('fourth','bool',[True,True,False])
- self.assertEquals(tab.Min('first'),'foo')
- self.assertEquals(tab.Min('second'),3)
- self.assertAlmostEquals(tab.Min('third'),2.2)
- self.assertEquals(tab.Min('fourth'),False)
+ self.assertEqual(tab.Min('first'),'foo')
+ self.assertEqual(tab.Min('second'),3)
+ self.assertAlmostEqual(tab.Min('third'),2.2)
+ self.assertEqual(tab.Min('fourth'),False)
self.assertRaises(ValueError,tab.Min,'fifth')
- self.assertEquals(tab.MinIdx('first'),1)
- self.assertEquals(tab.MinIdx('second'),0)
- self.assertAlmostEquals(tab.MinIdx('third'),1)
- self.assertEquals(tab.MinIdx('fourth'),2)
+ self.assertEqual(tab.MinIdx('first'),1)
+ self.assertEqual(tab.MinIdx('second'),0)
+ self.assertAlmostEqual(tab.MinIdx('third'),1)
+ self.assertEqual(tab.MinIdx('fourth'),2)
self.assertRaises(ValueError,tab.MinIdx,'fifth')
- self.assertEquals(tab.MinRow('first'),['foo', None, 2.20, True])
- self.assertEquals(tab.MinRow('second'),['x', 3, None, True])
- self.assertEquals(tab.MinRow('third'),['foo', None, 2.20, True])
- self.assertEquals(tab.MinRow('fourth'),[None, 9, 3.3, False])
+ self.assertEqual(tab.MinRow('first'),['foo', None, 2.20, True])
+ self.assertEqual(tab.MinRow('second'),['x', 3, None, True])
+ self.assertEqual(tab.MinRow('third'),['foo', None, 2.20, True])
+ self.assertEqual(tab.MinRow('fourth'),[None, 9, 3.3, False])
self.assertRaises(ValueError,tab.MinRow,'fifth')
def testMaxTable(self):
tab = self.CreateTestTable()
tab.AddCol('fourth','bool',[False,True,True])
- self.assertEquals(tab.Max('first'),'x')
- self.assertEquals(tab.Max('second'),9)
- self.assertAlmostEquals(tab.Max('third'),3.3)
- self.assertEquals(tab.Max('fourth'),True)
+ self.assertEqual(tab.Max('first'),'x')
+ self.assertEqual(tab.Max('second'),9)
+ self.assertAlmostEqual(tab.Max('third'),3.3)
+ self.assertEqual(tab.Max('fourth'),True)
self.assertRaises(ValueError,tab.Max,'fifth')
- self.assertEquals(tab.MaxIdx('first'),0)
- self.assertEquals(tab.MaxIdx('second'),2)
- self.assertAlmostEquals(tab.MaxIdx('third'),2)
- self.assertEquals(tab.MaxIdx('fourth'),1)
+ self.assertEqual(tab.MaxIdx('first'),0)
+ self.assertEqual(tab.MaxIdx('second'),2)
+ self.assertAlmostEqual(tab.MaxIdx('third'),2)
+ self.assertEqual(tab.MaxIdx('fourth'),1)
self.assertRaises(ValueError,tab.MaxIdx,'fifth')
- self.assertEquals(tab.MaxRow('first'),['x', 3, None, False])
- self.assertEquals(tab.MaxRow('second'),[None, 9, 3.3, True])
- self.assertEquals(tab.MaxRow('third'),[None, 9, 3.3, True])
- self.assertEquals(tab.MaxRow('fourth'),['foo', None, 2.2, True])
+ self.assertEqual(tab.MaxRow('first'),['x', 3, None, False])
+ self.assertEqual(tab.MaxRow('second'),[None, 9, 3.3, True])
+ self.assertEqual(tab.MaxRow('third'),[None, 9, 3.3, True])
+ self.assertEqual(tab.MaxRow('fourth'),['foo', None, 2.2, True])
self.assertRaises(ValueError,tab.MaxRow,'fifth')
def testSumTable(self):
@@ -1088,9 +1089,9 @@ class TestTable(unittest.TestCase):
tab.AddCol('fifth','string',['foo','bar',None])
self.assertRaises(TypeError,tab.Sum,'first')
- self.assertEquals(tab.Sum('second'),12)
- self.assertAlmostEquals(tab.Sum('third'),5.5)
- self.assertEquals(tab.Sum('fourth'),1)
+ self.assertEqual(tab.Sum('second'),12)
+ self.assertAlmostEqual(tab.Sum('third'),5.5)
+ self.assertEqual(tab.Sum('fourth'),1)
self.assertRaises(TypeError,tab.Sum,'fifth')
self.assertRaises(ValueError,tab.Sum,'sixth')
@@ -1100,9 +1101,9 @@ class TestTable(unittest.TestCase):
tab.AddCol('fifth','string',['foo','bar',None])
self.assertRaises(TypeError,tab.Median,'first')
- self.assertEquals(tab.Median('second'),6.0)
- self.assertAlmostEquals(tab.Median('third'),2.75)
- self.assertEquals(tab.Median('fourth'),False)
+ self.assertEqual(tab.Median('second'),6.0)
+ self.assertAlmostEqual(tab.Median('third'),2.75)
+ self.assertEqual(tab.Median('fourth'),False)
self.assertRaises(TypeError,tab.Median,'fifth')
self.assertRaises(ValueError,tab.Median,'sixth')
@@ -1112,9 +1113,9 @@ class TestTable(unittest.TestCase):
tab.AddCol('fifth','string',['foo','bar',None])
self.assertRaises(TypeError,tab.Mean,'first')
- self.assertAlmostEquals(tab.Mean('second'),6.0)
- self.assertAlmostEquals(tab.Mean('third'),2.75)
- self.assertAlmostEquals(tab.Mean('fourth'),0.33333333)
+ self.assertAlmostEqual(tab.Mean('second'),6.0)
+ self.assertAlmostEqual(tab.Mean('third'),2.75)
+ self.assertAlmostEqual(tab.Mean('fourth'),0.33333333)
self.assertRaises(TypeError,tab.Mean,'fifth')
self.assertRaises(ValueError,tab.Mean,'sixth')
@@ -1146,9 +1147,9 @@ class TestTable(unittest.TestCase):
tab.AddCol('fifth','string',['foo','bar',None])
self.assertRaises(TypeError,tab.StdDev,'first')
- self.assertAlmostEquals(tab.StdDev('second'),3.0)
- self.assertAlmostEquals(tab.StdDev('third'),0.55)
- self.assertAlmostEquals(tab.StdDev('fourth'),0.47140452079)
+ self.assertAlmostEqual(tab.StdDev('second'),3.0)
+ self.assertAlmostEqual(tab.StdDev('third'),0.55)
+ self.assertAlmostEqual(tab.StdDev('fourth'),0.47140452079)
self.assertRaises(TypeError,tab.StdDev,'fifth')
self.assertRaises(ValueError,tab.StdDev,'sixth')
@@ -1156,14 +1157,14 @@ class TestTable(unittest.TestCase):
tab = self.CreateTestTable()
tab.AddCol('fourth','bool',[False,True,False])
- self.assertEquals(tab.Count('first'),2)
- self.assertEquals(tab.Count('second'),2)
- self.assertEquals(tab.Count('third'),2)
- self.assertEquals(tab.Count('fourth'),3)
- self.assertEquals(tab.Count('first', ignore_nan=False),3)
- self.assertEquals(tab.Count('second', ignore_nan=False),3)
- self.assertEquals(tab.Count('third', ignore_nan=False),3)
- self.assertEquals(tab.Count('fourth', ignore_nan=False),3)
+ self.assertEqual(tab.Count('first'),2)
+ self.assertEqual(tab.Count('second'),2)
+ self.assertEqual(tab.Count('third'),2)
+ self.assertEqual(tab.Count('fourth'),3)
+ self.assertEqual(tab.Count('first', ignore_nan=False),3)
+ self.assertEqual(tab.Count('second', ignore_nan=False),3)
+ self.assertEqual(tab.Count('third', ignore_nan=False),3)
+ self.assertEqual(tab.Count('fourth', ignore_nan=False),3)
self.assertRaises(ValueError,tab.Count,'fifth')
def testCalcEnrichment(self):
@@ -1180,15 +1181,15 @@ class TestTable(unittest.TestCase):
class_dir='-')
for x,y,refx,refy in zip(enrx,enry,enrx_ref,enry_ref):
- self.assertAlmostEquals(x,refx)
- self.assertAlmostEquals(y,refy)
+ self.assertAlmostEqual(x,refx)
+ self.assertAlmostEqual(y,refy)
enrx,enry = tab.ComputeEnrichment(score_col='score', score_dir='-',
class_col='classific')
for x,y,refx,refy in zip(enrx,enry,enrx_ref,enry_ref):
- self.assertAlmostEquals(x,refx)
- self.assertAlmostEquals(y,refy)
+ self.assertAlmostEqual(x,refx)
+ self.assertAlmostEqual(y,refy)
tab.AddCol('bad','string','col')
@@ -1275,7 +1276,7 @@ class TestTable(unittest.TestCase):
class_col='rmsd', class_cutoff=2.0,
class_dir='-')
- self.assertAlmostEquals(auc, auc_ref)
+ self.assertAlmostEqual(auc, auc_ref)
def testPlotROC(self):
if not HAS_MPL or not HAS_PIL:
@@ -1297,7 +1298,7 @@ class TestTable(unittest.TestCase):
pl = tab.PlotROC(score_col='score', score_dir='+',
class_col='classific',
save=os.path.join("testfiles","roc-out.png"))
- self.assertEquals(pl, None)
+ self.assertEqual(pl, None)
def testPlotLogROC(self):
if not HAS_MPL or not HAS_PIL:
@@ -1319,7 +1320,7 @@ class TestTable(unittest.TestCase):
pl = tab.PlotLogROC(score_col='score', score_dir='+',
class_col='classific',
save=os.path.join("testfiles","logroc-out.png"))
- self.assertEquals(pl, None)
+ self.assertEqual(pl, None)
def testPlotROCSameValues(self):
if not HAS_MPL or not HAS_PIL:
@@ -1361,14 +1362,14 @@ class TestTable(unittest.TestCase):
classific=[True, True, False, True, True, True, False, False, True, False, True, False, True, False, False, False, True, False, True, False],
score=[0.9, 0.8, 0.7, 0.6, 0.55, 0.54, 0.53, 0.52, 0.51, 0.505, 0.4, 0.39, 0.38, 0.37, 0.36, 0.35, 0.34, 0.33, 0.30, 0.1])
auc = tab.ComputeROCAUC(score_col='score', score_dir='+', class_col='classific')
- self.assertAlmostEquals(auc, auc_ref)
+ self.assertAlmostEqual(auc, auc_ref)
# no true positives
tab = Table(['classific', 'score'], 'bf',
classific=[False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False],
score=[0.9, 0.8, 0.7, 0.6, 0.55, 0.54, 0.53, 0.52, 0.51, 0.505, 0.4, 0.39, 0.38, 0.37, 0.36, 0.35, 0.34, 0.33, 0.30, 0.1])
auc = tab.ComputeROCAUC(score_col='score', score_dir='+', class_col='classific')
- self.assertEquals(auc, None)
+ self.assertEqual(auc, None)
def testLogROCAUCforPerfectCurve(self):
if not HAS_NUMPY:
@@ -1380,11 +1381,11 @@ class TestTable(unittest.TestCase):
# test logAUC
auc = tab.ComputeLogROCAUC(score_col='score', score_dir='+', class_col='classific')
- self.assertAlmostEquals(auc, auc_ref)
+ self.assertAlmostEqual(auc, auc_ref)
# test linear AUC
auc = tab.ComputeROCAUC(score_col='score', score_dir='+', class_col='classific')
- self.assertAlmostEquals(auc, auc_ref)
+ self.assertAlmostEqual(auc, auc_ref)
def testCalcLogROCAUCRandomCurve(self):
if not HAS_NUMPY:
@@ -1396,12 +1397,12 @@ class TestTable(unittest.TestCase):
# test logAUC
auc_ref = 0.1440197405305
auc = tab.ComputeLogROCAUC(score_col='score', score_dir='+', class_col='classific')
- self.assertAlmostEquals(auc, auc_ref)
+ self.assertAlmostEqual(auc, auc_ref)
# test linear AUC
auc_ref = 0.5
auc = tab.ComputeROCAUC(score_col='score', score_dir='+', class_col='classific')
- self.assertAlmostEquals(auc, auc_ref)
+ self.assertAlmostEqual(auc, auc_ref)
def testCalcROCAUCWithCutoff(self):
@@ -1411,18 +1412,18 @@ class TestTable(unittest.TestCase):
classific=[0.9, 0.8, 0.7, 0.6, 0.55, 0.54, 0.53, 0.52, 0.51, 0.505, 0.4, 0.39, 0.38, 0.37, 0.36, 0.35, 0.34, 0.33, 0.30, 0.1],
score=[0.9, 0.8, 0.7, 0.6, 0.55, 0.54, 0.53, 0.52, 0.51, 0.505, 0.4, 0.39, 0.38, 0.37, 0.36, 0.35, 0.34, 0.33, 0.30, 0.1])
auc = tab.ComputeROCAUC(score_col='score', class_col='classific', class_cutoff=0.5)
- self.assertEquals(auc, 1.0)
+ self.assertEqual(auc, 1.0)
# no true positives
auc = tab.ComputeROCAUC(score_col='score', class_col='classific', class_cutoff=1.0)
- self.assertEquals(auc, None)
+ self.assertEqual(auc, None)
def testCalcROCFromFile(self):
if not HAS_NUMPY:
return
tab = Table.Load(os.path.join('testfiles','roc_table.dat'))
auc = tab.ComputeROCAUC(score_col='prediction', class_col='reference', class_cutoff=0.4)
- self.assertEquals(auc, 1.0)
+ self.assertEqual(auc, 1.0)
def testCalcROCAUCSameValues(self):
@@ -1433,7 +1434,7 @@ class TestTable(unittest.TestCase):
classific=[True, True, False, True, True, True, False, False, True, False, True, False, True, False, False, False, True, False, True, False],
score=[0.9, 0.8, 0.7, 0.7, 0.7, 0.7, 0.53, 0.52, 0.51, 0.505, 0.4, 0.4, 0.4, 0.4, 0.36, 0.35, 0.34, 0.33, 0.30, 0.1])
auc = tab.ComputeROCAUC(score_col='score', score_dir='+', class_col='classific')
- self.assertAlmostEquals(auc, auc_ref)
+ self.assertAlmostEqual(auc, auc_ref)
def testCalcMCC(self):
log = _FetchLog()
@@ -1447,18 +1448,18 @@ class TestTable(unittest.TestCase):
class_wrong=[False,False,False,False,False,False, False,False,False, False,False,False,False,False,False, False,False,False,False, False,False,False,False,False])
mcc = tab.ComputeMCC(score_col='score', score_dir='-', class_col='rmsd', class_dir='-', score_cutoff=1.0, class_cutoff=2.0)
- self.assertAlmostEquals(mcc, 0.1490711984)
+ self.assertAlmostEqual(mcc, 0.1490711984)
mcc = tab.ComputeMCC(score_col='class_score', class_col='class_rmsd')
- self.assertAlmostEquals(mcc, 0.1490711984)
+ self.assertAlmostEqual(mcc, 0.1490711984)
mcc = tab.ComputeMCC(score_col='score', score_dir='+', class_col='rmsd', class_dir='+', score_cutoff=1.0, class_cutoff=2.0)
- self.assertAlmostEquals(mcc, 0.1490711984)
+ self.assertAlmostEqual(mcc, 0.1490711984)
mcc = tab.ComputeMCC(score_col='score', score_dir='-', class_col='rmsd', class_dir='+', score_cutoff=1.0, class_cutoff=2.0)
- self.assertAlmostEquals(mcc, -0.1490711984)
+ self.assertAlmostEqual(mcc, -0.1490711984)
mcc = tab.ComputeMCC(score_col='score', score_dir='+', class_col='rmsd', class_dir='-', score_cutoff=1.0, class_cutoff=2.0)
- self.assertAlmostEquals(mcc, -0.1490711984)
+ self.assertAlmostEqual(mcc, -0.1490711984)
mcc = tab.ComputeMCC(score_col='class_wrong', class_col='class_rmsd')
- self.assertEquals(mcc,None)
- self.assertEquals(log.messages['WARNING'][0],
+ self.assertEqual(mcc,None)
+ self.assertEqual(log.messages['WARNING'][0],
'Could not compute MCC: MCC is not defined since factor (tp + fp) is zero')
def testCalcMCCPreclassified(self):
@@ -1467,11 +1468,11 @@ class TestTable(unittest.TestCase):
prediction1=[False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, True, False, True, False, True, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, True, False, False, True, False, True, False, False, False, False, False, False],
prediction2=[False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, True, False, False, True, False, False, False, False, False, False, False, False, False, False, False, False, False, False, True, False, True, False, False, True, False, True, True, False, False, False, False, False, False, False, False, False, False, True, False, False, True, False, False, False, True, False, False, False, False])
mcc = tab.ComputeMCC(score_col='prediction1', class_col='reference')
- self.assertAlmostEquals(mcc, 0.538389277)
+ self.assertAlmostEqual(mcc, 0.538389277)
mcc = tab.ComputeMCC(score_col='prediction2', class_col='reference')
- self.assertAlmostEquals(mcc, 0.882089673321)
+ self.assertAlmostEqual(mcc, 0.882089673321)
- def testTableAsNumpyMatrix(self):
+ def testTableAsNumpyMatrixAsArray(self):
if not HAS_NUMPY:
return
@@ -1487,24 +1488,24 @@ class TestTable(unittest.TestCase):
tab = self.CreateTestTable()
tab.AddCol('fourth','b',[True, False, False])
- m = tab.GetNumpyMatrix('second')
- mc = np.matrix([[3],[None],[9]])
+ m = tab.GetNumpyMatrixAsArray('second')
+ mc = np.array([[3],[None],[9]])
self.assertTrue(np.all(m==mc))
- mc = np.matrix([[3],[None],[10]])
+ mc = np.array([[3],[None],[10]])
self.assertFalse(np.all(m==mc))
- m = tab.GetNumpyMatrix('third')
- mc = np.matrix([[None],[2.200],[3.300]])
+ m = tab.GetNumpyMatrixAsArray('third')
+ mc = np.array([[None],[2.200],[3.300]])
self.assertTrue(np.all(m==mc))
- m = tab.GetNumpyMatrix('second','third')
- mc = np.matrix([[3, None],[None, 2.200],[9, 3.300]])
+ m = tab.GetNumpyMatrixAsArray('second','third')
+ mc = np.array([[3, None],[None, 2.200],[9, 3.300]])
self.assertTrue(np.all(m==mc))
- m = tab.GetNumpyMatrix('third','second')
- mc = np.matrix([[None, 3],[2.200, None],[3.300, 9]])
+ m = tab.GetNumpyMatrixAsArray('third','second')
+ mc = np.array([[None, 3],[2.200, None],[3.300, 9]])
self.assertTrue(np.all(m==mc))
- self.assertRaises(TypeError, tab.GetNumpyMatrix, 'fourth')
- self.assertRaises(TypeError, tab.GetNumpyMatrix, 'first')
- self.assertRaises(RuntimeError, tab.GetNumpyMatrix)
+ self.assertRaises(TypeError, tab.GetNumpyMatrixAsArray, 'fourth')
+ self.assertRaises(TypeError, tab.GetNumpyMatrixAsArray, 'first')
+ self.assertRaises(RuntimeError, tab.GetNumpyMatrixAsArray)
def testOptimalPrefactors(self):
if not HAS_NUMPY:
@@ -1519,24 +1520,24 @@ class TestTable(unittest.TestCase):
f=[9,9,9,9,9,9,9,9,9])
pref = tab.GetOptimalPrefactors('c','a','b')
- self.assertAlmostEquals(pref[0],0.799999999)
- self.assertAlmostEquals(pref[1],0.166666666666)
+ self.assertAlmostEqual(pref[0],0.799999999)
+ self.assertAlmostEqual(pref[1],0.166666666666)
pref = tab.GetOptimalPrefactors('c','b','a')
- self.assertAlmostEquals(pref[0],0.166666666666)
- self.assertAlmostEquals(pref[1],0.799999999)
+ self.assertAlmostEqual(pref[0],0.166666666666)
+ self.assertAlmostEqual(pref[1],0.799999999)
pref = tab.GetOptimalPrefactors('c','b','a',weights='e')
- self.assertAlmostEquals(pref[0],0.166666666666)
- self.assertAlmostEquals(pref[1],0.799999999)
+ self.assertAlmostEqual(pref[0],0.166666666666)
+ self.assertAlmostEqual(pref[1],0.799999999)
pref = tab.GetOptimalPrefactors('c','b','a',weights='f')
- self.assertAlmostEquals(pref[0],0.166666666666)
- self.assertAlmostEquals(pref[1],0.799999999)
+ self.assertAlmostEqual(pref[0],0.166666666666)
+ self.assertAlmostEqual(pref[1],0.799999999)
pref = tab.GetOptimalPrefactors('c','a','b',weights='d')
- self.assertAlmostEquals(pref[0],0.6078825445851)
- self.assertAlmostEquals(pref[1],0.3394613806088)
+ self.assertAlmostEqual(pref[0],0.6078825445851)
+ self.assertAlmostEqual(pref[1],0.3394613806088)
self.assertRaises(RuntimeError, tab.GetOptimalPrefactors, 'c','a','b',weight='d')
self.assertRaises(RuntimeError, tab.GetOptimalPrefactors, 'c',weights='d')
@@ -1580,12 +1581,12 @@ class TestTable(unittest.TestCase):
tab_list[i].append(v)
for i in range(len(ref_list[0])):
- self.assertAlmostEquals(tab_list[0][i],ref_list[0][i])
- self.assertAlmostEquals(tab_list[1][i],ref_list[1][i])
- self.assertAlmostEquals(tab_list[2][i],ref_list[2][i])
- self.assertAlmostEquals(tab_list[3][i],ref_list[3][i])
- self.assertAlmostEquals(tab_list[4][i],ref_list[4][i])
- self.assertAlmostEquals(tab_list[5][i],ref_list[5][i])
+ self.assertAlmostEqual(tab_list[0][i],ref_list[0][i])
+ self.assertAlmostEqual(tab_list[1][i],ref_list[1][i])
+ self.assertAlmostEqual(tab_list[2][i],ref_list[2][i])
+ self.assertAlmostEqual(tab_list[3][i],ref_list[3][i])
+ self.assertAlmostEqual(tab_list[4][i],ref_list[4][i])
+ self.assertAlmostEqual(tab_list[5][i],ref_list[5][i])
def testIsEmpty(self):
@@ -1641,30 +1642,30 @@ class TestTable(unittest.TestCase):
tab = self.CreateTestTable()
tab.AddRow(['foo',4, 3.3])
tab.AddRow([None,5, 6.3])
- self.assertEquals(tab.GetUnique('first'), ['x','foo'])
- self.assertEquals(tab.GetUnique('first', ignore_nan=False), ['x','foo', None])
- self.assertEquals(tab.GetUnique('second'), [3,9,4,5])
- self.assertEquals(tab.GetUnique('second', ignore_nan=False), [3,None,9,4,5])
- self.assertEquals(tab.GetUnique('third'), [2.2, 3.3, 6.3])
- self.assertEquals(tab.GetUnique('third', ignore_nan=False), [None, 2.2, 3.3, 6.3])
+ self.assertEqual(tab.GetUnique('first'), ['x','foo'])
+ self.assertEqual(tab.GetUnique('first', ignore_nan=False), ['x','foo', None])
+ self.assertEqual(tab.GetUnique('second'), [3,9,4,5])
+ self.assertEqual(tab.GetUnique('second', ignore_nan=False), [3,None,9,4,5])
+ self.assertEqual(tab.GetUnique('third'), [2.2, 3.3, 6.3])
+ self.assertEqual(tab.GetUnique('third', ignore_nan=False), [None, 2.2, 3.3, 6.3])
def testCorrel(self):
tab = self.CreateTestTable()
- self.assertEquals(tab.Correl('second','third'), None)
+ self.assertEqual(tab.Correl('second','third'), None)
tab.AddRow(['foo',4, 3.3])
tab.AddRow([None,5, 6.3])
tab.AddRow([None,8, 2])
- self.assertAlmostEquals(tab.Correl('second','third'), -0.4954982578)
+ self.assertAlmostEqual(tab.Correl('second','third'), -0.4954982578)
def testSpearmanCorrel(self):
if not HAS_SCIPY_STATS:
return
tab = self.CreateTestTable()
- self.assertEquals(tab.SpearmanCorrel('second','third'), None)
+ self.assertEqual(tab.SpearmanCorrel('second','third'), None)
tab.AddRow(['foo',4, 3.3])
tab.AddRow([None,5, 6.3])
tab.AddRow([None,8, 2])
- self.assertAlmostEquals(tab.SpearmanCorrel('second','third'), -0.316227766)
+ self.assertAlmostEqual(tab.SpearmanCorrel('second','third'), -0.316227766)
def testExtend(self):
'''
@@ -1804,8 +1805,8 @@ class TestTable(unittest.TestCase):
split_exp_two=selector._ExpressionLexer(query_two)
parsed_exp_two=selector._ParseExpression(split_exp_two)
rpn_two=['a', 1, '=', 'a', 2, '=', 'or', 'b', 5.0, 'a', '+', '>', 'b', 2.0, '<', 'or', 'or']
- self.assertEquals(selector._ShuntingYard(parsed_exp_one),rpn_one)
- self.assertEquals(selector._ShuntingYard(parsed_exp_two),rpn_two)
+ self.assertEqual(selector._ShuntingYard(parsed_exp_one),rpn_one)
+ self.assertEqual(selector._ShuntingYard(parsed_exp_two),rpn_two)
#check operator evaluations
self.assertTrue(selector._EvaluateOperator('=',False,False))
diff --git a/modules/base/tests/tests.cc b/modules/base/tests/tests.cc
index 8bf9b0a2357bd946b17b31d2e554684ef2e4f4da..60e7ed62da5952d40672fcb530c2a01c2488f7d6 100644
--- a/modules/base/tests/tests.cc
+++ b/modules/base/tests/tests.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/bindings/doc/dssp.rst b/modules/bindings/doc/dssp.rst
index bb9d2b57b0f081bd0f6ec0d7b82e0ef9bcf59089..3a51a870c9c740b495baa5caa53c0d1475818d77 100644
--- a/modules/bindings/doc/dssp.rst
+++ b/modules/bindings/doc/dssp.rst
@@ -39,7 +39,7 @@ using the mmCIF interface.
for chain in ent.chains:
if chain.is_polypeptide:
for res in chain.residues:
- print res.GetFloatProp('relative_solvent_accessibility')
+ print(res.GetFloatProp('relative_solvent_accessibility'))
DSSP bindings Usage
diff --git a/modules/bindings/doc/hhblits.rst b/modules/bindings/doc/hhblits.rst
index 9ffb1c0c6f5d81b2a35b4299e54a30165bf656e1..62b3262a0a79bfbc30f9b0ce537cf161d52cc4cb 100644
--- a/modules/bindings/doc/hhblits.rst
+++ b/modules/bindings/doc/hhblits.rst
@@ -54,7 +54,7 @@ First query by sequence:
with open(hit_file) as hit_fh:
header, hits = hhblits.ParseHHblitsOutput(hit_fh)
for hit in hits:
- print hit.aln
+ print(hit.aln)
# cleanup
hh.Cleanup()
@@ -82,7 +82,7 @@ Very similar going by file:
with open(hit_file) as hit_fh:
header, hits = hhblits.ParseHHblitsOutput(hit_fh)
for hit in hits:
- print hit.aln
+ print(hit.aln)
# cleanup
hh.Cleanup()
@@ -106,7 +106,7 @@ so one may want to extract them:
# note that ParseA3M is not a class method but a module function
output = hhblits.ParseA3M(open(a3m_file))
- print output['msa']
+ print(output['msa'])
# cleanup
hh.Cleanup()
diff --git a/modules/bindings/doc/tmtools.rst b/modules/bindings/doc/tmtools.rst
index 7a39ba987ece4c6ba688ae781802758dad6bd73b..823a35eca537d4a4b7b2d0d98d5e435c2fca3734 100644
--- a/modules/bindings/doc/tmtools.rst
+++ b/modules/bindings/doc/tmtools.rst
@@ -61,9 +61,9 @@ structures and print the RMSD as well as the GDT_TS and GDT_HA similarity measur
pdb1=io.LoadPDB('1ake.pdb', restrict_chains='A')
pdb2=io.LoadPDB('4ake.pdb', restrict_chains='A')
result=tmtools.TMScore(pdb1, pdb2)
- print result.rmsd_below_five # 1.9
- print result.gdt_ha # 0.41
- print result.gdt_ts # 0.56
+ print(result.rmsd_below_five) # 1.9
+ print(result.gdt_ha) # 0.41
+ print(result.gdt_ts) # 0.56
Usage of TMalign
--------------------------------------------------------------------------------
@@ -82,7 +82,7 @@ Usage of TMscore
TMalign C++ wrapper
--------------------------------------------------------------------------------
-.. module:: ost.bindings
+.. currentmodule:: ost.bindings
Instead of calling the TMalign executable, ost also provides a wrapper around
its C++ implementation. The advantage is that no intermediate files need to be
@@ -96,8 +96,8 @@ generated in order to call the executable.
pdb2=io.LoadPDB('4ake.pdb').Select("peptide=true")
result = bindings.WrappedTMAlign(pdb1.chains[0], pdb2.chains[0],
fast=True)
- print result.tm_score
- print result.alignment.ToString(80)
+ print(result.tm_score)
+ print(result.alignment.ToString(80))
.. class:: TMAlignResult(rmsd, tm_score, aligned_length, transform, alignment)
diff --git a/modules/bindings/pymod/CMakeLists.txt b/modules/bindings/pymod/CMakeLists.txt
index 468151bc5c2d0314a80efd525e8b9a243c721d35..17bd42b19f02c74e7587e8d795d6a433c16aab58 100644
--- a/modules/bindings/pymod/CMakeLists.txt
+++ b/modules/bindings/pymod/CMakeLists.txt
@@ -13,7 +13,6 @@ blast.py
cadscore.py
kclust.py
ialign.py
-align_3dcomb.py
)
set(OST_BINDINGS_PYMOD_SOURCES
diff --git a/modules/bindings/pymod/__init__.py b/modules/bindings/pymod/__init__.py
index 4510f10ef2e9b38d26efb8f5ba14c2263eb305ff..5e8e38a422b516c52680e3b8ec947bb951702cc8 100644
--- a/modules/bindings/pymod/__init__.py
+++ b/modules/bindings/pymod/__init__.py
@@ -7,5 +7,4 @@ from ost.bindings import naccess
from ost.bindings import hbplus
from ost.bindings import clustalw
from ost.bindings import cadscore
-from ost.bindings import align_3dcomb
-from _ost_bindings import *
+from ._ost_bindings import *
diff --git a/modules/bindings/pymod/align_3dcomb.py b/modules/bindings/pymod/align_3dcomb.py
deleted file mode 100644
index ca709fc15fcadfe8dbb0765466cf874e3b35c231..0000000000000000000000000000000000000000
--- a/modules/bindings/pymod/align_3dcomb.py
+++ /dev/null
@@ -1,129 +0,0 @@
-"""
-3DCOMB module
-
-Author: Niklaus Johner
-
-This module is for structural alignment from OpenStructure using the external program 3DCOMB.
-
-How To Use This Module:
- 1. Import it (e.g. as "from ost.bindings import align_3dcomb")
- 2. Use it (e.g. as "alignment,transformation_list = align_3dcomb.AlignStructures(view_list)")
-
-Requirement:
- - 3DCOMB installed
-"""
-
-from ost.bindings import utils
-import subprocess,os
-from ost import settings
-from ost import io
-import ost
-import ost.geom
-
-def _GetExecutable(comb_exe, comb_env):
- """
- Function to check if 3DCOMB executable is present
-
- :param comb_exe: Explicit path to 3DCOMB executable
- :param msms_env: Environment variable pointing to 3DCOMB executable
- :returns: Path to the executable
- :raises: :class:`~ost.FileNotFound` if executable is not found
- """
- return settings.Locate(['3DCOMB_linux','3DCOMB_win.exe'], explicit_file_name=comb_exe,
- env_name=comb_env)
-
-def _SetupFiles(structure_list):
- """
- Setup files for MSMS calculation in temporary directory
-
- :param structure_list: A list of EntityView that will be aligned.\
- each EntityView should contain a single chain and each residue needs to have a CA atom.
- :returns: calss:settings.TempDir
- :raises: class:`RuntimeError` if on of the Views is not valid
- """
-
- #write out temporary pdb files
- if not all([ev.IsValid() for ev in structure_list]):
- raise RuntimeError, "Invalid EntityView in structure_list"
- tpd=utils.TempDirWithFiles(structure_list)
-
- #Write out the file containing the list of all structures
- outfile=open(os.path.join(tpd.dirname,'list'),'w')
- outfile.write('\n'.join(tpd.files))
- outfile.close()
- return tpd
-
-
-def _Run3DCOMB(command,tpd):
- """
- Run the 3DCOMB alignment command
-
- This functions starts the external 3DCOMB executable and returns the stdout of
- 3DCOMB.
-
- :param command: Command to execute
- :returns: stdout of 3DCOMB
- :raises: :class:`CalledProcessError` for non-zero return value
- """
- outname=os.path.join(tpd.dirname,'align.out')
- outfile=open(outname,'w')
- returncode=subprocess.call(command, shell=True, stdout=outfile)
- outfile.close()
- #check for successful completion of 3DCOMB
- if returncode!=0:
- print "WARNING: 3DCOMB error\n"
- raise subprocess.CalledProcessError
- return returncode
-
-def _ParseOutput(tpd):
- #Read Alignment
- ali=io.LoadAlignment(os.path.join(tpd.dirname,'list.ali'),'fasta')
- for i in range(ali.GetCount()):
- ali.SetSequenceName(i,'struc{0}'.format(i))
- #Read Transformations
- f=open(os.path.join(tpd.dirname,'list.rmt'),'r')
- Tl=[]
- for l in f:
- if l.startswith('>'):
- fl=ost.FloatList()
- for i in range(3):
- l=f.next()
- sl=l.split(',')
- fl.extend([float(el) for el in sl[0].split()+[sl[1]]])
- fl.extend([0,0,0,1])
- T=ost.geom.Transform()
- M=ost.geom.Mat4(*fl)
- T.SetMatrix(M)
- Tl.append(T)
- #Read standard output
- outfile=open(os.path.join(tpd.dirname,'align.out'),'r')
- results={}
- for line in outfile:
- if line.startswith('Objective function value is'):results['objective_function']=float(line.split()[-1])
- if line.startswith('CORE_LEN'):
- l=line.split(',')
- for el in l:
- s=el.split('=')
- results[s[0]]=float(s[1])
- return ali,Tl,results
-
-
-def AlignStructures(structure_list,apply_transform=False,name_list=None,comb_exe=None,comb_env=None):
- comb_executable=_GetExecutable(comb_exe, comb_env)
- tpd=_SetupFiles(structure_list)
- command=' '.join([comb_executable,os.path.join(tpd.dirname,'list')])
- returncode=_Run3DCOMB(command,tpd)
- try:ali,Tl,results=_ParseOutput(tpd)
- except:
- print 'could not parse output'
- raise RuntimeError
- if apply_transform:
- for T,ev in zip(Tl,structure_list):
- ev.handle.FixTransform()
- ev.handle.SetTransform(T)
- tpd.Cleanup()
- return ali,Tl,results
-
-
-
-
diff --git a/modules/bindings/pymod/blast.py b/modules/bindings/pymod/blast.py
index e63007f40d5b9feb0fb0c838166f35b3142ad24b..2cff9231cffc91418d604e2caabb0c57292f647a 100644
--- a/modules/bindings/pymod/blast.py
+++ b/modules/bindings/pymod/blast.py
@@ -103,12 +103,12 @@ def ParseBlastOutput(string, seqid_thres=0, evalue_thres=float("infinity")):
aln=seq.CreateAlignment(query_seq, hit_seq)
return AlignedPatch(aln, bit_score, score, evalue, seqid)
- except Exception, e:
- print str(e), query_seq, hit_seq
+ except Exception as e:
+ print(str(e), query_seq, hit_seq)
try:
doc=minidom.parseString(string)
- except Exception, e:
+ except Exception as e:
ost.LogError('Error while parsing BLAST output: %s' % str(e))
return None
hits=[]
@@ -166,9 +166,10 @@ def CreateDB(infasta, dbout, mkdb_cmd=None):
else:
raise IOError('mkdb command must either be the path to formatdb or makeblastdb!')
- cmd=' '.join(args)
- ost.LogInfo('creating blast DB (%s)' % cmd)
- os.system(cmd)
+ ost.LogInfo('creating blast DB (%s)' % ' '.join(args))
+ blast_pipe=subprocess.Popen(args, stdout=subprocess.PIPE,
+ stderr=subprocess.PIPE)
+ blast_pipe.communicate()
def BlastVersion(blast_location=None):
"""
@@ -193,7 +194,8 @@ def BlastVersion(blast_location=None):
blast_pipe=subprocess.Popen(args, stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
- lines=blast_pipe.stdout.readlines()
+ stdout, _ = blast_pipe.communicate()
+ lines=stdout.decode().splitlines()
for line in lines:
m=pattern.match(line)
@@ -206,8 +208,8 @@ def BlastVersion(blast_location=None):
def Blast(query, database, gap_open=11, gap_ext=1, matrix='BLOSUM62',
blast_location=None, outfmt=0, filter_low_complexity=True):
"""
- Runs a protein vs. protein blast search. The results are returned as a
- list of :class:`BlastHit` instances.
+ Runs a protein vs. protein blast search. The results are returned
+ according to the value of the ``outfmt`` parameter.
:param query: the query sequence
:type query: :class:`seq.ConstSequenceHandle`
@@ -222,10 +224,13 @@ def Blast(query, database, gap_open=11, gap_ext=1, matrix='BLOSUM62',
:param gap_ext: Gap extension penalty. Only a subset of gap extension
penalties are supported for each of the substitution matrices. Consult the
blast docs for more information.
- :param outfmt: output format, where '0' corresponds to default output (parsed blast output and 1 to raw output)
+ :param outfmt: output format, where '0' corresponds to default output (parsed
+ blast output and 1 to raw string output).
:param filter_low_complexity: Mask off segments of the query sequence that
have low compositional complexity, as determined by the SEG program of
Wootton & Federhen (Computers and Chemistry, 1993)
+ :rtype: :class:`BlastHit` (with ``outfmt=0``) or :class:`str`
+ (with ``outfmt=1``)
"""
subst_mats=('BLOSUM45', 'BLOSUM62', 'BLOSUM80', 'PAM30', 'PAM70',)
if matrix not in subst_mats:
@@ -266,17 +271,17 @@ def Blast(query, database, gap_open=11, gap_ext=1, matrix='BLOSUM62',
blast_pipe=subprocess.Popen(args, stderr=subprocess.PIPE,
stdout=subprocess.PIPE, stdin=subprocess.PIPE)
if isinstance(query, str):
- stdout, stderr=blast_pipe.communicate(query)
+ stdout, stderr=blast_pipe.communicate(query.encode())
else:
- stdout, stderr=blast_pipe.communicate(io.SequenceToString(query, 'fasta'))
+ stdout, stderr=blast_pipe.communicate(io.SequenceToString(query, 'fasta').encode())
if len(stderr)>0:
pattern=re.compile(r'^\[.*\]\s+ERROR:\s+(.*)')
- lines=stderr.split('\n')
+ lines=stderr.decode().split('\n')
error_message=pattern.match(lines[0])
if error_message:
raise BlastError(error_message.group(1), '\n'.join(lines[1:]))
if outfmt==0:
- return ParseBlastOutput(stdout)
+ return ParseBlastOutput(stdout.decode())
else:
- return stdout
+ return stdout.decode()
diff --git a/modules/bindings/pymod/cadscore.py b/modules/bindings/pymod/cadscore.py
index 3b0fd0a0c1e1c04daa620d8a503cc67afbea4cf0..5d931b04fc865c3f28264de4f5fe9be944ebd741 100644
--- a/modules/bindings/pymod/cadscore.py
+++ b/modules/bindings/pymod/cadscore.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2009 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
@@ -186,17 +186,17 @@ def _RunCAD(tmp_dir, mode, cad_bin_path, old_regime):
"cadtemp"))
ps1=subprocess.Popen(command1, shell=True, stdout=subprocess.PIPE)
- ps1.wait()
+ ps1.communicate()
ps2=subprocess.Popen(command2, shell=True, stdout=subprocess.PIPE)
- ps2.wait()
- lines=ps2.stdout.readlines()
+ stdout,_ = ps2.communicate()
+ lines=stdout.decode().splitlines()
try:
globalAA=_ParseCADGlobal(lines)
except:
raise RuntimeError("CAD calculation failed")
ps3=subprocess.Popen(command3, shell=True, stdout=subprocess.PIPE)
- ps3.wait()
- lines=ps3.stdout.readlines()
+ stdout,_ = ps3.communicate()
+ lines=stdout.decode().splitlines()
try:
localAA=_ParseCADLocal(lines)
except:
@@ -226,13 +226,14 @@ def _RunCAD(tmp_dir, mode, cad_bin_path, old_regime):
cmd.append("--old-regime")
cmd = ' '.join(cmd)
ps = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE)
- ps.wait()
+ stdout, _ = ps.communicate()
try:
- globalAA = _ParseVoronotaGlobal(ps.stdout.readlines())
+ globalAA = _ParseVoronotaGlobal(stdout.decode().splitlines())
except:
raise RuntimeError("CAD calculation failed")
try:
- localAA = _ParseVoronotaLocal(open(local_score_filename).readlines())
+ with open(local_score_filename) as f:
+ localAA = _ParseVoronotaLocal(f.readlines())
except:
raise RuntimeError("CAD calculation failed")
@@ -246,16 +247,14 @@ def _RunCAD(tmp_dir, mode, cad_bin_path, old_regime):
def _HasInsertionCodes(model, reference):
for r in model.residues:
if r.GetNumber().GetInsCode() != "\0":
- print r
return True
for r in reference.residues:
if r.GetNumber().GetInsCode() != "\0":
- print r
return True
return False
def _MapLabels(model, cad_results, label):
- for k,v in cad_results.localAA.iteritems():
+ for k,v in cad_results.localAA.items():
r = model.FindResidue(k[0], k[1])
if not r.IsValid():
raise RuntimeError("Failed to map cadscore on residues: " +
diff --git a/modules/bindings/pymod/clustalw.py b/modules/bindings/pymod/clustalw.py
index 29af869f445f1c1353c2673770048125c507a4fc..f95422b79c7d956c462cd3cc17fe4bfc803726e1 100644
--- a/modules/bindings/pymod/clustalw.py
+++ b/modules/bindings/pymod/clustalw.py
@@ -72,8 +72,8 @@ def ClustalW(seq1, seq2=None, clustalw=None, keep_files=False, nopgap=False,
I isoleucine Y tyrosine
K lysine Z glutamate or glutamine
L leucine X any
- M methionine \* translation stop
- N asparagine \- gap of indeterminate length
+ M methionine \\* translation stop
+ N asparagine \\- gap of indeterminate length
======= ======================= ======= ============================
'''
@@ -129,8 +129,8 @@ def ClustalW(seq1, seq2=None, clustalw=None, keep_files=False, nopgap=False,
if clustalw_option_string!=False:
command=command+" "+clustalw_option_string #see useful flags: http://toolkit.tuebingen.mpg.de/clustalw/help_params
- ps=subprocess.Popen(command, shell=True, stdout=subprocess.PIPE)
- ps.stdout.readlines()
+ subprocess.run(command, shell=True, stdout=subprocess.DEVNULL)
+
aln=io.LoadAlignment(out)
diff --git a/modules/bindings/pymod/dssp.py b/modules/bindings/pymod/dssp.py
index 7fe206d0a10e0e6d701be941ef63a10eb32aa4ff..a31a6cebe3d6487b1d14049a5402e3d995cd33a9 100644
--- a/modules/bindings/pymod/dssp.py
+++ b/modules/bindings/pymod/dssp.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2009 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
@@ -55,9 +55,8 @@ def _ExecuteDSSP(path, dssp_bin, temp_dir=None):
if not os.access(dssp_abs_path, os.X_OK):
raise RuntimeError('"%s" is not executable' % dssp_abs_path)
- ps=subprocess.Popen([dssp_abs_path, path, temp_dssp_path],
- stderr=subprocess.PIPE)
- err_lines=ps.stderr.readlines()
+ subprocess.run([dssp_abs_path, path, temp_dssp_path])
+
return temp_dssp_path
@@ -116,9 +115,9 @@ def AssignDSSP(ent, pdb_path="", extract_burial_status=False, tmp_dir=None,
try:
LoadDSSP(temp_dssp_path, ent, extract_burial_status,
entity_saved)
- except Exception, e:
+ except Exception as e:
# clean up
- print "Exception in DSSP:", e
+ print("Exception in DSSP:", e)
_Cleanup(pdb_path, temp_dssp_path, entity_saved)
raise RuntimeError(e)
@@ -203,8 +202,8 @@ def LoadDSSP(file_name, model, extract_burial_status=False,
residue.SetStringProp("burial_status", 'b')
else:
residue.SetStringProp("burial_status", 'e')
- except Exception, e:
- print "ERROR:",e
+ except Exception as e:
+ print("ERROR:",e)
continue
rtype=line[16:17]
diff --git a/modules/bindings/pymod/export_tmalign.cc b/modules/bindings/pymod/export_tmalign.cc
index f416d8c2ac7a0f5d54474683ba19dcc79c4fb5b9..aefe33ec7de09fb20ab79558e1f685e2bff0f1cb 100644
--- a/modules/bindings/pymod/export_tmalign.cc
+++ b/modules/bindings/pymod/export_tmalign.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2019 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/bindings/pymod/hbplus.py b/modules/bindings/pymod/hbplus.py
index 5a97df2c9ed42138a1fe99da3365e9ae0a45e396..372809400cc0bb986abbeec2e6e2f9cbc7de34fb 100644
--- a/modules/bindings/pymod/hbplus.py
+++ b/modules/bindings/pymod/hbplus.py
@@ -8,6 +8,7 @@ from ost import settings
import subprocess
import re
import os
+import shutil
from ost import io
from ost import mol
@@ -62,20 +63,23 @@ def HBondList(ent, hbplus_bin=None):
"""
full_bin=_LocateHBPlus(hbplus_bin)
temp_d=tempfile.mkdtemp(prefix='hbplus_')
- hb_proc=subprocess.Popen(full_bin, shell=True, stdout=subprocess.PIPE,
- stdin=subprocess.PIPE)
file_name=os.path.join(temp_d, 'ent.pdb')
io.SaveEntity(ent, file_name)
- hb_proc.stdin.write('%s\n' % temp_d)
- hb_proc.stdin.write('%s\n\n' % file_name)
- for line in hb_proc.stdout:
+ hb_proc=subprocess.Popen(full_bin, shell=True, stdout=subprocess.PIPE,
+ stdin=subprocess.PIPE)
+ hb_proc.stdin.write(('%s\n' % temp_d).encode())
+ hb_proc.stdin.write(('%s\n\n' % file_name).encode())
+ stdout,_ = hb_proc.communicate()
+
+ for line in stdout.decode().splitlines():
match=re.match(r'Configured for (\d+) atoms and\s+(\d+) residues\.', line)
if match:
assert ent.atom_count<int(match.group(1))
assert ent.residue_count<int(match.group(2))
hb_out=open(os.path.join(temp_d, 'ent.hb2'), 'r')
hbonds=_ParseOutput(ent, hb_out)
- os.system('rm -rf "%s"' % temp_d)
+ hb_out.close()
+ shutil.rmtree(temp_d)
return hbonds
def HBondScore(ent1, ent2, hbplus_bin=None):
@@ -108,5 +112,5 @@ def HBondScore(ent1, ent2, hbplus_bin=None):
return 0.0
if __name__=='__main__':
- print 'HBond Score:', HBondScore(io.LoadPDB(sys.argv[1]),
- io.LoadPDB(sys.argv[2]))
\ No newline at end of file
+ print('HBond Score:', HBondScore(io.LoadPDB(sys.argv[1]),
+ io.LoadPDB(sys.argv[2])))
\ No newline at end of file
diff --git a/modules/bindings/pymod/hhblits.py b/modules/bindings/pymod/hhblits.py
index 6177847980ef1aaf711d73d9854c6d0933ed83a9..ff08319a4319cc562f6182df296ed20b7b92fe8b 100644
--- a/modules/bindings/pymod/hhblits.py
+++ b/modules/bindings/pymod/hhblits.py
@@ -161,42 +161,43 @@ def ParseHHblitsOutput(output):
value_start_column = 14
date_pattern = '%a %b %d %H:%M:%S %Y'
header = HHblitsHeader()
- line = lines.next()
+ line = next(lines)
assert line.startswith('Query')
header.query = line[value_start_column:].strip()
- line = lines.next()
+ line = next(lines)
assert line.startswith('Match_columns')
header.match_columns = int(line[value_start_column:].strip())
- line = lines.next()
+ line = next(lines)
assert line.startswith('No_of_seqs')
- line = lines.next()
+ line = next(lines)
assert line.startswith('Neff')
header.n_eff = float(line[value_start_column:].strip())
- line = lines.next()
+ line = next(lines)
assert line.startswith('Searched_HMMs')
header.searched_hmms = int(line[value_start_column:].strip())
- line = lines.next()
+ line = next(lines)
assert line.startswith('Date')
value = line[value_start_column:].strip()
header.date = datetime.datetime.strptime(value, date_pattern)
- line = lines.next()
+ line = next(lines)
assert line.startswith('Command')
header.command = line[value_start_column:].strip()
- line = lines.next()
+ line = next(lines)
assert len(line.strip()) == 0
return header
def _ParseTableOfContents(lines):
- assert lines.next().startswith(' No Hit')
+ line = next(lines)
+ assert line.startswith(' No Hit')
hits = []
while True:
- line = lines.next()
+ line = next(lines)
if len(line.strip()) == 0:
return hits
hits.append(ParseHeaderLine(line))
@@ -221,7 +222,7 @@ def ParseHHblitsOutput(output):
# - "T <hit_id> <start> <data> <end>"
# - "Q <query_id> <start> <data> <end>"
# -> rest is to be skipped
- line = lines.next()
+ line = next(lines)
if len(line.strip()) == 0:
continue
if line.startswith('Done!'):
@@ -236,12 +237,13 @@ def ParseHHblitsOutput(output):
query_id, hits[entry_index][0].hit_id,
query_str, templ_str, *hits[entry_index][1])
entry_index = int(line[3:].strip())-1
- hits[entry_index][0].hit_id = lines.next()[1:].strip()
+ line = next(lines)
+ hits[entry_index][0].hit_id = line[1:].strip()
query_str = ''
templ_str = ''
# skip the next line. It doesn't contain information we
# don't already know
- lines.next()
+ next(lines)
continue
assert entry_index != None
# Skip all "T ..." and "Q ..." lines besides the one we want
@@ -568,7 +570,7 @@ class HHblits:
job = subprocess.Popen(hhblits_cmd, shell=True, cwd=self.working_dir,
stdout=subprocess.PIPE, stderr=subprocess.PIPE)
sout, _ = job.communicate()
- lines = sout.splitlines()
+ lines = sout.decode().splitlines()
for line in lines:
ost.LogVerbose(line.strip())
if not os.path.exists(a3m_file):
@@ -588,7 +590,7 @@ class HHblits:
env=env, stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
sout, serr = job.communicate()
- lines = sout.splitlines()
+ lines = sout.decode().splitlines()
for line in lines:
if 'error' in line.lower():
ost.LogWarning('Predicting secondary structure for MSA '+
@@ -622,8 +624,17 @@ class HHblits:
return hhm_file
ost.LogVerbose('converting %s to %s' % (a3m_file, hhm_file))
os.putenv('HHLIB', self.hhlib_dir)
- if subprocess.call('%s -i %s -o %s' % (hhmake, a3m_file, hhm_file),
- shell=True):
+ job = subprocess.Popen('%s -i %s -o %s' % (hhmake, a3m_file, hhm_file),
+ shell=True, stdout=subprocess.PIPE,
+ stderr=subprocess.PIPE)
+ sout, serr = job.communicate()
+ lines = serr.decode().splitlines()
+ for line in lines:
+ ost.LogWarning(line)
+ lines = sout.decode().splitlines()
+ for line in lines:
+ ost.LogVerbose(line)
+ if job.returncode !=0:
raise IOError('could not convert a3m to hhm file')
return hhm_file
@@ -665,10 +676,9 @@ class HHblits:
job = subprocess.Popen(cs_cmd, shell=True, cwd=self.working_dir,
stdout=subprocess.PIPE, stderr=subprocess.PIPE)
sout, _ = job.communicate()
- lines = sout.splitlines()
- for line in lines:
- if 'Wrote abstract state sequence to' in line:
- return cs_file
+ if b'Wrote abstract state sequence to' in sout:
+ return cs_file
+
ost.LogWarning('Creating column state sequence file (%s) failed' % \
cs_file)
@@ -737,10 +747,10 @@ class HHblits:
stdout=subprocess.PIPE, stderr=subprocess.PIPE)
sout, serr = job.communicate()
if job.returncode != 0:
- lines = sout.splitlines()
+ lines = sout.decode().splitlines()
for line in lines:
ost.LogError(line.strip())
- lines = serr.splitlines()
+ lines = serr.decode().splitlines()
for line in lines:
ost.LogError(line.strip())
return None
@@ -758,7 +768,7 @@ def _ParseOptions(opts):
"""
opt_cmd = list()
opt_str = list()
- for k, val in opts.iteritems():
+ for k, val in opts.items():
if type(val) == type(True):
if val == True:
opt_cmd.append('-%s' % str(k))
diff --git a/modules/bindings/pymod/ialign.py b/modules/bindings/pymod/ialign.py
index d5c9f570d3a6abbaef00e2f8d1070727349b28f9..8409b98635e5f6cd0f45b951f8a32ad12a1e79bf 100644
--- a/modules/bindings/pymod/ialign.py
+++ b/modules/bindings/pymod/ialign.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2009 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
@@ -125,7 +125,7 @@ def _RuniAlign(ialign, tmp_dir, options={}):
}
opts.update(options)
cmd_opts = []
- for k, v in opts.iteritems():
+ for k, v in opts.items():
if type(v) == type(True):
if v == True:
cmd_opts.append('-%s' % str(k))
@@ -140,9 +140,11 @@ def _RuniAlign(ialign, tmp_dir, options={}):
else:
ialign_path=settings.Locate('ialign.pl', explicit_file_name=ialign)
command="\"%s\" \"%s\" \"%s\" %s" % (ialign_path, model1_filename, model2_filename, cmd_opts)
+
ps=subprocess.Popen(command, shell=True, stdout=subprocess.PIPE)
- ps.wait()
- lines=ps.stdout.readlines()
+ stdout,_=ps.communicate()
+ lines=stdout.decode().splitlines()
+
if (len(lines))<22:
_CleanupFiles(tmp_dir)
#for l in lines:
diff --git a/modules/bindings/pymod/kclust.py b/modules/bindings/pymod/kclust.py
index 5ecdf11d01a72ff8d9ba5812888b8674511ab5ba..076141f6bd55c6b895cf2a860fdd68f8ca2e618c 100644
--- a/modules/bindings/pymod/kclust.py
+++ b/modules/bindings/pymod/kclust.py
@@ -56,8 +56,10 @@ def _CleanupFiles(tmp_dir_name):
def _ParseOutput(tmp_dir_name):
- header_data=open(os.path.join(tmp_dir_name,'headers.dmp'),'r').readlines()
- cluster_data=open(os.path.join(tmp_dir_name,'clusters.dmp'),'r').readlines()
+ with open(os.path.join(tmp_dir_name,'headers.dmp'),'r') as f:
+ header_data=f.readlines()
+ with open(os.path.join(tmp_dir_name,'clusters.dmp'),'r') as f:
+ cluster_data=f.readlines()
sequences=io.LoadSequenceList(os.path.join(tmp_dir_name,'fastadb.fasta'))
clusters=dict()
@@ -84,7 +86,7 @@ def _ParseOutput(tmp_dir_name):
#translate into final output
res=list()
- for k, v in clusters.iteritems():
+ for k, v in clusters.items():
res.append(cluster(v, header_mapper[k]))
return res
diff --git a/modules/bindings/pymod/lga.py b/modules/bindings/pymod/lga.py
index 0f5410fe3ba543a960595808ae589c9bd9cfa879..59f5d53fb646042ea5da4e72069e58810b016965 100644
--- a/modules/bindings/pymod/lga.py
+++ b/modules/bindings/pymod/lga.py
@@ -52,8 +52,8 @@ def _ParseGDTSection(section, residue_count):
cutoffs=[float(e) for e in section[0].split()[2:]]
num_ca=[int(e) for e in section[1].split()[2:]]
gdt_ts=[float(e) for e in section[2].split()[2:]]
- scores=dict(zip(cutoffs, gdt_ts))
- numbers=dict(zip(cutoffs, num_ca))
+ scores=dict(list(zip(cutoffs, gdt_ts)))
+ numbers=dict(list(zip(cutoffs, num_ca)))
factor=(1.0/(4*residue_count))*100
ts_cutoffs=(1.0, 2.0, 4.0, 8.0)
ha_cutoffs=(0.5, 1.0, 2.0, 4.0)
@@ -109,7 +109,9 @@ def GDT(pdb1, pdb2, chain1='', chain2='', reference_length=None, lga_bin=None):
expanded_cmd=command % params
lga_proc=subprocess.Popen(expanded_cmd, shell=True,
stdout=subprocess.PIPE)
+ stdout, _ = lga_proc.communicate()
+
length=reference_length or max(pdb1.residue_count, pdb2.residue_count)
- result=_ParseLGAOutput(lga_proc.stdout.readlines(), reference_length)
+ result=_ParseLGAOutput(stdout.decode().splitlines(), reference_length)
os.system('rm -r %s' % temp_d)
return result
diff --git a/modules/bindings/pymod/msms.py b/modules/bindings/pymod/msms.py
index 534cd3d8e0be5c80fcfa4638896ffbfa23bcdbf9..38f37008a32ab37bfb8e6b8606b78448c520b870 100644
--- a/modules/bindings/pymod/msms.py
+++ b/modules/bindings/pymod/msms.py
@@ -47,7 +47,7 @@ def GetVersion(msms_exe=None, msms_env=None):
stdout_value, stderr_value = proc.communicate()
version = ""
- for l in stdout_value.splitlines():
+ for l in stdout_value.decode().splitlines():
if l[0:4]=='MSMS':
version = l.split(' ')[1]
return version
@@ -86,7 +86,7 @@ def _SetupFiles(entity, selection):
# select only heavy atoms if no_hydrogens is true
entity_view=entity.Select(selection)
if not entity_view.IsValid():
- raise RuntimeError, "Could not create view for selection (%s)"%(selection)
+ raise RuntimeError("Could not create view for selection (%s)"%(selection))
# write entity to tmp file
tmp_file_name=os.path.join(tmp_dir_name,"entity")
@@ -118,7 +118,7 @@ def _ParseAreaFile(entity, selection, file, asa_prop, esa_prop):
# shift first line
area_lines = area_lines[1:]
if view.GetAtomCount() != len(area_lines):
- raise RuntimeError, "Atom count (%d) unequeal to number of atoms in area file (%d)" % (view.GetAtomCount(), len(area_lines))
+ raise RuntimeError("Atom count (%d) unequeal to number of atoms in area file (%d)" % (view.GetAtomCount(), len(area_lines)))
for l in area_lines:
atom_no, sesa, sasa = l.split()
a = view.atoms[int(atom_no)]
@@ -154,10 +154,10 @@ def _RunMSMS(command):
#check for successful completion of msms
if proc.returncode!=0:
- print "WARNING: msms error\n", stdout_value
+ print("WARNING: msms error\n", stdout_value.decode())
raise MsmsProcessError(proc.returncode, command)
- return stdout_value
+ return stdout_value.decode()
diff --git a/modules/bindings/pymod/naccess.py b/modules/bindings/pymod/naccess.py
index 0d5566ea257d5ac69302cdcdd41ee0dc2feee088..57d1c5740c6621fb7fd85f3320ebde403acaa1c9 100644
--- a/modules/bindings/pymod/naccess.py
+++ b/modules/bindings/pymod/naccess.py
@@ -74,9 +74,9 @@ def _SetupFiles(entity, selection, scratch_dir, max_number_of_atoms):
else:
entity_view = entity
if len(entity_view.atoms) > max_number_of_atoms:
- raise RuntimeError, "Too much atoms for NACCESS (> %s)" % max_number_of_atoms
+ raise RuntimeError("Too much atoms for NACCESS (> %s)" % max_number_of_atoms)
if not entity_view.IsValid():
- raise RuntimeError, "Could not create view for selection (%s)"%(selection)
+ raise RuntimeError("Could not create view for selection (%s)"%(selection))
# write entity to tmp file
tmp_file_name = "entity.pdb"
@@ -162,7 +162,7 @@ def _ParseRsaFile(entity, file, asa_abs, asa_rel):
res.SetFloatProp(asa_rel, float(rel_all) )
res.SetFloatProp(asa_abs, float(abs_all) )
else:
- raise RuntimeError, "Residue Names are not the same for ResNumb: %s (%s vs %s)" % (res_number, res.name, res_name)
+ raise RuntimeError("Residue Names are not the same for ResNumb: %s (%s vs %s)" % (res_number, res.name, res_name))
def __CleanupFiles(dir_name):
@@ -190,17 +190,18 @@ def _RunACCALL(command, temp_dir, query):
:returns: stdout of command
:exception: CalledProcessError for non-zero return value
"""
- proc = subprocess.Popen(command, stdout=subprocess.PIPE,
- stderr=subprocess.PIPE, stdin=subprocess.PIPE,
- cwd=temp_dir)
- stdout_value, stderr_value = proc.communicate(query)
+
+ proc = subprocess.Popen(command, cwd=temp_dir, stdout=subprocess.PIPE,
+ stderr=subprocess.PIPE, stdin=subprocess.PIPE)
+ stdout_value, stderr_value = proc.communicate(query.encode())
# check for successful completion of naccess
if proc.returncode != 0:
- LogWarning("WARNING: naccess error\n%s\n%s" % (stdout_value, stderr_value))
+ LogWarning("WARNING: naccess error\n%s\n%s" % (stdout_value.decode(),
+ stderr_value.decode()))
raise subprocess.CalledProcessError(proc.returncode, command)
- return stdout_value
+ return stdout_value.decode()
def _RunNACCESS(command, temp_dir):
@@ -214,16 +215,16 @@ def _RunNACCESS(command, temp_dir):
:returns: stdout of command
:exception: CalledProcessError for non-zero return value
"""
- proc = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE,
- cwd=temp_dir)
+ proc = subprocess.Popen(command, cwd=temp_dir, shell=True,
+ stdout=subprocess.PIPE)
stdout_value, stderr_value = proc.communicate()
# check for successful completion of naccess
if proc.returncode != 0:
- LogWarning("WARNING: naccess error\n%s" % stdout_value)
+ LogWarning("WARNING: naccess error\n%s" % stdout_value.decode())
raise subprocess.CalledProcessError(proc.returncode, command)
- return stdout_value
+ return stdout_value.decode()
def CalculateSurfaceArea(entity, radius=1.4,
diff --git a/modules/bindings/pymod/tmtools.py b/modules/bindings/pymod/tmtools.py
index 0d158d77f402012df9fed8edc8692e5a313a51e1..94fc4ceed5b88113842fbebaa63995ae7469f7d7 100644
--- a/modules/bindings/pymod/tmtools.py
+++ b/modules/bindings/pymod/tmtools.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2015 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
@@ -81,8 +81,8 @@ def _RunTmAlign(tmalign, tmp_dir):
tmalign_path=settings.Locate('tmalign', explicit_file_name=tmalign)
command="\"%s\" \"%s\" \"%s\" -m \"%s\"" %(tmalign_path, model1_filename, model2_filename, os.path.join(tmp_dir,'matrix.txt'))
ps=subprocess.Popen(command, shell=True, stdout=subprocess.PIPE)
- ps.wait()
- lines=ps.stdout.readlines()
+ stdout,_=ps.communicate()
+ lines=stdout.decode().splitlines()
if (len(lines))<22:
_CleanupFiles(tmp_dir)
raise RuntimeError("tmalign superposition failed")
@@ -91,50 +91,6 @@ def _RunTmAlign(tmalign, tmp_dir):
matrix_file.close()
return _ParseTmAlign(lines,lines_matrix)
-class MMAlignResult:
- def __init__(self, rmsd, aligned_length, tm_score, transform, alignment):
- self.rmsd=rmsd
- self.tm_score=tm_score
- self.aligned_length=aligned_length
- self.transform=transform
- self.alignment=alignment
-
-def _ParseMmAlign(lines):
- info_line=lines[10].split(',')
- aln_length=float(info_line[0].split('=')[1].strip())
- rmsd=float(info_line[1].split('=')[1].strip())
- tm_score=float(info_line[2].split('=')[1].strip())
- tf1=[float(i.strip()) for i in lines[14].split()]
- tf2=[float(i.strip()) for i in lines[15].split()]
- tf3=[float(i.strip()) for i in lines[16].split()]
- rot=geom.Mat3(tf1[2], tf1[3], tf1[4], tf2[2], tf2[3],
- tf2[4], tf3[2], tf3[3], tf3[4])
- tf=geom.Mat4(rot)
- tf.PasteTranslation(geom.Vec3(tf1[1], tf2[1], tf3[1]))
- seq1 = seq.CreateSequence("1",lines[19].strip())
- seq2 = seq.CreateSequence("2",lines[21].strip())
- alignment = seq.CreateAlignment()
- alignment.AddSequence(seq2)
- alignment.AddSequence(seq1)
-
- return MMAlignResult(rmsd, tm_score, aln_length, tf, seq2, alignment)
-
-def _RunMmAlign(mmalign, tmp_dir):
- model1_filename=os.path.join(tmp_dir, 'model01.pdb')
- model2_filename=os.path.join(tmp_dir, 'model02.pdb')
- if platform.system() == "Windows":
- mmalign_path=settings.Locate('mmalign.exe', explicit_file_name=mmalign)
- command="\"%s\" %s %s" %(os.path.normpath(mmalign_path), model1_filename, model2_filename)
- else:
- mmalign_path=settings.Locate('MMalign', explicit_file_name=mmalign)
- command="\"%s\" \"%s\" \"%s\"" %(mmalign_path, model1_filename, model2_filename)
- ps=subprocess.Popen(command, shell=True, stdout=subprocess.PIPE)
- ps.wait()
- lines=ps.stdout.readlines()
- if (len(lines))<22:
- _CleanupFiles(tmp_dir)
- raise RuntimeError("mmalign superposition failed")
- return _ParseMmAlign(lines)
class TMScoreResult:
"""
@@ -206,8 +162,8 @@ def _RunTmScore(tmscore, tmp_dir):
command="\"%s\" \"%s\" \"%s\"" % (tmscore_path, model1_filename,
model2_filename)
ps=subprocess.Popen(command, shell=True, stdout=subprocess.PIPE)
- ps.wait()
- lines=ps.stdout.readlines()
+ stdout,_=ps.communicate()
+ lines=stdout.decode().splitlines()
if (len(lines))<22:
_CleanupFiles(tmp_dir)
raise RuntimeError("tmscore superposition failed")
@@ -238,16 +194,6 @@ def TMAlign(model1, model2, tmalign=None):
_CleanupFiles(tmp_dir_name)
return result
-def MMAlign(model1, model2, mmalign=None):
- """
- Run tmalign on two protein structures
- """
- tmp_dir_name=_SetupFiles((model1, model2))
- result=_RunMmAlign(mmalign, tmp_dir_name)
- model1.handle.EditXCS().ApplyTransform(result.transform)
- _CleanupFiles(tmp_dir_name)
- return result
-
def TMScore(model1, model2, tmscore=None):
"""
Performs a sequence dependent superposition of model1 onto model2,
diff --git a/modules/bindings/pymod/wrap_bindings.cc b/modules/bindings/pymod/wrap_bindings.cc
index 364a543a39c93b57e6c58464eaefe674ea9a41b6..c60893f21d62ca6082c5d57529ef46ccb40a88f3 100644
--- a/modules/bindings/pymod/wrap_bindings.cc
+++ b/modules/bindings/pymod/wrap_bindings.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2019 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/bindings/src/tmalign/TMalign.h b/modules/bindings/src/tmalign/TMalign.h
index 79abc61af1f744ae16032b5a42f1d83bee2ee63c..08caeec3a2b97f6cdb49a1a7d22b660b2c60b2eb 100644
--- a/modules/bindings/src/tmalign/TMalign.h
+++ b/modules/bindings/src/tmalign/TMalign.h
@@ -794,7 +794,7 @@ bool overlap(const int a1,const int b1,const int c1,const int d1,
void sec_str(int len,char *seq, const vector<vector<bool> >&bp,
int a, int b,int &c, int &d)
{
- int i,j;
+ int i;
for (i=0;i<len;i++)
{
@@ -811,8 +811,8 @@ void sec_str(int len,char *seq, const vector<vector<bool> >&bp,
* 1->unpair, 2->paired with upstream, 3->paired with downstream */
void make_sec(char *seq, double **x, int len, int *sec,const string atom_opt)
{
- int ii,jj,i,j;
-
+ int ii,jj,j;
+ unsigned int i;
float lb=12.5; // lower bound for " C3'"
float ub=15.0; // upper bound for " C3'"
if (atom_opt==" C4'") {lb=14.0;ub=16.0;}
@@ -825,7 +825,7 @@ void make_sec(char *seq, double **x, int len, int *sec,const string atom_opt)
vector<bool> bp_tmp(len,false);
vector<vector<bool> > bp(len,bp_tmp);
bp_tmp.clear();
- for (i=0; i<len; i++)
+ for (i=0;(int) i<len; i++)
{
sec[i]=1;
for (j=i+1; j<len; j++)
@@ -843,7 +843,7 @@ void make_sec(char *seq, double **x, int len, int *sec,const string atom_opt)
// From 5' to 3': A0 C0 D0 B0: A0 paired to B0, C0 paired to D0
vector<int> A0,B0,C0,D0;
- for (i=0; i<len-2; i++)
+ for (i=0;(int) i<len-2; i++)
{
for (j=i+3; j<len; j++)
{
@@ -858,8 +858,8 @@ void make_sec(char *seq, double **x, int len, int *sec,const string atom_opt)
}
}
- int sign;
- for (i=0;i<A0.size();i++)
+ //int sign;
+ for (i=0; i<A0.size();i++)
{
/*
sign=0;
@@ -1483,8 +1483,8 @@ void output_superpose(const string filename, const char *fname_super,
double x1[3]; // after transform
/* for PDBx/mmCIF only */
- map<string,int> _atom_site;
- int atom_site_pos;
+ map<string,unsigned int> _atom_site;
+ unsigned int atom_site_pos;
vector<string> line_vec;
while (compress_type?fin_gz.good():fin.good())
@@ -1545,7 +1545,7 @@ void output_superpose(const string filename, const char *fname_super,
transform(t, u, x, x1);
for (atom_site_pos=0; atom_site_pos<_atom_site.size(); atom_site_pos++)
- {
+ {
if (atom_site_pos==_atom_site["Cartn_x"])
buf<<setiosflags(ios::fixed)<<setprecision(3)
<<setw(8)<<x1[0]<<' ';
@@ -2324,7 +2324,6 @@ int TMalign_main(double **xa, double **ya,
TM2 = TMscore8_search(r1, r2, xtm, ytm, xt, n_ali8, t, u, simplify_step,
score_sum_method, &rmsd, local_d0_search, Lnorm, score_d8, d0);
- double Lnorm_d0;
if (a_opt>0)
{
//normalized by average length of structures A, B
@@ -2360,7 +2359,6 @@ int TMalign_main(double **xa, double **ya,
d0_out=d0_scale;
d0_0=d0_scale;
//Lnorm_0=ylen;
- Lnorm_d0=Lnorm_0;
local_d0_search = d0_search;
TM5 = TMscore8_search(r1, r2, xtm, ytm, xt, n_ali8, t0, u0,
simplify_step, score_sum_method, &rmsd, local_d0_search, Lnorm,
diff --git a/modules/bindings/src/tmalign/basic_fun.h b/modules/bindings/src/tmalign/basic_fun.h
index 8274428ee8d56b061180855f6205df214ed32e49..3dadccc30faf0dde5403b9adc123d2cf376bb867 100644
--- a/modules/bindings/src/tmalign/basic_fun.h
+++ b/modules/bindings/src/tmalign/basic_fun.h
@@ -124,7 +124,7 @@ void split(const string &line, vector<string> &line_vec,
const char delimiter=' ')
{
bool within_word = false;
- for (int pos=0;pos<line.size();pos++)
+ for (unsigned int pos=0;pos<line.size();pos++)
{
if (line[pos]==delimiter)
{
@@ -276,7 +276,7 @@ size_t get_PDB_lines(const string filename,
chainID_list.push_back(i8_stream.str());
PDB_lines.push_back(tmp_str_vec);
mol_vec.push_back(0);
- for (i=0;i<L;i++)
+ for (i=0;(int) i<L;i++)
{
if (compress_type) fin_gz>>x>>y>>z;
else fin >>x>>y>>z;
@@ -294,7 +294,6 @@ size_t get_PDB_lines(const string filename,
else if (infmt_opt==2) // xyz format
{
int L=0;
- char A;
stringstream i8_stream;
while (compress_type?fin_gz.good():fin.good())
{
@@ -309,7 +308,7 @@ size_t get_PDB_lines(const string filename,
chainID_list.push_back(':'+line.substr(0,i));
PDB_lines.push_back(tmp_str_vec);
mol_vec.push_back(0);
- for (i=0;i<L;i++)
+ for (i=0;(int) i<L;i++)
{
if (compress_type) getline(fin_gz, line);
else getline(fin, line);
@@ -511,7 +510,7 @@ size_t get_FASTA_lines(const string filename,
{
string line;
vector<string> tmp_str_vec;
- int l;
+ unsigned int l;
int compress_type=0; // uncompressed file
ifstream fin;
@@ -640,7 +639,7 @@ int extract_aln_from_resi(vector<string> &sequence, char *seqx, char *seqy,
int read_PDB(const vector<string> &PDB_lines, double **a, char *seq,
vector<string> &resi_vec, const int byresi_opt)
{
- int i;
+ unsigned int i;
for (i=0;i<PDB_lines.size();i++)
{
a[i][0] = atof(PDB_lines[i].substr(30, 8).c_str());
@@ -733,7 +732,7 @@ void read_user_alignment(vector<string>&sequence, const string &fname_lign,
if (I_opt)
{
int aligned_resNum=0;
- for (int i=0;i<sequence[0].size();i++)
+ for (unsigned int i=0;i<sequence[0].size();i++)
aligned_resNum+=(sequence[0][i]!='-' && sequence[1][i]!='-');
if (aligned_resNum<3)
PrintErrorAndQuit("ERROR! Superposition is undefined for <3 aligned residues.");
diff --git a/modules/bindings/src/wrap_tmalign.cc b/modules/bindings/src/wrap_tmalign.cc
index 5a707139649d7d6d08867c1230bfd97de45632ae..bbc2eb506a789b4aea3306b90e80b27c061af597 100644
--- a/modules/bindings/src/wrap_tmalign.cc
+++ b/modules/bindings/src/wrap_tmalign.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2019 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/bindings/src/wrap_tmalign.hh b/modules/bindings/src/wrap_tmalign.hh
index 124f51f05921fad25e13597671038fb8b2d241f8..4163d4644f8f4e703f15bff9ea6e6099f79a2f1f 100644
--- a/modules/bindings/src/wrap_tmalign.hh
+++ b/modules/bindings/src/wrap_tmalign.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2019 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/bindings/tests/CMakeLists.txt b/modules/bindings/tests/CMakeLists.txt
index dd257c1cb9819c3f71233d22216537ba9b68d6b9..d99953fe24f509c5f9cff16d95e86c2ea3be85e3 100644
--- a/modules/bindings/tests/CMakeLists.txt
+++ b/modules/bindings/tests/CMakeLists.txt
@@ -5,6 +5,11 @@ set(OST_BINDINGS_UNIT_TESTS
test_blast.py
test_kclust.py
test_naccess.py
+ test_cadscore.py
+ test_tmtools.py
+ test_ialign.py
+ test_lga.py
+ test_hbplus.py
)
ost_unittest(MODULE bindings
diff --git a/modules/bindings/tests/test_blast.py b/modules/bindings/tests/test_blast.py
index 18311abd9342e4b8408fc4c2a2d30534ef08ed12..9be501b00856249910d3fb45e962035e891fe7cb 100644
--- a/modules/bindings/tests/test_blast.py
+++ b/modules/bindings/tests/test_blast.py
@@ -52,7 +52,8 @@ class TestBlastBindings(unittest.TestCase):
def testBlastParseOutput(self):
- raw_out=open('testfiles/raw_blastout.txt','r').read()
+ with open('testfiles/raw_blastout.txt','r') as f:
+ raw_out=f.read()
parsed_out=blast.ParseBlastOutput(raw_out)
@@ -102,7 +103,7 @@ if __name__ == "__main__":
try:
blastpath=settings.Locate(('blastp','blastall'))
except(settings.FileNotFound):
- print "Could not find blast executable: ignoring unit tests"
+ print("Could not find blast executable: ignoring unit tests")
sys.exit(0)
from ost import testutils
testutils.RunTests()
diff --git a/modules/bindings/tests/test_cadscore.py b/modules/bindings/tests/test_cadscore.py
new file mode 100644
index 0000000000000000000000000000000000000000..be3bab50d0bc59943d760bb5dcc86054f479bc3c
--- /dev/null
+++ b/modules/bindings/tests/test_cadscore.py
@@ -0,0 +1,74 @@
+import unittest
+from ost import *
+from ost import settings
+from ost.bindings import cadscore
+from ost import testutils
+
+class TestCADBindings(unittest.TestCase):
+
+ def setUp(self):
+ self.protein = io.LoadEntity("testfiles/testprotein.pdb")
+
+
+ def testCADClassic(self):
+
+ try:
+ # all of the following need to be present
+ cad_calc_path = settings.Locate('CADscore_calc.bash')
+ cad_read_g_path = settings.Locate('CADscore_read_global_scores.bash')
+ cad_read_l_path = settings.Locate('CADscore_read_local_scores.bash')
+ executable_path = settings.Locate('voroprot2')
+ except:
+ print("Could not find CAD score classic executables: ignoring unit tests")
+ return
+
+ cad_result = cadscore.CADScore(self.protein, self.protein,
+ label="cad_classic")
+
+ # model and reference are the same, we expect a global CAD score of 1
+ self.assertEqual(cad_result.globalAA, 1.0)
+
+ # one score per residue
+ self.assertEqual(len(cad_result.localAA), len(self.protein.residues))
+
+ # model and reference are the same, we expect local CAD scores of 0.0
+ for score in cad_result.localAA.values():
+ self.assertEqual(score, 0.0)
+
+ # check whether this score is assigned to each residue as float property
+ for r in self.protein.residues:
+ self.assertTrue(r.HasProp("cad_classic"))
+ self.assertEqual(r.GetFloatProp("cad_classic"), 0.0)
+
+
+ def testCADVoronota(self):
+
+ try:
+ # all of the following need to be present
+ voronota_cadscore_path = settings.Locate("voronota-cadscore")
+ executable_path = settings.Locate("voronota")
+ except:
+ print("Could not find CAD score voronota executables: ignoring unit tests")
+ return
+
+ cad_result = cadscore.CADScore(self.protein, self.protein, mode="voronota",
+ label="cad_voronota")
+
+ # model and reference are the same, we expect a global CAD score of 1
+ self.assertEqual(cad_result.globalAA, 1.0)
+
+ # one score per residue
+ self.assertEqual(len(cad_result.localAA), len(self.protein.residues))
+
+ # model and reference are the same, we expect local CAD scores of 1.0
+ for score in cad_result.localAA.values():
+ self.assertEqual(score, 1.0)
+
+ # check whether this score is assigned to each residue as float property
+ for r in self.protein.residues:
+ self.assertTrue(r.HasProp("cad_voronota"))
+ self.assertEqual(r.GetFloatProp("cad_voronota"), 1.0)
+
+
+if __name__ == "__main__":
+ testutils.RunTests()
diff --git a/modules/bindings/tests/test_clustalw.py b/modules/bindings/tests/test_clustalw.py
index 8f295088ed235ab3ad401eff4525b985df51280d..222effed8a6b6924ad746a2f31eb2da9507cce15 100644
--- a/modules/bindings/tests/test_clustalw.py
+++ b/modules/bindings/tests/test_clustalw.py
@@ -76,7 +76,7 @@ if __name__ == "__main__":
try:
clustalw_path=settings.Locate(('clustalw', 'clustalw2'))
except(settings.FileNotFound):
- print "Could not find clustalw executable: ignoring unit tests"
+ print("Could not find clustalw executable: ignoring unit tests")
sys.exit(0)
from ost import testutils
testutils.RunTests()
diff --git a/modules/bindings/tests/test_hbplus.py b/modules/bindings/tests/test_hbplus.py
new file mode 100644
index 0000000000000000000000000000000000000000..ecc91fbc2f5427481dc46340ccafb593d16142ea
--- /dev/null
+++ b/modules/bindings/tests/test_hbplus.py
@@ -0,0 +1,26 @@
+import unittest
+import sys
+from ost import *
+from ost import settings
+from ost.bindings import hbplus
+
+class TestHBPlusBinding(unittest.TestCase):
+
+ def setUp(self):
+ self.protein = io.LoadEntity("testfiles/testprotein.pdb")
+
+ def testHBondList(self):
+ hbond_list = hbplus.HBondList(self.protein)
+ self.assertEqual(len(hbond_list), 499)
+
+ def testHBondScore(self):
+ self.assertEqual(hbplus.HBondScore(self.protein, self.protein), 1.0)
+
+if __name__ == "__main__":
+ try:
+ settings.Locate("hbplus")
+ except:
+ print("Could not find hbplus, could not test binding...")
+ sys.exit(0)
+ from ost import testutils
+ testutils.RunTests()
diff --git a/modules/bindings/tests/test_hhblits.py b/modules/bindings/tests/test_hhblits.py
index 2ba099ced0c4e7f5dd7d0856431cd48d22a326b2..7e0e3a7fcea983290755ac531812cc40f6c9d7ef 100644
--- a/modules/bindings/tests/test_hhblits.py
+++ b/modules/bindings/tests/test_hhblits.py
@@ -13,6 +13,24 @@ import ost
from ost import seq
from ost.bindings import hhblits
+class _UnitTestHHblitsLog(ost.LogSink):
+ """Dedicated logger to hide some expected warning/ error messages.
+ """
+ def __init__(self):
+ ost.LogSink.__init__(self)
+ self.lcwd = os.getcwd()
+
+ def LogMessage(self, message, severity):
+ message = message.strip()
+ dnem = "could not open file '%s'" % os.path.join(self.lcwd,
+ 'doesnotexist.a3m')
+ if message.endswith(dnem):
+ return
+ print(message)
+
+def setUpModule():
+ ost.PushLogSink(_UnitTestHHblitsLog())
+
class TestHHblitsBindings(unittest.TestCase):
def setUp(self):
self.hhroot = os.getenv('EBROOTHHMINSUITE')
@@ -129,10 +147,10 @@ class TestHHblitsBindings(unittest.TestCase):
os.remove(self.tmpfile)
hhfile = self.hh.A3MToProfile("testfiles/testali.a3m",
hhm_file=self.tmpfile)
- tfh = open(hhfile)
- efh = open("testfiles/test.hmm")
- elst = efh.readlines()
- tlst = tfh.readlines()
+ with open(hhfile) as tfh:
+ tlst = tfh.readlines()
+ with open("testfiles/test.hmm") as efh:
+ elst = efh.readlines()
self.assertEqual(len(elst), len(tlst))
for i in range(0, len(elst)):
if not elst[i].startswith(('FILE', 'COM', 'DATE')):
@@ -147,10 +165,10 @@ class TestHHblitsBindings(unittest.TestCase):
'TSKYR')
self.hh = hhblits.HHblits(query_seq, self.hhroot)
hhfile = self.hh.A3MToProfile("testfiles/testali.a3m")
- tfh = open(hhfile)
- efh = open("testfiles/test.hmm")
- elst = efh.readlines()
- tlst = tfh.readlines()
+ with open(hhfile) as tfh:
+ tlst = tfh.readlines()
+ with open("testfiles/test.hmm") as efh:
+ elst = efh.readlines()
self.assertEqual(len(elst), len(tlst))
for i in range(0, len(elst)):
if not elst[i].startswith(('FILE', 'COM', 'DATE')):
@@ -182,7 +200,7 @@ class TestHHblitsBindings(unittest.TestCase):
with self.assertRaises(IOError) as ioe:
self.hh.A3MToProfile("doesnotexist.a3m")
self.assertEqual(ioe.exception.errno, None)
- self.assertEqual(ioe.exception.message,
+ self.assertEqual(ioe.exception.args[0],
"could not convert a3m to hhm file")
def testA3mToCSFileName(self):
@@ -244,10 +262,12 @@ class TestHHblitsBindings(unittest.TestCase):
self.hh = hhblits.HHblits(query_seq, self.hhroot)
search_file = self.hh.Search("testfiles/testali.a3m",
'testfiles/hhblitsdb/hhblitsdb')
- tfh = open(search_file)
- efh = open("testfiles/test.hhr")
- elst = efh.readlines()
- tlst = tfh.readlines()
+
+ with open(search_file) as tfh:
+ tlst = tfh.readlines()
+ with open("testfiles/test.hhr") as efh:
+ elst = efh.readlines()
+
self.assertEqual(len(elst), len(tlst))
for i in range(0, len(elst)):
if not elst[i].startswith(('Date', 'Command')):
@@ -286,8 +306,9 @@ class TestHHblitsBindings(unittest.TestCase):
def testParseHHMNotWorking(self):
# get info from an HHM file
with self.assertRaises(IOError) as ioe:
- hhblits.ParseHHM(open('testfiles/testali.a3m'))
- self.assertEqual(ioe.exception.message,
+ with open('testfiles/testali.a3m') as f:
+ hhblits.ParseHHM(f)
+ self.assertEqual(ioe.exception.args[0],
'Profile file "testfiles/testali.a3m" is missing '+
'the "Consensus" section')
@@ -317,7 +338,8 @@ class TestHHblitsBindings(unittest.TestCase):
self.assertAlmostEqual(hit.ss_score, 34.1)
def testParseHHblitsOutput(self):
- header, hits = hhblits.ParseHHblitsOutput(open("testfiles/test.hhr"))
+ with open("testfiles/test.hhr") as f:
+ header, hits = hhblits.ParseHHblitsOutput(f)
self.assertEqual(header.query, 'Test')
self.assertEqual(header.match_columns, 141)
self.assertEqual(header.n_eff, 9.4)
@@ -399,8 +421,8 @@ class TestHHblitsBindings(unittest.TestCase):
if __name__ == "__main__":
hhsuite_root_dir = os.getenv('EBROOTHHMINSUITE')
if not hhsuite_root_dir:
- print "No environment variable 'EBROOTHHMINSUITE'. To enable the "+\
- "unit test, this needs to point to your HHsuite installation."
+ print("No environment variable 'EBROOTHHMINSUITE'. To enable the "+\
+ "unit test, this needs to point to your HHsuite installation.")
sys.exit(0)
from ost import testutils
testutils.RunTests()
diff --git a/modules/bindings/tests/test_ialign.py b/modules/bindings/tests/test_ialign.py
new file mode 100644
index 0000000000000000000000000000000000000000..33b6f610d18b094c66a7a1bde944e69184a4d9f5
--- /dev/null
+++ b/modules/bindings/tests/test_ialign.py
@@ -0,0 +1,37 @@
+import unittest
+from ost import *
+from ost import settings
+from ost import testutils
+from ost.seq.alg import SequenceIdentity
+from ost.bindings import ialign
+
+class TestIAlign(unittest.TestCase):
+
+ def setUp(self):
+ self.protein = io.LoadEntity("testfiles/testprotein.pdb")
+
+
+ def testIAlign(self):
+
+ try:
+ ialign_exec = settings.Locate('ialign.pl')
+ except:
+ print("Could not find ialign master perl script: ignoring unit tests")
+ return
+
+ ialign_result = ialign.iAlign(self.protein, self.protein)
+
+ # model and reference are the same, we expect pretty good results
+ self.assertEqual(ialign_result.rmsd, 0.0)
+ self.assertEqual(ialign_result.is_score, 1.0)
+ self.assertEqual(SequenceIdentity(ialign_result.alignment), 100.0)
+ self.assertEqual(ialign_result.aligned_residues, 78)
+ self.assertEqual(ialign_result.aligned_contacts, 91)
+
+ # transformation should be identity matrix (no transformation at all...)
+ identity = geom.Mat4(1,0,0,0, 0,1,0,0, 0,0,1,0, 0,0,0,1)
+ self.assertEqual(ialign_result.transform, identity)
+
+
+if __name__ == "__main__":
+ testutils.RunTests()
diff --git a/modules/bindings/tests/test_kclust.py b/modules/bindings/tests/test_kclust.py
index fe7251613484b55ad248f21edb2df12f61c0ca3e..707288d0757ae1453b6e254348b0bfab5b26a935 100644
--- a/modules/bindings/tests/test_kclust.py
+++ b/modules/bindings/tests/test_kclust.py
@@ -38,7 +38,7 @@ if __name__ == "__main__":
try:
blastpath=settings.Locate(('kClust'))
except(settings.FileNotFound):
- print "Could not find kClust executable: ignoring unit tests"
+ print("Could not find kClust executable: ignoring unit tests")
sys.exit(0)
from ost import testutils
testutils.RunTests()
diff --git a/modules/bindings/tests/test_lga.py b/modules/bindings/tests/test_lga.py
new file mode 100644
index 0000000000000000000000000000000000000000..dfdcea972465c9ac49f3114724c1eaff3b3c384a
--- /dev/null
+++ b/modules/bindings/tests/test_lga.py
@@ -0,0 +1,30 @@
+import unittest
+from ost import *
+from ost import settings
+from ost.bindings import lga
+from ost import testutils
+
+class TestLGABindings(unittest.TestCase):
+
+ def setUp(self):
+ self.protein = io.LoadEntity("testfiles/testprotein.pdb")
+ self.chain_a = self.protein.Select("cname=A")
+
+ def testLGA(self):
+
+ try:
+ lga_path = settings.Locate('lga')
+ except:
+ print("Could not find lga executable: ignoring unit tests")
+ return
+
+ lga_result = lga.GDT(self.chain_a, self.chain_a,
+ reference_length=len(self.chain_a.residues))
+
+ expected_transform = geom.Mat4(1,0,0,0, 0,1,0,0, 0,0,1,0, 0,0,0,1)
+ self.assertEqual(lga_result.gdt_ts, 100.0)
+ self.assertEqual(lga_result.gdt_ha, 100.0)
+ self.assertEqual(lga_result.GetTransform(), expected_transform)
+
+if __name__ == "__main__":
+ testutils.RunTests()
diff --git a/modules/bindings/tests/test_msms.py b/modules/bindings/tests/test_msms.py
index 9041f94fab817441da03ae794fe63d793ad7d208..fb49a2cfa1183263200fe30e1e8eb4b7c97bb3fe 100755
--- a/modules/bindings/tests/test_msms.py
+++ b/modules/bindings/tests/test_msms.py
@@ -12,24 +12,32 @@ class TestMSMSBindings(unittest.TestCase):
self.num_vert=55762
self.ases=20051.928
self.asas=21574.324
+ self.volume=60229.848
def testCalculateSurface(self):
surf=msms.CalculateSurface(self.protein,
msms_env='MSMSSERVER',
density=3,
- radius=1.4)[0]
- assert self.num_vert==len(surf.GetVertexIDList()) \
- and self.num_tri==len(surf.GetTriIDList()), \
- "Number of surface vertices (%i) or triangles (%i) do not match precalculated values (%i/%i)"%(len(surf.GetVertexIDList()),len(surf.GetTriIDList()),self.num_vert,self.num_tri)
-
- def testCalculateSurfaceAres(self):
- (msms_ases, msms_asas)=msms.CalculateSurfaceArea(self.protein, \
- msms_env='MSMSSERVER',
- density=3,
- radius=1.4)
- assert self.ases==msms_ases[0] and self.asas==msms_asas[0], \
- "SASA (%f) or SESA (%f) do not match precalculated values (%f/%f)"%(msms_asas[0],msms_ases[0],self.asas,self.ases)
+ radius=1.4,
+ attach_asa="asa",
+ attach_esa="esa")[0]
+ self.assertEqual(self.num_vert, len(surf.GetVertexIDList()))
+ self.assertEqual(self.num_tri, len(surf.GetTriIDList()))
+
+ def testCalculateSurfaceArea(self):
+ (msms_ases, msms_asas)=msms.CalculateSurfaceArea(self.protein, \
+ msms_env='MSMSSERVER',
+ density=3,
+ radius=1.4)
+ self.assertAlmostEqual(self.ases, msms_ases[0], 1)
+ self.assertAlmostEqual(self.asas, msms_asas[0], 1)
+ def testCalculateSurfaceVolume(self):
+ volume=msms.CalculateSurfaceVolume(self.protein, \
+ msms_env='MSMSSERVER',
+ density=3,
+ radius=1.4)
+ self.assertAlmostEqual(self.volume, volume, 1)
if __name__ == "__main__":
# test if msms package is available on system, otherwise ignore tests
@@ -37,10 +45,10 @@ if __name__ == "__main__":
try:
msms._GetExecutable(msms_exe=None, msms_env='MSMSSERVER')
except(settings.FileNotFound):
- print "Could not find msms executable: ignoring unit tests"
+ print("Could not find msms executable: ignoring unit tests")
exit(0)
version = msms.GetVersion(msms_exe=None, msms_env='MSMSSERVER')
if version!=VERSION_REQUIRED:
- print "MSMS version (%s) does not match required version %s: ignoring unit tests"%(version, VERSION_REQUIRED)
+ print("MSMS version (%s) does not match required version %s: ignoring unit tests"%(version, VERSION_REQUIRED))
from ost import testutils
testutils.RunTests()
diff --git a/modules/bindings/tests/test_naccess.py b/modules/bindings/tests/test_naccess.py
index c2b33b06315340b10eecca93c9adfab25cf37bb7..95949301da14c109872c5b0bafba6822bf35eb68 100644
--- a/modules/bindings/tests/test_naccess.py
+++ b/modules/bindings/tests/test_naccess.py
@@ -25,7 +25,7 @@ class TestNaccessBindings(unittest.TestCase):
except:
excp_raised = True
raise
- self.assertEquals(excp_raised, False, msg="Naccess raised an "+
+ self.assertEqual(excp_raised, False, msg="Naccess raised an "+
"exception on a path containing a '.'. This is not "+
"supposed to happen.")
@@ -33,7 +33,7 @@ if __name__ == "__main__":
try:
settings.Locate("naccess")
except:
- print "Could not find NACCESS, could not test binding..."
+ print("Could not find NACCESS, could not test binding...")
sys.exit(0)
from ost import testutils
testutils.RunTests()
diff --git a/modules/bindings/tests/test_tmtools.py b/modules/bindings/tests/test_tmtools.py
new file mode 100644
index 0000000000000000000000000000000000000000..148e6263c39fc06dc6514b91d2c0c76d78f759b2
--- /dev/null
+++ b/modules/bindings/tests/test_tmtools.py
@@ -0,0 +1,59 @@
+import unittest
+from ost import *
+from ost import settings
+from ost import testutils
+from ost.seq.alg import SequenceIdentity
+from ost.bindings import tmtools
+
+class TestTMBindings(unittest.TestCase):
+
+ def setUp(self):
+ self.protein = io.LoadEntity("testfiles/testprotein.pdb")
+
+
+ def testTMAlign(self):
+
+ try:
+ cad_calc_path = settings.Locate('tmalign')
+ except:
+ print("Could not find tmalign executable: ignoring unit tests")
+ return
+
+ tm_result = tmtools.TMAlign(self.protein, self.protein)
+
+ # model and reference are the same, we expect pretty good results
+ self.assertEqual(tm_result.rmsd, 0.0)
+ self.assertEqual(tm_result.tm_score, 1.0)
+ self.assertEqual(tm_result.aligned_length, len(self.protein.chains[0].residues))
+ self.assertEqual(SequenceIdentity(tm_result.alignment), 100.0)
+
+ # transformation should be identity matrix (no transformation at all...)
+ identity = geom.Mat4(1,0,0,0, 0,1,0,0, 0,0,1,0, 0,0,0,1)
+ self.assertEqual(tm_result.transform, identity)
+
+
+ def testTMScore(self):
+
+ try:
+ cad_calc_path = settings.Locate('tmscore')
+ except:
+ print("Could not find tmalign executable: ignoring unit tests")
+ return
+
+ tm_result = tmtools.TMScore(self.protein, self.protein)
+
+ # model and reference are the same, we expect pretty good results
+ self.assertEqual(tm_result.rmsd_common, 0.0)
+ self.assertEqual(tm_result.tm_score, 1.0)
+ self.assertEqual(tm_result.max_sub, 1.0)
+ self.assertEqual(tm_result.gdt_ts, 1.0)
+ self.assertEqual(tm_result.gdt_ha, 1.0)
+ self.assertEqual(tm_result.rmsd_below_five, 0.0)
+
+ # transformation should be identity matrix (no transformation at all...)
+ identity = geom.Mat4(1,0,0,0, 0,1,0,0, 0,0,1,0, 0,0,0,1)
+ self.assertEqual(tm_result.transform, identity)
+
+
+if __name__ == "__main__":
+ testutils.RunTests()
diff --git a/modules/config/base.hh b/modules/config/base.hh
index b10638e7ede8f4a6f301aad7db6dd8d05b243bc0..a3aada65db0594238032d49d3add69467b3d4083 100644
--- a/modules/config/base.hh
+++ b/modules/config/base.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/config/config.hh.in b/modules/config/config.hh.in
index 7e8a96579478b0d1010ffe3197618d7cbd076619..9cc959a3654af7bbc4808fcca2f24a521a814e9d 100644
--- a/modules/config/config.hh.in
+++ b/modules/config/config.hh.in
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/config/dllexport.hh b/modules/config/dllexport.hh
index 3cacc7c0b5625ea85b82cc6b0cfaa762df78e282..7471428dc18328e2fef2fea79cacddba6a481d29 100755
--- a/modules/config/dllexport.hh
+++ b/modules/config/dllexport.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/config/version.hh.in b/modules/config/version.hh.in
index 94948475f862b2876ccdd459638f8c781735f784..fc132e16463d1c833c6134f9fcf1b1b8417616c1 100644
--- a/modules/config/version.hh.in
+++ b/modules/config/version.hh.in
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2009 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/conop/doc/aminoacid.rst b/modules/conop/doc/aminoacid.rst
index a33104ca6b91085b63a3a0df02b100ebd1d9c2d7..7867e8a0cfcf312f80202782b23a59563e6a636d 100644
--- a/modules/conop/doc/aminoacid.rst
+++ b/modules/conop/doc/aminoacid.rst
@@ -23,7 +23,7 @@ Converter functions
--------------------------------------------------------------------------------
.. function:: ResidueToAminoAcid(residue)
ResidueNameToAminoAcid(rname)
- OneLetterCodeNameToAminoAcid(olc)
+ OneLetterCodeToAminoAcid(olc)
:return: Amino acid from residue, residue name (three-letter-code)
or one-letter-code. Returns XXX if residue, residue name or
diff --git a/modules/conop/doc/compoundlib.rst b/modules/conop/doc/compoundlib.rst
index 195614fbd6d962dda1f2dff29f98515debc8b897..194979cfd388b4c1c129e1904cf83e1d26f01925 100644
--- a/modules/conop/doc/compoundlib.rst
+++ b/modules/conop/doc/compoundlib.rst
@@ -194,7 +194,7 @@ In this example we will translate the three-letter-codes given in the SEQRES rec
compound=compound_lib.FindCompound(tlc)
if compound:
sequence+=compound.one_letter_code
- print sequence # prints 'AGMVF'
+ print(sequence) # prints 'AGMVF'
.. _mmcif-convert:
diff --git a/modules/conop/pymod/__init__.py b/modules/conop/pymod/__init__.py
index 3b7856fe1634cd5d9ec3dfb7e22218618ae2655e..96f2130d748315d1901801578aa06e909a1fbb48 100644
--- a/modules/conop/pymod/__init__.py
+++ b/modules/conop/pymod/__init__.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
@@ -16,7 +16,7 @@
# along with this library; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
#------------------------------------------------------------------------------
-from _ost_conop import *
+from ._ost_conop import *
# The 20 standard amino acids in no particular order
STANDARD_AMINOACIDS=(
diff --git a/modules/conop/pymod/cleanup.py b/modules/conop/pymod/cleanup.py
index 1a51673d778e3e51237a3d576db8e67fca75279f..6866a913aecab022914a963cf743bc45428dea72 100644
--- a/modules/conop/pymod/cleanup.py
+++ b/modules/conop/pymod/cleanup.py
@@ -79,7 +79,7 @@ def _CanonicalizeResidues(clean_entity, ed, compound_lib) :
_DeleteSidechain(res, ed)
for atom in res.atoms:
atom.is_hetatom = False
- print "Removing sidechain of %s, beacuse it has not been found in the compound library"% parent_tlc
+ print("Removing sidechain of %s, beacuse it has not been found in the compound library"% parent_tlc)
else:
#collect atom's names
modif_atom_names = set([atom.name for atom in res.atoms
diff --git a/modules/conop/pymod/export_amino_acids.cc b/modules/conop/pymod/export_amino_acids.cc
index b1422c409a91c05193b2f7ad4474a50170b10d79..8b4f0525ff86d3d6bf6e293751d65e31b4e0fcc6 100644
--- a/modules/conop/pymod/export_amino_acids.cc
+++ b/modules/conop/pymod/export_amino_acids.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/conop/pymod/export_compound.cc b/modules/conop/pymod/export_compound.cc
index 661fa9db11019c805f6eb8d032aa06d8b50c9990..400fad7738b0d3acad1df591aeb380e91146a2f8 100644
--- a/modules/conop/pymod/export_compound.cc
+++ b/modules/conop/pymod/export_compound.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/conop/pymod/export_conop.cc b/modules/conop/pymod/export_conop.cc
index 9f72861bd6a038648b02e6d49926615527e0fdbf..3ffbbad532cb2a35a70676df0557ed05156b8329 100644
--- a/modules/conop/pymod/export_conop.cc
+++ b/modules/conop/pymod/export_conop.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/conop/pymod/export_diag.cc b/modules/conop/pymod/export_diag.cc
index c50c92cce9e864d94048a74423fee26ef30d12a8..acb8e406f8dd10e5e29ce75921894e3a0c8c1025 100644
--- a/modules/conop/pymod/export_diag.cc
+++ b/modules/conop/pymod/export_diag.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/conop/pymod/export_heuristic.cc b/modules/conop/pymod/export_heuristic.cc
index 66e5a894f14b4bb8cad996696205838d1a323f77..275245a7eaeeac0ef66b571556a9d64161ceb36a 100644
--- a/modules/conop/pymod/export_heuristic.cc
+++ b/modules/conop/pymod/export_heuristic.cc
@@ -2,7 +2,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/conop/pymod/export_processor.cc b/modules/conop/pymod/export_processor.cc
index 37e4d8bfcdffccfd569216b4d6085231ab9c486d..262a1dffffbc80e4343693d493f2098f6d12a623 100644
--- a/modules/conop/pymod/export_processor.cc
+++ b/modules/conop/pymod/export_processor.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/conop/pymod/export_ring_finder.cc b/modules/conop/pymod/export_ring_finder.cc
index 7f48ced622ca4d419c0d5186957ce7d94ca57796..55945575514307b3cc59d6bc2cc3c5cb51da2001 100644
--- a/modules/conop/pymod/export_ring_finder.cc
+++ b/modules/conop/pymod/export_ring_finder.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/conop/pymod/export_rule_based.cc b/modules/conop/pymod/export_rule_based.cc
index 053cfd75ca5fdc78a8ae248666b20e6feb113979..7b22b6d2d8f29cf474ae5fd367786835a5edb34c 100644
--- a/modules/conop/pymod/export_rule_based.cc
+++ b/modules/conop/pymod/export_rule_based.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/conop/pymod/wrap_conop.cc b/modules/conop/pymod/wrap_conop.cc
index 04bcfce147b3ebf986cee454c2594e242ade7059..bc52575737b80c062804463601bb1519c178aa66 100644
--- a/modules/conop/pymod/wrap_conop.cc
+++ b/modules/conop/pymod/wrap_conop.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/conop/src/amino_acids.cc b/modules/conop/src/amino_acids.cc
index 2ce42a48510479ffcb5c7cfe1dc0c801a25a5aca..cf11ae0a843788f5ce12fdc9efd047275520f6fe 100644
--- a/modules/conop/src/amino_acids.cc
+++ b/modules/conop/src/amino_acids.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/conop/src/amino_acids.hh b/modules/conop/src/amino_acids.hh
index f79bb68ac9d25f5fda38aa8f94168c720ee7ecda..85aef04878cb3f59f8a7f026a13dbc3cd327c39a 100644
--- a/modules/conop/src/amino_acids.hh
+++ b/modules/conop/src/amino_acids.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/conop/src/chemdict_tool.cc b/modules/conop/src/chemdict_tool.cc
index 9cd043f00fd6a76875447a4908d73401f8d709fe..0286e525ff3eb4a1cf257624533385370ad2e3db 100644
--- a/modules/conop/src/chemdict_tool.cc
+++ b/modules/conop/src/chemdict_tool.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/conop/src/compound.cc b/modules/conop/src/compound.cc
index 6e496ad1074bd67fdbde80cf79f772b865b12ba1..10c330192b2c5164f5f2e206eb5d58ce2e4f3eb3 100644
--- a/modules/conop/src/compound.cc
+++ b/modules/conop/src/compound.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/conop/src/compound.hh b/modules/conop/src/compound.hh
index dff839494c72b842dadbc9e325f5d32c18a2bea9..948cecee588ed3a594ea8775c4524f1d5ff87c4e 100644
--- a/modules/conop/src/compound.hh
+++ b/modules/conop/src/compound.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/conop/src/compound_lib.cc b/modules/conop/src/compound_lib.cc
index 8c901e1ecedc794ffc0f4772bb08c7846e3457a6..7c3fc9eebf33058e3d468609710613b436bbd538 100644
--- a/modules/conop/src/compound_lib.cc
+++ b/modules/conop/src/compound_lib.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/conop/src/compound_lib.hh b/modules/conop/src/compound_lib.hh
index e7192c51eddf99b07c03ca76481e29c0836570dc..2199c1c60511fb46eb6b8ed6c086332751fc7fae 100644
--- a/modules/conop/src/compound_lib.hh
+++ b/modules/conop/src/compound_lib.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/conop/src/conop.cc b/modules/conop/src/conop.cc
index 7ca7d961dae49164d3ff39d7027ab3ed648850da..2bdd6e3b1df34384c804852f9f259e9c3b8f043d 100644
--- a/modules/conop/src/conop.cc
+++ b/modules/conop/src/conop.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/conop/src/conop.hh b/modules/conop/src/conop.hh
index 69a4c92204e322231d9b01c022c8de46f7536070..abf43ca1c0a67369c539682b6c3a8c3efdaf28a0 100644
--- a/modules/conop/src/conop.hh
+++ b/modules/conop/src/conop.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/conop/src/diag.cc b/modules/conop/src/diag.cc
index cf7147ede8fab30eca26dbf22dfe977b6350ed51..3d0838170b825708d6389e963356d713ed905d63 100644
--- a/modules/conop/src/diag.cc
+++ b/modules/conop/src/diag.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/conop/src/diag.hh b/modules/conop/src/diag.hh
index ba7297dd63766ede1e5dd067852b99b61fd14cae..75c13630de10223afc390289a869fa079f089ae4 100644
--- a/modules/conop/src/diag.hh
+++ b/modules/conop/src/diag.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/conop/src/heuristic.cc b/modules/conop/src/heuristic.cc
index a2f931848be7de153884c77358c6804e96d6fed3..b69317c8f5a1f2cd4c38109b24e32b097c358605 100644
--- a/modules/conop/src/heuristic.cc
+++ b/modules/conop/src/heuristic.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/conop/src/heuristic.hh b/modules/conop/src/heuristic.hh
index 40dbdb878f10a41f50dd498437a53d86dad011f9..2b70864aa12e5111b98923accb57cddcc4643495 100644
--- a/modules/conop/src/heuristic.hh
+++ b/modules/conop/src/heuristic.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/conop/src/module_config.hh b/modules/conop/src/module_config.hh
index 224a38c88d6340b96e8a3f7ee0f18c709b0c32ae..ce6369d3e21e019747daaa6145c2b1efc6b5344f 100644
--- a/modules/conop/src/module_config.hh
+++ b/modules/conop/src/module_config.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/conop/src/processor.cc b/modules/conop/src/processor.cc
index 7727bd704d8e09e54573ac517275d8d8d0f3e0a3..844256a3c00ff4c5eb1f8a0a23d0e15d19478909 100644
--- a/modules/conop/src/processor.cc
+++ b/modules/conop/src/processor.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/conop/src/processor.hh b/modules/conop/src/processor.hh
index 65d340ecc1f8fd40fee6935406e97e65c011643f..81add923d0886fd88aa75f47d2093d5b312e5eaf 100644
--- a/modules/conop/src/processor.hh
+++ b/modules/conop/src/processor.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/conop/src/ring_finder.cc b/modules/conop/src/ring_finder.cc
index 04351f1d4b4f2875f5b5a59b4891a17e93ee8068..0af0dd06c9a9bafb5aa39e6601c801c6a6eb0379 100755
--- a/modules/conop/src/ring_finder.cc
+++ b/modules/conop/src/ring_finder.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/conop/src/ring_finder.hh b/modules/conop/src/ring_finder.hh
index e617e85c1c62a6afbf7790fa266ce92c126f754f..6697c76ab264a32d27efed239f35e337f09d1f1d 100755
--- a/modules/conop/src/ring_finder.hh
+++ b/modules/conop/src/ring_finder.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/conop/src/rule_based.cc b/modules/conop/src/rule_based.cc
index fe2013e254b80f5b4ff5b52474ff672873adb72c..47dae10ed054ae9fd83e9be05b5e222b80c35c68 100644
--- a/modules/conop/src/rule_based.cc
+++ b/modules/conop/src/rule_based.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/conop/src/rule_based.hh b/modules/conop/src/rule_based.hh
index 719ba78030003cae44dfa881d8339757b3008102..cea8d5fd3c087c2b1efe0c8429bc8b97f5def4a7 100644
--- a/modules/conop/src/rule_based.hh
+++ b/modules/conop/src/rule_based.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/conop/tests/test_amino_acids.cc b/modules/conop/tests/test_amino_acids.cc
index 58c842a57e7281e2111bf88495fc43f71b49799e..60b8ee3b9fa0bd86321ffb8a6733282d9ea7774c 100644
--- a/modules/conop/tests/test_amino_acids.cc
+++ b/modules/conop/tests/test_amino_acids.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2016 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
@@ -76,7 +76,7 @@ BOOST_AUTO_TEST_CASE(test_one_letter_code_to_residue_name) {
BOOST_CHECK_EQUAL(OneLetterCodeToResidueName('W'), "TRP");
BOOST_CHECK_EQUAL(OneLetterCodeToResidueName('Y'), "TYR");
BOOST_CHECK_EQUAL(OneLetterCodeToResidueName('V'), "VAL");
- // should also wiork if not uppercase!
+ // should also work if not uppercase!
BOOST_CHECK_EQUAL(OneLetterCodeToResidueName('a'), "ALA");
BOOST_CHECK_EQUAL(OneLetterCodeToResidueName('r'), "ARG");
BOOST_CHECK_EQUAL(OneLetterCodeToResidueName('n'), "ASN");
@@ -124,7 +124,7 @@ BOOST_AUTO_TEST_CASE(test_one_letter_code_to_amino_acid) {
BOOST_CHECK_EQUAL(OneLetterCodeToAminoAcid('W'), TRP);
BOOST_CHECK_EQUAL(OneLetterCodeToAminoAcid('Y'), TYR);
BOOST_CHECK_EQUAL(OneLetterCodeToAminoAcid('V'), VAL);
- // should also wiork if not uppercase!
+ // should also work if not uppercase!
BOOST_CHECK_EQUAL(OneLetterCodeToAminoAcid('a'), ALA);
BOOST_CHECK_EQUAL(OneLetterCodeToAminoAcid('r'), ARG);
BOOST_CHECK_EQUAL(OneLetterCodeToAminoAcid('n'), ASN);
@@ -172,7 +172,7 @@ BOOST_AUTO_TEST_CASE(test_residue_name_to_one_letter_code) {
BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("TRP"), 'W');
BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("TYR"), 'Y');
BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("VAL"), 'V');
- // should also wiork if not uppercase!
+ // should also work if not uppercase!
BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("Ala"), 'A');
BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("Arg"), 'R');
BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("Asn"), 'N');
@@ -193,6 +193,11 @@ BOOST_AUTO_TEST_CASE(test_residue_name_to_one_letter_code) {
BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("Trp"), 'W');
BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("Tyr"), 'Y');
BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("Val"), 'V');
+ // non-standard amino acids
+ BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("MSE"), 'X');
+ BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("SEC"), 'X');
+ BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("PYL"), 'X');
+ BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("PCA"), 'X');
// unknown ones
BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("MUH"), 'X');
BOOST_CHECK_EQUAL(ResidueNameToOneLetterCode("FOO"), 'X');
@@ -220,7 +225,7 @@ BOOST_AUTO_TEST_CASE(test_residue_name_to_amino_acid) {
BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("TRP"), TRP);
BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("TYR"), TYR);
BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("VAL"), VAL);
- // should also wiork if not uppercase!
+ // should also work if not uppercase!
BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("Ala"), ALA);
BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("Arg"), ARG);
BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("Asn"), ASN);
@@ -241,6 +246,11 @@ BOOST_AUTO_TEST_CASE(test_residue_name_to_amino_acid) {
BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("Trp"), TRP);
BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("Tyr"), TYR);
BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("Val"), VAL);
+ // non-standard amino acids
+ BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("MSE"), XXX);
+ BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("SEC"), XXX);
+ BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("PYL"), XXX);
+ BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("PCA"), XXX);
// unknown ones
BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("MUH"), XXX);
BOOST_CHECK_EQUAL(ResidueNameToAminoAcid("FOO"), XXX);
diff --git a/modules/conop/tests/test_cleanup.py b/modules/conop/tests/test_cleanup.py
index b0579127a404330c7de3e2b14eea8c9a840ae5e8..54d33a8bc67bf1b95d2df425ea76b8ac5927a09c 100644
--- a/modules/conop/tests/test_cleanup.py
+++ b/modules/conop/tests/test_cleanup.py
@@ -163,4 +163,4 @@ if __name__ == "__main__":
if testutils.SetDefaultCompoundLib():
testutils.RunTests()
else:
- print 'No compound library available. Ignoring test_cleanup.py tests.'
+ print('No compound library available. Ignoring test_cleanup.py tests.')
diff --git a/modules/conop/tests/test_compound.py b/modules/conop/tests/test_compound.py
index bd54b7dfaf94dda8fc2112eb56f58d831df74f44..01c59a233e263e1c9d538c6ae303a7cf5442a8d3 100644
--- a/modules/conop/tests/test_compound.py
+++ b/modules/conop/tests/test_compound.py
@@ -28,4 +28,4 @@ if __name__=='__main__':
if testutils.SetDefaultCompoundLib():
testutils.RunTests()
else:
- print 'No compound library available. Ignoring test_compound.py tests.'
\ No newline at end of file
+ print('No compound library available. Ignoring test_compound.py tests.')
\ No newline at end of file
diff --git a/modules/conop/tests/test_heuristic_builder.cc b/modules/conop/tests/test_heuristic_builder.cc
index cf6efa96f28187ded714133b97b87b955ca2b76f..8ec8b697c5db071f340b3b0e8a28d62a8ba19468 100644
--- a/modules/conop/tests/test_heuristic_builder.cc
+++ b/modules/conop/tests/test_heuristic_builder.cc
@@ -1,7 +1,7 @@
// ------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// This library 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
diff --git a/modules/conop/tests/test_heuristic_conop.cc b/modules/conop/tests/test_heuristic_conop.cc
index 65e0a7fc2d7e9f5de8754b8668eedb28db1e5b44..d6ba9f058b1add565219187ee55c402623fc0402 100644
--- a/modules/conop/tests/test_heuristic_conop.cc
+++ b/modules/conop/tests/test_heuristic_conop.cc
@@ -1,7 +1,7 @@
// ------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// This library 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
diff --git a/modules/conop/tests/test_rule_based_conop.cc b/modules/conop/tests/test_rule_based_conop.cc
index 485454611462364f4a77f75d0fff4f3dd3672daf..4e52222423b61268614b9d11fb28007daa4b5848 100644
--- a/modules/conop/tests/test_rule_based_conop.cc
+++ b/modules/conop/tests/test_rule_based_conop.cc
@@ -2,7 +2,7 @@
// -----------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// This library 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
diff --git a/modules/conop/tests/tests.cc b/modules/conop/tests/tests.cc
index 21dd70140444ba26a29e3c3ce7a85b8d7faaa2b2..a7b157852aeabb6feea5e32a40f77d46de9b40dc 100644
--- a/modules/conop/tests/tests.cc
+++ b/modules/conop/tests/tests.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/db/pymod/__init__.py b/modules/db/pymod/__init__.py
index d443def87175ede548bcd9ff0140f3068e391c36..5133a9694bb24127c8223f1b50d17d1be3d6486e 100644
--- a/modules/db/pymod/__init__.py
+++ b/modules/db/pymod/__init__.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
@@ -16,4 +16,4 @@
# along with this library; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
#------------------------------------------------------------------------------
-from _ost_db import *
+from ._ost_db import *
diff --git a/modules/db/pymod/export_linear_db.cc b/modules/db/pymod/export_linear_db.cc
index 8b9f7f942551a7bd5105dc0cdff59b607416e200..597f4243e1f447d47d39f771b12a09a56e6c5e57 100644
--- a/modules/db/pymod/export_linear_db.cc
+++ b/modules/db/pymod/export_linear_db.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2019 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/db/pymod/wrap_db.cc b/modules/db/pymod/wrap_db.cc
index 883c6a33eb374e82acdd4882afe3fa00a86066be..2bc2223a481615800ca96b765b7f8865dc234727 100644
--- a/modules/db/pymod/wrap_db.cc
+++ b/modules/db/pymod/wrap_db.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2019 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/db/src/binary_container.cc b/modules/db/src/binary_container.cc
index a82723c52e67121acb08675a3313429886115d3c..37f01e402075f49f6b53af23e336f4a36294aba6 100644
--- a/modules/db/src/binary_container.cc
+++ b/modules/db/src/binary_container.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2019 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/db/src/binary_container.hh b/modules/db/src/binary_container.hh
index 3648513d43129fa0b8fd16789710c465ca5a917b..6477e7452bcbd2c0867c5d4d55779e6b54ead351 100644
--- a/modules/db/src/binary_container.hh
+++ b/modules/db/src/binary_container.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2019 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/db/src/extract_data_helper.cc b/modules/db/src/extract_data_helper.cc
index 607499e8fd009972a163c21f9327b4ceadac0e09..f95ff73e3c1b5e20d026af755f2c36b76d3f389e 100644
--- a/modules/db/src/extract_data_helper.cc
+++ b/modules/db/src/extract_data_helper.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2019 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/db/src/extract_data_helper.hh b/modules/db/src/extract_data_helper.hh
index 288ed953688f50b7a806aab8416fa6896fe6bdc1..271d03b3d920bf7c5cd1670d99ceaf9496e13191 100644
--- a/modules/db/src/extract_data_helper.hh
+++ b/modules/db/src/extract_data_helper.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2019 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
@@ -46,4 +46,4 @@ void ExtractTemplateData(const String& entry_name, const String& chain_name,
}} //ns
-#endif
\ No newline at end of file
+#endif
diff --git a/modules/db/src/linear_indexer.cc b/modules/db/src/linear_indexer.cc
index c0a586582525222d2fb4ff8e1cbcc56413d4f4dd..d03471f08bf63045449719b98f8d122c8ff21749 100644
--- a/modules/db/src/linear_indexer.cc
+++ b/modules/db/src/linear_indexer.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2019 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/db/src/linear_indexer.hh b/modules/db/src/linear_indexer.hh
index 3507ae12d3769d960b59e8cdfda1c90639aa552c..a6c77a1d15488bb06a0f20b48a0b0ba3ef29cda4 100644
--- a/modules/db/src/linear_indexer.hh
+++ b/modules/db/src/linear_indexer.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2019 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/db/src/module_config.hh b/modules/db/src/module_config.hh
index cdc876ae17a29f1fea30a39b34a65292c8692b43..03b1a08348045196609e3caea90bf3e0ba9d1d8c 100644
--- a/modules/db/src/module_config.hh
+++ b/modules/db/src/module_config.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/db/src/paged_array.hh b/modules/db/src/paged_array.hh
index 5512c7a9d758f0c017ad3623c9c42866a939cb59..776754bc7cb37118cdd9bd11376b21862f49b8d5 100644
--- a/modules/db/src/paged_array.hh
+++ b/modules/db/src/paged_array.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2019 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/db/src/sqlite_conv.hh b/modules/db/src/sqlite_conv.hh
index 8e4cf959dd7cdccf87851eaee51cc7b91b4b968a..136c5ff6477d4cf67b3209c4172776dd5376661d 100644
--- a/modules/db/src/sqlite_conv.hh
+++ b/modules/db/src/sqlite_conv.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/db/src/sqlite_wrap.cc b/modules/db/src/sqlite_wrap.cc
index f67d85cb0bbef59149882652329aaa7e154e1ee2..8c626ee83d78e26db80ba7de9d223ff121cfd585 100644
--- a/modules/db/src/sqlite_wrap.cc
+++ b/modules/db/src/sqlite_wrap.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/db/src/sqlite_wrap.hh b/modules/db/src/sqlite_wrap.hh
index db9a8d352275d6c8aede7081663342ee663f41fb..a40c725096ad023b9342f8f50c23f7bb6e43afa7 100644
--- a/modules/db/src/sqlite_wrap.hh
+++ b/modules/db/src/sqlite_wrap.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/doc/actions.rst b/modules/doc/actions.rst
index 993612233e4650e6f76287864fe29bcfa9f7f1d2..6d7391a2128ef36d0722d7ab6b98635d49b77065 100644
--- a/modules/doc/actions.rst
+++ b/modules/doc/actions.rst
@@ -26,6 +26,10 @@ In summary it performs the following steps:
- Read structures (PDB or mmCIF format, can be gzipped) and split into
biological assemblies (all possible pairs are scored).
+- Mandatory cleanup of hydrogen atoms, ligand and water chains, small
+ (< 20 residues) peptides or chains with no amino acids as described in
+ :attr:`QSscoreEntity.ent <ost.mol.alg.qsscoring.QSscoreEntity.ent>` and
+ :attr:`QSscoreEntity.removed_chains <ost.mol.alg.qsscoring.QSscoreEntity.removed_chains>`.
- Optional cleanup of structures with :func:`~ost.mol.alg.Molck`.
- Optional structural checks with :func:`~ost.mol.alg.CheckStructure`.
- Unless user-provided, find chain mapping between complexes (see
diff --git a/modules/doc/external.rst b/modules/doc/external.rst
index 3d75fa80b3fa1cc2217892159e0e4e9ca8f03d93..0d7f7d2047bc7319e0d168fb3b3b65a11afcf7b8 100644
--- a/modules/doc/external.rst
+++ b/modules/doc/external.rst
@@ -26,7 +26,7 @@ As an example, we would like to obtain the full path of the msms executable (a p
from ost import settings
exe_path = settings.Locate('msms', search_paths=['/opt/app','/home/app'],
env_name='MSMS', search_system_paths=True)
- print exe_path
+ print(exe_path)
The :func:`~ost.settings.Locate` command looks for the program with the name
`msms`. If env_name is set, it first looks if an environment variable with the
@@ -52,12 +52,12 @@ An example how to generate a temporary directory, open a file in this directory
# generate a temporary directory
tmp_dir_name = tempfile.mkdtemp()
- print 'temporary directory:',tmp_dir_name
+ print('temporary directory:',tmp_dir_name)
# generate and open a file in the temp directory
tmp_file_name = os.path.join(tmp_dir_name,"entity")
tmp_file_handle = open(tmp_file_name, 'w')
- print 'temporary file:',tmp_file_handle
+ print('temporary file:',tmp_file_handle)
# write position and radius of all atoms to file
for a in entity.GetAtomList():
@@ -82,7 +82,7 @@ To run the external program msms from the above example, with the temporary file
# set the command to execute
command = "%s -if %s -of %s" % (exe_path,
tmp_file_name, tmp_file_name)
- print 'command:',command
+ print('command:',command)
# run the executable with the command
proc = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE)
@@ -90,11 +90,11 @@ To run the external program msms from the above example, with the temporary file
# check for successful completion of msms
if proc.returncode != 0:
- print "WARNING: msms error\n", stdout_value
+ print("WARNING: msms error\n", stdout_value)
raise subprocess.CalledProcessError(proc.returncode, command)
# print everything written to the command line (stdout)
- print stdout_value
+ print(stdout_value)
Read Generated Output
--------------------------------------------------------------------------------
@@ -106,8 +106,8 @@ Here we first print the command line output and then load the generated msms sur
.. code-block:: python
# print everything written to the command line (stdout)
- print stdout_value
+ print(stdout_value)
# read msms surface from file
surface = io.LoadSurface(tmp_file_name, "msms")
- print 'number of vertices:',len(surface.GetVertexIDList())
+ print('number of vertices:',len(surface.GetVertexIDList()))
diff --git a/modules/doc/install.rst b/modules/doc/install.rst
index cfea868bf996b792f7942aff96324fa692ab73f7..37af4de496f075f6b401cecb49406de907085111 100644
--- a/modules/doc/install.rst
+++ b/modules/doc/install.rst
@@ -7,9 +7,11 @@ Brief Overview
For a simple and portable way to use OpenStructure we recommend using a
container solution. We provide recipes to build images for
`Docker <https://www.docker.com/>`_ and
-`Singularity <https://www.sylabs.io/guides/2.5.1/user-guide>`_.
-The latest recipes and instructions can be found on our GitLab site
-(`Docker instructions`_ and `Singularity instructions`_).
+`Singularity <https://sylabs.io/singularity/>`_.
+The latest recipes and instructions can be found on our
+`GitLab site <https://git.scicore.unibas.ch/schwede/openstructure/>`_, including
+a link to OpenStructure's own `GitLab Docker registry <https://git.scicore.unibas.ch/schwede/openstructure/container_registry>`_ (`Docker instructions`_ and
+`Singularity instructions`_).
If you wish to compile OpenStructure outside of a container, you need to follow
the steps which we describe in detail below. In essence, these steps are:
@@ -23,13 +25,14 @@ the steps which we describe in detail below. In essence, these steps are:
Installing the Dependencies
--------------------------------------------------------------------------------
-OpenStructure uses a bunch of open-source libraries. If you haven't already
-installed them, please install them now! Where appropriate, the minimally
-required version is given in parentheses.
+OpenStructure requires a C++11 enabled compiler (e.g. recent gcc/clang) and uses
+a bunch of open-source libraries. If you haven't already installed them, please
+install them now! Where appropriate, the minimally required version is given in
+parentheses.
-* `CMake <http://cmake.org>`_ (2.6.4)
-* `Python2 <http://python.org>`_ (2.7)
-* `Boost <http://boost.org>`_ (1.53)
+* `CMake <http://cmake.org>`_ (3.10.2)
+* `Python3 <http://python.org>`_ (3.6)
+* `Boost <http://boost.org>`_ (1.65)
* `zlib <https://zlib.net/>`_ (usually comes with Boost or system)
* `Eigen3 <http://eigen.tuxfamily.org>`_ (3.2.0)
* `SQLite3 <https://www3.sqlite.org>`_ (3.7.13)
@@ -45,7 +48,7 @@ When you enable support for image processing, you will need:
If you would like to use the info module, also install:
-* `Qt5 <http://qt-project.org/>`_ and a C++11 compatible compiler
+* `Qt5 <http://qt-project.org/>`_
If you would like to use the graphical user interface (GUI), also install:
@@ -56,6 +59,9 @@ If you would like to use the :mod:`molecular mechanics <ost.mol.mm>` module:
* `OpenMM <https://simtk.org/home/openmm>`_ (6.1)
+We do not provide backwards compatibility to Python 2.7. The last
+release supporting Python 2.7 is 1.11.0.
+
Getting the Source Code
--------------------------------------------------------------------------------
@@ -69,7 +75,7 @@ get the source code, use git clone:
git clone https://git.scicore.unibas.ch/schwede/openstructure.git <directory-name>
The above command will clone OpenStructure into the directory specified by
-`<directory-name>`. If omitted, the directory will be called ost.
+`<directory-name>`. If omitted, the directory will be called openstructure.
.. note::
@@ -222,6 +228,10 @@ can influence it.
* Usually, you will receive errors for those variables when executing `cmake`
and set them accordingly as needed.
+* `OPENGLPREFERENCE_LEGACY` switches the GL implementation to be used by OpenGL.
+ The default is what should be used on modern systems. But since there are some
+ reports on the internet claiming that the default does not work everywhere,
+ this switch enables the usage of the legacy implementation of GL.
Build Options
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -291,14 +301,14 @@ observed for OpenMM versions 6.1 until 7.1.1 when compiling with gcc versions >=
from source.
-**Ubuntu 18.04 LTS / Debian 9 with GUI**
+**Ubuntu 18.04 LTS / Debian 10.3.0 with GUI**
All the dependencies can be installed from the package manager as follows:
.. code-block:: bash
sudo apt-get install cmake g++ sip-dev libtiff-dev libfftw3-dev libeigen3-dev \
- libpng-dev python-all python2.7 python-pyqt5 libboost-all-dev \
+ libpng-dev python3-all python3-pyqt5 libboost-all-dev \
qt5-qmake qtbase5-dev libpng-dev libsqlite3-dev
Now, all dependencies are located in standard locations and cmake will
@@ -309,15 +319,19 @@ version of OpenStructure.
.. code-block:: bash
- cmake . -DPYTHON_LIBRARIES=/usr/lib/x86_64-linux-gnu/libpython2.7.so \
+ cmake . -DPYTHON_LIBRARIES=/usr/lib/x86_64-linux-gnu/libpython3.6m.so \
-DOPTIMIZE=ON
-
-**macOS (Mojave/ High Sierra) with Homebrew**
+Be careful at -DPYTHON_LIBRARIES, Debian 10 comes with Python 3.7 so that needs
+to be substituted.
+
+**macOS (Catalina) with Homebrew**
`Homebrew <https://brew.sh/>`_ can be used to conveniently install all
-dependencies. The current Boost version, as of writing these instructions, is
-1.70.0 but works so far. Do not forget to also install `boost-python`.
+dependencies. The current Python version, as of writing these instructions, is
+3.7.6 but works so far. Boost comes as 1.72.0 which seems to be OK. Do not
+forget to also install `boost-python3`. Eigen and SQLite also seem to be
+unproblematic concerning higher version numbers.
If you want to build the info module or the graphical user interface, make sure
you have the Xcode app installed. Just the Xcode command line tools which are
@@ -340,18 +354,36 @@ binaries in your Path for CMake to determine its configuration:
Homebrew installs all the software under /usr/local. Thus we have to tell cmake
where to find Boost and Python. Also the Python headers and libraries are not
-located as they are on Linux and hence they must be specified too:
+located as they are on Linux and hence they must be specified too. To get rid of
+a ton of compilation warnings from third party software, we add some dedicated
+C flags:
.. code-block:: bash
- cmake . -DPYTHON_INCLUDE_PATH=/usr/local/Cellar/python@2/2.7.16/\
- Frameworks/Python.framework/Versions/2.7/include/python2.7 \
- -DPYTHON_LIBRARIES=/usr/local/Cellar/python@2/2.7.16/\
- Frameworks/Python.framework/Versions/2.7/lib/libpython2.7.dylib \
- -DPYTHON_ROOT=/usr/local/ \
- -DBOOST_ROOT=/usr/local \
- -DSYS_ROOT=/usr/local \
- -DOPTIMIZE=ON
+ cmake . -DPYTHON_INCLUDE_PATH=/usr/local/Cellar/python3/3.7.6_1/\
+ Frameworks/Python.framework/Versions/Current/include/python3.7m \
+ -DPYTHON_LIBRARIES=/usr/local/Cellar/python3/3.7.6_1/\
+ Frameworks/Python.framework/Versions/Current/lib/libpython3.7m.dylib \
+ -DPYTHON_ROOT=/usr/local/ \
+ -DBOOST_ROOT=/usr/local \
+ -DSYS_ROOT=/usr/local \
+ -DOPTIMIZE=ON \
+ -DCMAKE_C_FLAGS="-isystem /Applications/Xcode.app/Contents/\
+ Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/System/\
+ Library/Frameworks/OpenGL.framework/Headers/ -isystem /usr/local/opt/\
+ qt/lib/QtCore.framework/Headers/ -isystem /usr/local/opt/qt/lib/\
+ QtWidgets.framework/Headers/ -isystem /Applications/Xcode.app/\
+ Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/\
+ MacOSX.sdk/System/Library/Frameworks/Security.framework/ \
+ -isystem /usr/local/opt/qt/lib/QtGui.framework/Headers/" \
+ -DCMAKE_CXX_FLAGS="-isystem /Applications/Xcode.app/Contents/\
+ Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/System/\
+ Library/Frameworks/OpenGL.framework/Headers/ -isystem /usr/local/opt/\
+ qt/lib/QtCore.framework/Headers/ -isystem /usr/local/opt/qt/lib/\
+ QtWidgets.framework/Headers/ -isystem /Applications/Xcode.app/\
+ Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/\
+ MacOSX.sdk/System/Library/Frameworks/Security.framework/ \
+ -isystem /usr/local/opt/qt/lib/QtGui.framework/Headers/"
Building the Project
--------------------------------------------------------------------------------
@@ -394,4 +426,4 @@ in your terminal. This will fetch the newest changes.
.. LocalWords: Homebrew cmake CMake zlib SQLite FFTW libtiff libpng PyQt
.. LocalWords: SSL macOS Makefiles PDB qmake PNG libz libsqlite OPTIMIZE
.. LocalWords: DNDEBUG RPATH rpath SHADER shader SPNAV DConnexion profiler
-.. LocalWords: DOPTIMIZE DENABLE DOPEN DPYTHON DBOOST DSYS Xcode
+.. LocalWords: DOPTIMIZE DENABLE DOPEN DPYTHON DBOOST DSYS Xcode Eigen
diff --git a/modules/doc/intro-01.rst b/modules/doc/intro-01.rst
index 25c092f8ae5801f258b206d2b409498ea0e3ae8d..98c3427e7a445adab8f4e5ad020996ad0e18d50b 100644
--- a/modules/doc/intro-01.rst
+++ b/modules/doc/intro-01.rst
@@ -47,9 +47,9 @@ The loaded structure is an instance of :class:`~ost.mol.EntityHandle` which offe
.. code-block:: python
- print len(fragment.chains), fragment.chains
- print len(fragment.residues), fragment.residues
- print len(fragment.atoms), fragment.atoms
+ print(len(fragment.chains), fragment.chains)
+ print(len(fragment.residues), fragment.residues)
+ print(len(fragment.atoms), fragment.atoms)
As you can see, our fragment consists of one peptide chain of 12 amino acids and
has 81 atoms in total. Now let's examine our fragment in more detail. Enter the
@@ -58,9 +58,9 @@ command
.. code-block:: python
for residue in fragment.residues:
- print residue, 'has', len(residue.atoms), 'atom(s).'
+ print(residue, 'has', len(residue.atoms), 'atom(s).')
for atom in residue.atoms:
- print ' ', atom.name, atom.pos
+ print(' ', atom.name, atom.pos)
This will group the atoms by residue. And, for completeness, we will first group them by chain, then by residues.
@@ -68,11 +68,11 @@ This will group the atoms by residue. And, for completeness, we will first group
.. code-block:: python
for chain in fragment.chains:
- print 'chain', chain.name, 'has', len(chain.residues), 'residue(s)'
+ print('chain', chain.name, 'has', len(chain.residues), 'residue(s)')
for residue in chain.residues:
- print ' ', residue, 'has', len(residue.atoms), 'atom(s).'
+ print(' ', residue, 'has', len(residue.atoms), 'atom(s).')
for atom in residue.atoms:
- print ' ', atom.name, atom.pos
+ print(' ', atom.name, atom.pos)
A protein fragment would not be complete without bonds. Let's see
what bonds we have in there:
@@ -80,7 +80,7 @@ what bonds we have in there:
.. code-block:: python
for bond in fragment.bonds:
- print bond
+ print(bond)
Let There Be Shiny Graphics
--------------------------------------------------------------------------------
diff --git a/modules/doc/intro-02.rst b/modules/doc/intro-02.rst
index 4470a9d8c21746abe5c2a3f1b9bcc8deacebe33f..67bfc4ddbed9cefbf05f52e871c1d835578cc6d2 100644
--- a/modules/doc/intro-02.rst
+++ b/modules/doc/intro-02.rst
@@ -30,7 +30,7 @@ Now let's inspect what we just loaded:
.. code-block:: python
- print map.GetPixelSampling(), map.GetSize()
+ print(map.GetPixelSampling(), map.GetSize())
We can see that the sampling is set to 1.0 Angstrom in all three dimensions. The loaded map is an instance of :class:`~ost.img.ImageHandle`, a class to represent images in one, two and three dimensions.
diff --git a/modules/doc/table.rst b/modules/doc/table.rst
index d0dd45691b89094bba4815fab8ded65e7badd206..4a8748e50bd9a72c7fa1ab01d02c2f926bc33d3b 100644
--- a/modules/doc/table.rst
+++ b/modules/doc/table.rst
@@ -42,14 +42,14 @@ Iterating over table items:
# iterate over all rows
for row in tab.rows:
# print complete row
- print row
+ print(row)
# print value for column 'foo'
- print row[idx]
+ print(row[idx])
# iterate over all rows of selected columns
for foo, bar in tab.Zip('foo','bar'):
- print foo, bar
+ print(foo, bar)
Doing element wise mathematical operations on entire colums:
@@ -63,7 +63,7 @@ Doing element wise mathematical operations on entire colums:
# addition of column foo and column bar
tab.AddCol('qux', 'f', tab['foo']+tab['bar'])
- print tab
+ print(tab)
Select part of the table based on a query:
@@ -76,11 +76,11 @@ Select part of the table based on a query:
# select all rows where foo>=2 and bar<10
subtab = tab.Select('foo>=2 and bar<10')
- print subtab
+ print(subtab)
# select all rows where foo>3 or bar=1
subtab = tab.Select('foo>3 or bar=1')
- print subtab
+ print(subtab)
Functions You Might be Interested In
diff --git a/modules/geom/doc/mat.rst b/modules/geom/doc/mat.rst
index c8736733a7a18533cf18e6fcf40ddecf6b3a52c7..a05dab46569994c22ba46d1064e1ba0b52e7b444 100644
--- a/modules/geom/doc/mat.rst
+++ b/modules/geom/doc/mat.rst
@@ -11,8 +11,8 @@ the following code examples:
.. code-block:: python
m=geom.Mat2(1, 2, 3, 4)
- print m # will print {{1,2},{3,4}}
- print m[(0,0)], m[(0,1)], m[(1,0)], m[(1,1)] # will print 1, 2, 3, 4
+ print(m) # will print {{1,2},{3,4}}
+ print(m[(0,0)], m[(0,1)], m[(1,0)], m[(1,1)]) # will print 1, 2, 3, 4
Matrices support arithmetic via overloaded operators. The following operations are
supported:
@@ -164,4 +164,4 @@ Functions Operating on Matrices
(0, 0, 0).
:param vec: A vector of arbitrary length
- :type vec: :class:`Vec3`
\ No newline at end of file
+ :type vec: :class:`Vec3`
diff --git a/modules/geom/doc/vec.rst b/modules/geom/doc/vec.rst
index bc88b3f2b0e020bdfa0b96480c561414e8f2fa7f..c55dcbb658b82859514addc548884e7fcd6edc6d 100644
--- a/modules/geom/doc/vec.rst
+++ b/modules/geom/doc/vec.rst
@@ -16,9 +16,9 @@ This is shown in the following example:
vec_a=geom.Vec2(1, 0)
vec_b=geom.Vec2(0, 1)
- print vec_a, vec_b
- print vec_a+vec_b
- print vec_a*3-vec_b
+ print(vec_a, vec_b)
+ print(vec_a+vec_b)
+ print(vec_a*3-vec_b)
The standard vector operations are implemented as :ref:`free standing functions
<vector-functions>`:
@@ -29,12 +29,12 @@ The standard vector operations are implemented as :ref:`free standing functions
vec_a=geom.Vec3(1, 0, 0)
vec_b=geom.Vec3(0, 1, 0)
- print geom.Dot(vec_a, vec_b)
- print geom.Cross(vec_a, vec_b)
+ print(geom.Dot(vec_a, vec_b))
+ print(geom.Cross(vec_a, vec_b))
- print geom.Normalize(geom.Vec3(1, 1, 0))
+ print(geom.Normalize(geom.Vec3(1, 1, 0)))
- print geom.Length(geom.Vec3(1, 1, 1))
+ print(geom.Length(geom.Vec3(1, 1, 1)))
Vector Classes
diff --git a/modules/geom/pymod/__init__.py b/modules/geom/pymod/__init__.py
index bd4691781fd76f8e22f507b9cab9a311e8c93a29..4a8e70608fbb710e1a0c6c2306c5eb63fd92cf7e 100644
--- a/modules/geom/pymod/__init__.py
+++ b/modules/geom/pymod/__init__.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
@@ -16,4 +16,4 @@
# along with this library; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
#------------------------------------------------------------------------------
-from _ost_geom import *
+from ._ost_geom import *
diff --git a/modules/geom/pymod/export_composite2.cc b/modules/geom/pymod/export_composite2.cc
index d208ab107d5963cbb21bab5a707a131d65b319a8..c4748c0371c2d1fecd851b3b7391cb73c1116370 100644
--- a/modules/geom/pymod/export_composite2.cc
+++ b/modules/geom/pymod/export_composite2.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/pymod/export_composite2_op.cc b/modules/geom/pymod/export_composite2_op.cc
index 2ea8462b119a89e11532ab8532a83d9054e053fc..334f5532bfe2e6bb77f13778fe5660a5c453240a 100644
--- a/modules/geom/pymod/export_composite2_op.cc
+++ b/modules/geom/pymod/export_composite2_op.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/pymod/export_composite3.cc b/modules/geom/pymod/export_composite3.cc
index 4a37c79f70939446f4a131a1e219ce7e6dc73a21..14fb9d4de5f14fd69cb94b8c8bc853281aadcf7c 100644
--- a/modules/geom/pymod/export_composite3.cc
+++ b/modules/geom/pymod/export_composite3.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/pymod/export_composite3_op.cc b/modules/geom/pymod/export_composite3_op.cc
index ba6faf85fead4627a88ab9ec1b558c2a82edebb5..50414ed43002541d6573bb16ecb1e37c545ba59e 100644
--- a/modules/geom/pymod/export_composite3_op.cc
+++ b/modules/geom/pymod/export_composite3_op.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/pymod/export_mat2.cc b/modules/geom/pymod/export_mat2.cc
index 446aca95ce24f013b8fa3c3c58953f0d28383973..0dcce1b07b3ca8e173ac42eff3c14a9f293ccffc 100644
--- a/modules/geom/pymod/export_mat2.cc
+++ b/modules/geom/pymod/export_mat2.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/pymod/export_mat3.cc b/modules/geom/pymod/export_mat3.cc
index c12f6402c86e1b1a8426007bfa71fec4044bba74..53910aa0b8ebad2caa6ff639c851d1b033a624f4 100644
--- a/modules/geom/pymod/export_mat3.cc
+++ b/modules/geom/pymod/export_mat3.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/pymod/export_mat4.cc b/modules/geom/pymod/export_mat4.cc
index c457eb2618833c699cc8dd925ee235dcb015d0ff..b152e1904759d9e5d5bd6b488a77e7e40adb13b2 100644
--- a/modules/geom/pymod/export_mat4.cc
+++ b/modules/geom/pymod/export_mat4.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/pymod/export_quat.cc b/modules/geom/pymod/export_quat.cc
index 7e233f69c363e9a5c568545c302f8c0a6df3fa1d..c9f1b5656907b750b93ad8229b1c73e396d42e92 100644
--- a/modules/geom/pymod/export_quat.cc
+++ b/modules/geom/pymod/export_quat.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/pymod/export_transform.cc b/modules/geom/pymod/export_transform.cc
index b2f921246bd2b6bedc90fa786aaa58f58b045ac5..9c9b59464247ce3e2f06effefede6040f0e82581 100644
--- a/modules/geom/pymod/export_transform.cc
+++ b/modules/geom/pymod/export_transform.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/pymod/export_vec2.cc b/modules/geom/pymod/export_vec2.cc
index f760d7e7032f74cd89d2690f76d24e1096b8c6ec..77c66017818002cb1a2354709c9233f226e711ab 100644
--- a/modules/geom/pymod/export_vec2.cc
+++ b/modules/geom/pymod/export_vec2.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/pymod/export_vec3.cc b/modules/geom/pymod/export_vec3.cc
index 8adf113fcfd5fb1ae09fd6bbb097212489a65ab5..7d7aba3f9604d83c587d1d9361d83a053ab8641b 100644
--- a/modules/geom/pymod/export_vec3.cc
+++ b/modules/geom/pymod/export_vec3.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/pymod/export_vec4.cc b/modules/geom/pymod/export_vec4.cc
index 810c9de1c7cde2d5a19e6e1c3d2931ade3bb893b..c089319a87a2789696aed59eff27840b1281f23f 100644
--- a/modules/geom/pymod/export_vec4.cc
+++ b/modules/geom/pymod/export_vec4.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/pymod/export_vecmat2_op.cc b/modules/geom/pymod/export_vecmat2_op.cc
index 8f594681fd9a58b2e50595ece974fa63396fddc9..34f9f11f5429a5a4ba902daebe67526dd70041c3 100644
--- a/modules/geom/pymod/export_vecmat2_op.cc
+++ b/modules/geom/pymod/export_vecmat2_op.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/pymod/export_vecmat3_op.cc b/modules/geom/pymod/export_vecmat3_op.cc
index 0cdc3e37358693f63215c0bb8fe05adf17b6617e..f90b24cddb95c1b419e0fe68b44123aa24badbf7 100644
--- a/modules/geom/pymod/export_vecmat3_op.cc
+++ b/modules/geom/pymod/export_vecmat3_op.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/pymod/export_vecmat4_op.cc b/modules/geom/pymod/export_vecmat4_op.cc
index af64cef7476c00ee2c31db423ec40af4d3674aa9..31895316e14dd79732d1fe504d9cde957e9dcfd2 100644
--- a/modules/geom/pymod/export_vecmat4_op.cc
+++ b/modules/geom/pymod/export_vecmat4_op.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/pymod/import_wrapper.hh b/modules/geom/pymod/import_wrapper.hh
index fa687fa2410b200d159c94ef9e8233e1bfee4bae..70c8175fb8d8f7158b98ddcf686ea0f50ea2d0c6 100644
--- a/modules/geom/pymod/import_wrapper.hh
+++ b/modules/geom/pymod/import_wrapper.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/pymod/wrap_geom.cc b/modules/geom/pymod/wrap_geom.cc
index 14df2fa8b1fc2dbcff97f1f9913ca2861bc584e7..8abd01c72099beb90d0be3cc042ae005082c847b 100644
--- a/modules/geom/pymod/wrap_geom.cc
+++ b/modules/geom/pymod/wrap_geom.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/src/aligned_cuboid.cc b/modules/geom/src/aligned_cuboid.cc
index ebd772733cec30960210fdcb915b977866bda396..9e9c840d3b75f3863dcb52517bce651cda5047d8 100644
--- a/modules/geom/src/aligned_cuboid.cc
+++ b/modules/geom/src/aligned_cuboid.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/src/aligned_cuboid.hh b/modules/geom/src/aligned_cuboid.hh
index 9d2298942f8f791942ccabd556ced21617951d70..6a4a6c9d1d108f5746caf2c124ae9c530c5e80b9 100644
--- a/modules/geom/src/aligned_cuboid.hh
+++ b/modules/geom/src/aligned_cuboid.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/src/circular_iterator.hh b/modules/geom/src/circular_iterator.hh
index 2e8755944dab9e47e4f2419b286657a9a93c72d6..58d47ab462e3b2eb6cd0e5c2af0e18552659eb4e 100644
--- a/modules/geom/src/circular_iterator.hh
+++ b/modules/geom/src/circular_iterator.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/src/composite.hh b/modules/geom/src/composite.hh
index 6d1ad48c174073de5aa64272f354c86213bd57e6..f374e970ca2d7a4dd2d2c0a57615884f48e31965 100644
--- a/modules/geom/src/composite.hh
+++ b/modules/geom/src/composite.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/src/composite2.cc b/modules/geom/src/composite2.cc
index 8a6aec909cdd9a9a8bbda1ffbf49e20add92f770..7bfd58e9acb570095840c0751242f9b1ecb26b9b 100644
--- a/modules/geom/src/composite2.cc
+++ b/modules/geom/src/composite2.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/src/composite2.hh b/modules/geom/src/composite2.hh
index bcbc9a77924d65b8111ed7f9470c21a0beaeff34..13c3f80a777433eccb928002b6ed1f061f1fb544 100644
--- a/modules/geom/src/composite2.hh
+++ b/modules/geom/src/composite2.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/src/composite2_op.cc b/modules/geom/src/composite2_op.cc
index ad25008f88a9e9d2c4d3a02d021d1a087773e18a..a31f5f76cbb5328ed4f3f386c34a64dd96ab2200 100644
--- a/modules/geom/src/composite2_op.cc
+++ b/modules/geom/src/composite2_op.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/src/composite2_op.hh b/modules/geom/src/composite2_op.hh
index 71eb1b3c6d9b662450c15dfd0f96a5818f33d5f1..86281e1c5bcfdad093012cc9b1eddfd76b413878 100644
--- a/modules/geom/src/composite2_op.hh
+++ b/modules/geom/src/composite2_op.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/src/composite3.cc b/modules/geom/src/composite3.cc
index b2d795247fe3858c11fb2ee2262746aa9c495d1e..5abcd778ad21ce4db881ed5d6e3a2cc5615d33e8 100644
--- a/modules/geom/src/composite3.cc
+++ b/modules/geom/src/composite3.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/src/composite3.hh b/modules/geom/src/composite3.hh
index 8e88050366915bac120bcaf5ccdf4c8d43164a5c..02f1c7d61580b267df44cf551325bc1dc4c4a1d3 100644
--- a/modules/geom/src/composite3.hh
+++ b/modules/geom/src/composite3.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/src/composite3_op.cc b/modules/geom/src/composite3_op.cc
index 09fb2c72e7430c2fc938534ff4167052485a4b24..283659e397f0551ce4220f179dbdf1166c6aa615 100644
--- a/modules/geom/src/composite3_op.cc
+++ b/modules/geom/src/composite3_op.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/src/composite3_op.hh b/modules/geom/src/composite3_op.hh
index 23bdf3e5e4d4e3d18f8206a01b9cd1c8bf45780b..00dfd14ee740e88e3938f6e8a5c11e6f8f3f10c2 100644
--- a/modules/geom/src/composite3_op.hh
+++ b/modules/geom/src/composite3_op.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/src/composite_op.hh b/modules/geom/src/composite_op.hh
index b81c5a32d8b137637399eb919af799e4f49e2f19..ab3b016d7cbf85ba20d6032bbe756e6ebe6a6261 100644
--- a/modules/geom/src/composite_op.hh
+++ b/modules/geom/src/composite_op.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/src/constants.hh b/modules/geom/src/constants.hh
index 45b8b111e2e1f6c516cd8113e2b6be46117db7f2..e00404ea42b5c1d79847b711e01bfe5ace45dd04 100644
--- a/modules/geom/src/constants.hh
+++ b/modules/geom/src/constants.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/src/def.hh b/modules/geom/src/def.hh
index fb100fa795f9cc8c2cd72fc81a2f8ffe17242622..6fe7306d1bc08a078daa4bd00af329ae4617a4a6 100644
--- a/modules/geom/src/def.hh
+++ b/modules/geom/src/def.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/src/exc.hh b/modules/geom/src/exc.hh
index 0c4390030e9d6d3c520a9876722e8ce564be4134..9d7f636bc4d3fd229ea42fb0d7203fe1194aace8 100644
--- a/modules/geom/src/exc.hh
+++ b/modules/geom/src/exc.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/src/fnc.hh b/modules/geom/src/fnc.hh
index 0062db1f7ce2d50214baf4a3c34e337d65707ad4..48d19131cbd98a457afe145c89013018c2f5d4c1 100644
--- a/modules/geom/src/fnc.hh
+++ b/modules/geom/src/fnc.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/src/geom.hh b/modules/geom/src/geom.hh
index 2bf028ab5b825a8a9eb100ba1c4d35e27626a640..255839d94e082d5e01254e65478c4c5c54dbb1b5 100644
--- a/modules/geom/src/geom.hh
+++ b/modules/geom/src/geom.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/src/mat.hh b/modules/geom/src/mat.hh
index 8127088ac0e27488266facb0636154aec1425995..e0ef21819adde8aaa0900e2d5a824cf734563b2d 100644
--- a/modules/geom/src/mat.hh
+++ b/modules/geom/src/mat.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/src/mat2.cc b/modules/geom/src/mat2.cc
index d0bf5809d15e7d9641cc702ae476f85419626688..3b6804879b42c06d1bb2f060bb033ceb118b5120 100644
--- a/modules/geom/src/mat2.cc
+++ b/modules/geom/src/mat2.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/src/mat2.hh b/modules/geom/src/mat2.hh
index b7743dfc03e18656648513bf48be068d901f4038..9e6524a6d99ece22919d32de1f9fab7fcdb1a59d 100644
--- a/modules/geom/src/mat2.hh
+++ b/modules/geom/src/mat2.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/src/mat3.cc b/modules/geom/src/mat3.cc
index edf414eb82517336696866389405fdd95cf73388..7b1a502c35716a6210d2b3ef623c5ed5c60fe0b6 100644
--- a/modules/geom/src/mat3.cc
+++ b/modules/geom/src/mat3.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/src/mat3.hh b/modules/geom/src/mat3.hh
index 35cae2f03f078e7d7c7fa9e97c5bf06ba09c0344..1a24ce73b183bc7e4eb0c06653b59c3974b67ee9 100644
--- a/modules/geom/src/mat3.hh
+++ b/modules/geom/src/mat3.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/src/mat4.cc b/modules/geom/src/mat4.cc
index c43780e0a44f1b35447b82a6af60422f25ffc8cc..c082bcd8aab5c070c3f249bf9d1250ea5b0a905e 100644
--- a/modules/geom/src/mat4.cc
+++ b/modules/geom/src/mat4.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/src/mat4.hh b/modules/geom/src/mat4.hh
index 3888fa873b0b48bc799d48eda7b52ed4ca5325d0..67cef15c0f70a1cc37929101a882a0de1e014690 100644
--- a/modules/geom/src/mat4.hh
+++ b/modules/geom/src/mat4.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/src/module_config.hh b/modules/geom/src/module_config.hh
index 760e1ae87ecc43af6dc1337cbb58ee8e1a21e7a9..525726e3fcdc6e6ac730970fe0fee29989abffde 100644
--- a/modules/geom/src/module_config.hh
+++ b/modules/geom/src/module_config.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/src/point_cloud.cc b/modules/geom/src/point_cloud.cc
index 72a7552005cd8bd4651073fbee20dfc18bb68925..218af5f40696f1a474d25e7f67ae6047254a8545 100644
--- a/modules/geom/src/point_cloud.cc
+++ b/modules/geom/src/point_cloud.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/src/point_cloud.hh b/modules/geom/src/point_cloud.hh
index 6188dbf26a7a3645d44f8c5976af81bb2e3ed631..1707b622fff8c24b04a16d62a342060046c5e7db 100644
--- a/modules/geom/src/point_cloud.hh
+++ b/modules/geom/src/point_cloud.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/src/quat.cc b/modules/geom/src/quat.cc
index 84fcb872a5a3deff62d114ecd15b3a734a273cc7..99a7a7246ef17fcbb99af15820ec7a7ca56f376b 100644
--- a/modules/geom/src/quat.cc
+++ b/modules/geom/src/quat.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/src/quat.hh b/modules/geom/src/quat.hh
index 881f69b5bdd8a8112eefe3ffc642ceed525efe42..edae2c1875df3f4b5911821c5e71620eab8da70b 100644
--- a/modules/geom/src/quat.hh
+++ b/modules/geom/src/quat.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/src/transform.cc b/modules/geom/src/transform.cc
index 9c00d5e8c4fc2aa1cc3b5b71e498e99585aa0ee0..4b064aca8bde62e1d42f173eb51339fced47619b 100644
--- a/modules/geom/src/transform.cc
+++ b/modules/geom/src/transform.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/src/transform.hh b/modules/geom/src/transform.hh
index 6965c48437dd5b4c041aabf46eb705ec87bd9ec4..40e764fcbc014ca8ae2233b8c3ebabbcae507518 100644
--- a/modules/geom/src/transform.hh
+++ b/modules/geom/src/transform.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/src/vec.hh b/modules/geom/src/vec.hh
index 70871d2274b41c87086d3310b120ad06093d65b3..e31b363fb0d0885e767170cdf671b07b36b9a28a 100644
--- a/modules/geom/src/vec.hh
+++ b/modules/geom/src/vec.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/src/vec2.hh b/modules/geom/src/vec2.hh
index b0191ac7f4be32ef99592e46f91f02288bcffae3..83ea4a0de74e40bf1f56f70ff52767a1e849c1ba 100644
--- a/modules/geom/src/vec2.hh
+++ b/modules/geom/src/vec2.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/src/vec3.cc b/modules/geom/src/vec3.cc
index a69b2682d7d53aaaf8970b165d068c1adb228988..0bda96a8b0022f39033488ff0678d80d4ed15f51 100644
--- a/modules/geom/src/vec3.cc
+++ b/modules/geom/src/vec3.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/src/vec3.hh b/modules/geom/src/vec3.hh
index 47137476eb9aa8c2a9d6286de9da7954a97f269b..527928f455a32271d10b8e479e37f164c4e7b183 100644
--- a/modules/geom/src/vec3.hh
+++ b/modules/geom/src/vec3.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
@@ -73,6 +73,23 @@ public:
//! explicit initialization with an array of floats
explicit Vec3(const float v[3]): x(v[0]), y(v[1]), z(v[2]) { }
+ /* The "=" operator for Vec3 gives the "maybe-uninitialize" warning in
+ combination with GenericPropValue with GCC when optimisation is turned on.
+ GenericPropValue is implemented via boost::variant which may confuse GCC
+ tracking variables through the compilation process. As boost::variant is
+ able to search for a "=" operator of different type if no direct match is
+ provided, maybe GCC mixes the Real and Vec3 operators where Real used for
+ Vec3 would indeed lack the y and z component. According to the GCC manual,
+ the "maybe-uninitialize" warnings are prone to produce false positives.
+ There is actually an initiative to get rid of them.
+
+ We ignore them for this particular case by saving the current diagnostic
+ settings (push), disabling the warning in the diagnostics
+ (ignored "-Wmaybe-uninitialized") and afterwards restoring the old
+ diagnostics context (pop).
+ */
+ #pragma GCC diagnostic push
+ #pragma GCC diagnostic ignored "-Wmaybe-uninitialized"
//! assignement op
Vec3& operator=(const Vec3& v)
{
@@ -81,7 +98,8 @@ public:
z=v.z;
return *this;
}
-
+ #pragma GCC diagnostic pop
+
//! comparable
bool operator==(const Vec3& rhs) const
{
diff --git a/modules/geom/src/vec4.hh b/modules/geom/src/vec4.hh
index 5947a1c06a1d18c898c0ff08a4ff84e364d5e451..f003002cf71c14a1d224eccd73ca0da95a620eab 100644
--- a/modules/geom/src/vec4.hh
+++ b/modules/geom/src/vec4.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/src/vec_mat_predicates.hh b/modules/geom/src/vec_mat_predicates.hh
index bbe639f3b70f7e68cafaf96e30668027d3c95b33..64542ec0bfe37eb33ef6d69b5e663eaa6cc2e68e 100644
--- a/modules/geom/src/vec_mat_predicates.hh
+++ b/modules/geom/src/vec_mat_predicates.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/src/vecmat2_op.cc b/modules/geom/src/vecmat2_op.cc
index 221a6bbf2a4401da31dd118d04c86f4e0ca9723e..ef9a903237858be7440a556fbd9f52811b96cbb7 100644
--- a/modules/geom/src/vecmat2_op.cc
+++ b/modules/geom/src/vecmat2_op.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/src/vecmat2_op.hh b/modules/geom/src/vecmat2_op.hh
index 65a027f74cae3463e52bc3f76d73e70521bbfaa0..ac8e9332a25b4f05d5c9fd4779937163ec7ce6ed 100644
--- a/modules/geom/src/vecmat2_op.hh
+++ b/modules/geom/src/vecmat2_op.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/src/vecmat3_op.cc b/modules/geom/src/vecmat3_op.cc
index f476eca3098fcde019427da37960a0bf826f0933..f29419223b9411228c71a2ab2d2b833b02bb3228 100644
--- a/modules/geom/src/vecmat3_op.cc
+++ b/modules/geom/src/vecmat3_op.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/src/vecmat3_op.hh b/modules/geom/src/vecmat3_op.hh
index d7762cccfe7240647b34049c257152d4ba67e17a..c4378d166fe9673d2e6db3234eeec5ab7b2c19a8 100644
--- a/modules/geom/src/vecmat3_op.hh
+++ b/modules/geom/src/vecmat3_op.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/src/vecmat4_op.cc b/modules/geom/src/vecmat4_op.cc
index b1bce87d4d38b647d1b95252285eb2309f34eee4..a1e791ce64834ac10128bc9a9e49cc81212d4c67 100644
--- a/modules/geom/src/vecmat4_op.cc
+++ b/modules/geom/src/vecmat4_op.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/src/vecmat4_op.hh b/modules/geom/src/vecmat4_op.hh
index a3cbf8531e971cc8e41e007f2edfae097d71f8cf..bd823cb7ef1c56ca4402adcd8046a1e3a412f740 100644
--- a/modules/geom/src/vecmat4_op.hh
+++ b/modules/geom/src/vecmat4_op.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/src/vecmat_op.hh b/modules/geom/src/vecmat_op.hh
index 400d5f1aa29fa66eef5ac5a8f7680e96c53609c6..f8664f1a5b9f706ca514b94d3185036a15c65c54 100644
--- a/modules/geom/src/vecmat_op.hh
+++ b/modules/geom/src/vecmat_op.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/tests/test_composite2.cc b/modules/geom/tests/test_composite2.cc
index a459f74d1123ff14855470eb41f49f573078301b..cd6110af4f4df6e0a0a004cfc78e2a11c477a662 100644
--- a/modules/geom/tests/test_composite2.cc
+++ b/modules/geom/tests/test_composite2.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/tests/test_composite3.cc b/modules/geom/tests/test_composite3.cc
index 48309acd0476adbced427021e1ffb23af061079a..13450ded0365539708086f8ad7e3908d98d0cc4d 100644
--- a/modules/geom/tests/test_composite3.cc
+++ b/modules/geom/tests/test_composite3.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/tests/test_geom.py b/modules/geom/tests/test_geom.py
index 46063eb4fb1dab5c1f28796bb4d077710f08a097..d076c9c946e7c1b97fcd3de75341285835f81187 100644
--- a/modules/geom/tests/test_geom.py
+++ b/modules/geom/tests/test_geom.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
@@ -30,7 +30,7 @@ import ost.geom as geom
# which do not convert std::out_of_range to IndexError correctly.
try:
geom.Vec2()[3]
-except Exception, e:
+except Exception as e:
pass
IndexError = type(e)
diff --git a/modules/geom/tests/test_mat2.cc b/modules/geom/tests/test_mat2.cc
index 944de8e9a5276af0c1e33c0c414fc5032379eeb8..7316b929fdee5a489b01cca8ee7ecce670b078b0 100644
--- a/modules/geom/tests/test_mat2.cc
+++ b/modules/geom/tests/test_mat2.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/tests/test_mat3.cc b/modules/geom/tests/test_mat3.cc
index 2d4ce923eb4d276b2c3b6acece0e56dd5f286009..eb8f65f80bc82948ebc9cdd212cba1db4b432405 100644
--- a/modules/geom/tests/test_mat3.cc
+++ b/modules/geom/tests/test_mat3.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/tests/test_mat4.cc b/modules/geom/tests/test_mat4.cc
index bee468108bc8c038caae0b2156dcd67d6f3a3b2d..d51c49ba83771f69a00db92b70f61f34df282bbe 100644
--- a/modules/geom/tests/test_mat4.cc
+++ b/modules/geom/tests/test_mat4.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/tests/test_op2.cc b/modules/geom/tests/test_op2.cc
index 3805cc879bbf5caa0df7d1ab885b7add4f30e744..5d96e51c9f51900a924d210e4dfb3505c631a796 100644
--- a/modules/geom/tests/test_op2.cc
+++ b/modules/geom/tests/test_op2.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/tests/test_op3.cc b/modules/geom/tests/test_op3.cc
index 519b19f8eb38cf3126d7a1ee083f769f7023b5b2..63ec98bd338de7ed4bc2eb02c31c16ed70e41382 100644
--- a/modules/geom/tests/test_op3.cc
+++ b/modules/geom/tests/test_op3.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/tests/test_op4.cc b/modules/geom/tests/test_op4.cc
index 96edec9175189a3e4b30446b215ad3e65a43cc71..db6edc4d4ada2aeed87b9450ef0548aee776364f 100644
--- a/modules/geom/tests/test_op4.cc
+++ b/modules/geom/tests/test_op4.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/tests/test_quat.cc b/modules/geom/tests/test_quat.cc
index 158f44d1ee415c6ab32a475ef89ad543e819350e..c1c5d7a670074528ed95773bdac0b766f516779b 100644
--- a/modules/geom/tests/test_quat.cc
+++ b/modules/geom/tests/test_quat.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/tests/test_transform.cc b/modules/geom/tests/test_transform.cc
index f52a47628f635d8c01a9889e77a0fbdbef8bde78..104905acb0a742610065c3c4425fee35f9609276 100644
--- a/modules/geom/tests/test_transform.cc
+++ b/modules/geom/tests/test_transform.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/tests/test_vec2.cc b/modules/geom/tests/test_vec2.cc
index 3ea6090b2c3d3ce4e4cf348d360ede46bfc75ce8..ff561e774986b4bab55f177dbc07e287a42b01dd 100644
--- a/modules/geom/tests/test_vec2.cc
+++ b/modules/geom/tests/test_vec2.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/tests/test_vec3.cc b/modules/geom/tests/test_vec3.cc
index b7c03ff7f2a3ec7f5b43d55c7a498a00df9caad6..97cb8906dc542e429741d4e723e4e7db0aec21a9 100644
--- a/modules/geom/tests/test_vec3.cc
+++ b/modules/geom/tests/test_vec3.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/tests/test_vec4.cc b/modules/geom/tests/test_vec4.cc
index 44b87bcf19a9aee5018159ddd02b93cecaa98dbb..ad493244a8f5db12d347c836e2c17d524a53420e 100644
--- a/modules/geom/tests/test_vec4.cc
+++ b/modules/geom/tests/test_vec4.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/geom/tests/tests.cc b/modules/geom/tests/tests.cc
index c0b2b30306327a8892ab74e9bbc22923711f2c84..87cf43c09db05a08f1920c3ce836b85e21111bce 100644
--- a/modules/geom/tests/tests.cc
+++ b/modules/geom/tests/tests.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/pymod/__init__.py b/modules/gfx/pymod/__init__.py
index d1b59f1a7cd7e59807cd7d16b7c3ce5a68d623e8..1d84a86c47f4078f33ad1a8efd88b8a4c226e02f 100644
--- a/modules/gfx/pymod/__init__.py
+++ b/modules/gfx/pymod/__init__.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
@@ -16,8 +16,9 @@
# along with this library; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
#------------------------------------------------------------------------------
-from _ost_gfx import *
-from py_gfx_obj import PyGfxObj
+from ._ost_gfx import *
+from .py_gfx_obj import PyGfxObj
+import functools
WHITE=RGB(1.0,1.0,1.0)
BLACK=RGB(0.0,0.0,0.0)
@@ -94,8 +95,10 @@ def FitToScreen(gfx_ent, width=None, height=None, margin=0.05):
max_proj=max(proj, max_proj)
lengths.append(max_proj-min_proj)
def cmp_x(rhs, lhs):
- return cmp(lhs[1], rhs[1])
- sorted_axes=sorted(zip(rows, lengths), cmp_x)
+ # replaced cmp when porting to Python 3
+ #return cmp(lhs[1], rhs[1])
+ return (lhs[1] > rhs[1]) - (lhs[1] < rhs[1])
+ sorted_axes=sorted(zip(rows, lengths), key=functools.cmp_to_key(cmp_x))
return [r*l for r,l in sorted_axes]
scene=Scene()
if not isinstance(gfx_ent, Entity):
@@ -282,7 +285,7 @@ def _entity_reset(self,*args,**kwargs):
else:
raise TypeError("Reset: unknown option of type '%s' given"%type(a))
- for key,val in kwargs.iteritems():
+ for key,val in kwargs.items():
if key=="entity":
if not isinstance(val,mol.EntityHandle):
raise TypeError("Reset: expected mol.EntityHandle for 'entity' option")
diff --git a/modules/gfx/pymod/color_by_def.hh b/modules/gfx/pymod/color_by_def.hh
index 41436d83382e1e0ced0eef780e0eeadc0a5c9aed..86938289d454a379c3c714bfad11b5cbdba6ba6a 100644
--- a/modules/gfx/pymod/color_by_def.hh
+++ b/modules/gfx/pymod/color_by_def.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/pymod/export_bitmap.cc b/modules/gfx/pymod/export_bitmap.cc
index d8e944d21462cfaa90d72b7c99920882c6887722..d5a6f1e79deffdf6d5453cb9a8cb8b8529b59fb4 100644
--- a/modules/gfx/pymod/export_bitmap.cc
+++ b/modules/gfx/pymod/export_bitmap.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/pymod/export_color.cc b/modules/gfx/pymod/export_color.cc
index e673212501ffa23d1331e9682e995866857125fb..009255badefaf116cd95060afeb93a866b690315 100644
--- a/modules/gfx/pymod/export_color.cc
+++ b/modules/gfx/pymod/export_color.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/pymod/export_color_ops.cc b/modules/gfx/pymod/export_color_ops.cc
index fd974b22d46c85a8806dd67c11b730c012031f10..c77458b6773dfdb870ebb6e11b9e1f15c49cc435 100644
--- a/modules/gfx/pymod/export_color_ops.cc
+++ b/modules/gfx/pymod/export_color_ops.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/pymod/export_entity.cc b/modules/gfx/pymod/export_entity.cc
index 0a3ca83624e815e57878fe8a92680d42e46912a6..334a96c5b3d359c0560e72857dea29a377b423ad 100644
--- a/modules/gfx/pymod/export_entity.cc
+++ b/modules/gfx/pymod/export_entity.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/pymod/export_exporter.cc b/modules/gfx/pymod/export_exporter.cc
index 22c9a97432477c8f8c47b4ba6fd7d2cfac58451d..2cfefea2942d784119f31367f853d0be0936a05f 100644
--- a/modules/gfx/pymod/export_exporter.cc
+++ b/modules/gfx/pymod/export_exporter.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/pymod/export_gfx_node.cc b/modules/gfx/pymod/export_gfx_node.cc
index 9a1ed0c5e6d9bc486e2ca08f329cdaa16cce8291..43dde9fb4b072a2aa2db084f16c793cc858b5e1f 100644
--- a/modules/gfx/pymod/export_gfx_node.cc
+++ b/modules/gfx/pymod/export_gfx_node.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/pymod/export_gfx_obj.cc b/modules/gfx/pymod/export_gfx_obj.cc
index 68e88f90169ae1c1f190a3b778da26d0f63160a1..6952ddab006a4b595c768797ff3918b69ceef9dc 100644
--- a/modules/gfx/pymod/export_gfx_obj.cc
+++ b/modules/gfx/pymod/export_gfx_obj.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/pymod/export_glwin_base.cc b/modules/gfx/pymod/export_glwin_base.cc
index a2cb803ba2b8a865285094d47b12f7f206661570..6772994d85424a6401616a6b48e8054653fa1706 100644
--- a/modules/gfx/pymod/export_glwin_base.cc
+++ b/modules/gfx/pymod/export_glwin_base.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/pymod/export_gradient.cc b/modules/gfx/pymod/export_gradient.cc
index fa09e623bdcb139da989f295174d8ce25c11ef56..cfff11ac0a1edf97db20e96f43676c78134d0b0d 100644
--- a/modules/gfx/pymod/export_gradient.cc
+++ b/modules/gfx/pymod/export_gradient.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/pymod/export_map.cc b/modules/gfx/pymod/export_map.cc
index ea334ead8a8e3dc69808af841d26c1fee46d805a..0cfee858af946bab7e7d87176f4f84028abfa666 100644
--- a/modules/gfx/pymod/export_map.cc
+++ b/modules/gfx/pymod/export_map.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/pymod/export_primitives.cc b/modules/gfx/pymod/export_primitives.cc
index 01b328d7288116ab8c6dcd9e7d86c5c3ad97fb07..5762646ce65764de0a093e008ff932679ccb217e 100644
--- a/modules/gfx/pymod/export_primitives.cc
+++ b/modules/gfx/pymod/export_primitives.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/pymod/export_primlist.cc b/modules/gfx/pymod/export_primlist.cc
index d11d7465625d24a9f849fb7b916b4c4f703bc508..4538f366e1a2b5c4f2c4e5280194ddbbf5f6e3e2 100644
--- a/modules/gfx/pymod/export_primlist.cc
+++ b/modules/gfx/pymod/export_primlist.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
@@ -137,6 +137,8 @@ namespace {
void export_primlist()
{
#if OST_NUMPY_SUPPORT_ENABLED
+ // The following define enforces no return value when calling import_array
+ #define NUMPY_IMPORT_ARRAY_RETVAL
import_array(); // magic handshake for numpy module
#endif
diff --git a/modules/gfx/pymod/export_render_options.cc b/modules/gfx/pymod/export_render_options.cc
index 4f1de36c40d87559161c82c3a1a8b571b685328b..8116d84fbb8fc3bfa7a688e0d397f0a32863a77d 100644
--- a/modules/gfx/pymod/export_render_options.cc
+++ b/modules/gfx/pymod/export_render_options.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/pymod/export_scene.cc b/modules/gfx/pymod/export_scene.cc
index 746c958f7c8ee041252b79687e2cfb0c4a029342..d3982dfa96d0b082c4bd80942c6383a3affccf96 100644
--- a/modules/gfx/pymod/export_scene.cc
+++ b/modules/gfx/pymod/export_scene.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/pymod/export_surface.cc b/modules/gfx/pymod/export_surface.cc
index b954a414a26173a211f3a275e8ea83990efe279e..f6b8efa5d4aac6da7f10ce7a91da14a48378e782 100644
--- a/modules/gfx/pymod/export_surface.cc
+++ b/modules/gfx/pymod/export_surface.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/pymod/export_symmetry_node.cc b/modules/gfx/pymod/export_symmetry_node.cc
index f89d54a4b0edf44304399d13b4d3a54263e6873e..b97f309022ab14f7190e6ee1b47bd734d719f1f6 100644
--- a/modules/gfx/pymod/export_symmetry_node.cc
+++ b/modules/gfx/pymod/export_symmetry_node.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/pymod/py_gfx_obj.py b/modules/gfx/pymod/py_gfx_obj.py
index ac91e9073a47b061ee57145e0d3d7b6b6a51dcc5..33dcb5361fb0f901f62da24444b4f28fe542bb99 100644
--- a/modules/gfx/pymod/py_gfx_obj.py
+++ b/modules/gfx/pymod/py_gfx_obj.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
@@ -17,7 +17,7 @@
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
#------------------------------------------------------------------------------
import traceback
-from _ost_gfx import *
+from ._ost_gfx import *
class PyGfxObj(GfxObj):
def __init__(self,name):
diff --git a/modules/gfx/pymod/wrap_gfx.cc b/modules/gfx/pymod/wrap_gfx.cc
index b28c496597e9ae55489a1a0930fdfe2b00fcc620..10967df666492b09bdbca2e318e42067d547a010 100644
--- a/modules/gfx/pymod/wrap_gfx.cc
+++ b/modules/gfx/pymod/wrap_gfx.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/bitmap_io.cc b/modules/gfx/src/bitmap_io.cc
index 4245c32ec0b7b70daf17f56f73349b10cd39dfa8..8437de3975fbeb601727deb904bca4659d24ace9 100644
--- a/modules/gfx/src/bitmap_io.cc
+++ b/modules/gfx/src/bitmap_io.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/bitmap_io.hh b/modules/gfx/src/bitmap_io.hh
index dacb9dbe36b95a32c6d9b8273999ebbac7efe8eb..68111dd7e8f75614cbf4ae0ea45a66964215403d 100644
--- a/modules/gfx/src/bitmap_io.hh
+++ b/modules/gfx/src/bitmap_io.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/collada_exporter.cc b/modules/gfx/src/collada_exporter.cc
index d2b45c21e76db54c311f10ff1e8c7389049151b6..02c6923264630eded00372359af4f5da75813b26 100644
--- a/modules/gfx/src/collada_exporter.cc
+++ b/modules/gfx/src/collada_exporter.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/collada_exporter.hh b/modules/gfx/src/collada_exporter.hh
index 7a05417c6826528bc49d956e33dc8109a3803a6d..d7ddc4b5fb4eec84cd1e218b987d8d01851dacc0 100644
--- a/modules/gfx/src/collada_exporter.hh
+++ b/modules/gfx/src/collada_exporter.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/color.cc b/modules/gfx/src/color.cc
index 60607ad0ed0fd0c85a0a67342b4b2929cfcbe426..a98e961d674b64bcfdd58907f4beb60cb72bf093 100644
--- a/modules/gfx/src/color.cc
+++ b/modules/gfx/src/color.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/color.hh b/modules/gfx/src/color.hh
index 1340967f9b61d53d1aa4b5e307b0f9f560413d2d..458f39fceccffecf7ddc70b1327bfc07708bf7b8 100644
--- a/modules/gfx/src/color.hh
+++ b/modules/gfx/src/color.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/color_ops/basic_gradient_color_op.cc b/modules/gfx/src/color_ops/basic_gradient_color_op.cc
index 397ed3d41303e8c57544a053826bbe55949eda22..49ba30e4d6630c3e6971c24de114cd7116cfe76a 100644
--- a/modules/gfx/src/color_ops/basic_gradient_color_op.cc
+++ b/modules/gfx/src/color_ops/basic_gradient_color_op.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/color_ops/basic_gradient_color_op.hh b/modules/gfx/src/color_ops/basic_gradient_color_op.hh
index 6da2b9006363d843f874f4972d47324b418075d4..4024fa3cec21e38a0fed3abd2cdc282a37a1340b 100644
--- a/modules/gfx/src/color_ops/basic_gradient_color_op.hh
+++ b/modules/gfx/src/color_ops/basic_gradient_color_op.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/color_ops/by_chain_color_op.cc b/modules/gfx/src/color_ops/by_chain_color_op.cc
index d2c6789f9c5b6d4b21239f490b9b29a70bad8de4..53bf367f52f68d53886a323988cbec4aa0fd1599 100644
--- a/modules/gfx/src/color_ops/by_chain_color_op.cc
+++ b/modules/gfx/src/color_ops/by_chain_color_op.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/color_ops/by_chain_color_op.hh b/modules/gfx/src/color_ops/by_chain_color_op.hh
index 58485af37577c0d5848992020608c9a54c593fbd..5f06c7079edbf8154c0e9dd0a8d1440c6205864d 100644
--- a/modules/gfx/src/color_ops/by_chain_color_op.hh
+++ b/modules/gfx/src/color_ops/by_chain_color_op.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/color_ops/by_element_color_op.cc b/modules/gfx/src/color_ops/by_element_color_op.cc
index 031fe5e322f9574a777dfe3cb4da98d7a98a6c45..e5ff19c172e4c4edb09d20f89eba031b4e327a98 100644
--- a/modules/gfx/src/color_ops/by_element_color_op.cc
+++ b/modules/gfx/src/color_ops/by_element_color_op.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/color_ops/by_element_color_op.hh b/modules/gfx/src/color_ops/by_element_color_op.hh
index 0ad7c60d826c4d3953daea2ef37206dd9a7f5ac1..0fe606ef3e339aa558bb05f91c937cdb8aab9af9 100644
--- a/modules/gfx/src/color_ops/by_element_color_op.hh
+++ b/modules/gfx/src/color_ops/by_element_color_op.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/color_ops/color_op.cc b/modules/gfx/src/color_ops/color_op.cc
index 514650f84b9cdb2e4083f83e24fc666b3a62b7ca..670bd8add1e6514eefbbe619f97ab371a98de54d 100644
--- a/modules/gfx/src/color_ops/color_op.cc
+++ b/modules/gfx/src/color_ops/color_op.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/color_ops/color_op.hh b/modules/gfx/src/color_ops/color_op.hh
index 7e9e433a726ae936ae1c9c88fce50e23368e1118..e51678417de55da765309a7f8d09a7b902d9a88e 100644
--- a/modules/gfx/src/color_ops/color_op.hh
+++ b/modules/gfx/src/color_ops/color_op.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/color_ops/entity_view_color_op.cc b/modules/gfx/src/color_ops/entity_view_color_op.cc
index de44bf1a059141f5ecf686e97a1a49f3d267569a..fc412439a962c76ca898975312909fdefc3cdf34 100644
--- a/modules/gfx/src/color_ops/entity_view_color_op.cc
+++ b/modules/gfx/src/color_ops/entity_view_color_op.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/color_ops/entity_view_color_op.hh b/modules/gfx/src/color_ops/entity_view_color_op.hh
index 49e6e294bd70f3f2c20d1e49734147121263881b..1995f7266bf119a6fa17ffb6843fad2449668876 100644
--- a/modules/gfx/src/color_ops/entity_view_color_op.hh
+++ b/modules/gfx/src/color_ops/entity_view_color_op.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/color_ops/gradient_color_op.cc b/modules/gfx/src/color_ops/gradient_color_op.cc
index 0a9e95952d1eb01c7e45232c887a6f4944dfbf3b..7ac2bb99c9e3cc21b3dc63ddf7495f33295c66db 100644
--- a/modules/gfx/src/color_ops/gradient_color_op.cc
+++ b/modules/gfx/src/color_ops/gradient_color_op.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/color_ops/gradient_color_op.hh b/modules/gfx/src/color_ops/gradient_color_op.hh
index 9c7f37345e9a6e3f9898d112ad50b8712f18f282..97b611f3564b939adef3b076202b27748bde2f4f 100644
--- a/modules/gfx/src/color_ops/gradient_color_op.hh
+++ b/modules/gfx/src/color_ops/gradient_color_op.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/color_ops/gradient_level_color_op.cc b/modules/gfx/src/color_ops/gradient_level_color_op.cc
index 32429a095344d56b8de72e904bf3e29dd4555cfd..f3501d98ea94d6c33143f7c9d846d4ccc0738086 100644
--- a/modules/gfx/src/color_ops/gradient_level_color_op.cc
+++ b/modules/gfx/src/color_ops/gradient_level_color_op.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/color_ops/gradient_level_color_op.hh b/modules/gfx/src/color_ops/gradient_level_color_op.hh
index 1b453a48f9c1ec4613727862895bca9311c65e0c..282c25800bbc41b4c19dc98a52d8b2de6059c686 100644
--- a/modules/gfx/src/color_ops/gradient_level_color_op.hh
+++ b/modules/gfx/src/color_ops/gradient_level_color_op.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/color_ops/map_handle_color_op.cc b/modules/gfx/src/color_ops/map_handle_color_op.cc
index d09be806cb84bdcfab5123ef2f1066604a318bad..1f580bf495a87cde6250138e13253a1d5d5bb8c3 100644
--- a/modules/gfx/src/color_ops/map_handle_color_op.cc
+++ b/modules/gfx/src/color_ops/map_handle_color_op.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/color_ops/map_handle_color_op.hh b/modules/gfx/src/color_ops/map_handle_color_op.hh
index b0d1c15fb0ed07364b81de7bf5f0b94c98332b2b..bca982bb33cf39eed1d80c0cb3488a5717ea752d 100644
--- a/modules/gfx/src/color_ops/map_handle_color_op.hh
+++ b/modules/gfx/src/color_ops/map_handle_color_op.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/color_ops/uniform_color_op.cc b/modules/gfx/src/color_ops/uniform_color_op.cc
index 8447317067950edd823a41a926c42e7710968565..b76ecff619be1a25e1d5f245576f662c3cfe7383 100644
--- a/modules/gfx/src/color_ops/uniform_color_op.cc
+++ b/modules/gfx/src/color_ops/uniform_color_op.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/color_ops/uniform_color_op.hh b/modules/gfx/src/color_ops/uniform_color_op.hh
index 518fc5792e84032eac27c953b57f3eee0e5c2c19..c322cb4e57d364d78ecb5f2a7883599a0aba65b9 100644
--- a/modules/gfx/src/color_ops/uniform_color_op.hh
+++ b/modules/gfx/src/color_ops/uniform_color_op.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/entity.cc b/modules/gfx/src/entity.cc
index 6b8468a249a469a4e256f62834d91ba74aae36d8..1d1f232baec883f490e86a592a9a33fa6347c4bf 100644
--- a/modules/gfx/src/entity.cc
+++ b/modules/gfx/src/entity.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/entity.hh b/modules/gfx/src/entity.hh
index 9106e260769091b06aac55bc9f346514c73f5e8a..f16fe32924ba035911a314108f908ad812614d52 100644
--- a/modules/gfx/src/entity.hh
+++ b/modules/gfx/src/entity.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/entity_fw.hh b/modules/gfx/src/entity_fw.hh
index 192ad391322da684abb6590365c8e2b89530ea56..b877a0ff14cddaf5cd50ca5b40f4d0cc011e0ed3 100644
--- a/modules/gfx/src/entity_fw.hh
+++ b/modules/gfx/src/entity_fw.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/exporter.cc b/modules/gfx/src/exporter.cc
index 5100490c1d1ed852b9788f05d57ad3a05e38beaa..88bd074cd1531c56fbbe6cb45da709c0b2ef7190 100644
--- a/modules/gfx/src/exporter.cc
+++ b/modules/gfx/src/exporter.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/exporter.hh b/modules/gfx/src/exporter.hh
index 1780851eb94e5470f778ea648fed821782717f66..a663bde27c5d4338f08611d8bbecf97f06ddf662 100644
--- a/modules/gfx/src/exporter.hh
+++ b/modules/gfx/src/exporter.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/exporter_fw.hh b/modules/gfx/src/exporter_fw.hh
index 499248014e24d9df5374569c7a66d5227a4c8443..c0c9fe4ff847976689e548a00476b34afeffb569 100644
--- a/modules/gfx/src/exporter_fw.hh
+++ b/modules/gfx/src/exporter_fw.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/gfx.hh b/modules/gfx/src/gfx.hh
index 2a0d2303d23786caf0d2feae24a5487ecac842c6..dfc2e55ebca39b18123b539091cab839a034cfb2 100644
--- a/modules/gfx/src/gfx.hh
+++ b/modules/gfx/src/gfx.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/gfx_fw.hh b/modules/gfx/src/gfx_fw.hh
index e5efaacf9eba4255c11524c2f3f6a50d422ef734..d87ad16e3a175b77cf8642cf646bee89aa01983e 100644
--- a/modules/gfx/src/gfx_fw.hh
+++ b/modules/gfx/src/gfx_fw.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/gfx_node.cc b/modules/gfx/src/gfx_node.cc
index 657068c9ef836eeb73db31a956fa627d1b1e321a..716523f1df54883e4c692929b301d8bbb82a4505 100644
--- a/modules/gfx/src/gfx_node.cc
+++ b/modules/gfx/src/gfx_node.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/gfx_node.hh b/modules/gfx/src/gfx_node.hh
index 6cff8388518b96924eec6802dad40e5631cf8c4c..d3c01d425455ba5f4025a8e7f2dc0916300421c2 100644
--- a/modules/gfx/src/gfx_node.hh
+++ b/modules/gfx/src/gfx_node.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/gfx_node_fw.hh b/modules/gfx/src/gfx_node_fw.hh
index 744b350efb52cc300e4e8a320cf6d9032991aecf..b265f1ac963a97e4d788fe45ddbf1555ad598166 100644
--- a/modules/gfx/src/gfx_node_fw.hh
+++ b/modules/gfx/src/gfx_node_fw.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/gfx_node_visitor.hh b/modules/gfx/src/gfx_node_visitor.hh
index 5b1d49a6b21f59316c5d516809cae052745c50d5..ff41b28f3d4fa8180bef813c6decb602304bf504 100644
--- a/modules/gfx/src/gfx_node_visitor.hh
+++ b/modules/gfx/src/gfx_node_visitor.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/gfx_object.cc b/modules/gfx/src/gfx_object.cc
index 97e235f418f2e50dee56a33d55f285919d138175..dbfe17cddd122612c98a977e76ba9138654a7ee1 100644
--- a/modules/gfx/src/gfx_object.cc
+++ b/modules/gfx/src/gfx_object.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/gfx_object.hh b/modules/gfx/src/gfx_object.hh
index 03d76a8c4e719861452c7b1c9e1bc8f2b5226d75..4049eb77fdfb51d06565c7f25cf0497f8ba6c527 100644
--- a/modules/gfx/src/gfx_object.hh
+++ b/modules/gfx/src/gfx_object.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/gfx_object_base.hh b/modules/gfx/src/gfx_object_base.hh
index 07e49a92eb4df39fa9359b3f09e37f4e3eb9ef40..c2072ab89febaac523e82e77616e62f7b4beffeb 100644
--- a/modules/gfx/src/gfx_object_base.hh
+++ b/modules/gfx/src/gfx_object_base.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/gfx_object_fw.hh b/modules/gfx/src/gfx_object_fw.hh
index 73118a522dd2a6c459046147c86bbe8df156d0ea..8bc44c1f6ba82df3e800f35de4de65c64162cf11 100644
--- a/modules/gfx/src/gfx_object_fw.hh
+++ b/modules/gfx/src/gfx_object_fw.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/gfx_prim.cc b/modules/gfx/src/gfx_prim.cc
index a5af981b12f83256f4af14332ab3f8a45a4a8cb4..8d55b87d043c9759316de70709eaef664e88f8ca 100644
--- a/modules/gfx/src/gfx_prim.cc
+++ b/modules/gfx/src/gfx_prim.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/gfx_prim.hh b/modules/gfx/src/gfx_prim.hh
index cb545425462042868a60be6b0a49c99adda6d065..fa050c68af0190719a716a5fec47825ec720f97d 100644
--- a/modules/gfx/src/gfx_prim.hh
+++ b/modules/gfx/src/gfx_prim.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/gfx_test_object.cc b/modules/gfx/src/gfx_test_object.cc
index 7e60ab6d8657d35b44d2eb0840a0c0f7640ad76a..381f3c19a0db1a57e53def0be5905d8d0c8f8197 100644
--- a/modules/gfx/src/gfx_test_object.cc
+++ b/modules/gfx/src/gfx_test_object.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/gfx_test_object.hh b/modules/gfx/src/gfx_test_object.hh
index 8d878d7c213ca7f8d8fa31241934a0c7a114baa6..9053101aaf83beb37a7e58a719846ba751319c65 100644
--- a/modules/gfx/src/gfx_test_object.hh
+++ b/modules/gfx/src/gfx_test_object.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/gl_helper.hh b/modules/gfx/src/gl_helper.hh
index 77346056346c4ec937b90dba4bebaedd9fe5fb59..82aa630383ee3e327d99c8fd0f07856287892c4d 100644
--- a/modules/gfx/src/gl_helper.hh
+++ b/modules/gfx/src/gl_helper.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/gl_include.hh b/modules/gfx/src/gl_include.hh
index 69761cce04882a18b174bca19a295d50a1af8a18..9ea90d473cae9955db1705ce08db685539389171 100644
--- a/modules/gfx/src/gl_include.hh
+++ b/modules/gfx/src/gl_include.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
@@ -39,8 +39,10 @@
# if defined(__APPLE__)
+# define GL_SILENCE_DEPRECATION
# include <OpenGL/gl.h>
# include <OpenGL/glu.h>
+# undef GL_SILENCE_DEPRECATION
# else
# include <GL/gl.h>
# include <GL/glu.h>
diff --git a/modules/gfx/src/glext_include.hh b/modules/gfx/src/glext_include.hh
index 874b70a31137e6839574c48f712e7ec4978bb7fb..3c39256dbb74ecb7b2be55b423319d5f85769d05 100644
--- a/modules/gfx/src/glext_include.hh
+++ b/modules/gfx/src/glext_include.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/glwin_base.hh b/modules/gfx/src/glwin_base.hh
index 77d30ee76ea8cedb30a80d615b74e968439b65a8..9bcaed92caeaff04bfc0e26223c9df7c33c41859 100644
--- a/modules/gfx/src/glwin_base.hh
+++ b/modules/gfx/src/glwin_base.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/gost_exporter.cc b/modules/gfx/src/gost_exporter.cc
index 525a70aba0334a0dcdc1e0bfbbccee7ff28975e3..5be10034e6d4bf89323eb1f68b8bb8f549128acd 100644
--- a/modules/gfx/src/gost_exporter.cc
+++ b/modules/gfx/src/gost_exporter.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/gost_exporter.hh b/modules/gfx/src/gost_exporter.hh
index 03f47680eeabba9fe36236ff057b5e13f4385c9c..509dca86cdaef938dd14ab18f13f2bcef9c263fc 100644
--- a/modules/gfx/src/gost_exporter.hh
+++ b/modules/gfx/src/gost_exporter.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/gradient.cc b/modules/gfx/src/gradient.cc
index 0018f3aa6bbd8c9eb07fd7a0b6f13b5eb70ec91b..4f3fd3ebab6e0c458997af4aa5f2539dd53c4de7 100644
--- a/modules/gfx/src/gradient.cc
+++ b/modules/gfx/src/gradient.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/gradient.hh b/modules/gfx/src/gradient.hh
index e08a24edaf22bdc3841fed3514574a5f9cd5650b..ae1efbdcfa6985c721f642b9671164213e3561f4 100644
--- a/modules/gfx/src/gradient.hh
+++ b/modules/gfx/src/gradient.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/gradient_manager.cc b/modules/gfx/src/gradient_manager.cc
index ab807ad1848bdd1df4e972a5921428e124c092d2..7f8894a092fd85a566680debce13023306ca4569 100644
--- a/modules/gfx/src/gradient_manager.cc
+++ b/modules/gfx/src/gradient_manager.cc
@@ -1,4 +1,4 @@
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/gradient_manager.hh b/modules/gfx/src/gradient_manager.hh
index fe73bbe19aa5f3d50b869ccaf1f457378ed41c26..756ee127d01401f93ab996a803959d82a511472e 100644
--- a/modules/gfx/src/gradient_manager.hh
+++ b/modules/gfx/src/gradient_manager.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/impl/backbone_trace.cc b/modules/gfx/src/impl/backbone_trace.cc
index da56ae1796004e52c4ceca18cc8e1df287035be5..26bd1e1ff24e6764bf26fb3ed87e3b6aa34dcb5e 100644
--- a/modules/gfx/src/impl/backbone_trace.cc
+++ b/modules/gfx/src/impl/backbone_trace.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/impl/backbone_trace.hh b/modules/gfx/src/impl/backbone_trace.hh
index 677f02f12341036757606410e8328458e776c2e8..7eca13bbb13c310f41caa598c50207d2e668ec0a 100644
--- a/modules/gfx/src/impl/backbone_trace.hh
+++ b/modules/gfx/src/impl/backbone_trace.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/impl/cartoon_renderer.cc b/modules/gfx/src/impl/cartoon_renderer.cc
index 3dfedd48460b8ca116341a6b4b5d2aab8ab7696b..87ba15c42642ce5e0e2f936b7dfa7d939bf21e0e 100644
--- a/modules/gfx/src/impl/cartoon_renderer.cc
+++ b/modules/gfx/src/impl/cartoon_renderer.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/impl/cartoon_renderer.hh b/modules/gfx/src/impl/cartoon_renderer.hh
index 1d60eec76b775923e6b51ddc98ca8f815add45e0..220dcecd53163da82abc00dbe2ac70a00ed9a1b9 100644
--- a/modules/gfx/src/impl/cartoon_renderer.hh
+++ b/modules/gfx/src/impl/cartoon_renderer.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/impl/cgl_offscreen_buffer.cc b/modules/gfx/src/impl/cgl_offscreen_buffer.cc
index fa56d00ce9ea6eb1a3bee4b9bab8e0882bb9a013..29d255c8049cb02ef124bd193b14af01c30f85c7 100644
--- a/modules/gfx/src/impl/cgl_offscreen_buffer.cc
+++ b/modules/gfx/src/impl/cgl_offscreen_buffer.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/impl/cgl_offscreen_buffer.hh b/modules/gfx/src/impl/cgl_offscreen_buffer.hh
index 17d7854cb48cc5bb95ef04d7988fd0d72aa27526..619b6065448a9158c2de63eda0cf7b165c79b1ec 100644
--- a/modules/gfx/src/impl/cgl_offscreen_buffer.hh
+++ b/modules/gfx/src/impl/cgl_offscreen_buffer.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/impl/connect_renderer_base.cc b/modules/gfx/src/impl/connect_renderer_base.cc
index 5f0ed4a6b8f821866eb587ac7110a0df28a307d4..51afae44fa6cf9d343cce17c13b88c447c304122 100644
--- a/modules/gfx/src/impl/connect_renderer_base.cc
+++ b/modules/gfx/src/impl/connect_renderer_base.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/impl/connect_renderer_base.hh b/modules/gfx/src/impl/connect_renderer_base.hh
index 0f4c7f23724dd2547ab809a5dc89614713361fb5..bcf8691eae2cd3fd3db3b1451305548598ac00b6 100644
--- a/modules/gfx/src/impl/connect_renderer_base.hh
+++ b/modules/gfx/src/impl/connect_renderer_base.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/impl/cpk_renderer.cc b/modules/gfx/src/impl/cpk_renderer.cc
index f780647b745c51658d12fd3e97dbc05359159baf..46cf90c10ef1501a29720570965652cd9f4660b2 100644
--- a/modules/gfx/src/impl/cpk_renderer.cc
+++ b/modules/gfx/src/impl/cpk_renderer.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/impl/cpk_renderer.hh b/modules/gfx/src/impl/cpk_renderer.hh
index 1a6dcd2dcb12e0d811603dcf141a7203aa074aea..e5090aa7ec830b623a11ed0df64a7fa4504f831b 100644
--- a/modules/gfx/src/impl/cpk_renderer.hh
+++ b/modules/gfx/src/impl/cpk_renderer.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/impl/custom_renderer.cc b/modules/gfx/src/impl/custom_renderer.cc
index ec3195464d969141b80cc9305766a59854cd0853..cedd9567ee40ef59bb6d3e846692ec38b8915520 100644
--- a/modules/gfx/src/impl/custom_renderer.cc
+++ b/modules/gfx/src/impl/custom_renderer.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/impl/custom_renderer.hh b/modules/gfx/src/impl/custom_renderer.hh
index 8c5c1bd3d2c566f4f85fcd4721b2068ff051c0cc..245fbbd09c74eb82afeff5d92b7251f645d0c821 100644
--- a/modules/gfx/src/impl/custom_renderer.hh
+++ b/modules/gfx/src/impl/custom_renderer.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/impl/debug_renderer.cc b/modules/gfx/src/impl/debug_renderer.cc
index 3ff579078643ca36c0fbd42b31dd766521bb899c..1c2752714da2b53e3c7ef26732a47dea5651949a 100644
--- a/modules/gfx/src/impl/debug_renderer.cc
+++ b/modules/gfx/src/impl/debug_renderer.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/impl/debug_renderer.hh b/modules/gfx/src/impl/debug_renderer.hh
index 22a6d432ce2a6d379dd3757bdaeeabd3cdf0a837..f8ea2f078d2ecf7b24f6c6a5191e83e1d407f44a 100644
--- a/modules/gfx/src/impl/debug_renderer.hh
+++ b/modules/gfx/src/impl/debug_renderer.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/impl/entity_detail.cc b/modules/gfx/src/impl/entity_detail.cc
index 7e7f65989bca37bfdbba9ef8c68e2208492cfec9..b597ee31dbf274f81022df89da84c64659fbefa8 100644
--- a/modules/gfx/src/impl/entity_detail.cc
+++ b/modules/gfx/src/impl/entity_detail.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/impl/entity_detail.hh b/modules/gfx/src/impl/entity_detail.hh
index 12412f680236afc25f67556971b76f8eac8f643d..932d6a0b4abab8cd45e1a7c502ffa5c9c2028fcd 100644
--- a/modules/gfx/src/impl/entity_detail.hh
+++ b/modules/gfx/src/impl/entity_detail.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/impl/entity_renderer.cc b/modules/gfx/src/impl/entity_renderer.cc
index 9b623cc11455a1a93737045f576e3279cf6d3637..dc6f056f72668f791bae9952665fddd854f636de 100644
--- a/modules/gfx/src/impl/entity_renderer.cc
+++ b/modules/gfx/src/impl/entity_renderer.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/impl/entity_renderer.hh b/modules/gfx/src/impl/entity_renderer.hh
index 14c0332c3b5a15d0d0f101b19aad3e9363d03047..0157c5b08d4420c7ceb71a66c7dc6109e99cd785 100644
--- a/modules/gfx/src/impl/entity_renderer.hh
+++ b/modules/gfx/src/impl/entity_renderer.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/impl/entity_renderer_fw.hh b/modules/gfx/src/impl/entity_renderer_fw.hh
index f07fbd625d2d3c0b362c0dfe99f27cbc8cd8aad8..fdecafc7389d60a7247371f358a6eab2b533db6d 100644
--- a/modules/gfx/src/impl/entity_renderer_fw.hh
+++ b/modules/gfx/src/impl/entity_renderer_fw.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/impl/fast_spheres.cc b/modules/gfx/src/impl/fast_spheres.cc
index 905791c34a539d691885c10f2ce7a07cf1e20af6..5a5cae22fe8ee325d09b8debc31b532df8272d48 100644
--- a/modules/gfx/src/impl/fast_spheres.cc
+++ b/modules/gfx/src/impl/fast_spheres.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/impl/fast_spheres.hh b/modules/gfx/src/impl/fast_spheres.hh
index 72402ef9b36f81fca897f0a2484b39def3a7a932..e6374352bf1158e3015e1737dba2a13d2a2d3705 100644
--- a/modules/gfx/src/impl/fast_spheres.hh
+++ b/modules/gfx/src/impl/fast_spheres.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/impl/generate_map_iso_spec.py b/modules/gfx/src/impl/generate_map_iso_spec.py
index 74a9f58dbcdc786e3946bb47b6c79202847fdcab..5c655aeda8af805bd0d2edf8f2a4f0523fd9e17e 100644
--- a/modules/gfx/src/impl/generate_map_iso_spec.py
+++ b/modules/gfx/src/impl/generate_map_iso_spec.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
diff --git a/modules/gfx/src/impl/glx_offscreen_buffer.cc b/modules/gfx/src/impl/glx_offscreen_buffer.cc
index 41bca43a363a7c873f0ee719e2ca68c0859a893b..0f4e691d89b591079184242d0353ca7a0466c806 100644
--- a/modules/gfx/src/impl/glx_offscreen_buffer.cc
+++ b/modules/gfx/src/impl/glx_offscreen_buffer.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/impl/glx_offscreen_buffer.hh b/modules/gfx/src/impl/glx_offscreen_buffer.hh
index e089e8ace66d32b46cf9f4d3d6884211d225a449..304b5b68cc01f29a227311fbdc6063bd657d4ae3 100644
--- a/modules/gfx/src/impl/glx_offscreen_buffer.hh
+++ b/modules/gfx/src/impl/glx_offscreen_buffer.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/impl/line_trace_renderer.cc b/modules/gfx/src/impl/line_trace_renderer.cc
index bb6622ac84e6de1d5138c3810760975d2744dffb..e953f034a108a2a7581accbb3048b4e6b07a4623 100644
--- a/modules/gfx/src/impl/line_trace_renderer.cc
+++ b/modules/gfx/src/impl/line_trace_renderer.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/impl/line_trace_renderer.hh b/modules/gfx/src/impl/line_trace_renderer.hh
index 110492ccd1942442fbe8a6e8170fc42da3e0136e..b880f8b4adece9619d7a8f9ee8489ce8d242befd 100644
--- a/modules/gfx/src/impl/line_trace_renderer.hh
+++ b/modules/gfx/src/impl/line_trace_renderer.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/impl/map_iso_gen.cc b/modules/gfx/src/impl/map_iso_gen.cc
index 603a7a0dd26bd315bb02da5262d8bf139a4f755b..ada35ee1a1fe58935c658f60cba1ffb4ff85f7b1 100644
--- a/modules/gfx/src/impl/map_iso_gen.cc
+++ b/modules/gfx/src/impl/map_iso_gen.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/impl/map_iso_gen.hh b/modules/gfx/src/impl/map_iso_gen.hh
index cd3f937c6a301108f912ba1fac10bdd3c9d4e401..6a9cfddb221393311ab37387e4cd464337a88c32 100644
--- a/modules/gfx/src/impl/map_iso_gen.hh
+++ b/modules/gfx/src/impl/map_iso_gen.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/impl/map_iso_gen_o.cc b/modules/gfx/src/impl/map_iso_gen_o.cc
index 50bae81d5f8ca45229c0915038ef7a56fef7b0fa..eeb6c071da9d07f2ae1d5cbdcba2632042e70a23 100644
--- a/modules/gfx/src/impl/map_iso_gen_o.cc
+++ b/modules/gfx/src/impl/map_iso_gen_o.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/impl/map_iso_gen_o.hh b/modules/gfx/src/impl/map_iso_gen_o.hh
index 64e9cac0791bea1587ea4e7b8ca8f1206469a853..476e23825fe9cb6e70201e25932944c619f7545b 100644
--- a/modules/gfx/src/impl/map_iso_gen_o.hh
+++ b/modules/gfx/src/impl/map_iso_gen_o.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/impl/map_iso_gen_s.cc b/modules/gfx/src/impl/map_iso_gen_s.cc
index c16461c691c6888725c392978e8b2709a2a4781d..1dab8b44cbc934cfb5045b3176bada6ab57e0e35 100644
--- a/modules/gfx/src/impl/map_iso_gen_s.cc
+++ b/modules/gfx/src/impl/map_iso_gen_s.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/impl/map_iso_gen_s.hh b/modules/gfx/src/impl/map_iso_gen_s.hh
index c0a925b84eab810cb3b57ff31d66f46f8496a4f4..ca98facf444b5f9775727691133a4022d98b2c9e 100644
--- a/modules/gfx/src/impl/map_iso_gen_s.hh
+++ b/modules/gfx/src/impl/map_iso_gen_s.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/impl/map_iso_spec.hh b/modules/gfx/src/impl/map_iso_spec.hh
index c4520e078ab4cfee989c8adc511c78070e8a70a5..1f93463d2a86da9537369df5def1ca8009e4a43a 100644
--- a/modules/gfx/src/impl/map_iso_spec.hh
+++ b/modules/gfx/src/impl/map_iso_spec.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/impl/map_octree.cc b/modules/gfx/src/impl/map_octree.cc
index 3190ff74cd5b276b02efa44f11b89f30dede5475..f6cff0a990b8da731d86da981dd6901b2b4c5975 100644
--- a/modules/gfx/src/impl/map_octree.cc
+++ b/modules/gfx/src/impl/map_octree.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/impl/map_octree.hh b/modules/gfx/src/impl/map_octree.hh
index 0666880c169a79c4268c9b6c5fe3fd28cd5f288f..60b06da8dddcb2c1ca2485814e22bead5cff90cf 100644
--- a/modules/gfx/src/impl/map_octree.hh
+++ b/modules/gfx/src/impl/map_octree.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/impl/mapped_property.cc b/modules/gfx/src/impl/mapped_property.cc
index 26b08d6537f23ff2fee45718597f785d9f636d31..bb6dbf378aca5ac4aa4120e442e4acda7215da47 100644
--- a/modules/gfx/src/impl/mapped_property.cc
+++ b/modules/gfx/src/impl/mapped_property.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/impl/mapped_property.hh b/modules/gfx/src/impl/mapped_property.hh
index 096e775667f130c9e76e6c70625231dd171cc32e..bc380f068eba71334933d7de1ea71bbfdf5347df 100644
--- a/modules/gfx/src/impl/mapped_property.hh
+++ b/modules/gfx/src/impl/mapped_property.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/impl/mesa_offscreen_buffer.cc b/modules/gfx/src/impl/mesa_offscreen_buffer.cc
index 39ed73b5cfd090c4f451e0881364e9ba5778e05b..98f62a3a0597b258636c68f044475f43238849a6 100644
--- a/modules/gfx/src/impl/mesa_offscreen_buffer.cc
+++ b/modules/gfx/src/impl/mesa_offscreen_buffer.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/impl/mesa_offscreen_buffer.hh b/modules/gfx/src/impl/mesa_offscreen_buffer.hh
index 5ed38b942e7ab7a8b5c41924d1f3f2fcb7a44e24..62a371ddf9f1e415467866b8f13d50763c1c7ba0 100644
--- a/modules/gfx/src/impl/mesa_offscreen_buffer.hh
+++ b/modules/gfx/src/impl/mesa_offscreen_buffer.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/impl/octree_isocont.cc b/modules/gfx/src/impl/octree_isocont.cc
index 2fccd83d8c95a75ff5031f3a947c4fbb266d1690..ff82c50dc0a32645648118e4ffe85e366445c159 100644
--- a/modules/gfx/src/impl/octree_isocont.cc
+++ b/modules/gfx/src/impl/octree_isocont.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/impl/octree_isocont.hh b/modules/gfx/src/impl/octree_isocont.hh
index b6c277ffbef421e84d5cb43f703b41455c5adc69..47c04356e127681d61f06b89754e2489319f569c 100644
--- a/modules/gfx/src/impl/octree_isocont.hh
+++ b/modules/gfx/src/impl/octree_isocont.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/impl/scene_fx.hh b/modules/gfx/src/impl/scene_fx.hh
index ad8d2a787c57a7b4e9eb1433fd5d8e1f4c63d173..7da2ee0f1e4eb03fc5433be2bcc2ad2b491a5fec 100644
--- a/modules/gfx/src/impl/scene_fx.hh
+++ b/modules/gfx/src/impl/scene_fx.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/impl/simple_renderer.cc b/modules/gfx/src/impl/simple_renderer.cc
index 97d2e50bc1bc71ef3e79a17d61d54ef04bba60e1..7e36c96062664a03ffadb82a0e6f302628fcbd12 100644
--- a/modules/gfx/src/impl/simple_renderer.cc
+++ b/modules/gfx/src/impl/simple_renderer.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/impl/simple_renderer.hh b/modules/gfx/src/impl/simple_renderer.hh
index 95fd8bf03e05b966426d5808b457376761b19ffa..df5ec2ca7df30d72cf50477a876ead2cc7b2fbae 100644
--- a/modules/gfx/src/impl/simple_renderer.hh
+++ b/modules/gfx/src/impl/simple_renderer.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/impl/sline_renderer.cc b/modules/gfx/src/impl/sline_renderer.cc
index eae42acad4c0afd38374b3b5f384c314e729b60a..42bfca1fb81341df811e50dc17a0792a3430067c 100644
--- a/modules/gfx/src/impl/sline_renderer.cc
+++ b/modules/gfx/src/impl/sline_renderer.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/impl/sline_renderer.hh b/modules/gfx/src/impl/sline_renderer.hh
index 88c03e5b3062bb4645c5abde8e2c1be521833c4b..cc52307f199888f3362e3c58f5cf9980647adba7 100644
--- a/modules/gfx/src/impl/sline_renderer.hh
+++ b/modules/gfx/src/impl/sline_renderer.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/impl/tabulated_trig.cc b/modules/gfx/src/impl/tabulated_trig.cc
index d46059c085fc48378b02e583637f3061d8e6db65..ca7d9c2ad62d67f17d33424d615c385fcfcac24f 100644
--- a/modules/gfx/src/impl/tabulated_trig.cc
+++ b/modules/gfx/src/impl/tabulated_trig.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/impl/tabulated_trig.hh b/modules/gfx/src/impl/tabulated_trig.hh
index 673f4e20bb0a8c6ee7573a252c96b6175361bebe..1afa4054d6ef2c628e7a4d3938d326c1873f8e35 100644
--- a/modules/gfx/src/impl/tabulated_trig.hh
+++ b/modules/gfx/src/impl/tabulated_trig.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/impl/trace_renderer.cc b/modules/gfx/src/impl/trace_renderer.cc
index f901c77cdf7fa93424bcf6557e02557fd67377f3..940a0f2a2526ef8813aff9d018b1cd9433c03704 100644
--- a/modules/gfx/src/impl/trace_renderer.cc
+++ b/modules/gfx/src/impl/trace_renderer.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/impl/trace_renderer.hh b/modules/gfx/src/impl/trace_renderer.hh
index 380572adc8eaf9449aa843947a70735b9c712fa1..2cad26f71bc9b427b5b025ddaa9c67b2c469a63b 100644
--- a/modules/gfx/src/impl/trace_renderer.hh
+++ b/modules/gfx/src/impl/trace_renderer.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/impl/trace_renderer_base.cc b/modules/gfx/src/impl/trace_renderer_base.cc
index 1b4c47fe5320f3a118d8ffff66a26412640b9201..b78dad0ab5d90aaecbc1f7bb5878bccebb5b8b0a 100644
--- a/modules/gfx/src/impl/trace_renderer_base.cc
+++ b/modules/gfx/src/impl/trace_renderer_base.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/impl/trace_renderer_base.hh b/modules/gfx/src/impl/trace_renderer_base.hh
index 7cba4e75203b22d038be2e948dedc4d12b6e441d..d8f4acdeb8e2c39f053e91df32cc17bc837ccf5c 100644
--- a/modules/gfx/src/impl/trace_renderer_base.hh
+++ b/modules/gfx/src/impl/trace_renderer_base.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/impl/wgl_offscreen_buffer.cc b/modules/gfx/src/impl/wgl_offscreen_buffer.cc
index f9420de6217ebd931591668414a60ee29a84632e..40ce2b04b01cfb0c15d04251664605a1dd1a95bc 100644
--- a/modules/gfx/src/impl/wgl_offscreen_buffer.cc
+++ b/modules/gfx/src/impl/wgl_offscreen_buffer.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/impl/wgl_offscreen_buffer.hh b/modules/gfx/src/impl/wgl_offscreen_buffer.hh
index 7874e838a55b41f954606b23a363f1d0715bdfd2..caec031f250d71f74880e68ad22505d39f252454 100644
--- a/modules/gfx/src/impl/wgl_offscreen_buffer.hh
+++ b/modules/gfx/src/impl/wgl_offscreen_buffer.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/input.cc b/modules/gfx/src/input.cc
index 5c677322671a52e56ee60ef18c76b123e7488bfc..be69ad680d4b578afdf1c1995bcb17414ad91d64 100644
--- a/modules/gfx/src/input.cc
+++ b/modules/gfx/src/input.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/input.hh b/modules/gfx/src/input.hh
index 128358cda5141ecf32b277e87ef3a8287fe33383..c3a640b8b241b22649e600c4e0961fdc9b96e31a 100644
--- a/modules/gfx/src/input.hh
+++ b/modules/gfx/src/input.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/map_iso.cc b/modules/gfx/src/map_iso.cc
index fdcf0a3fe95724e0d5082d144b25835fb2615378..8d29f50fdac1c58bf0fd39b4a872f56a43121fec 100644
--- a/modules/gfx/src/map_iso.cc
+++ b/modules/gfx/src/map_iso.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/map_iso.hh b/modules/gfx/src/map_iso.hh
index cee9025fa6e60598d3a08df3642cf7c4fff8781b..6edb51cf76b4900771a41c633fecd01fa802b57b 100644
--- a/modules/gfx/src/map_iso.hh
+++ b/modules/gfx/src/map_iso.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/map_iso_prop.hh b/modules/gfx/src/map_iso_prop.hh
index 3aa49b7078c11f29f9b9ec32a7eb938178349f33..68021b6b684122e3918c2a4ea634312a1a11d145 100644
--- a/modules/gfx/src/map_iso_prop.hh
+++ b/modules/gfx/src/map_iso_prop.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/map_slab.cc b/modules/gfx/src/map_slab.cc
index 3af16f422257a6a1dea44aa2dd0da13bb20fd7b7..46b0618c31c249a98f859d535dabb96475fd1deb 100644
--- a/modules/gfx/src/map_slab.cc
+++ b/modules/gfx/src/map_slab.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/map_slab.hh b/modules/gfx/src/map_slab.hh
index c38a88864a5fc129733571c2be34971ce73339fd..2f8c361b11903b8e708514bb436662cf81b5e26f 100644
--- a/modules/gfx/src/map_slab.hh
+++ b/modules/gfx/src/map_slab.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/material.cc b/modules/gfx/src/material.cc
index b0e039471f1038523c880d62b4f1f9c98b9740df..28454d43ee526b4fcd79ddbb1ff266c1ea36b407 100644
--- a/modules/gfx/src/material.cc
+++ b/modules/gfx/src/material.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/material.hh b/modules/gfx/src/material.hh
index 12e67481a34ed0067d0d971573d0490330a6c784..8054fc46583870f4bcf646948f26f72c45b3c1b5 100644
--- a/modules/gfx/src/material.hh
+++ b/modules/gfx/src/material.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/module_config.hh b/modules/gfx/src/module_config.hh
index 0deb631474bc426fbdf3ef349d39354b8e1784e7..90949b4ecc4ad80b050aaa3eb455713892901d48 100644
--- a/modules/gfx/src/module_config.hh
+++ b/modules/gfx/src/module_config.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/offscreen_buffer.hh b/modules/gfx/src/offscreen_buffer.hh
index f623190621c66c2f3f151edff06a8c4ec5b7f539..a2c2829957d8aced1c76d85cfede931e864afbfc 100644
--- a/modules/gfx/src/offscreen_buffer.hh
+++ b/modules/gfx/src/offscreen_buffer.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/povray.cc b/modules/gfx/src/povray.cc
index f630974d7ccdaacc2cf5da557c17dac9a9376709..e50c4ad6f32b233eb5ebe026e736676a845b025d 100644
--- a/modules/gfx/src/povray.cc
+++ b/modules/gfx/src/povray.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/povray.hh b/modules/gfx/src/povray.hh
index c8ef79461b8380c9c870d547fe1f6e26b180d0eb..d1a998afb753b2a0936a940d56295c00f2e4fbc9 100644
--- a/modules/gfx/src/povray.hh
+++ b/modules/gfx/src/povray.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/povray_fw.hh b/modules/gfx/src/povray_fw.hh
index a2c0c58a667c97d074388883c10080d2d2f0134e..ff14bd8c183223174baba69299773e45ec4051e5 100644
--- a/modules/gfx/src/povray_fw.hh
+++ b/modules/gfx/src/povray_fw.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/prim_list.cc b/modules/gfx/src/prim_list.cc
index 0b06442fdc30bf8ebc9901415a0f34e368170abd..16840a3b14d52f73905b3197c50a6bb8fe6e4028 100644
--- a/modules/gfx/src/prim_list.cc
+++ b/modules/gfx/src/prim_list.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/prim_list.hh b/modules/gfx/src/prim_list.hh
index 84247aa78d954965cfad0e9f6a3ee524a468e2e9..7fadee42a70ff208a42f37323b7e223a65ba232f 100644
--- a/modules/gfx/src/prim_list.hh
+++ b/modules/gfx/src/prim_list.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/primitives.cc b/modules/gfx/src/primitives.cc
index 46552aa5861447fc343f88b9ab159096f8f8a51b..71758da14628a9a7f5ee652e8564a54f5975de31 100644
--- a/modules/gfx/src/primitives.cc
+++ b/modules/gfx/src/primitives.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/primitives.hh b/modules/gfx/src/primitives.hh
index 04ce67de9f9d92e46c86ae291122605af7653339..fefff88424c98728e0a16bab4fe5c6b6d2323b80 100644
--- a/modules/gfx/src/primitives.hh
+++ b/modules/gfx/src/primitives.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/render_mode.hh b/modules/gfx/src/render_mode.hh
index 06c275632ed47751d3639254185c787f9f4cd5ad..92eb300cbc112721f28454898b794c6c5d6ebbaa 100644
--- a/modules/gfx/src/render_mode.hh
+++ b/modules/gfx/src/render_mode.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/render_options/cartoon_render_options.cc b/modules/gfx/src/render_options/cartoon_render_options.cc
index 4b20f63d7ede94f81998d1bf653536ebaee60272..2a8801e53a0182566854f1920e228d1a9ecca79c 100644
--- a/modules/gfx/src/render_options/cartoon_render_options.cc
+++ b/modules/gfx/src/render_options/cartoon_render_options.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/render_options/cartoon_render_options.hh b/modules/gfx/src/render_options/cartoon_render_options.hh
index f279d00266648bd5a14da2c97e997948c6e86b31..5b50613a9c86f23878e7ab4fafd859651db314ef 100644
--- a/modules/gfx/src/render_options/cartoon_render_options.hh
+++ b/modules/gfx/src/render_options/cartoon_render_options.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/render_options/cpk_render_options.cc b/modules/gfx/src/render_options/cpk_render_options.cc
index 93f0206e56590c503134131959cd9fed0bd0e704..b9626a56741fc3b2a8c379462d93edc2a5d9506b 100644
--- a/modules/gfx/src/render_options/cpk_render_options.cc
+++ b/modules/gfx/src/render_options/cpk_render_options.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/render_options/cpk_render_options.hh b/modules/gfx/src/render_options/cpk_render_options.hh
index abc469cc1ebd9a9fa5d6abcc3f7fba8eb226c849..882ae2512028f0683b44e713ac2b456f378e714b 100644
--- a/modules/gfx/src/render_options/cpk_render_options.hh
+++ b/modules/gfx/src/render_options/cpk_render_options.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/render_options/custom_render_options.cc b/modules/gfx/src/render_options/custom_render_options.cc
index 1712c02437b071baad8490d4c8829a1f47f35eee..1a992024203432b4d9cb2eaac61bc4c8348b69f2 100644
--- a/modules/gfx/src/render_options/custom_render_options.cc
+++ b/modules/gfx/src/render_options/custom_render_options.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/render_options/custom_render_options.hh b/modules/gfx/src/render_options/custom_render_options.hh
index dfd7ddd4c68b37fe1f55ea51e78997622607c8f4..e9b275beacf61a6e56a3fc411a6028877578699c 100644
--- a/modules/gfx/src/render_options/custom_render_options.hh
+++ b/modules/gfx/src/render_options/custom_render_options.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/render_options/line_render_options.cc b/modules/gfx/src/render_options/line_render_options.cc
index fbc42af37ab9faaecab7d3d474096e622f1259a0..a9fd4746ce3a1f9f9f8782912066acac9648581c 100644
--- a/modules/gfx/src/render_options/line_render_options.cc
+++ b/modules/gfx/src/render_options/line_render_options.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/render_options/line_render_options.hh b/modules/gfx/src/render_options/line_render_options.hh
index ea6865040ef324d8e62edae0e5d3936e4c5e61c3..fdb5be5c5d5942a72721b4974ad0a7fd4b690cce 100644
--- a/modules/gfx/src/render_options/line_render_options.hh
+++ b/modules/gfx/src/render_options/line_render_options.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/render_options/line_trace_render_options.cc b/modules/gfx/src/render_options/line_trace_render_options.cc
index 2029ab482742d97f18477020ccacefb54ab7aeaf..a702da10ab57d343bc3664c3236384a601eba216 100644
--- a/modules/gfx/src/render_options/line_trace_render_options.cc
+++ b/modules/gfx/src/render_options/line_trace_render_options.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/render_options/line_trace_render_options.hh b/modules/gfx/src/render_options/line_trace_render_options.hh
index 96e1532bc65dc7f7095b73be1528a71b7877ace0..ab12432411e0f61dea75ef0c53252d79da39f4f5 100644
--- a/modules/gfx/src/render_options/line_trace_render_options.hh
+++ b/modules/gfx/src/render_options/line_trace_render_options.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/render_options/render_options.cc b/modules/gfx/src/render_options/render_options.cc
index 12690d8207402fe96557347b168a8b717e11eb68..591437815280bbf54171cbba5ef7a6a6f5fd223e 100644
--- a/modules/gfx/src/render_options/render_options.cc
+++ b/modules/gfx/src/render_options/render_options.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/render_options/render_options.hh b/modules/gfx/src/render_options/render_options.hh
index ce9dfc60209876eea3a142f08599022c86e041a2..4aae7e034f83d74d34d3d5f0d54817d83ae2f881 100644
--- a/modules/gfx/src/render_options/render_options.hh
+++ b/modules/gfx/src/render_options/render_options.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/render_options/simple_render_options.cc b/modules/gfx/src/render_options/simple_render_options.cc
index 72ad4e82960618a292ad298a14a7e67235fbf00f..33bac6f8e0f40148fe801847d57ca6678485c99c 100644
--- a/modules/gfx/src/render_options/simple_render_options.cc
+++ b/modules/gfx/src/render_options/simple_render_options.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/render_options/simple_render_options.hh b/modules/gfx/src/render_options/simple_render_options.hh
index 1817ea62a9b0fe08ae93188658fc9ff8258acfc9..74c9bb2557f95642b130ef28d1d7e94b5197f920 100644
--- a/modules/gfx/src/render_options/simple_render_options.hh
+++ b/modules/gfx/src/render_options/simple_render_options.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/render_options/sline_render_options.cc b/modules/gfx/src/render_options/sline_render_options.cc
index a3c66383822794d71753971f756c8ab69ea470af..215ec030ee842b4836e8898a46bc528d4d165264 100644
--- a/modules/gfx/src/render_options/sline_render_options.cc
+++ b/modules/gfx/src/render_options/sline_render_options.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/render_options/sline_render_options.hh b/modules/gfx/src/render_options/sline_render_options.hh
index fcd336de13d16cf8a279c276064c758921ec1031..df814fab958e91453e6a0d3ac74f69f79810b7ff 100644
--- a/modules/gfx/src/render_options/sline_render_options.hh
+++ b/modules/gfx/src/render_options/sline_render_options.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/render_options/trace_render_options.cc b/modules/gfx/src/render_options/trace_render_options.cc
index e5e9c026372699dc9dd7b21f29ab28133d61c177..615f38b0b97714ac07b185a8a4444f91ebb1049c 100644
--- a/modules/gfx/src/render_options/trace_render_options.cc
+++ b/modules/gfx/src/render_options/trace_render_options.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/render_options/trace_render_options.hh b/modules/gfx/src/render_options/trace_render_options.hh
index e8817ed3e08c95f82aaa3e7722a75d64e6c05015..d32523e288068c65e20770580a670cbe035f4cab 100644
--- a/modules/gfx/src/render_options/trace_render_options.hh
+++ b/modules/gfx/src/render_options/trace_render_options.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/render_pass.hh b/modules/gfx/src/render_pass.hh
index badbebe30a677d64255a6d70918ae5a28c8b8a31..2c00c9e1860fd259901269ee335c69f268900877 100644
--- a/modules/gfx/src/render_pass.hh
+++ b/modules/gfx/src/render_pass.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/scene.cc b/modules/gfx/src/scene.cc
index 1ce2a44ebfa553a035c5cb285fa9f97b5c493409..f53323a54302e8f26325048e07cd00084f93b695 100644
--- a/modules/gfx/src/scene.cc
+++ b/modules/gfx/src/scene.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/scene.hh b/modules/gfx/src/scene.hh
index c10bec64dd15d022017c1324c6c9bd3d76f59c12..714e60a637567086c9e4c6b1a0313411ef3c7c6c 100644
--- a/modules/gfx/src/scene.hh
+++ b/modules/gfx/src/scene.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/scene_observer.hh b/modules/gfx/src/scene_observer.hh
index 6e9eea0fca0b75f15dacb457b73d434617a28651..8101038399e5e418f7794db58081a556b7cbc51e 100644
--- a/modules/gfx/src/scene_observer.hh
+++ b/modules/gfx/src/scene_observer.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/selection.cc b/modules/gfx/src/selection.cc
index ab0d2c6b550d74ffc3bc96618f7b85be299d4d1c..a204c40f6a9c80b172e15bb9eded1fb6655fd37e 100644
--- a/modules/gfx/src/selection.cc
+++ b/modules/gfx/src/selection.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/selection.hh b/modules/gfx/src/selection.hh
index 41d0b02d9a862c65a7cb3a9970133b183e42d88f..10aa33aa92a235d7e93be4f71b2dbf8dacf3d676 100644
--- a/modules/gfx/src/selection.hh
+++ b/modules/gfx/src/selection.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/shader.cc b/modules/gfx/src/shader.cc
index 03f88696bb5abeccd334cef35608b88fcca1eac5..211d9d24444c57775d51665cf5c86b3902103a9d 100644
--- a/modules/gfx/src/shader.cc
+++ b/modules/gfx/src/shader.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/shader.hh b/modules/gfx/src/shader.hh
index 149c8fc8668e773f651ffa0866fb27a7860f0b1d..6520f0570a033ff0ded521764e6c9a76eced462b 100644
--- a/modules/gfx/src/shader.hh
+++ b/modules/gfx/src/shader.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/surface.cc b/modules/gfx/src/surface.cc
index 390f2d27a6453d10e01cbd3aee31373e9cdfdf98..c0adbef6c5af9d1c01f21af5ac680e6df4d1880b 100644
--- a/modules/gfx/src/surface.cc
+++ b/modules/gfx/src/surface.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/surface.hh b/modules/gfx/src/surface.hh
index ff3ea292c6940cce040d5600aa370250f2868105..52b7166f14da0ac893f3144f2aad6f13f5c1b8a0 100644
--- a/modules/gfx/src/surface.hh
+++ b/modules/gfx/src/surface.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/symmetry_node.cc b/modules/gfx/src/symmetry_node.cc
index 266f008d614eae796a8c8acbf99b045f842c7d43..86dc6d9094525d14049bcb0b92315d6d1e50154f 100644
--- a/modules/gfx/src/symmetry_node.cc
+++ b/modules/gfx/src/symmetry_node.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/symmetry_node.hh b/modules/gfx/src/symmetry_node.hh
index 7298a19e85ea353611893d577433953850171ca1..80946172e6cd78d8f813372cca29e3799778fba5 100644
--- a/modules/gfx/src/symmetry_node.hh
+++ b/modules/gfx/src/symmetry_node.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/texture.hh b/modules/gfx/src/texture.hh
index cf25b9d4f83a8c86d442d4b82db0ac0346d8b433..731f3185ee6d559b1dd0b687187ebd65af32eea7 100644
--- a/modules/gfx/src/texture.hh
+++ b/modules/gfx/src/texture.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/vertex_array.cc b/modules/gfx/src/vertex_array.cc
index 89dbaa728405ab3b0adf50fb3a21a60ba7d195e3..566d289c72ddb5769a90ac45c60c707849174053 100644
--- a/modules/gfx/src/vertex_array.cc
+++ b/modules/gfx/src/vertex_array.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/vertex_array.hh b/modules/gfx/src/vertex_array.hh
index ac24ef85a01f8e6b0680af7d47729a7e154c4725..69c8b3dbd5884d8b566d416f8dd0fb5f7fa732a9 100644
--- a/modules/gfx/src/vertex_array.hh
+++ b/modules/gfx/src/vertex_array.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/vertex_array_helper.cc b/modules/gfx/src/vertex_array_helper.cc
index 4354996e8235deb85d26beee4d9287829b767e2d..ea8020a607aaa40462f7b2f4793a52a8ad8922a8 100644
--- a/modules/gfx/src/vertex_array_helper.cc
+++ b/modules/gfx/src/vertex_array_helper.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/src/vertex_array_helper.hh b/modules/gfx/src/vertex_array_helper.hh
index f810c511c71e10e40610a8844dadc00584545a31..0ec375b4d5f3c5f45d6bdca9a08dfcd7ba7981b0 100644
--- a/modules/gfx/src/vertex_array_helper.hh
+++ b/modules/gfx/src/vertex_array_helper.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/tests/test_color.cc b/modules/gfx/tests/test_color.cc
index 21f82f2c3e54f06eaae81c0affad095f106d7d33..630260542177d8763362f2bddcfd4922c2ced0f2 100644
--- a/modules/gfx/tests/test_color.cc
+++ b/modules/gfx/tests/test_color.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/tests/test_ent_pov_export.cc b/modules/gfx/tests/test_ent_pov_export.cc
index c7730806a1476ce02728b42bcc194c6353908b3d..83a42917d72e6dbc46714819cfa7e7bfa9908022 100644
--- a/modules/gfx/tests/test_ent_pov_export.cc
+++ b/modules/gfx/tests/test_ent_pov_export.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/tests/test_gfx.py b/modules/gfx/tests/test_gfx.py
index fcd0f8510660904a4f07459fa4f28c6391b8489d..2baf689d8a4054663826426340bc9026974872df 100644
--- a/modules/gfx/tests/test_gfx.py
+++ b/modules/gfx/tests/test_gfx.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
@@ -32,7 +32,7 @@ if ost.WITH_NUMPY:
has_numpy=True
try:
import numpy
- except ImportError, e:
+ except ImportError as e:
has_numpy=False
else:
has_numpy=False
diff --git a/modules/gfx/tests/test_gfx_node.cc b/modules/gfx/tests/test_gfx_node.cc
index 95e7e222f0080ac809034726e7561e76ad50856c..2d38d7e132b81f669691aa6bc9050fa5b6812e82 100644
--- a/modules/gfx/tests/test_gfx_node.cc
+++ b/modules/gfx/tests/test_gfx_node.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/tests/test_gost_import.py b/modules/gfx/tests/test_gost_import.py
index deebd2d31d805c7c0cc190d5ad273262dc7728bf..357a0678d0e60f3b9b1aecb1d1e852340e123bb5 100644
--- a/modules/gfx/tests/test_gost_import.py
+++ b/modules/gfx/tests/test_gost_import.py
@@ -9,7 +9,7 @@ with open("test.gost","rb") as gf:
while raw:
(type, subtype,size) = struct.unpack("iiL",raw)
- print "found type=%d, subtype=%d and blocksize=%u"%(type,subtype,size)
+ print("found type=%d, subtype=%d and blocksize=%u"%(type,subtype,size))
if size>0:
data = gf.read(size)
raw = gf.read(16)
diff --git a/modules/gfx/tests/test_map_octree.cc b/modules/gfx/tests/test_map_octree.cc
index 41bfba860b39a425fa3c39229721faacd22cedaa..245817b54702e36bb580cd8cd8e5dd5aa6dc75f0 100644
--- a/modules/gfx/tests/test_map_octree.cc
+++ b/modules/gfx/tests/test_map_octree.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gfx/tests/tests.cc b/modules/gfx/tests/tests.cc
index bb712952ea2cbacc92179c9e0ad78406e294df5f..50c8c17ce094706a15db5ebe48272218e154d915 100644
--- a/modules/gfx/tests/tests.cc
+++ b/modules/gfx/tests/tests.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/doc/python_cpp.rst b/modules/gui/doc/python_cpp.rst
index 0f4be50a63797040a7965daa68b143f9b9b8204c..f7f726251dbae3740036eaa3a06d6cae0b397ecb 100644
--- a/modules/gui/doc/python_cpp.rst
+++ b/modules/gui/doc/python_cpp.rst
@@ -12,7 +12,7 @@ which wraps the Object into a Python SIP Object.
seq_viewer = gui.SequenceViewer() # Create SequenceViewer Object
qobj = seq_viewer.qobject #Get Python SIP Object
- print qobj.size() # Call function on QWidget
+ print(qobj.size()) # Call function on QWidget
The other way around, each boost::python Qt Object accepts Python objects as
input for Qt Objects. It handles the cast to a C++ Qt Object internally.
diff --git a/modules/gui/pymod/__init__.py b/modules/gui/pymod/__init__.py
index da6b1599a0b8378ba6153054c1ce72d0ca5f1581..78c1617af5a25907fa2f21472e59fe4ec4aa45cb 100644
--- a/modules/gui/pymod/__init__.py
+++ b/modules/gui/pymod/__init__.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
@@ -17,16 +17,16 @@
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
#------------------------------------------------------------------------------
import ost.gui.trajectory_viewer
-from _ost_gui import *
+from ._ost_gui import *
import sip
## \brief Opens a DataViewer
# \sa \example fft_li.py "View Fourier Transform Example" \sa \ref modulate_image.py "Modulate Image Example"
def _close_event_override_(event):
- print "close event"
+ print("close event")
def _set_data_override_(data):
- print "set data"
+ print("set data")
def CreateDataViewer(ih,flag=False):
viewer=GostyApp.Instance().CreateDataViewer(ih)
diff --git a/modules/gui/pymod/data_viewer_proxy.cc b/modules/gui/pymod/data_viewer_proxy.cc
index d4d418e1f378588c09dfed18f7541788df47b07a..84930db5c968542f07c5dea24c59fb9de980f655 100644
--- a/modules/gui/pymod/data_viewer_proxy.cc
+++ b/modules/gui/pymod/data_viewer_proxy.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2010 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/gui/pymod/data_viewer_proxy.hh b/modules/gui/pymod/data_viewer_proxy.hh
index 096485b406fa07b36082936fa0c966e9e862e155..bfacf0c05378de3684bb20f35d845684c440bbd9 100644
--- a/modules/gui/pymod/data_viewer_proxy.hh
+++ b/modules/gui/pymod/data_viewer_proxy.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2010 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/gui/pymod/dng/init.py b/modules/gui/pymod/dng/init.py
index 070cace7b8fbca2f9a157c1236490ebbcb605704..c555d91661e942c1b286ffa6c9f83fa9fd73fefe 100644
--- a/modules/gui/pymod/dng/init.py
+++ b/modules/gui/pymod/dng/init.py
@@ -13,7 +13,7 @@ except ImportError:
_img_present=False
pass
-import httplib
+import http.client
from PyQt5 import QtGui, QtWidgets, QtCore
from ost.gui.scene.init_inspector import _InitInspector
@@ -116,7 +116,7 @@ def _execute_script():
sys_argv_backup=sys.argv
sys.argv=script_argv
try:
- execfile(script, __main__.__dict__)
+ exec(compile(open(script).read(), script, 'exec'), __main__.__dict__)
finally:
sys.argv=sys_argv_backup
@@ -150,7 +150,7 @@ class OstOptionParser(optparse.OptionParser):
def __init__(self, **kwargs):
optparse.OptionParser.__init__(self, **kwargs)
def exit(self, status_code, error_message):
- print error_message,
+ print(error_message, end=' ')
QtWidgets.QApplication.instance().exit()
sys.exit(-1)
@@ -171,7 +171,7 @@ if len(parser.rargs)!=0:
if not rargs_string.endswith('.py'):
loading_list.append(rargs_string)
else:
- print 'Error: one of the files to load is a Python script, use -s flag to execute it\n'
+ print('Error: one of the files to load is a Python script, use -s flag to execute it\n')
QtWidgets.QApplication.instance().exit()
sys.exit(-1)
@@ -189,16 +189,16 @@ home = os.getenv('HOME') or os.getenv('USERPROFILE')
_ostrc=os.path.join(home, '.ostrc')
if os.path.exists(_ostrc):
try:
- exec(open(_ostrc))
- except Exception, e:
- print e
+ exec(compile(open(_ostrc).read(), _ostrc, 'exec'))
+ except Exception as e:
+ print(e)
else:
rcfile=open(_ostrc,"w")
- print >> rcfile, '# This python file is parsed by ost and dng at startup'
- print >> rcfile, '# Its content is made available in the global namespace'
- print >> rcfile, '# It can be used to define custom variables and functions'
- print >> rcfile, '# For example:'
- print >> rcfile, '# IMPORTANT_DIR="path/to/important/dir"'
+ print('# This python file is parsed by ost and dng at startup', file=rcfile)
+ print('# Its content is made available in the global namespace', file=rcfile)
+ print('# It can be used to define custom variables and functions', file=rcfile)
+ print('# For example:', file=rcfile)
+ print('# IMPORTANT_DIR="path/to/important/dir"', file=rcfile)
rcfile.close()
ost.gui.PushVerbosityLevel(options.vlevel)
diff --git a/modules/gui/pymod/dng/menu.py b/modules/gui/pymod/dng/menu.py
index 425cf6ca75ff6666938fa2cc1d45e4b754f5275e..487eec75c1b28fb7e1b414f197a0ec1e44c7c7fe 100644
--- a/modules/gui/pymod/dng/menu.py
+++ b/modules/gui/pymod/dng/menu.py
@@ -52,8 +52,8 @@ class ClipWidget(QWidget):
self.far_.setMinimum(int(bounds_near.text()))
self.far_.setMaximum(int(bounds_far.text()))
far = int(gfx.Scene().far)
- if far>sys.maxint:
- far = sys.maxint
+ if far>sys.maxsize:
+ far = sys.maxsize
self.far_.setValue(far)
self.auto_ = QCheckBox("Continuous Automatic Clipping")
self.auto_.setChecked(gfx.Scene().GetAutoAutoslab())
diff --git a/modules/gui/pymod/dng/superpositiondialog.py b/modules/gui/pymod/dng/superpositiondialog.py
index a6851c372899b6e4c73f91f08fac1e8fd13e2cc2..351cf4f97d5dc3537636d071e095857c95cfd27d 100644
--- a/modules/gui/pymod/dng/superpositiondialog.py
+++ b/modules/gui/pymod/dng/superpositiondialog.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
diff --git a/modules/gui/pymod/export_alignment_view.cc b/modules/gui/pymod/export_alignment_view.cc
index 1d6e22bfdf42f3436b8f5bd13c2b8a063a0a075a..2a8cee63b801798e746bbc490e01b922f10f4c72 100644
--- a/modules/gui/pymod/export_alignment_view.cc
+++ b/modules/gui/pymod/export_alignment_view.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/pymod/export_data_viewer.cc b/modules/gui/pymod/export_data_viewer.cc
index d5e03fe5e3888bd86c74ba531f5e01afdcc4c796..3ce93fe7459b5bac2bcaed6f8cb7baf283e20dbd 100644
--- a/modules/gui/pymod/export_data_viewer.cc
+++ b/modules/gui/pymod/export_data_viewer.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/gui/pymod/export_file_loader.cc b/modules/gui/pymod/export_file_loader.cc
index b39d6dadd8383cbe9b42c31d085528ace7dc6aca..4bef89833057a493ceaef42c73c6402ef7815c0e 100644
--- a/modules/gui/pymod/export_file_loader.cc
+++ b/modules/gui/pymod/export_file_loader.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/pymod/export_file_viewer.cc b/modules/gui/pymod/export_file_viewer.cc
index 66b704d84233a7adfcdc425bfcffe3a3635bf241..e92246cb195452f290e88bbacdd4ae4754f569a1 100644
--- a/modules/gui/pymod/export_file_viewer.cc
+++ b/modules/gui/pymod/export_file_viewer.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/pymod/export_gl_canvas.cc b/modules/gui/pymod/export_gl_canvas.cc
index daf2eec4ef6fd6b482c5ec9ef4d685ac8f8b6d90..93f6cbd3d800ee38615fd0de661051591b6433f2 100644
--- a/modules/gui/pymod/export_gl_canvas.cc
+++ b/modules/gui/pymod/export_gl_canvas.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/pymod/export_gl_win.cc b/modules/gui/pymod/export_gl_win.cc
index 044cf417aafdefdd5485c923b5e7c5399d75165d..ec0fae15dad355425e457b2088955e744bc5b81d 100644
--- a/modules/gui/pymod/export_gl_win.cc
+++ b/modules/gui/pymod/export_gl_win.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/pymod/export_gosty.cc b/modules/gui/pymod/export_gosty.cc
index ef7ee6777b43c63ad6c0e8ce0e296b6a0c73c48c..18f945e2e226ff363618c39e345ec3ea5956050d 100644
--- a/modules/gui/pymod/export_gosty.cc
+++ b/modules/gui/pymod/export_gosty.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/pymod/export_input.cc b/modules/gui/pymod/export_input.cc
index b6ecb5c0b5787264315354848db56c723e93adb7..06846fc98ace3c57af3d7435f3bbf72fe7dc6687 100644
--- a/modules/gui/pymod/export_input.cc
+++ b/modules/gui/pymod/export_input.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/pymod/export_main_area.cc b/modules/gui/pymod/export_main_area.cc
index bc3adaa08636ee86bc7bf10a58f6dac153543a0d..84d18c6c1bd2b3dd036734808317fdf376b994e6 100644
--- a/modules/gui/pymod/export_main_area.cc
+++ b/modules/gui/pymod/export_main_area.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/pymod/export_menu_bar.cc b/modules/gui/pymod/export_menu_bar.cc
index 35220c9665511ba442f741f6e242bed1c1b8fb22..9bb9c118b3947ff3a2b60b5adddadbc9b3c78856 100644
--- a/modules/gui/pymod/export_menu_bar.cc
+++ b/modules/gui/pymod/export_menu_bar.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/pymod/export_message_widget.cc b/modules/gui/pymod/export_message_widget.cc
index 1893c7e874e2c05cf40f12939fa4862e99e101b1..cd3ffcc4c8135e33fc6e26baa093adbb21a59726 100644
--- a/modules/gui/pymod/export_message_widget.cc
+++ b/modules/gui/pymod/export_message_widget.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
@@ -39,9 +39,9 @@ void log_message_a(MessageWidget* message_widget, const QString& message, QMessa
void log_message_b(MessageWidget * message_widget, object py_object)
{
if(py_object.ptr() != Py_None){
- if(PyObject_IsInstance(py_object.ptr(), (PyObject*)&PyString_Type)){
- String message = extract < std::string > (py_object);
- message_widget->LogMessage(QString(message.c_str()));
+ if(PyObject_IsInstance(py_object.ptr(), (PyObject*)&PyUnicode_Type)){
+ String message = extract < std::string > (py_object);
+ message_widget->LogMessage(QString(message.c_str()));
}
else if(QStandardItem* item = get_cpp_qobject<QStandardItem>(py_object)){
message_widget->LogMessage(item);
diff --git a/modules/gui/pymod/export_overlay.cc b/modules/gui/pymod/export_overlay.cc
index 4b95814e243575934200cdfff4b4fe8b767e07cd..11db3c6e8dd6179f15bdfe4617fef194af73258e 100644
--- a/modules/gui/pymod/export_overlay.cc
+++ b/modules/gui/pymod/export_overlay.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/gui/pymod/export_panels.cc b/modules/gui/pymod/export_panels.cc
index 71920ef1aece9406b6799da87ea28e027ceb02a1..9f988000531cac98bdea923ab1ad45e3c187b408 100644
--- a/modules/gui/pymod/export_panels.cc
+++ b/modules/gui/pymod/export_panels.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/pymod/export_perspective.cc b/modules/gui/pymod/export_perspective.cc
index fbc5b6c5902a057ae84934c846f7d0518874375c..20af5c8bd4b8f1ff9a70d77a8ed6315371b1cf02 100644
--- a/modules/gui/pymod/export_perspective.cc
+++ b/modules/gui/pymod/export_perspective.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/pymod/export_py_shell.cc b/modules/gui/pymod/export_py_shell.cc
index 84dfbe16db263865d5dd45ae17545fa52efa1bd2..ea7d4d02ce4989bae831a64b0308dde364746287 100644
--- a/modules/gui/pymod/export_py_shell.cc
+++ b/modules/gui/pymod/export_py_shell.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/pymod/export_scene_selection.cc b/modules/gui/pymod/export_scene_selection.cc
index 7b05d2bf804a2df04081e07c1753af61885b4372..a74d3155ee589d57fa7823e75012debdbf6a0cc4 100644
--- a/modules/gui/pymod/export_scene_selection.cc
+++ b/modules/gui/pymod/export_scene_selection.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/pymod/export_scene_win.cc b/modules/gui/pymod/export_scene_win.cc
index b814c257e90ce7fee36e15a07c819109c7e2123a..3ef9546b547fda7a6fc67ca5c9672f83b6732951 100644
--- a/modules/gui/pymod/export_scene_win.cc
+++ b/modules/gui/pymod/export_scene_win.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/pymod/export_sequence_viewer.cc b/modules/gui/pymod/export_sequence_viewer.cc
index caecdc4d6b68678203a1298485da609bbcb677a4..c4f68a7586908a2ffdbb4507bdd6636f17162b1b 100644
--- a/modules/gui/pymod/export_sequence_viewer.cc
+++ b/modules/gui/pymod/export_sequence_viewer.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/pymod/export_sip_handler.cc b/modules/gui/pymod/export_sip_handler.cc
index 6606e7875668da7ce4c0690e67023bcbce6776a8..40c01dc8a8ec07e337101ffcf0549d23cbf40842 100644
--- a/modules/gui/pymod/export_sip_handler.cc
+++ b/modules/gui/pymod/export_sip_handler.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/pymod/export_tool.cc b/modules/gui/pymod/export_tool.cc
index 3d968fd8840e2369699aed3da179418e9dc6f18b..5a9f83469d8df05216dc0ce5214d8449e455531e 100644
--- a/modules/gui/pymod/export_tool.cc
+++ b/modules/gui/pymod/export_tool.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/pymod/export_widget.cc b/modules/gui/pymod/export_widget.cc
index fe6bd46fbf6490ab753f8b4116d65b39c1b15aac..9393b6919b5f37feeb551ce3efe2fbc87c70fb8d 100644
--- a/modules/gui/pymod/export_widget.cc
+++ b/modules/gui/pymod/export_widget.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/pymod/helpwidget.py b/modules/gui/pymod/helpwidget.py
index 9ac28e2059c2805d276b798572f48b4ecd5ebb83..aee9b19ac45e7477bbe1b4203a0bbea99d7df810 100644
--- a/modules/gui/pymod/helpwidget.py
+++ b/modules/gui/pymod/helpwidget.py
@@ -30,7 +30,7 @@ class Help:
else:
try:
s=d.document(pydoc.resolve(what)[0])
- except ImportError, detail:
+ except ImportError as detail:
s=str(detail)
doc_widget.doctext.setHtml(s)
doc_widget.searchbox.setText('')
diff --git a/modules/gui/pymod/init_menubar.py b/modules/gui/pymod/init_menubar.py
index 03930fc53230a7c94f93e1bce6bb9b081466ed3b..c245f0f3ceccfd682d40a22d7df94562be2feb9b 100644
--- a/modules/gui/pymod/init_menubar.py
+++ b/modules/gui/pymod/init_menubar.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
diff --git a/modules/gui/pymod/qptr.hh b/modules/gui/pymod/qptr.hh
index 24d53b8e527a0cf48127a1a53f3f02bf0a4a4e54..f7c7f85e8920f6866311d9b7c4452e72f28ef781 100644
--- a/modules/gui/pymod/qptr.hh
+++ b/modules/gui/pymod/qptr.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/pymod/scene/__init__.py b/modules/gui/pymod/scene/__init__.py
index 4d1c5111982932c3898bc189c5814c448aaefe32..18460a92a80b1b5be878baae40ee5cb5cebc5b0a 100644
--- a/modules/gui/pymod/scene/__init__.py
+++ b/modules/gui/pymod/scene/__init__.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
diff --git a/modules/gui/pymod/scene/color_options_widget.py b/modules/gui/pymod/scene/color_options_widget.py
index c99eb41e2993459d5fb062353b15e7cc278af9a9..5cf29fab3848be4d7d51a9f149e95ed58df7253a 100644
--- a/modules/gui/pymod/scene/color_options_widget.py
+++ b/modules/gui/pymod/scene/color_options_widget.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
@@ -30,10 +30,10 @@ except ImportError:
pass
from PyQt5 import QtCore, QtWidgets, QtWidgets
-from scene_selection_helper import SelHelper
-from gradient_editor_widget import GradientEditor
-from uniform_color_widget import UniformColorWidget
-from combo_options_widget import ComboOptionsWidget
+from .scene_selection_helper import SelHelper
+from .gradient_editor_widget import GradientEditor
+from .uniform_color_widget import UniformColorWidget
+from .combo_options_widget import ComboOptionsWidget
class ColorOptionsWidget(ComboOptionsWidget):
def __init__(self, parent=None):
diff --git a/modules/gui/pymod/scene/color_select_widget.py b/modules/gui/pymod/scene/color_select_widget.py
index 737fd8c48db892a48510e8fb2f86d8afe0e3bba4..25547e70843a2e5a4cd7f616ee68e884037f21d7 100644
--- a/modules/gui/pymod/scene/color_select_widget.py
+++ b/modules/gui/pymod/scene/color_select_widget.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
diff --git a/modules/gui/pymod/scene/combo_options_widget.py b/modules/gui/pymod/scene/combo_options_widget.py
index 28bacce3f156cfc6ecde2bb4d23d7db8a78a15d3..4fda5cb177e863fae20b517f189ac828db39efd4 100644
--- a/modules/gui/pymod/scene/combo_options_widget.py
+++ b/modules/gui/pymod/scene/combo_options_widget.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
@@ -90,7 +90,7 @@ class ComboOptionsWidget(QtWidgets.QWidget):
This abstract method must be implemented by all subclasses.
It can be used to do something ;-) whenever the combobox changes its value.
"""
- raise NotImplementedError, "Subclasses must define OnComboChange()"
+ raise NotImplementedError("Subclasses must define OnComboChange()")
def OnActivate(self, item):
return self.OnComboChange(self, item)
diff --git a/modules/gui/pymod/scene/cpk_widget.py b/modules/gui/pymod/scene/cpk_widget.py
index c40819abe636a81a94279b3f14fa96d6e3f08cd7..408cde497aa8161152c2641b48209d8a240fec35 100644
--- a/modules/gui/pymod/scene/cpk_widget.py
+++ b/modules/gui/pymod/scene/cpk_widget.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
@@ -21,7 +21,7 @@
from ost import gui
from ost import gfx
from PyQt5 import QtCore, QtWidgets
-from render_mode_widget import RenderModeWidget
+from .render_mode_widget import RenderModeWidget
#CPK Render Options
class CPKWidget(RenderModeWidget):
diff --git a/modules/gui/pymod/scene/custom_widget.py b/modules/gui/pymod/scene/custom_widget.py
index e94eabd2d1bb9dafb173f8db951ef21b4d5ba7d1..be2e434a3455d36ea702d4af00442f370c3fb4fc 100644
--- a/modules/gui/pymod/scene/custom_widget.py
+++ b/modules/gui/pymod/scene/custom_widget.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
@@ -21,7 +21,7 @@
from ost import gui
from ost import gfx
from PyQt5 import QtCore, QtWidgets
-from render_mode_widget import RenderModeWidget
+from .render_mode_widget import RenderModeWidget
#Custom Render Options
class CustomWidget(RenderModeWidget):
diff --git a/modules/gui/pymod/scene/file_loader.py b/modules/gui/pymod/scene/file_loader.py
index fedca454330ce6a5c006cdc0ac32bd610781c373..adf747d10b27ff9b7c19b682fb9aa86d0c33f03f 100644
--- a/modules/gui/pymod/scene/file_loader.py
+++ b/modules/gui/pymod/scene/file_loader.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
diff --git a/modules/gui/pymod/scene/gradient_editor_widget.py b/modules/gui/pymod/scene/gradient_editor_widget.py
index 370bd51cd21eb5029e60bee9bf26c05f4fd669ca..2b5a69f227e16b39524e0cab2695d0da6eb8774f 100644
--- a/modules/gui/pymod/scene/gradient_editor_widget.py
+++ b/modules/gui/pymod/scene/gradient_editor_widget.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
@@ -22,8 +22,8 @@ from ost import gui
from ost import gfx
from ost import mol
from PyQt5 import QtCore, QtGui, QtWidgets
-from color_select_widget import ColorSelectWidget
-from gradient_preset_widget import GradientPresetWidget
+from .color_select_widget import ColorSelectWidget
+from .gradient_preset_widget import GradientPresetWidget
#Gradient Editor
class GradientEditor(QtWidgets.QWidget):
diff --git a/modules/gui/pymod/scene/gradient_info_handler.py b/modules/gui/pymod/scene/gradient_info_handler.py
index 747b058605f243e20c71310e5383e1f5b2ae3d42..eac8de236c50e738088e4f596c718c6ba092c1a8 100644
--- a/modules/gui/pymod/scene/gradient_info_handler.py
+++ b/modules/gui/pymod/scene/gradient_info_handler.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
@@ -22,7 +22,7 @@ from ost import gui
from ost import gfx
from ost import info
from PyQt5 import QtCore
-from immutable_gradient_info_handler import ImmutableGradientInfoHandler
+from .immutable_gradient_info_handler import ImmutableGradientInfoHandler
#Gradient Info Handler
class GradientInfoHandler(ImmutableGradientInfoHandler):
diff --git a/modules/gui/pymod/scene/gradient_list_model.py b/modules/gui/pymod/scene/gradient_list_model.py
index 43f3f95dbdaea38bc37d7c5a6bfdcd75a379d402..5195e7f9f5962a6be26ec8bfbe45be149dd5a497 100644
--- a/modules/gui/pymod/scene/gradient_list_model.py
+++ b/modules/gui/pymod/scene/gradient_list_model.py
@@ -3,8 +3,8 @@ from ost import gfx
import os
import ost
from PyQt5 import QtCore, QtWidgets, QtGui
-from immutable_gradient_info_handler import ImmutableGradientInfoHandler
-from gradient_info_handler import GradientInfoHandler
+from .immutable_gradient_info_handler import ImmutableGradientInfoHandler
+from .gradient_info_handler import GradientInfoHandler
class GradientListModel(QtCore.QAbstractListModel):
@@ -57,11 +57,11 @@ class GradientListModel(QtCore.QAbstractListModel):
def LoadGradientFromInfo(self):
if self.immutable_infoh_:
qgradients = self.immutable_infoh_.GetQGradients()
- for k, v in qgradients.iteritems():
+ for k, v in qgradients.items():
self.AddItem(k, v, self.GetLastRow(), False, False)
qgradients = self.infoh_.GetQGradients()
- for k, v in qgradients.iteritems():
+ for k, v in qgradients.items():
self.AddItem(k, v, self.GetLastRow(), True, False)
def GetGradient(self, model_index):
diff --git a/modules/gui/pymod/scene/gradient_preset_widget.py b/modules/gui/pymod/scene/gradient_preset_widget.py
index 998714befd2ad9c900d634bfc55f37cfce1873cd..fd22117cc0e6496aa095dfa2e8e8ba4f72f50f07 100644
--- a/modules/gui/pymod/scene/gradient_preset_widget.py
+++ b/modules/gui/pymod/scene/gradient_preset_widget.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
@@ -27,8 +27,8 @@ from datetime import datetime
from datetime import datetime
from PyQt5 import QtCore, QtWidgets, QtGui
-from gradient_info_handler import GradientInfoHandler
-from gradient_list_model import GradientListModel
+from .gradient_info_handler import GradientInfoHandler
+from .gradient_list_model import GradientListModel
#Gradient Preset Widget
diff --git a/modules/gui/pymod/scene/hsc_widget.py b/modules/gui/pymod/scene/hsc_widget.py
index 442639a7107e82e1224135ddfa4197e14079c24b..ea6292258fd4dc5263344cfdbe53cd0d97c63892 100644
--- a/modules/gui/pymod/scene/hsc_widget.py
+++ b/modules/gui/pymod/scene/hsc_widget.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
@@ -21,7 +21,7 @@
from ost import gui
from ost import gfx
from PyQt5 import QtCore, QtWidgets
-from render_mode_widget import RenderModeWidget
+from .render_mode_widget import RenderModeWidget
#Tube Render Options
class HSCWidget(RenderModeWidget):
diff --git a/modules/gui/pymod/scene/immutable_gradient_info_handler.py b/modules/gui/pymod/scene/immutable_gradient_info_handler.py
index 65ecf0d9c935f129ffe08f47f122d48f426055d0..ca59ac92d4f62f0ce56f4a811885a1978d191594 100644
--- a/modules/gui/pymod/scene/immutable_gradient_info_handler.py
+++ b/modules/gui/pymod/scene/immutable_gradient_info_handler.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
diff --git a/modules/gui/pymod/scene/immutable_info_handler.py b/modules/gui/pymod/scene/immutable_info_handler.py
index e766c840267f60300567351728a4d748c229eb2c..d302f20d5fd3670fdd59b98e26a3ced60f11ddbf 100644
--- a/modules/gui/pymod/scene/immutable_info_handler.py
+++ b/modules/gui/pymod/scene/immutable_info_handler.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
diff --git a/modules/gui/pymod/scene/immutable_preset_info_handler.py b/modules/gui/pymod/scene/immutable_preset_info_handler.py
index 83dd1c741bee02f4560bf152b59cec6eeef22dc0..e6882892f8d38738908f0fff1f27086489f6c6fd 100644
--- a/modules/gui/pymod/scene/immutable_preset_info_handler.py
+++ b/modules/gui/pymod/scene/immutable_preset_info_handler.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
diff --git a/modules/gui/pymod/scene/init_inspector.py b/modules/gui/pymod/scene/init_inspector.py
index 0e2803daea72e4ab6f4dd7b86a65e5025c4412a1..99fea817bfbe79c96479494e8b040c46c4c19a37 100644
--- a/modules/gui/pymod/scene/init_inspector.py
+++ b/modules/gui/pymod/scene/init_inspector.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
diff --git a/modules/gui/pymod/scene/inspector_widget.py b/modules/gui/pymod/scene/inspector_widget.py
index 503d3acdceddf27afb5248f5d842706a66e530a6..f1d98d3778ef603cf3cc9849b3a01661b60fba16 100644
--- a/modules/gui/pymod/scene/inspector_widget.py
+++ b/modules/gui/pymod/scene/inspector_widget.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
@@ -24,12 +24,12 @@ from ost import gfx
import ost
import os
from PyQt5 import QtCore, QtWidgets
-from toolbar_options_widget import ToolBarOptionsWidget
-from render_options_widget import RenderOptionsWidget
-from color_options_widget import ColorOptionsWidget
+from .toolbar_options_widget import ToolBarOptionsWidget
+from .render_options_widget import RenderOptionsWidget
+from .color_options_widget import ColorOptionsWidget
from ost.gui.scene.scene_observer_impl import SceneObserverImpl
-from map_level_widget import AdditionalSettingsWidget
-from scene_selection_helper import SelHelper
+from .map_level_widget import AdditionalSettingsWidget
+from .scene_selection_helper import SelHelper
class InspectorWidget(ToolBarOptionsWidget):
ICONS_PATH = os.path.join(ost.GetSharedDataPath(), "scene", "icons/")
diff --git a/modules/gui/pymod/scene/line_trace_widget.py b/modules/gui/pymod/scene/line_trace_widget.py
index 569f6dfcc904cce41a41e0177000e685c6b99f05..283ce9c667e3b43c3708dc4b063e7905015a27d3 100644
--- a/modules/gui/pymod/scene/line_trace_widget.py
+++ b/modules/gui/pymod/scene/line_trace_widget.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
@@ -21,7 +21,7 @@
from ost import gui
from ost import gfx
from PyQt5 import QtCore, QtWidgets
-from render_mode_widget import RenderModeWidget
+from .render_mode_widget import RenderModeWidget
#Simple Render Options
class LineTraceWidget(RenderModeWidget):
diff --git a/modules/gui/pymod/scene/map_level_widget.py b/modules/gui/pymod/scene/map_level_widget.py
index b5c0905de1472dc4dbef3d122caaa3cda608074b..32b083e55e94d5a0cc0797fe92631eccbfaff47a 100644
--- a/modules/gui/pymod/scene/map_level_widget.py
+++ b/modules/gui/pymod/scene/map_level_widget.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
@@ -28,7 +28,7 @@ except ImportError:
pass
from PyQt5 import QtCore, QtWidgets
-from preset_widget import PresetWidget
+from .preset_widget import PresetWidget
class AdditionalSettingsWidget(QtWidgets.QStackedWidget):
def __init__(self, parent=None):
diff --git a/modules/gui/pymod/scene/preset.py b/modules/gui/pymod/scene/preset.py
index 279765d7cb6f609c93a44a68e4ccdb02c66b6620..de2a9524ae241306bdc65e17f2557308c30edf53 100644
--- a/modules/gui/pymod/scene/preset.py
+++ b/modules/gui/pymod/scene/preset.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
@@ -106,7 +106,7 @@ class Preset:
op = op_class.FromInfo(op_group)
class_order_dict[index]=op
for i in range(0, len(class_order_dict)):
- if(class_order_dict.has_key(i)):
+ if(i in class_order_dict):
preset.AddOp(class_order_dict[i])
return preset
diff --git a/modules/gui/pymod/scene/preset_editor_list_model.py b/modules/gui/pymod/scene/preset_editor_list_model.py
index 35fac9836008178d43be9e80849bcbdc907f8249..a878006956656e70f2bb8e5e41fb7491cbdd694a 100644
--- a/modules/gui/pymod/scene/preset_editor_list_model.py
+++ b/modules/gui/pymod/scene/preset_editor_list_model.py
@@ -3,7 +3,7 @@ from ost import gfx
import os
import ost
from PyQt5 import QtCore
-from preset import Preset
+from .preset import Preset
class PresetEditorListModel(QtCore.QAbstractListModel):
def __init__(self, preset, parent=None, *args):
diff --git a/modules/gui/pymod/scene/preset_editor_widget.py b/modules/gui/pymod/scene/preset_editor_widget.py
index c5a314efb6129d1db2d3b24d7b1da9f326d9c034..f3cb3f509820c91d6d87d75b06afeea8b27146ba 100644
--- a/modules/gui/pymod/scene/preset_editor_widget.py
+++ b/modules/gui/pymod/scene/preset_editor_widget.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
@@ -24,21 +24,21 @@ from ost import mol
from datetime import datetime
from datetime import datetime
from PyQt5 import QtCore, QtWidgets, QtGui
-from color_select_widget import ColorSelectWidget
-from gradient_preset_widget import GradientPresetWidget
-from gradient_editor_widget import GradientPreview
-from gradient_editor_widget import GradientEdit
-from preset_editor_list_model import PresetEditorListModel
-from immutable_gradient_info_handler import ImmutableGradientInfoHandler
-from query_editor import QueryEditorWidget
+from .color_select_widget import ColorSelectWidget
+from .gradient_preset_widget import GradientPresetWidget
+from .gradient_editor_widget import GradientPreview
+from .gradient_editor_widget import GradientEdit
+from .preset_editor_list_model import PresetEditorListModel
+from .immutable_gradient_info_handler import ImmutableGradientInfoHandler
+from .query_editor import QueryEditorWidget
from ost.mol import Prop
from ost.gfx import ByElementColorOp
from ost.gfx import ByChainColorOp
from ost.gfx import GradientLevelColorOp
from ost.gfx import UniformColorOp
-from preset import Preset
-from render_op import RenderOp
-from visibility_op import VisibilityOp
+from .preset import Preset
+from .render_op import RenderOp
+from .visibility_op import VisibilityOp
#Preset Editor
class PresetEditor(QtWidgets.QDialog):
diff --git a/modules/gui/pymod/scene/preset_info_handler.py b/modules/gui/pymod/scene/preset_info_handler.py
index 25237b3bd96072905b4578791d1177b71614345e..cc0c5867ee00d5d79086e27ac5f3bb65214f63ff 100644
--- a/modules/gui/pymod/scene/preset_info_handler.py
+++ b/modules/gui/pymod/scene/preset_info_handler.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
@@ -21,7 +21,7 @@
from ost import gui
from ost import gfx
from ost import info
-from immutable_preset_info_handler import ImmutablePresetInfoHandler
+from .immutable_preset_info_handler import ImmutablePresetInfoHandler
#Preset Info Handler
class PresetInfoHandler(ImmutablePresetInfoHandler):
diff --git a/modules/gui/pymod/scene/preset_list_model.py b/modules/gui/pymod/scene/preset_list_model.py
index dbe1926ade00e007ccffa8fb051d4a5f4730b81d..6bdf05db722822ad3e0227dde2315eaaa8e7a8a0 100644
--- a/modules/gui/pymod/scene/preset_list_model.py
+++ b/modules/gui/pymod/scene/preset_list_model.py
@@ -3,8 +3,8 @@ from ost import gfx
import os
import ost
from PyQt5 import QtCore, QtWidgets, QtGui
-from immutable_preset_info_handler import ImmutablePresetInfoHandler
-from preset_info_handler import PresetInfoHandler
+from .immutable_preset_info_handler import ImmutablePresetInfoHandler
+from .preset_info_handler import PresetInfoHandler
class PresetListModel(QtCore.QAbstractListModel):
IMMUTABLE_PRESET_PATH = os.path.join(ost.GetSharedDataPath(),"scene",
@@ -64,11 +64,11 @@ class PresetListModel(QtCore.QAbstractListModel):
def LoadPresetsFromInfo(self):
if self.immutable_infoh_:
presets = self.immutable_infoh_.GetPresets()
- for k, v in presets.iteritems():
+ for k, v in presets.items():
self.AddItem(v, self.GetLastRow(), False, False)
presets = self.infoh_.GetPresets()
- for k, v in presets.iteritems():
+ for k, v in presets.items():
self.AddItem(v, self.GetLastRow(), True, False)
def GetPreset(self, model_index):
diff --git a/modules/gui/pymod/scene/preset_widget.py b/modules/gui/pymod/scene/preset_widget.py
index aec2f2d29e1bc8ef51c39f5357a7d4d6f15c6c5c..34f6bccb158c708ca0f8605bed95e9f4fc878daf 100644
--- a/modules/gui/pymod/scene/preset_widget.py
+++ b/modules/gui/pymod/scene/preset_widget.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
@@ -23,10 +23,10 @@ import ost
import os
from datetime import datetime
from PyQt5 import QtCore, QtWidgets, QtGui
-from scene_selection_helper import SelHelper
-from preset_list_model import PresetListModel
-from preset_editor_widget import PresetEditor
-from preset import Preset
+from .scene_selection_helper import SelHelper
+from .preset_list_model import PresetListModel
+from .preset_editor_widget import PresetEditor
+from .preset import Preset
class PresetWidget(QtWidgets.QWidget):
PRESET_XML_FILE = os.path.join(ost.GetSharedDataPath(), "scene", "presets.xml")
diff --git a/modules/gui/pymod/scene/remote.py b/modules/gui/pymod/scene/remote.py
index 3f4459914957e68e201f163d6a880726fd51102a..dea7de08d7ec9db00b309c92db634941ee2ecae2 100644
--- a/modules/gui/pymod/scene/remote.py
+++ b/modules/gui/pymod/scene/remote.py
@@ -28,7 +28,7 @@ class RemoteLoader(QtWidgets.QWidget):
def _RemoteMenu(self):
menu = QtWidgets.QMenu()
action_group = QtWidgets.QActionGroup(menu)
- for k,v in REMOTE_REPOSITORIES.iteritems():
+ for k,v in REMOTE_REPOSITORIES.items():
action = menu.addAction(v.name)
action.setCheckable(True)
if k == 'pdb':
@@ -56,13 +56,13 @@ class RemoteLoader(QtWidgets.QWidget):
for split_id in split_ids:
try:
ent = RemoteLoad(split_id, from_repo=self._current_repo)
- except Exception, e:
+ except Exception as e:
LogError(str(e))
continue
g = gfx.Entity(split_id, ent)
try:
gfx.Scene().Add(g)
- except Exception, e:
+ except Exception as e:
LogError(str(e))
remote_loader=RemoteLoader()
diff --git a/modules/gui/pymod/scene/render_mode_widget.py b/modules/gui/pymod/scene/render_mode_widget.py
index 31b33ddd7ce25071f0387d460e2b04a3dfead903..72100a95059e198af92406d4556a5d51c0fe1f18 100644
--- a/modules/gui/pymod/scene/render_mode_widget.py
+++ b/modules/gui/pymod/scene/render_mode_widget.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
@@ -31,10 +31,10 @@ class RenderModeWidget(QtWidgets.QWidget):
self.entities_ = set()
def GetText(self):
- raise NotImplementedError, "Subclasses must define GetText()"
+ raise NotImplementedError("Subclasses must define GetText()")
def GetRenderMode(self):
- raise NotImplementedError, "Subclasses must define GetRenderMode()"
+ raise NotImplementedError("Subclasses must define GetRenderMode()")
def UpdateGui(self, options):
pass
diff --git a/modules/gui/pymod/scene/render_op.py b/modules/gui/pymod/scene/render_op.py
index ea2b54263e1a9a17da6f51e42d5c406fa0e1c5cb..3ce5c9da9fd20438bc39cf8f40bf9ea6a0a853f4 100644
--- a/modules/gui/pymod/scene/render_op.py
+++ b/modules/gui/pymod/scene/render_op.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
diff --git a/modules/gui/pymod/scene/render_options_widget.py b/modules/gui/pymod/scene/render_options_widget.py
index 90cc213e827c648244487c9e23737a37d43ad635..7367cecfe3d1e29374df995f4b18c7be6ff1562c 100644
--- a/modules/gui/pymod/scene/render_options_widget.py
+++ b/modules/gui/pymod/scene/render_options_widget.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
@@ -23,22 +23,22 @@ from ost import gui
from ost import gfx
try:
from ost import img
- from wireframe_widget import WireframeWidget
+ from .wireframe_widget import WireframeWidget
_img_present=True
except ImportError:
_img_present=False
pass
from PyQt5 import QtCore, QtWidgets
-from scene_selection_helper import SelHelper
-from combo_options_widget import ComboOptionsWidget
-from custom_widget import CustomWidget
-from cpk_widget import CPKWidget
-from tube_widget import TubeWidget
-from simple_widget import SimpleWidget
-from sline_widget import SlineWidget
-from hsc_widget import HSCWidget
-from trace_widget import TraceWidget
-from line_trace_widget import LineTraceWidget
+from .scene_selection_helper import SelHelper
+from .combo_options_widget import ComboOptionsWidget
+from .custom_widget import CustomWidget
+from .cpk_widget import CPKWidget
+from .tube_widget import TubeWidget
+from .simple_widget import SimpleWidget
+from .sline_widget import SlineWidget
+from .hsc_widget import HSCWidget
+from .trace_widget import TraceWidget
+from .line_trace_widget import LineTraceWidget
class RenderOptionsWidget(ComboOptionsWidget):
def __init__(self, parent=None):
diff --git a/modules/gui/pymod/scene/scene_observer_impl.py b/modules/gui/pymod/scene/scene_observer_impl.py
index b4a0096fab48b23e740fb8235eb47e649531a690..987662ab59284fdf73418d19c66252012f93cefa 100644
--- a/modules/gui/pymod/scene/scene_observer_impl.py
+++ b/modules/gui/pymod/scene/scene_observer_impl.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
diff --git a/modules/gui/pymod/scene/scene_selection_helper.py b/modules/gui/pymod/scene/scene_selection_helper.py
index 80d35b9b4f1d692de27e9e5a053d27d6f2aa6d67..91686daf2270378337e2935cb8ad75c733854e7f 100644
--- a/modules/gui/pymod/scene/scene_selection_helper.py
+++ b/modules/gui/pymod/scene/scene_selection_helper.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
diff --git a/modules/gui/pymod/scene/simple_widget.py b/modules/gui/pymod/scene/simple_widget.py
index 53e172afd94d9b9620830dc9dd841c3f8d702478..0811a4c2174683e6db0c8e363aeb028b4cc4b5cd 100644
--- a/modules/gui/pymod/scene/simple_widget.py
+++ b/modules/gui/pymod/scene/simple_widget.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
@@ -21,7 +21,7 @@
from ost import gui
from ost import gfx
from PyQt5 import QtCore, QtWidgets
-from render_mode_widget import RenderModeWidget
+from .render_mode_widget import RenderModeWidget
#Simple Render Options
class SimpleWidget(RenderModeWidget):
diff --git a/modules/gui/pymod/scene/sline_widget.py b/modules/gui/pymod/scene/sline_widget.py
index c42f2f98ffd5875ab7501110beeb552a03d26a5c..74ddaed1083b999f0d689e1dd7b9120e8ee2e6dd 100644
--- a/modules/gui/pymod/scene/sline_widget.py
+++ b/modules/gui/pymod/scene/sline_widget.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
@@ -21,7 +21,7 @@
from ost import gui
from ost import gfx
from PyQt5 import QtCore, QtWidgets
-from render_mode_widget import RenderModeWidget
+from .render_mode_widget import RenderModeWidget
#Simple Render Options
class SlineWidget(RenderModeWidget):
diff --git a/modules/gui/pymod/scene/toolbar_options_widget.py b/modules/gui/pymod/scene/toolbar_options_widget.py
index 55e45b04652bd35f57e7a89983fb346bd7c0f663..0113f9dc0a8855636179c62239548bebc95da9a5 100644
--- a/modules/gui/pymod/scene/toolbar_options_widget.py
+++ b/modules/gui/pymod/scene/toolbar_options_widget.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
@@ -100,7 +100,7 @@ class ToolBarOptionsWidget(QtWidgets.QWidget):
This abstract method must be implemented by all subclasses.
It can be used to do something ;-) whenever the combobox changes its value.
"""
- raise NotImplementedError, "Subclasses must define OnComboChange()"
+ raise NotImplementedError("Subclasses must define OnComboChange()")
def DoResize(self):
item = self.__GetCurrentWidget()
diff --git a/modules/gui/pymod/scene/trace_widget.py b/modules/gui/pymod/scene/trace_widget.py
index 8705d18d8628e92c7a7d1d4ed6033883c02feb5f..b0eaf20c2d777069d6d3205af5ac6fba4dc615d0 100644
--- a/modules/gui/pymod/scene/trace_widget.py
+++ b/modules/gui/pymod/scene/trace_widget.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
@@ -21,7 +21,7 @@
from ost import gui
from ost import gfx
from PyQt5 import QtCore, QtWidgets
-from render_mode_widget import RenderModeWidget
+from .render_mode_widget import RenderModeWidget
#Trace Render Options
class TraceWidget(RenderModeWidget):
diff --git a/modules/gui/pymod/scene/tube_widget.py b/modules/gui/pymod/scene/tube_widget.py
index 682fd0b05796c8bec84639204d0b3faf95eb4b85..3413373d92698c2df01111bb4619b7c33b01498f 100644
--- a/modules/gui/pymod/scene/tube_widget.py
+++ b/modules/gui/pymod/scene/tube_widget.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
@@ -21,7 +21,7 @@
from ost import gui
from ost import gfx
from PyQt5 import QtCore, QtWidgets
-from render_mode_widget import RenderModeWidget
+from .render_mode_widget import RenderModeWidget
#Tube Render Options
class TubeWidget(RenderModeWidget):
diff --git a/modules/gui/pymod/scene/uniform_color_widget.py b/modules/gui/pymod/scene/uniform_color_widget.py
index 2459cbc4c1a3db3e8b01cb5b6abe7e250145630e..4f4f8ccc0b7400b84db71b93c688dbe54c417924 100644
--- a/modules/gui/pymod/scene/uniform_color_widget.py
+++ b/modules/gui/pymod/scene/uniform_color_widget.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
@@ -28,7 +28,7 @@ except ImportError:
_img_present=False
pass
from PyQt5 import QtCore, QtWidgets, QtGui
-from color_select_widget import ColorSelectWidget
+from .color_select_widget import ColorSelectWidget
#Uniform Color Widget
class UniformColorWidget(QtWidgets.QWidget):
diff --git a/modules/gui/pymod/scene/visibility_op.py b/modules/gui/pymod/scene/visibility_op.py
index 4b5fc7fb88b2164048057efc8e2bc895685baf18..51874f02c01aba9790442043627237db680f406a 100644
--- a/modules/gui/pymod/scene/visibility_op.py
+++ b/modules/gui/pymod/scene/visibility_op.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
diff --git a/modules/gui/pymod/scene/wireframe_widget.py b/modules/gui/pymod/scene/wireframe_widget.py
index 458a8f09b1d466b36b75e92a482626f16c9adb73..d729f56c179fac31655c8a4349d2bdce4f9c9356 100644
--- a/modules/gui/pymod/scene/wireframe_widget.py
+++ b/modules/gui/pymod/scene/wireframe_widget.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
@@ -27,7 +27,7 @@ try:
except ImportError:
_img_present=False
pass
-from scene_selection_helper import SelHelper
+from .scene_selection_helper import SelHelper
#Wireframe Options
class WireframeWidget(QtWidgets.QWidget):
diff --git a/modules/gui/pymod/sip_handler.hh b/modules/gui/pymod/sip_handler.hh
index a244bdf82a076a4c17c58cb3645d20538eb8d20d..c2f9c189a1a2a4710e88e125360c8e36b498a244 100644
--- a/modules/gui/pymod/sip_handler.hh
+++ b/modules/gui/pymod/sip_handler.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/pymod/table.py b/modules/gui/pymod/table.py
index d45b5d74e2b98c928f139273f4fc0ef9e8170b49..cc6537a9b941acd4df1276fb97457269640a5e50 100644
--- a/modules/gui/pymod/table.py
+++ b/modules/gui/pymod/table.py
@@ -51,7 +51,7 @@ class Table(QTableView):
QObject.connect(self, SIGNAL('doubleClicked(QModelIndex)'),
self.OnDoubleClick)
def OnDoubleClick(self, model_index):
- print 'DOUBLE'
+ print('DOUBLE')
if not self.double_click:
return
row = table.TableRow(self._model.table.rows[model_index.row()],
diff --git a/modules/gui/pymod/trajectory_viewer.py b/modules/gui/pymod/trajectory_viewer.py
index 133091fce1b3b1a4c7b6e876f7789c1c3a8b846c..ece7a3bc51bed5f913ff0804683d3141227afd31 100644
--- a/modules/gui/pymod/trajectory_viewer.py
+++ b/modules/gui/pymod/trajectory_viewer.py
@@ -8,7 +8,7 @@ __all__=('TrajWidget','SetTimeUnit','AddTrajectory','RemoveTrajectory','SetSpeed
#-------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
@@ -255,9 +255,9 @@ class TrajWidget(_QWidget):
ref_eh=self.ehlist_[self.ref_index_]
ref_v=ref_eh.Select(str(self._align_selection.text()))
if ref_v.GetAtomCount()<=3:
- print 'not enough atoms for alignment'
+ print('not enough atoms for alignment')
return
- for i,t,eh in zip(range(len(self.trajlist_)),self.trajlist_,self.ehlist_):
+ for i,t,eh in zip(list(range(len(self.trajlist_))),self.trajlist_,self.ehlist_):
t=_ost.mol.alg.SuperposeFrames(t,eh.Select(str(self._align_selection.text())),ref_v)
self.trajlist_[i]=t
@@ -342,10 +342,10 @@ class TrajWidget(_QWidget):
def SetSpeed(self,val):
#Value should be between 0 and 1
if not (val<=1. and val >=0.):
- print 'Speed should be set between 0 and 1'
+ print('Speed should be set between 0 and 1')
return
else:
val=self._speed_slider_min-val*(self._speed_slider_min-self._speed_slider_max)
self._SetSpeedSliderPos(val)
- print val
+ print(val)
diff --git a/modules/gui/pymod/wrap_gui.cc b/modules/gui/pymod/wrap_gui.cc
index b24863ca8b04e04d9b6125e77e4074fb988c57e2..3dc8058875e0e6145112162d1006855dda6129e5 100644
--- a/modules/gui/pymod/wrap_gui.cc
+++ b/modules/gui/pymod/wrap_gui.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
@@ -77,7 +77,7 @@ namespace {
static void* convertible(PyObject* obj_ptr)
{
- if (!PyString_Check(obj_ptr)) return 0;
+ if (!PyUnicode_Check(obj_ptr)) return 0;
return obj_ptr;
}
@@ -85,8 +85,15 @@ namespace {
PyObject* obj_ptr,
boost::python::converter::rvalue_from_python_stage1_data* data)
{
- const char* value = PyString_AsString(obj_ptr);
- if (value == 0) boost::python::throw_error_already_set();
+ PyObject* temp_bytes = PyUnicode_AsEncodedString(obj_ptr, "UTF-8", "strict");
+ char* value = NULL;
+ if (temp_bytes != NULL) {
+ value = PyBytes_AS_STRING(temp_bytes);
+ value = strdup(value);
+ Py_DECREF(temp_bytes);
+ }
+ if (value == NULL) boost::python::throw_error_already_set();
+
void* storage = (
(boost::python::converter::rvalue_from_python_storage<QString>*)
data)->storage.bytes;
diff --git a/modules/gui/src/admin.cc b/modules/gui/src/admin.cc
index d82e384bd36fa0f1ee5311e75bd22110184e76a8..05704842964fa735cc27531650a1c35ed6fa33c0 100644
--- a/modules/gui/src/admin.cc
+++ b/modules/gui/src/admin.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/admin.hh b/modules/gui/src/admin.hh
index cfaa482be4ff801bcbf8d642e89b75f991e99e11..0b9019339411bf3c437aa4e3e57e722dd43002cf 100644
--- a/modules/gui/src/admin.hh
+++ b/modules/gui/src/admin.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/data_viewer/argand.cc b/modules/gui/src/data_viewer/argand.cc
index f53fb0fed48900a1de6a4cec734bb1ddf9c478a6..077f8fe0a1896d19f3345a64b6e2abec33208342 100644
--- a/modules/gui/src/data_viewer/argand.cc
+++ b/modules/gui/src/data_viewer/argand.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/gui/src/data_viewer/argand.hh b/modules/gui/src/data_viewer/argand.hh
index 8f09c241499b55a900e1a33b560f726cfedd5ba7..c1c04fc4023148a35a2cd61692f087f7fb0aa6a3 100644
--- a/modules/gui/src/data_viewer/argand.hh
+++ b/modules/gui/src/data_viewer/argand.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/gui/src/data_viewer/data_viewer.cc b/modules/gui/src/data_viewer/data_viewer.cc
index 5a75d518126e747a9ac98f8a9f1cf8314f90faf8..be46724af590ca688681539c721a224974ceaea1 100644
--- a/modules/gui/src/data_viewer/data_viewer.cc
+++ b/modules/gui/src/data_viewer/data_viewer.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/gui/src/data_viewer/data_viewer.hh b/modules/gui/src/data_viewer/data_viewer.hh
index c1f18847ec36c270de0d93183342c8427dd604a1..7146a173208dbb45499e99986e5d34247db872dc 100644
--- a/modules/gui/src/data_viewer/data_viewer.hh
+++ b/modules/gui/src/data_viewer/data_viewer.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/gui/src/data_viewer/data_viewer_panel.cc b/modules/gui/src/data_viewer/data_viewer_panel.cc
index 9de780147ac2c43179d6f4d2cd80d36029c439d7..8f2967c9d0883b0fa050166cbede79827c284542 100644
--- a/modules/gui/src/data_viewer/data_viewer_panel.cc
+++ b/modules/gui/src/data_viewer/data_viewer_panel.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/gui/src/data_viewer/data_viewer_panel.hh b/modules/gui/src/data_viewer/data_viewer_panel.hh
index 71fe55351ca6038afc73d138d4f9cca87d78b3d9..77f06107e21593c22abd8cbe1b888a523eb21e26 100644
--- a/modules/gui/src/data_viewer/data_viewer_panel.hh
+++ b/modules/gui/src/data_viewer/data_viewer_panel.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/gui/src/data_viewer/data_viewer_panel_base.cc b/modules/gui/src/data_viewer/data_viewer_panel_base.cc
index 3f145e555ed84c3d216fc0382b5f46d4f01de7ce..f946bc5c8793d152d4e0a2780cf9a9c87bf8febb 100644
--- a/modules/gui/src/data_viewer/data_viewer_panel_base.cc
+++ b/modules/gui/src/data_viewer/data_viewer_panel_base.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/gui/src/data_viewer/data_viewer_panel_base.hh b/modules/gui/src/data_viewer/data_viewer_panel_base.hh
index be3ac007ec7550c4242e8cbc607654c5eca12fea..68ffa086ecd4122fb02136d67f0c7daf6f72d35a 100644
--- a/modules/gui/src/data_viewer/data_viewer_panel_base.hh
+++ b/modules/gui/src/data_viewer/data_viewer_panel_base.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/gui/src/data_viewer/draw_overlay.cc b/modules/gui/src/data_viewer/draw_overlay.cc
index 86c05bb07d849056a3ee2c94a3b80392199450c6..2d362a23de065a985c7f9b13e60f73ee3f873457 100644
--- a/modules/gui/src/data_viewer/draw_overlay.cc
+++ b/modules/gui/src/data_viewer/draw_overlay.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/gui/src/data_viewer/draw_overlay.hh b/modules/gui/src/data_viewer/draw_overlay.hh
index 8ec433c4de1164d0774582c1f006bc6fb0543967..33487455c6d19da713f4e260395feae9001b39df 100644
--- a/modules/gui/src/data_viewer/draw_overlay.hh
+++ b/modules/gui/src/data_viewer/draw_overlay.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/gui/src/data_viewer/drawing_functions.cc b/modules/gui/src/data_viewer/drawing_functions.cc
index f27b3eb0dfe2894527b1d3658d716027e35c50b9..ff0393f14c87750b7c5ec5f44d126e91ecfb1588 100644
--- a/modules/gui/src/data_viewer/drawing_functions.cc
+++ b/modules/gui/src/data_viewer/drawing_functions.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/gui/src/data_viewer/drawing_functions.hh b/modules/gui/src/data_viewer/drawing_functions.hh
index 0d94bd69ba27ed89a9348b0106f7b89ffc987a6e..2b73ede453b23345407a7821e5e529c4fae9d7ef 100644
--- a/modules/gui/src/data_viewer/drawing_functions.hh
+++ b/modules/gui/src/data_viewer/drawing_functions.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/gui/src/data_viewer/fft_panel.cc b/modules/gui/src/data_viewer/fft_panel.cc
index 554cc67c2a6c5ec3a62139042a9c66e0ae7172d3..c519ff6bd985ba406022fad034c2a34a3b0cd692 100644
--- a/modules/gui/src/data_viewer/fft_panel.cc
+++ b/modules/gui/src/data_viewer/fft_panel.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/gui/src/data_viewer/fft_panel.hh b/modules/gui/src/data_viewer/fft_panel.hh
index ac0df0f56e39d148ab16735fe6e7fe3ce082244e..5fdf759c56b4f0080c4def9346febdb55468fe03 100644
--- a/modules/gui/src/data_viewer/fft_panel.hh
+++ b/modules/gui/src/data_viewer/fft_panel.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/gui/src/data_viewer/img2qt.cc b/modules/gui/src/data_viewer/img2qt.cc
index fdf5b8cb415b72fa918069162208fea2ff36505e..9b104aed6a056c3dac8aaf9fe73c6ef00bad4703 100644
--- a/modules/gui/src/data_viewer/img2qt.cc
+++ b/modules/gui/src/data_viewer/img2qt.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/gui/src/data_viewer/img2qt.hh b/modules/gui/src/data_viewer/img2qt.hh
index 3088a2f3e3c450e8ce1e93114b53c79fe69536fc..bf2aeecbddff74f22f35dd25ab125671a18fa560 100644
--- a/modules/gui/src/data_viewer/img2qt.hh
+++ b/modules/gui/src/data_viewer/img2qt.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/gui/src/data_viewer/info_panel.cc b/modules/gui/src/data_viewer/info_panel.cc
index a593884b16e90db34d864fa075c118adab3f22bf..f21fc357127f04491e8c63f7bd176c995f26ab5d 100644
--- a/modules/gui/src/data_viewer/info_panel.cc
+++ b/modules/gui/src/data_viewer/info_panel.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/gui/src/data_viewer/info_panel.hh b/modules/gui/src/data_viewer/info_panel.hh
index 69f125d6169d4b078bd7f850ab073ba2b24a2004..6ff4ced57b3fedadf1d5bbc368d91c1b80ed45cb 100644
--- a/modules/gui/src/data_viewer/info_panel.hh
+++ b/modules/gui/src/data_viewer/info_panel.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/gui/src/data_viewer/mask_overlay.cc b/modules/gui/src/data_viewer/mask_overlay.cc
index dc18830debf329c45e6869def2f681b572e7952d..1a9dd95312e63cdbff986ea597f124e2e17da375 100644
--- a/modules/gui/src/data_viewer/mask_overlay.cc
+++ b/modules/gui/src/data_viewer/mask_overlay.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/gui/src/data_viewer/mask_overlay.hh b/modules/gui/src/data_viewer/mask_overlay.hh
index a6ee6bc2b588b6c462c22b430457a2bd524b1de1..4f7b26132989e25d4b2a555ff26275ecdf4b304c 100644
--- a/modules/gui/src/data_viewer/mask_overlay.hh
+++ b/modules/gui/src/data_viewer/mask_overlay.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/gui/src/data_viewer/null_overlay.cc b/modules/gui/src/data_viewer/null_overlay.cc
index 1fa56b5e6ec24bc944553936defeca05650da1b5..e273de13bf5d6488ec5afbcf6d5c7809832a6a26 100644
--- a/modules/gui/src/data_viewer/null_overlay.cc
+++ b/modules/gui/src/data_viewer/null_overlay.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/gui/src/data_viewer/null_overlay.hh b/modules/gui/src/data_viewer/null_overlay.hh
index 59cbce5b9def8d1719ee7fa2ddc94586ec4b0712..b6ed1d3ba804f7bb4cd58718955ff04b0bf38374 100644
--- a/modules/gui/src/data_viewer/null_overlay.hh
+++ b/modules/gui/src/data_viewer/null_overlay.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/gui/src/data_viewer/overlay.hh b/modules/gui/src/data_viewer/overlay.hh
index 96d440a27d328b1864f990978f68636eb7ef8f5f..b1c0238ac88ee994c40dd68e14bc3e6d8fd8bbcd 100644
--- a/modules/gui/src/data_viewer/overlay.hh
+++ b/modules/gui/src/data_viewer/overlay.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/gui/src/data_viewer/overlay_base.cc b/modules/gui/src/data_viewer/overlay_base.cc
index c1505e2d992616721dc5807ab01b5aa8d494f3bc..3de2f4de3aee9624e15f2a27e215f8585da2ee99 100644
--- a/modules/gui/src/data_viewer/overlay_base.cc
+++ b/modules/gui/src/data_viewer/overlay_base.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/gui/src/data_viewer/overlay_base.hh b/modules/gui/src/data_viewer/overlay_base.hh
index b64475e6cbe901b85c3e5c13544c847d5ac66e9b..b0e71c2c05c003556025e31db29cd3457d4d184d 100644
--- a/modules/gui/src/data_viewer/overlay_base.hh
+++ b/modules/gui/src/data_viewer/overlay_base.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/gui/src/data_viewer/overlay_base_fw.hh b/modules/gui/src/data_viewer/overlay_base_fw.hh
index 7a38205b868cf8193545c94cb48f5acb9f6c1040..5c87342ff124adda1b0cb53b057d30bf6e622c15 100644
--- a/modules/gui/src/data_viewer/overlay_base_fw.hh
+++ b/modules/gui/src/data_viewer/overlay_base_fw.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/gui/src/data_viewer/overlay_manager.cc b/modules/gui/src/data_viewer/overlay_manager.cc
index ac2a709fbff4888096c6877a08b919e3e1dbc93d..f3da585343c29c9ef662e7f17134cc74b35e5c18 100644
--- a/modules/gui/src/data_viewer/overlay_manager.cc
+++ b/modules/gui/src/data_viewer/overlay_manager.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/gui/src/data_viewer/overlay_manager.hh b/modules/gui/src/data_viewer/overlay_manager.hh
index 2a3bb76573b3052656a0533ec3798dc377bff1e6..fa21eeaf05757969a5058d2fe98e29c13d780c85 100644
--- a/modules/gui/src/data_viewer/overlay_manager.hh
+++ b/modules/gui/src/data_viewer/overlay_manager.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/gui/src/data_viewer/overlay_manager_fw.hh b/modules/gui/src/data_viewer/overlay_manager_fw.hh
index a80d843da8cd90931493d8afbed40c6cc28b1de7..ba266f0417702179d4ed8a7eac0145a0ea4940be 100644
--- a/modules/gui/src/data_viewer/overlay_manager_fw.hh
+++ b/modules/gui/src/data_viewer/overlay_manager_fw.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/gui/src/data_viewer/overlay_manager_gui.cc b/modules/gui/src/data_viewer/overlay_manager_gui.cc
index 69bb6a5dd91f740aec70fea1a4684fcbaed7a2da..cfb85454f8b6b53b712f37258ba5172226d59844 100644
--- a/modules/gui/src/data_viewer/overlay_manager_gui.cc
+++ b/modules/gui/src/data_viewer/overlay_manager_gui.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/gui/src/data_viewer/overlay_manager_gui.hh b/modules/gui/src/data_viewer/overlay_manager_gui.hh
index 13ba39f87dedfcdeb5c78bdb5e633dd2ed7a77d6..b356d31d01c24222dcd71f9ef8a11695004ff97d 100644
--- a/modules/gui/src/data_viewer/overlay_manager_gui.hh
+++ b/modules/gui/src/data_viewer/overlay_manager_gui.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/gui/src/data_viewer/overlay_manager_observer.hh b/modules/gui/src/data_viewer/overlay_manager_observer.hh
index a4bf9b058a4a7cc27295ecf55c5a2aea98f4f68a..825ac242ce32fb6088eef957d379caa565a32b9e 100644
--- a/modules/gui/src/data_viewer/overlay_manager_observer.hh
+++ b/modules/gui/src/data_viewer/overlay_manager_observer.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/gui/src/data_viewer/pointlist_overlay.cc b/modules/gui/src/data_viewer/pointlist_overlay.cc
index 84f10563fa904c526619135d4f836a67f24696d8..06db7a9d17408083c9cf8bf946b39dc1916a1de5 100644
--- a/modules/gui/src/data_viewer/pointlist_overlay.cc
+++ b/modules/gui/src/data_viewer/pointlist_overlay.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/gui/src/data_viewer/pointlist_overlay.hh b/modules/gui/src/data_viewer/pointlist_overlay.hh
index 9244f445701c415be14d7522a7e63933794892da..15d635e5c82a3bdd09d566e8c11d1d0ff545bc1f 100644
--- a/modules/gui/src/data_viewer/pointlist_overlay.hh
+++ b/modules/gui/src/data_viewer/pointlist_overlay.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/gui/src/data_viewer/pointlist_overlay_base.cc b/modules/gui/src/data_viewer/pointlist_overlay_base.cc
index 3bf47d6d9d6d0e1bec284fc8c95e8d0364f2370f..05b23eb4ee85b4df29f3fe8c012e62e50a39df2d 100644
--- a/modules/gui/src/data_viewer/pointlist_overlay_base.cc
+++ b/modules/gui/src/data_viewer/pointlist_overlay_base.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/gui/src/data_viewer/pointlist_overlay_base.hh b/modules/gui/src/data_viewer/pointlist_overlay_base.hh
index 43e82562a12e88ae0fe78d154be928b5430c6fa0..4a7702e5630795d314b82dad41850335cd68cd22 100644
--- a/modules/gui/src/data_viewer/pointlist_overlay_base.hh
+++ b/modules/gui/src/data_viewer/pointlist_overlay_base.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/gui/src/data_viewer/strategies.cc b/modules/gui/src/data_viewer/strategies.cc
index e78a7183715dec6646da31ab0ddfd0115c9b768a..b603941851e253f3ae39671bdd0428c17e155ce5 100644
--- a/modules/gui/src/data_viewer/strategies.cc
+++ b/modules/gui/src/data_viewer/strategies.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/gui/src/data_viewer/strategies.hh b/modules/gui/src/data_viewer/strategies.hh
index a37f3f8ef544d563922fee1307193e65050f15d6..5f42db71107c691de0fcd462d8d13561d6c9a0b4 100644
--- a/modules/gui/src/data_viewer/strategies.hh
+++ b/modules/gui/src/data_viewer/strategies.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/gui/src/data_viewer/strategies_fw.hh b/modules/gui/src/data_viewer/strategies_fw.hh
index f66a4e66a9cce121e1e433ebf272944842f9d974..217a3097cc53b9c027d3b4296e020a7e1c8ec397 100644
--- a/modules/gui/src/data_viewer/strategies_fw.hh
+++ b/modules/gui/src/data_viewer/strategies_fw.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/gui/src/data_viewer/viewer_normalizer.cc b/modules/gui/src/data_viewer/viewer_normalizer.cc
index 09a21eaf51611cbcff4f213be1f038f578ed0d37..ad20766cddf85613c3945fc9cf0cf4edf41d2e05 100644
--- a/modules/gui/src/data_viewer/viewer_normalizer.cc
+++ b/modules/gui/src/data_viewer/viewer_normalizer.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/gui/src/data_viewer/viewer_normalizer.hh b/modules/gui/src/data_viewer/viewer_normalizer.hh
index 63b78a1886114862a54b3b165a0f957a65b405f7..071dc27fc8e686ab3d38bfbc9e634f477945e875 100644
--- a/modules/gui/src/data_viewer/viewer_normalizer.hh
+++ b/modules/gui/src/data_viewer/viewer_normalizer.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/gui/src/dock_widget.cc b/modules/gui/src/dock_widget.cc
index 53b7d7ea70f32d44f965a0f1d65de3029ebc3c1a..edf2a1d94afdb9232e780c74ee121495b53ab910 100644
--- a/modules/gui/src/dock_widget.cc
+++ b/modules/gui/src/dock_widget.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/gui/src/dock_widget.hh b/modules/gui/src/dock_widget.hh
index 4bb5f3c733fb4fc2695ca3134e46bfb878105139..5cebbc73c4a59a74699dda67884345a90c7a0323 100644
--- a/modules/gui/src/dock_widget.hh
+++ b/modules/gui/src/dock_widget.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/gui/src/file_browser.cc b/modules/gui/src/file_browser.cc
index 7c33f7d1f48ba176eaae8df1990ee98d121dc910..b390e911121a0e16145e0030f79a2462ed1e37c1 100644
--- a/modules/gui/src/file_browser.cc
+++ b/modules/gui/src/file_browser.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/file_browser.hh b/modules/gui/src/file_browser.hh
index b68b837febd88cfbc19a9f47114c877bbf888a16..04d1cb4208a6453293abc373444208cb290675cd 100644
--- a/modules/gui/src/file_browser.hh
+++ b/modules/gui/src/file_browser.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/file_loader.cc b/modules/gui/src/file_loader.cc
index 476c6e89fc2a0a5f032b304c3e3427dd918f1d84..0aef387175d695c453d309bf44e7eec53f2808b6 100644
--- a/modules/gui/src/file_loader.cc
+++ b/modules/gui/src/file_loader.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/file_loader.hh b/modules/gui/src/file_loader.hh
index 8e2e50758643ae67df2ea8f9d668f2e0128b7bde..805fa5cab3c039e2b20c7946425650fd1a636092 100644
--- a/modules/gui/src/file_loader.hh
+++ b/modules/gui/src/file_loader.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/file_type_dialog.cc b/modules/gui/src/file_type_dialog.cc
index ed226aba88370a95a16f710fa9b398f51e969c60..01cac724d9918f3e6be28a502c68d34f7f7997d0 100644
--- a/modules/gui/src/file_type_dialog.cc
+++ b/modules/gui/src/file_type_dialog.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/file_type_dialog.hh b/modules/gui/src/file_type_dialog.hh
index 270d35131d96f77ebfee4de64420abe4f933590d..3b650a9254cf90b9bf1bdf630ffb478cc5f04751 100644
--- a/modules/gui/src/file_type_dialog.hh
+++ b/modules/gui/src/file_type_dialog.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/file_viewer.cc b/modules/gui/src/file_viewer.cc
index 3d64433a96b5898a6df8886dd6b1c5d6a2facce4..4234bf81cc2f23bd5588ce60470bb9f7d9bf56ee 100644
--- a/modules/gui/src/file_viewer.cc
+++ b/modules/gui/src/file_viewer.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/file_viewer.hh b/modules/gui/src/file_viewer.hh
index d82217ccddd67c0613eb5d7b9162f6bda23b6992..6f3510be3aeb6e4e4fa3b804fe288f1ba3fb7ae0 100644
--- a/modules/gui/src/file_viewer.hh
+++ b/modules/gui/src/file_viewer.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/gl_canvas.cc b/modules/gui/src/gl_canvas.cc
index 8bec7a90773e7e5bbd8851a661ab7d0da8b97057..1dfdbdb7d04598ab34b820eec8dbfcac214acc5b 100644
--- a/modules/gui/src/gl_canvas.cc
+++ b/modules/gui/src/gl_canvas.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/gl_canvas.hh b/modules/gui/src/gl_canvas.hh
index 36d74b2a77bcb582e22dbf58c7a27b5ca241a254..4a85adb436c15094be47166f173b760dfced8894 100644
--- a/modules/gui/src/gl_canvas.hh
+++ b/modules/gui/src/gl_canvas.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/gl_win.cc b/modules/gui/src/gl_win.cc
index ee29b1f719014bbb291b0a2b617d9440fb758738..f6d00bfb571f1d024d97e147576217be7994d0a5 100644
--- a/modules/gui/src/gl_win.cc
+++ b/modules/gui/src/gl_win.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/gl_win.hh b/modules/gui/src/gl_win.hh
index 2daf43d3d876a715b9f7b6969c65155c503c556c..2b003ca9dcca4a1bf141b949a8aa35e9b20925dd 100644
--- a/modules/gui/src/gl_win.hh
+++ b/modules/gui/src/gl_win.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/gosty.cc b/modules/gui/src/gosty.cc
index b5275bb3e694c37359aad5eb2d5140544aae58f8..689cbf9eee7c0f6f341eecdb33e32d4e4f70889d 100644
--- a/modules/gui/src/gosty.cc
+++ b/modules/gui/src/gosty.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
@@ -185,14 +185,18 @@ int init_python_interpreter()
String python_loc=setup_python_search_path(root, py);
//py.RunCommand("from ost import *");
//py.RunCommand("gui_mode=True");
- std::stringstream cmd;
- cmd << "execfile('" << python_loc;
+ std::stringstream script_path;
+ script_path << python_loc;
#ifdef _MSC_VER
- cmd << "\\ost\\gui\\";
+ script_path << "\\ost\\gui\\";
#else
- cmd << "/ost/gui/";
+ script_path << "/ost/gui/";
#endif
- cmd << "gosty_startup.py')";
+ script_path << "gosty_startup.py";
+
+ std::stringstream cmd;
+ cmd << "exec(compile(open('" << script_path.str() << "').read(),'";
+ cmd << script_path.str() << "', 'exec'))";
py.RunCommand(QString::fromStdString(cmd.str()));
return 0;
}
diff --git a/modules/gui/src/gosty.hh b/modules/gui/src/gosty.hh
index a4c3f25bab74b0251044f717bc232b255c00d61c..ebebdbc80ce79dea1223119a03311bfc790ed723 100644
--- a/modules/gui/src/gosty.hh
+++ b/modules/gui/src/gosty.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/gosty_app.cc b/modules/gui/src/gosty_app.cc
index de0b008cc42957e2f5a60efd975d1f86935b5231..58bd7dd890f630f5fd1a629df49907dcae1ff9fd 100644
--- a/modules/gui/src/gosty_app.cc
+++ b/modules/gui/src/gosty_app.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/gosty_app.hh b/modules/gui/src/gosty_app.hh
index 5398c01c83a71474a29cf9c3c394bb600f0c83b9..0831e1316b5de9a82eec5b88a7a3037e4d3184f1 100644
--- a/modules/gui/src/gosty_app.hh
+++ b/modules/gui/src/gosty_app.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/input/spnav_input.cc b/modules/gui/src/input/spnav_input.cc
index 10022c6aef7fd6154cbe5246c4d24b10b82906f1..36c7002948becc9a75c6d25d6d888ccb94af8924 100644
--- a/modules/gui/src/input/spnav_input.cc
+++ b/modules/gui/src/input/spnav_input.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/input/spnav_input.hh b/modules/gui/src/input/spnav_input.hh
index fe6eec7e651421da882acced300b3aa5e3c52e2b..5d15bb9cc6b00b460dbab3c4358180ef80e62d4a 100644
--- a/modules/gui/src/input/spnav_input.hh
+++ b/modules/gui/src/input/spnav_input.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/main.cc b/modules/gui/src/main.cc
index e68f5fcf8e68dab588048543c8e19f3b93588028..3de15cda80e38801d0d9796b74c83faf6cac4e77 100644
--- a/modules/gui/src/main.cc
+++ b/modules/gui/src/main.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/main.hh b/modules/gui/src/main.hh
index 86105fb96e78180d0b56c17058bf1348ea5ca26d..2ead5affd0cee34f202619c42c5308ee3516b147 100644
--- a/modules/gui/src/main.hh
+++ b/modules/gui/src/main.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/main_area.cc b/modules/gui/src/main_area.cc
index 3c931ca8e74859b43eae25db173d3d2785b6fad2..bdfb451951c04f5719b93e7218c91cb82867bbfa 100644
--- a/modules/gui/src/main_area.cc
+++ b/modules/gui/src/main_area.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/main_area.hh b/modules/gui/src/main_area.hh
index 9e03d53a07a873574e909bbe2f09161bdbc3167b..76ac61168128a05aa8a7ca8da9cc723fd3feabd4 100644
--- a/modules/gui/src/main_area.hh
+++ b/modules/gui/src/main_area.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/main_window.cc b/modules/gui/src/main_window.cc
index 2ddeea9f7e30e3c4d1adc1ec99c08c5f127b7de3..b7eee29ab108f7c43ccbaab588c0ebff858f2499 100644
--- a/modules/gui/src/main_window.cc
+++ b/modules/gui/src/main_window.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/gui/src/main_window.hh b/modules/gui/src/main_window.hh
index 61c6055d15225830ab30b1ba8ac476f43a6e6801..56f956000fd9c40222a1b0313a91a77a95c34377 100644
--- a/modules/gui/src/main_window.hh
+++ b/modules/gui/src/main_window.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/gui/src/messages/log_reader.cc b/modules/gui/src/messages/log_reader.cc
index 33ad612ba2e73ce8245c481c5e2701e17aaec82c..b41b949ad31c93556339f42912db129711e6cf14 100644
--- a/modules/gui/src/messages/log_reader.cc
+++ b/modules/gui/src/messages/log_reader.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/messages/log_reader.hh b/modules/gui/src/messages/log_reader.hh
index 95c8e035ed8971c5caec8ec672f3fd00978c56b6..8fd500aea3dc0d1e610f74733914ead133624c97 100644
--- a/modules/gui/src/messages/log_reader.hh
+++ b/modules/gui/src/messages/log_reader.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/messages/message_box_widget.cc b/modules/gui/src/messages/message_box_widget.cc
index 2af0d5e0176956fe4af27eda6a87342b3368d6ed..26a8ddc4cf6a50bdcd9fddb91068313c91c86a04 100644
--- a/modules/gui/src/messages/message_box_widget.cc
+++ b/modules/gui/src/messages/message_box_widget.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/messages/message_box_widget.hh b/modules/gui/src/messages/message_box_widget.hh
index 60d0e7bb7be62042eba1a633068d03846eac2172..82680d349a1e5974aa8e02c47fe663363350a2d4 100644
--- a/modules/gui/src/messages/message_box_widget.hh
+++ b/modules/gui/src/messages/message_box_widget.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/messages/message_widget.cc b/modules/gui/src/messages/message_widget.cc
index b16df9afe9a950a5e2071222a56aa9ad6d462ffb..714c5f0c8ab0b3050101be3122fbefb44d04f951 100644
--- a/modules/gui/src/messages/message_widget.cc
+++ b/modules/gui/src/messages/message_widget.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/messages/message_widget.hh b/modules/gui/src/messages/message_widget.hh
index e9c0d224e890ff7cef626fa49c6a351c4dfe042d..2d48e79aa4a29d658d61034d74573535d35f0df5 100644
--- a/modules/gui/src/messages/message_widget.hh
+++ b/modules/gui/src/messages/message_widget.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/module_config.hh.in b/modules/gui/src/module_config.hh.in
index a45752148678c6e460b8d6bdcd4b0203cab07c59..baac49c7ab93a514c7346362a069583955abce6b 100644
--- a/modules/gui/src/module_config.hh.in
+++ b/modules/gui/src/module_config.hh.in
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/panels/bottom_bar.cc b/modules/gui/src/panels/bottom_bar.cc
index 5a19dc35839f208e948ff2f413338181a6691a4b..508cddf5ca3d0e054bb968f698946d344b5f1ba4 100644
--- a/modules/gui/src/panels/bottom_bar.cc
+++ b/modules/gui/src/panels/bottom_bar.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/panels/bottom_bar.hh b/modules/gui/src/panels/bottom_bar.hh
index e1927445cebdaae7d6153a733cd7ebf565732a5a..ab88057c809154b7963fd0e1ca9fa9fd7701ef38 100644
--- a/modules/gui/src/panels/bottom_bar.hh
+++ b/modules/gui/src/panels/bottom_bar.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/panels/button_bar.cc b/modules/gui/src/panels/button_bar.cc
index 72f3eebf92a6f9653bec74f1f6a4a5a04bd120ae..ea2e31ff7a848eb28194a6390d9fae4bdbf6ac97 100644
--- a/modules/gui/src/panels/button_bar.cc
+++ b/modules/gui/src/panels/button_bar.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/panels/button_bar.hh b/modules/gui/src/panels/button_bar.hh
index 987d667094bfa7768e9bfce6dd6eeb0733e28ec1..e255e4497c13f1ea788f877937b152e5c6aaf119 100644
--- a/modules/gui/src/panels/button_bar.hh
+++ b/modules/gui/src/panels/button_bar.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/panels/button_box.cc b/modules/gui/src/panels/button_box.cc
index 318e4f3b4c27483c2e4ae5429a7ce9fae693674f..ec52d04fead26affbcc2a88fdb3efc8b428d649b 100644
--- a/modules/gui/src/panels/button_box.cc
+++ b/modules/gui/src/panels/button_box.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/panels/button_box.hh b/modules/gui/src/panels/button_box.hh
index e65cea90d9991ef3cb47d12bb3a5b68c3da5235c..880f6a774409f80b08e51eb96e9d2dcbffa86e76 100644
--- a/modules/gui/src/panels/button_box.hh
+++ b/modules/gui/src/panels/button_box.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/panels/drop_box.cc b/modules/gui/src/panels/drop_box.cc
index d81a44cd740bc9cdf5487517bf22960058af4ad5..57b7c0dda1cb9f1464fcf87bdb01d8656c985ef1 100644
--- a/modules/gui/src/panels/drop_box.cc
+++ b/modules/gui/src/panels/drop_box.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/panels/drop_box.hh b/modules/gui/src/panels/drop_box.hh
index a474c0608031a2d14097c7cc3771b27314fd21c4..285794a3df1c28ddf25f29030f742f5e3c86ef20 100644
--- a/modules/gui/src/panels/drop_box.hh
+++ b/modules/gui/src/panels/drop_box.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/panels/event_button.cc b/modules/gui/src/panels/event_button.cc
index 3c789644068865af3cd69966d29d58e763a0bc96..a01a2f882329b8b93262010224417e7ac1088169 100644
--- a/modules/gui/src/panels/event_button.cc
+++ b/modules/gui/src/panels/event_button.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/panels/event_button.hh b/modules/gui/src/panels/event_button.hh
index f3763a1b6dcefa5be900e6b775f4aa20e4650371..f880d204072a58d9669798feaa5d05c3dd4fcd1b 100644
--- a/modules/gui/src/panels/event_button.hh
+++ b/modules/gui/src/panels/event_button.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/panels/panel_bar.cc b/modules/gui/src/panels/panel_bar.cc
index 81312afb1016eff513857e790ec64bcadce9962f..8654056163fa8466ac78efc3bd47eac35a7f535b 100644
--- a/modules/gui/src/panels/panel_bar.cc
+++ b/modules/gui/src/panels/panel_bar.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/panels/panel_bar.hh b/modules/gui/src/panels/panel_bar.hh
index 463641357c99248957c51e7ed8394c870eef8bf1..abb98607cee75ee5d061044d90496fc22b82d8a9 100644
--- a/modules/gui/src/panels/panel_bar.hh
+++ b/modules/gui/src/panels/panel_bar.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/panels/panel_bar_widget_holder.cc b/modules/gui/src/panels/panel_bar_widget_holder.cc
index 0d979e8221710c8ced9ea8466249c6d091aadd3a..a3866207ee3244cfc65855cbb5781901a120ead5 100644
--- a/modules/gui/src/panels/panel_bar_widget_holder.cc
+++ b/modules/gui/src/panels/panel_bar_widget_holder.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/panels/panel_bar_widget_holder.hh b/modules/gui/src/panels/panel_bar_widget_holder.hh
index 8aea1cbdc9a8211f071a687731169fd31b7c20f3..8cf6cbf9dfd03db76af79fe04c2e8a9d152527b7 100644
--- a/modules/gui/src/panels/panel_bar_widget_holder.hh
+++ b/modules/gui/src/panels/panel_bar_widget_holder.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/panels/panel_manager.cc b/modules/gui/src/panels/panel_manager.cc
index 1c30ad993cd90d7ab7265f071e9f6469489cc12b..8bbf2f179a86b05624d1144d8b3cb6341b0a7170 100644
--- a/modules/gui/src/panels/panel_manager.cc
+++ b/modules/gui/src/panels/panel_manager.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/panels/panel_manager.hh b/modules/gui/src/panels/panel_manager.hh
index e35feb05948203bd28e31381098a4de48073e6eb..37847c6fa7db26e384122d3f4037777056189b35 100644
--- a/modules/gui/src/panels/panel_manager.hh
+++ b/modules/gui/src/panels/panel_manager.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/panels/panel_widget_container.cc b/modules/gui/src/panels/panel_widget_container.cc
index 5b1e033137464be5bea21255b7e7d02bca0e05b9..06996c8a225677f58f79657cc2e0bfc2933d28b3 100644
--- a/modules/gui/src/panels/panel_widget_container.cc
+++ b/modules/gui/src/panels/panel_widget_container.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/panels/panel_widget_container.hh b/modules/gui/src/panels/panel_widget_container.hh
index 1b05717e25f79d50f647a34b0ad102190ca95c27..d1a1d586718d353830f2e8f56f1e8dffd7416da1 100644
--- a/modules/gui/src/panels/panel_widget_container.hh
+++ b/modules/gui/src/panels/panel_widget_container.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/panels/side_bar.cc b/modules/gui/src/panels/side_bar.cc
index 92025d0b071d2eddfa49eda2402fbf61d3435efc..3b7dd73ab7a703c2a75f853b1b9c99e2201a756d 100644
--- a/modules/gui/src/panels/side_bar.cc
+++ b/modules/gui/src/panels/side_bar.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/panels/side_bar.hh b/modules/gui/src/panels/side_bar.hh
index 879807a966daadda7fd5246f9b784735206f5162..5a152a4eba7fef85426ea2544917699211dae642 100644
--- a/modules/gui/src/panels/side_bar.hh
+++ b/modules/gui/src/panels/side_bar.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/panels/splitter_panel_bar.cc b/modules/gui/src/panels/splitter_panel_bar.cc
index dacc1ec21bb524af7fca74abe31fe67e6cb1b3f7..63b75218801315d690293d7653ed810421811ff5 100644
--- a/modules/gui/src/panels/splitter_panel_bar.cc
+++ b/modules/gui/src/panels/splitter_panel_bar.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/panels/splitter_panel_bar.hh b/modules/gui/src/panels/splitter_panel_bar.hh
index 8f20c9b756597b441df80796a449426ea0f62441..e42b1aed5d1951e92aa9e612fa037dd94a1cb07d 100644
--- a/modules/gui/src/panels/splitter_panel_bar.hh
+++ b/modules/gui/src/panels/splitter_panel_bar.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/panels/tabbed_panel_bar.cc b/modules/gui/src/panels/tabbed_panel_bar.cc
index b025507622dec5fd425576d279379416fc70b430..125815578428e34c5c48f6d38344b523cfde60b4 100644
--- a/modules/gui/src/panels/tabbed_panel_bar.cc
+++ b/modules/gui/src/panels/tabbed_panel_bar.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/panels/tabbed_panel_bar.hh b/modules/gui/src/panels/tabbed_panel_bar.hh
index 32237a89b611930661a019dc0964bbf5a47665d8..9b0a7f34735f215be8af99f72cea6461ba651350 100644
--- a/modules/gui/src/panels/tabbed_panel_bar.hh
+++ b/modules/gui/src/panels/tabbed_panel_bar.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/perspective.cc b/modules/gui/src/perspective.cc
index 318f01f2c3343627ad7b15c07c053c4876981f38..5cfb399b92fabf94fd192531b9db55af3a248ca4 100644
--- a/modules/gui/src/perspective.cc
+++ b/modules/gui/src/perspective.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/perspective.hh b/modules/gui/src/perspective.hh
index 573133e73b8d871b001bfd315d202afd43af7222..d9debf2a9cece928b33d30cb4de341950a0e4efd 100644
--- a/modules/gui/src/perspective.hh
+++ b/modules/gui/src/perspective.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/python_shell/completer_base.cc b/modules/gui/src/python_shell/completer_base.cc
index 292657027d2ef91cc88aa7cf517a202a465f4e83..738527d29e0afa87acd7930aa0717ed0f34a2f64 100644
--- a/modules/gui/src/python_shell/completer_base.cc
+++ b/modules/gui/src/python_shell/completer_base.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/python_shell/completer_base.hh b/modules/gui/src/python_shell/completer_base.hh
index 8699aab5a168e21f385c876d95ec44a1310a219e..f60a030b4eb6d10b70aadc0d6599b0d5be79937c 100644
--- a/modules/gui/src/python_shell/completer_base.hh
+++ b/modules/gui/src/python_shell/completer_base.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/python_shell/dir_model.cc b/modules/gui/src/python_shell/dir_model.cc
index 1add06e696af83fac081da461ef8b3570670118c..4dce53f9b513d9ae021c22d5ba9aa7ad24c360ae 100644
--- a/modules/gui/src/python_shell/dir_model.cc
+++ b/modules/gui/src/python_shell/dir_model.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/python_shell/dir_model.hh b/modules/gui/src/python_shell/dir_model.hh
index ea882f6b469836ee9978fecb3bb83ed8bede51ee..524a74edb803d4c0d6b58986513aa5764c65f319 100644
--- a/modules/gui/src/python_shell/dir_model.hh
+++ b/modules/gui/src/python_shell/dir_model.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/python_shell/gutter.cc b/modules/gui/src/python_shell/gutter.cc
index eed96f4573cc1b8ea35d5d5e51cd8de0ae1c257e..ae6f900d9bc3ee8951c78ce552f59216bf5e246e 100644
--- a/modules/gui/src/python_shell/gutter.cc
+++ b/modules/gui/src/python_shell/gutter.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/python_shell/gutter.hh b/modules/gui/src/python_shell/gutter.hh
index 57df034707851233903a74779329f41b26aee832..b3962c859415daf4d9a5d8d59946a671c65660bd 100644
--- a/modules/gui/src/python_shell/gutter.hh
+++ b/modules/gui/src/python_shell/gutter.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/python_shell/main_thread_runner.cc b/modules/gui/src/python_shell/main_thread_runner.cc
index 4dcb382da80c5fc4599b55cacc2b31cce619aab6..67eb9bd2a9a41b8d4959e19ae6d84e3c2737cd4a 100644
--- a/modules/gui/src/python_shell/main_thread_runner.cc
+++ b/modules/gui/src/python_shell/main_thread_runner.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/python_shell/main_thread_runner.hh b/modules/gui/src/python_shell/main_thread_runner.hh
index 97c818762e94f4aaa2ac635da606c1bbb5415c5a..9c3b56769b8058f05e3df804e8edbea6bcddb2df 100644
--- a/modules/gui/src/python_shell/main_thread_runner.hh
+++ b/modules/gui/src/python_shell/main_thread_runner.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/python_shell/output_redirector.cc b/modules/gui/src/python_shell/output_redirector.cc
index 39195d850a7a36c986238a4ac66c5c3b4fe16816..01fbb205c5dac1d415d919f4d040ce51ba19f93b 100644
--- a/modules/gui/src/python_shell/output_redirector.cc
+++ b/modules/gui/src/python_shell/output_redirector.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/python_shell/output_redirector.hh b/modules/gui/src/python_shell/output_redirector.hh
index 99057d7e86cdaa14bc4c46d1c35764aa7b2b181e..c440a2d2422d8b8f3324272816b81d6092e7e01b 100644
--- a/modules/gui/src/python_shell/output_redirector.hh
+++ b/modules/gui/src/python_shell/output_redirector.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/python_shell/path_completer.cc b/modules/gui/src/python_shell/path_completer.cc
index 922e88d9839268b1cf55699388602d7a644ec827..86c62358cc268ba7dd9c40cfc9087c54b73e3eda 100644
--- a/modules/gui/src/python_shell/path_completer.cc
+++ b/modules/gui/src/python_shell/path_completer.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/python_shell/path_completer.hh b/modules/gui/src/python_shell/path_completer.hh
index fbca0a890f6e067d198a9f39914efa1fa0a7e544..f9b527ba9ab18397ffbc2f2b24d76996ab9614bd 100644
--- a/modules/gui/src/python_shell/path_completer.hh
+++ b/modules/gui/src/python_shell/path_completer.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/python_shell/python_completer.cc b/modules/gui/src/python_shell/python_completer.cc
index af7f93d380726b0d520f496645a2f519f2fd09b8..bd548d14363aa6c5cef6420da31b0c989a85df80 100644
--- a/modules/gui/src/python_shell/python_completer.cc
+++ b/modules/gui/src/python_shell/python_completer.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/python_shell/python_completer.hh b/modules/gui/src/python_shell/python_completer.hh
index a2fcedbcc1dfaebcb258996c044d533f441ff8e5..216fe915a635cd6c65658873901152ce5cf21eef 100644
--- a/modules/gui/src/python_shell/python_completer.hh
+++ b/modules/gui/src/python_shell/python_completer.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/python_shell/python_context_parser.cc b/modules/gui/src/python_shell/python_context_parser.cc
index 944951114d44e1936d4c32265c9206dc9d39a5d2..18008a10c520155273ea0a55234a843e87a82620 100644
--- a/modules/gui/src/python_shell/python_context_parser.cc
+++ b/modules/gui/src/python_shell/python_context_parser.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/python_shell/python_context_parser.hh b/modules/gui/src/python_shell/python_context_parser.hh
index 0e5df593f494fb57edb1c3dc188ca5e5b32533b6..e8c483f7485c22c6243d88980f03ae065fcc884e 100644
--- a/modules/gui/src/python_shell/python_context_parser.hh
+++ b/modules/gui/src/python_shell/python_context_parser.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/python_shell/python_interpreter.cc b/modules/gui/src/python_shell/python_interpreter.cc
index 29178f2c0a7816459f4838f8b7efe75b447851ea..93c9af99b92f7b246aa41acbe1c7d63402faf1cd 100644
--- a/modules/gui/src/python_shell/python_interpreter.cc
+++ b/modules/gui/src/python_shell/python_interpreter.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
@@ -54,7 +54,7 @@ PythonInterpreter::PythonInterpreter():
main_module_ = bp::import("__main__");
main_namespace_ = bp::extract<bp::dict>(main_module_.attr("__dict__"));
main_namespace_["os"]=bp::import("os");
- main_namespace_["__builtin__"]=bp::import("__builtin__");
+ main_namespace_["builtins"]=bp::import("builtins");
main_namespace_["keyword"]=bp::import("keyword");
bp::object code=bp::import("code");
compile_command_=code.attr("compile_command");
diff --git a/modules/gui/src/python_shell/python_interpreter.hh b/modules/gui/src/python_shell/python_interpreter.hh
index 3cbe055cbb6dc0afd060a19b1c54b495e4372bb2..43083cc61e44b148adf8ddd2018417f457c08450 100644
--- a/modules/gui/src/python_shell/python_interpreter.hh
+++ b/modules/gui/src/python_shell/python_interpreter.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/gui/src/python_shell/python_interpreter_proxy.cc b/modules/gui/src/python_shell/python_interpreter_proxy.cc
index 693273bc2ba70a6857cef1cd297cd0e71debb797..37b2216afd6a1d5af9dbde3c533b043f70fdedb3 100644
--- a/modules/gui/src/python_shell/python_interpreter_proxy.cc
+++ b/modules/gui/src/python_shell/python_interpreter_proxy.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/python_shell/python_interpreter_proxy.hh b/modules/gui/src/python_shell/python_interpreter_proxy.hh
index 4dfd0f3ba60b9a523f2cac35f73c431f57d9b3b7..67991a6c04d784666b8eeb5b2e9d1d24d81ea5c6 100644
--- a/modules/gui/src/python_shell/python_interpreter_proxy.hh
+++ b/modules/gui/src/python_shell/python_interpreter_proxy.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/python_shell/python_interpreter_worker.cc b/modules/gui/src/python_shell/python_interpreter_worker.cc
index 5f7fb42a6db98946d27656124c82b8b5fa396ea2..c65a6d002815d9b894cc3b2400334ccc711807e3 100644
--- a/modules/gui/src/python_shell/python_interpreter_worker.cc
+++ b/modules/gui/src/python_shell/python_interpreter_worker.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2014 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/python_shell/python_interpreter_worker.hh b/modules/gui/src/python_shell/python_interpreter_worker.hh
index 557604900e046dee0c46fec77550a4b1e2292ad4..c8dc4ba3f9f8ef9bce55abb8e3f2adddd8916125 100644
--- a/modules/gui/src/python_shell/python_interpreter_worker.hh
+++ b/modules/gui/src/python_shell/python_interpreter_worker.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2014 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
@@ -23,8 +23,12 @@
// workaround for QTBUG-22829: https://bugreports.qt-project.org/browse/QTBUG-22829
#ifndef Q_MOC_RUN
+ // https://stackoverflow.com/questions/23068700/embedding-python3-in-qt-5
+ #pragma push_macro("slots")
+ #undef slots
#include <boost/python.hpp>
#include <boost/shared_ptr.hpp>
+ #pragma pop_macro("slots")
#endif
#include "output_redirector.hh"
#include <csignal>
diff --git a/modules/gui/src/python_shell/python_namespace_tree_item.cc b/modules/gui/src/python_shell/python_namespace_tree_item.cc
index e03444f692f1f18962f970b2132d85a79409610d..1524d17e931aa06d83f43eacaf814e35e4d7ca84 100644
--- a/modules/gui/src/python_shell/python_namespace_tree_item.cc
+++ b/modules/gui/src/python_shell/python_namespace_tree_item.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/python_shell/python_namespace_tree_item.hh b/modules/gui/src/python_shell/python_namespace_tree_item.hh
index c1cee49ef15f8e24597ae807543dd5579f63e4b1..c0c3591413269ecf67b74651f5edcf55e49704a9 100644
--- a/modules/gui/src/python_shell/python_namespace_tree_item.hh
+++ b/modules/gui/src/python_shell/python_namespace_tree_item.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/python_shell/python_namespace_tree_model.cc b/modules/gui/src/python_shell/python_namespace_tree_model.cc
index 6b05294f8148151f76f26f3f02e4758bcfd8fe6f..1d3694e5491d2e7f4cce864bf7427d013547f30f 100644
--- a/modules/gui/src/python_shell/python_namespace_tree_model.cc
+++ b/modules/gui/src/python_shell/python_namespace_tree_model.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/python_shell/python_namespace_tree_model.hh b/modules/gui/src/python_shell/python_namespace_tree_model.hh
index 21b283e6b57616237f84bb2d3f52dc05cd89b81b..79e88e3b2f1c65f9dd85e85dab74b0c060dabc26 100644
--- a/modules/gui/src/python_shell/python_namespace_tree_model.hh
+++ b/modules/gui/src/python_shell/python_namespace_tree_model.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/python_shell/python_shell.cc b/modules/gui/src/python_shell/python_shell.cc
index b651747b8d522c10eb3b9514491c4997539ff627..b9c0d0dd3216b77d5e447413eb874aa2920c4ab0 100644
--- a/modules/gui/src/python_shell/python_shell.cc
+++ b/modules/gui/src/python_shell/python_shell.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/python_shell/python_shell.hh b/modules/gui/src/python_shell/python_shell.hh
index 11cc3fad0c62397022c54824085f2fced1caf499..38bdf9445e1b0ae9057f1995f5363fceaa34f7d7 100644
--- a/modules/gui/src/python_shell/python_shell.hh
+++ b/modules/gui/src/python_shell/python_shell.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/python_shell/python_shell_fw.hh b/modules/gui/src/python_shell/python_shell_fw.hh
index 9abb7cae16532955fe0d1177fab66a4988b91492..492d833f9211675725323135db656dadd7cdec70 100644
--- a/modules/gui/src/python_shell/python_shell_fw.hh
+++ b/modules/gui/src/python_shell/python_shell_fw.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/python_shell/python_shell_text_document_layout.cc b/modules/gui/src/python_shell/python_shell_text_document_layout.cc
index bb95922f0d6bcf5b248b25757c71b20a43318b14..4f33754665dc3872aa9f9f937e17d122ad35d069 100644
--- a/modules/gui/src/python_shell/python_shell_text_document_layout.cc
+++ b/modules/gui/src/python_shell/python_shell_text_document_layout.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/python_shell/python_shell_text_document_layout.hh b/modules/gui/src/python_shell/python_shell_text_document_layout.hh
index 903867a3f811820287f0d7bdb73e4f59892ad466..6cb32f768d0b7625586ee680af745c800ac130c7 100644
--- a/modules/gui/src/python_shell/python_shell_text_document_layout.hh
+++ b/modules/gui/src/python_shell/python_shell_text_document_layout.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/python_shell/python_shell_widget.cc b/modules/gui/src/python_shell/python_shell_widget.cc
index 93d3f3896713216902cb5b3ac37deb324ed17202..023bdb22f720f01023dd2f40b724cf75e9086178 100644
--- a/modules/gui/src/python_shell/python_shell_widget.cc
+++ b/modules/gui/src/python_shell/python_shell_widget.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/python_shell/python_shell_widget.hh b/modules/gui/src/python_shell/python_shell_widget.hh
index 090272bbbd00e3b5155a917e2fc566c2c41cfc44..3b246addf540a10e3596a6b22b84755f5b042c1a 100644
--- a/modules/gui/src/python_shell/python_shell_widget.hh
+++ b/modules/gui/src/python_shell/python_shell_widget.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/python_shell/python_syntax_highlighter.cc b/modules/gui/src/python_shell/python_syntax_highlighter.cc
index 72ab4be2a096a3cab15fc0849eff8fcbb42dbc6d..b4ae78bdabcb3129fd9dd067e60df8a37482a979 100644
--- a/modules/gui/src/python_shell/python_syntax_highlighter.cc
+++ b/modules/gui/src/python_shell/python_syntax_highlighter.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/python_shell/python_syntax_highlighter.hh b/modules/gui/src/python_shell/python_syntax_highlighter.hh
index aaa97a529501aa66a21b406d3823376ac4708a8b..6280ac72c94e8b45d594065a92e48974ab1abf1a 100644
--- a/modules/gui/src/python_shell/python_syntax_highlighter.hh
+++ b/modules/gui/src/python_shell/python_syntax_highlighter.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/python_shell/python_tokenizer.cc b/modules/gui/src/python_shell/python_tokenizer.cc
index 3c6b2d3d89a1ee4991d62534c5735a0695b91d62..a44f0c60c1725049fa39e305b72cdf9df715ebe4 100644
--- a/modules/gui/src/python_shell/python_tokenizer.cc
+++ b/modules/gui/src/python_shell/python_tokenizer.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/gui/src/python_shell/python_tokenizer.hh b/modules/gui/src/python_shell/python_tokenizer.hh
index 49dc6c5c9ccd59617ac9f879a8c42e307247340f..8b2f43467b010a6b717fdea1db862d2e869db3a9 100644
--- a/modules/gui/src/python_shell/python_tokenizer.hh
+++ b/modules/gui/src/python_shell/python_tokenizer.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/python_shell/shell_history.cc b/modules/gui/src/python_shell/shell_history.cc
index 08d96cd6eea8b4646745fde34b8e78687aa9da43..7a687c301817a95f88cb6e7b668c3534797100d4 100644
--- a/modules/gui/src/python_shell/shell_history.cc
+++ b/modules/gui/src/python_shell/shell_history.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/python_shell/shell_history.hh b/modules/gui/src/python_shell/shell_history.hh
index 87e082af623c137959144216a5778698a545630d..8c5982cb1fbc5a2cf2370aeea6ba3230492f9b5a 100644
--- a/modules/gui/src/python_shell/shell_history.hh
+++ b/modules/gui/src/python_shell/shell_history.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/python_shell/state.cc b/modules/gui/src/python_shell/state.cc
index f5b7c522306c5f96df8b0817005f30f02a70800a..26566ae7f5cd7a7564f01f569ba474c8b4b77545 100644
--- a/modules/gui/src/python_shell/state.cc
+++ b/modules/gui/src/python_shell/state.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2014 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/python_shell/state.hh b/modules/gui/src/python_shell/state.hh
index 679542078d8a17086c099b0dfa6e9df04173ae68..88543975d097ccb34460018da710c768c8fb2b20 100644
--- a/modules/gui/src/python_shell/state.hh
+++ b/modules/gui/src/python_shell/state.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2014 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/python_shell/state_machine.cc b/modules/gui/src/python_shell/state_machine.cc
index 048ed68eb83a0bdd2324d451e7f4f6f7aea65ed2..82d8ee15a39bd817435167c6778fb1ef76708e42 100644
--- a/modules/gui/src/python_shell/state_machine.cc
+++ b/modules/gui/src/python_shell/state_machine.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2014 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/python_shell/state_machine.hh b/modules/gui/src/python_shell/state_machine.hh
index 8db26c10a64f521ab5e27021e78e4db391b7b245..197317ec90b87aef4c57ae186f7de409157da66a 100644
--- a/modules/gui/src/python_shell/state_machine.hh
+++ b/modules/gui/src/python_shell/state_machine.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2014 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/python_shell/string_literal_positions.cc b/modules/gui/src/python_shell/string_literal_positions.cc
index d1dd8ce5cf582acf2e39a58e3cd36a729e627e02..f14d4a025b26a5bfe5faf41373dcdfe676df842d 100644
--- a/modules/gui/src/python_shell/string_literal_positions.cc
+++ b/modules/gui/src/python_shell/string_literal_positions.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/python_shell/string_literal_positions.hh b/modules/gui/src/python_shell/string_literal_positions.hh
index d7d9e17d26e6193dfd7f24fa6b4a7d84e6ad0fc6..79711be961d4ed803bf1a42161d5c0f3b0d10ff4 100644
--- a/modules/gui/src/python_shell/string_literal_positions.hh
+++ b/modules/gui/src/python_shell/string_literal_positions.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/python_shell/text_logger.cc b/modules/gui/src/python_shell/text_logger.cc
index 1dda3afbb92bb8cb307fb7101c446eaad1f6bb8f..9fb389b64430b5635b64988bc60868cdc6ada08c 100644
--- a/modules/gui/src/python_shell/text_logger.cc
+++ b/modules/gui/src/python_shell/text_logger.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/python_shell/text_logger.hh b/modules/gui/src/python_shell/text_logger.hh
index 444092c07d2a6584a61560c32b304289d9ba9de3..9d1913e7cc452d8670cbb0abd060f088ae40e271 100644
--- a/modules/gui/src/python_shell/text_logger.hh
+++ b/modules/gui/src/python_shell/text_logger.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/python_shell/transition.cc b/modules/gui/src/python_shell/transition.cc
index 9916657713fe9be0a0c56913cffaf5dc312b468c..140e0fbe43b6c172c5f7c6f5b3fa873c2d8d8279 100644
--- a/modules/gui/src/python_shell/transition.cc
+++ b/modules/gui/src/python_shell/transition.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2014 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/python_shell/transition.hh b/modules/gui/src/python_shell/transition.hh
index a3550f4280f8f186023f5750aeb7feee8fb5da92..97ed93c8fc3d54d51a90e7d875ae32b90bb9f11c 100644
--- a/modules/gui/src/python_shell/transition.hh
+++ b/modules/gui/src/python_shell/transition.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2014 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/python_shell/transition_guard.cc b/modules/gui/src/python_shell/transition_guard.cc
index acf6ff2c95a35cef4b689c22a3c22822e82ff7c0..d01fdfad694e02c455f9519e9603640de2e0f243 100644
--- a/modules/gui/src/python_shell/transition_guard.cc
+++ b/modules/gui/src/python_shell/transition_guard.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2014 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/python_shell/transition_guard.hh b/modules/gui/src/python_shell/transition_guard.hh
index c3b20201a7d5f7a3b0e1c2d21c34f819a7294ac3..514bf979bf8b4db4103cc4d21c0ba5f7c77e3172 100644
--- a/modules/gui/src/python_shell/transition_guard.hh
+++ b/modules/gui/src/python_shell/transition_guard.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2014 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/remote_loader.hh b/modules/gui/src/remote_loader.hh
index 1d33e6d0bd27b17b0baf725c2895e72e5d83e3dc..a066325d0ad17dd519ad7fad9207f2957ce35fff 100644
--- a/modules/gui/src/remote_loader.hh
+++ b/modules/gui/src/remote_loader.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/remote_site_loader.cc b/modules/gui/src/remote_site_loader.cc
index 8146166972d95c016d2d792e20f5c8f7ddb9dc7c..9dc1647af1457612f6165f174236860b206028ad 100644
--- a/modules/gui/src/remote_site_loader.cc
+++ b/modules/gui/src/remote_site_loader.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/remote_site_loader.hh b/modules/gui/src/remote_site_loader.hh
index 5412441a1d61785c6f7b8c3ecaa10a4326fbc83d..e300b61b33179debdcc0254f69c8d566f19a4e6d 100644
--- a/modules/gui/src/remote_site_loader.hh
+++ b/modules/gui/src/remote_site_loader.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/scene_menu.cc b/modules/gui/src/scene_menu.cc
index bedcf0df437f5feb57243056dbbebd2bd1ebd02e..bd1adb113140c8837a242e83c7f4b381c5641dff 100644
--- a/modules/gui/src/scene_menu.cc
+++ b/modules/gui/src/scene_menu.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/scene_menu.hh b/modules/gui/src/scene_menu.hh
index 68fc6421f363d881bfa51e53c3077a5f053da010..7bf862a319404fc9189645dd147d93c3fe11e980 100644
--- a/modules/gui/src/scene_menu.hh
+++ b/modules/gui/src/scene_menu.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/scene_selection.cc b/modules/gui/src/scene_selection.cc
index be66a839918dcaa10d6f71db4bcc99ff989f89b6..7057b6a9d2aaaea7ffbf6acba5ac7d1d09b58903 100644
--- a/modules/gui/src/scene_selection.cc
+++ b/modules/gui/src/scene_selection.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/scene_selection.hh b/modules/gui/src/scene_selection.hh
index 53419a3ae90df316aec25877bffddc1e145568c3..70ce89365ee7e99ffabbd13a5fa0540ff680b039 100644
--- a/modules/gui/src/scene_selection.hh
+++ b/modules/gui/src/scene_selection.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/scene_win/context_menu.cc b/modules/gui/src/scene_win/context_menu.cc
index 70a8c2bdcd088308fa5073fa6a8093df7fb9fbf6..aae03ae53ae07212e033045d7c9490ab7451df97 100644
--- a/modules/gui/src/scene_win/context_menu.cc
+++ b/modules/gui/src/scene_win/context_menu.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/scene_win/context_menu.hh b/modules/gui/src/scene_win/context_menu.hh
index 56ca0929a2693f65756584341463c24dfa09f26f..12c844b1889b371cff30e7b11d8051e0028931ed 100644
--- a/modules/gui/src/scene_win/context_menu.hh
+++ b/modules/gui/src/scene_win/context_menu.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/scene_win/current_selection_node.cc b/modules/gui/src/scene_win/current_selection_node.cc
index d10da3813b9407334e072729162a257b6545407e..8f006a982b7fda197c99d866e40865851520d46d 100644
--- a/modules/gui/src/scene_win/current_selection_node.cc
+++ b/modules/gui/src/scene_win/current_selection_node.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2009 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/scene_win/current_selection_node.hh b/modules/gui/src/scene_win/current_selection_node.hh
index 45d97225c2b9134453007643004f59a324846bce..0d9fa00496c2a9794214679ff8107c4f4d67a62b 100644
--- a/modules/gui/src/scene_win/current_selection_node.hh
+++ b/modules/gui/src/scene_win/current_selection_node.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2009 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/scene_win/custom_part_node.cc b/modules/gui/src/scene_win/custom_part_node.cc
index e18e6d62c9cc898bda2713a7eadeba9c2e40de13..9dc79522b47cbfc6c6f8ba711a5009f2115232a7 100644
--- a/modules/gui/src/scene_win/custom_part_node.cc
+++ b/modules/gui/src/scene_win/custom_part_node.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2009 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/scene_win/custom_part_node.hh b/modules/gui/src/scene_win/custom_part_node.hh
index 9c9eba9f4bc609178e0e3577a0144657088b3de9..be5ceb9f9ff5447401e861c3a12aba60b1439ed3 100644
--- a/modules/gui/src/scene_win/custom_part_node.hh
+++ b/modules/gui/src/scene_win/custom_part_node.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2009 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/scene_win/entity_node.cc b/modules/gui/src/scene_win/entity_node.cc
index 1fa74f165a1318011fb6ede4708485723469fdc7..216723b053b339b50786263b60b7d84aec68e24e 100644
--- a/modules/gui/src/scene_win/entity_node.cc
+++ b/modules/gui/src/scene_win/entity_node.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2009 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/scene_win/entity_node.hh b/modules/gui/src/scene_win/entity_node.hh
index a9e58912440c0afcf7a963f66662e9f15c938f15..638f8ea476c5fded4b0bd3b7cd6ec17e3f5a9201 100644
--- a/modules/gui/src/scene_win/entity_node.hh
+++ b/modules/gui/src/scene_win/entity_node.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2009 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/scene_win/entity_part_node.cc b/modules/gui/src/scene_win/entity_part_node.cc
index bc1fb5a9f3f698ffa94d1c93b2569d7a1ac52f8b..c5994b8fc54fbaa20eb4d8ae1b74c7c6c3b96f58 100644
--- a/modules/gui/src/scene_win/entity_part_node.cc
+++ b/modules/gui/src/scene_win/entity_part_node.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2009 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/scene_win/entity_part_node.hh b/modules/gui/src/scene_win/entity_part_node.hh
index 2eb308cbedae85349e627cc31e9d05abe9b68413..c25c9d48738cd972a54b9a1e2f1c5058ef694fde 100644
--- a/modules/gui/src/scene_win/entity_part_node.hh
+++ b/modules/gui/src/scene_win/entity_part_node.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2009 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/scene_win/gfx_scene_node.cc b/modules/gui/src/scene_win/gfx_scene_node.cc
index ca06e19c844a54e5fc36bd75c627d0cd9d042d5c..8a8c0182380d4f082e9a10ae0b219b31de422800 100644
--- a/modules/gui/src/scene_win/gfx_scene_node.cc
+++ b/modules/gui/src/scene_win/gfx_scene_node.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/scene_win/gfx_scene_node.hh b/modules/gui/src/scene_win/gfx_scene_node.hh
index 9d779dcb7ebc6ee8260cd0749b927b6d067ae06a..882bc5ba6e8590004d7bef887ddfc9dae1766be0 100644
--- a/modules/gui/src/scene_win/gfx_scene_node.hh
+++ b/modules/gui/src/scene_win/gfx_scene_node.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/scene_win/label_node.cc b/modules/gui/src/scene_win/label_node.cc
index f71c832680aa5b0a8f601d61173b4f4aa6befbbe..4f5dd843b6509c1995bf4ee8d14b4042d1ead461 100644
--- a/modules/gui/src/scene_win/label_node.cc
+++ b/modules/gui/src/scene_win/label_node.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2009 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/scene_win/label_node.hh b/modules/gui/src/scene_win/label_node.hh
index 4a9722f7f01ccf09b5afa3609f91f53566f0c5e3..a449492d0406a3e1454df5048182d1b3651d1748 100644
--- a/modules/gui/src/scene_win/label_node.hh
+++ b/modules/gui/src/scene_win/label_node.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2009 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/scene_win/render_mode_node.cc b/modules/gui/src/scene_win/render_mode_node.cc
index bba7f59abd2ddb12c721c372a0edab85b1dc8dde..1f789ac864b99346f003f05227267c8d79c21601 100644
--- a/modules/gui/src/scene_win/render_mode_node.cc
+++ b/modules/gui/src/scene_win/render_mode_node.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2009 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/scene_win/render_mode_node.hh b/modules/gui/src/scene_win/render_mode_node.hh
index 45984b7ce9fefac5d20e820f765f4ace2bff4103..4b08a8d8247c2c5d16e66a6f4ae1a73f1d9daf8a 100644
--- a/modules/gui/src/scene_win/render_mode_node.hh
+++ b/modules/gui/src/scene_win/render_mode_node.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2009 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/scene_win/render_modes_node.cc b/modules/gui/src/scene_win/render_modes_node.cc
index 68661b0973f984f9cb583a48ae354255496fa2aa..bb4420cdb3b871736acfa723661b8a666750daa3 100644
--- a/modules/gui/src/scene_win/render_modes_node.cc
+++ b/modules/gui/src/scene_win/render_modes_node.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2009 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/scene_win/render_modes_node.hh b/modules/gui/src/scene_win/render_modes_node.hh
index 024d45f8e1ba2a6a7bcf3c40ac005d27b3ff39b1..dd574f97d41e529994a0def7b9c2961c94ce8577 100644
--- a/modules/gui/src/scene_win/render_modes_node.hh
+++ b/modules/gui/src/scene_win/render_modes_node.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2009 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/scene_win/root_node.cc b/modules/gui/src/scene_win/root_node.cc
index 6c61c775d3fa167ea76ca33df9954d9d726f645b..dbe8956fb3c4cab3c01234b3b710a2dabca3307e 100644
--- a/modules/gui/src/scene_win/root_node.cc
+++ b/modules/gui/src/scene_win/root_node.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/scene_win/root_node.hh b/modules/gui/src/scene_win/root_node.hh
index ef2292c4d41a19e75f8408b5325381d0a4660069..e9b32b5f296df1c145924358b1eafe4935145706 100644
--- a/modules/gui/src/scene_win/root_node.hh
+++ b/modules/gui/src/scene_win/root_node.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/scene_win/scene_node.cc b/modules/gui/src/scene_win/scene_node.cc
index 3e99b51ccfbdcef37d0ddaeaf08bd558ac8b6c43..c63619d9d274b76e7988d27696bdadf13d355729 100644
--- a/modules/gui/src/scene_win/scene_node.cc
+++ b/modules/gui/src/scene_win/scene_node.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/scene_win/scene_node.hh b/modules/gui/src/scene_win/scene_node.hh
index 6b183788d5e336f97e9e44e257e752d3f98905c0..cf370596f72c8d1130481ca3faddf6d70d5f4c4c 100644
--- a/modules/gui/src/scene_win/scene_node.hh
+++ b/modules/gui/src/scene_win/scene_node.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/scene_win/scene_win.cc b/modules/gui/src/scene_win/scene_win.cc
index 2e8375075c4f2c403b331e21c2feaae97c1b945e..f3601709f1299f682d664302da036ce7ad23b6cc 100644
--- a/modules/gui/src/scene_win/scene_win.cc
+++ b/modules/gui/src/scene_win/scene_win.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/scene_win/scene_win.hh b/modules/gui/src/scene_win/scene_win.hh
index d84669079fabfca8255af0156f35c5f3db54c60e..644672914a1a2e44c0b45c109916ebe53dc34bb0 100644
--- a/modules/gui/src/scene_win/scene_win.hh
+++ b/modules/gui/src/scene_win/scene_win.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/scene_win/scene_win_model.cc b/modules/gui/src/scene_win/scene_win_model.cc
index c9cf6d681304cc733a079344b440d810bc8d2e51..144d366005da250b0228ea684e3d0cc29c93b55d 100644
--- a/modules/gui/src/scene_win/scene_win_model.cc
+++ b/modules/gui/src/scene_win/scene_win_model.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/scene_win/scene_win_model.hh b/modules/gui/src/scene_win/scene_win_model.hh
index 3382331640b0e9b74166d784cb43be15095ee349..35808af619efa24bfcdc12993e66686666a8aa64 100644
--- a/modules/gui/src/scene_win/scene_win_model.hh
+++ b/modules/gui/src/scene_win/scene_win_model.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/sequence_viewer/align_properties_painter.cc b/modules/gui/src/sequence_viewer/align_properties_painter.cc
index c761267e4fbcfa4be432d81fe8cc7184b3c653e1..fdf9256abad0ed49217e897986e5741eb3537bd1 100644
--- a/modules/gui/src/sequence_viewer/align_properties_painter.cc
+++ b/modules/gui/src/sequence_viewer/align_properties_painter.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/sequence_viewer/align_properties_painter.hh b/modules/gui/src/sequence_viewer/align_properties_painter.hh
index 50a36a11cf56abd1b9d377aabac808d569dbeff4..90ac3c7da74eda074f2fd2a32ee3dc7276a2c7de 100644
--- a/modules/gui/src/sequence_viewer/align_properties_painter.hh
+++ b/modules/gui/src/sequence_viewer/align_properties_painter.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/sequence_viewer/alignment_view_object.cc b/modules/gui/src/sequence_viewer/alignment_view_object.cc
index 9084ee7fa74c76efa22992d547b964e27ca416b4..1fd0526bbced4684551f69eb66b234e0c63e0b49 100644
--- a/modules/gui/src/sequence_viewer/alignment_view_object.cc
+++ b/modules/gui/src/sequence_viewer/alignment_view_object.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/sequence_viewer/alignment_view_object.hh b/modules/gui/src/sequence_viewer/alignment_view_object.hh
index 9c96d31c5b4da314e75ada911350b50c0276946f..78646d8cec2054be6e427e7bb5737b5d33204258 100644
--- a/modules/gui/src/sequence_viewer/alignment_view_object.hh
+++ b/modules/gui/src/sequence_viewer/alignment_view_object.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/sequence_viewer/background_painter.cc b/modules/gui/src/sequence_viewer/background_painter.cc
index b2c86168fffd85d6d2970a850e1e9f76572704a6..7d7ccfdf16b8746da80ce20e2b37bdd555bbf2c3 100644
--- a/modules/gui/src/sequence_viewer/background_painter.cc
+++ b/modules/gui/src/sequence_viewer/background_painter.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/sequence_viewer/background_painter.hh b/modules/gui/src/sequence_viewer/background_painter.hh
index ec496675be23307d92f4907d048fb3d7487d52bd..b013214a986fd1503f96362dfd3d70763aa47711 100644
--- a/modules/gui/src/sequence_viewer/background_painter.hh
+++ b/modules/gui/src/sequence_viewer/background_painter.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/sequence_viewer/base_row.cc b/modules/gui/src/sequence_viewer/base_row.cc
index c4c2a76ae9d86048a7ac4859f977adc3af0e08f6..15cf1f6c956cdf6e6801b1db8616674402609994 100644
--- a/modules/gui/src/sequence_viewer/base_row.cc
+++ b/modules/gui/src/sequence_viewer/base_row.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/sequence_viewer/base_row.hh b/modules/gui/src/sequence_viewer/base_row.hh
index 544a7d7559c5cb051770cfb926280c6b3d279ba8..1782e2f3a1791bd7dc1296f396be439eab88ac61 100644
--- a/modules/gui/src/sequence_viewer/base_row.hh
+++ b/modules/gui/src/sequence_viewer/base_row.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/sequence_viewer/base_view_object.cc b/modules/gui/src/sequence_viewer/base_view_object.cc
index 5f567bab79a389be4f30e8cf21a980a805ee1b16..70277b361708f84a90dcad291e3dd08fd2b23572 100644
--- a/modules/gui/src/sequence_viewer/base_view_object.cc
+++ b/modules/gui/src/sequence_viewer/base_view_object.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/sequence_viewer/base_view_object.hh b/modules/gui/src/sequence_viewer/base_view_object.hh
index 80842f8779333d61585e79f92ce9948d31485b8c..fab8435ff0c9099daa52f9fe9fd47b9a85ecc740 100644
--- a/modules/gui/src/sequence_viewer/base_view_object.hh
+++ b/modules/gui/src/sequence_viewer/base_view_object.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/sequence_viewer/conservation_painter.cc b/modules/gui/src/sequence_viewer/conservation_painter.cc
index 91babf268081bc58cbb055cc88cc499680c1423a..d4247c4412f11e7f85b7fdba6b00bd5a9cdb4703 100644
--- a/modules/gui/src/sequence_viewer/conservation_painter.cc
+++ b/modules/gui/src/sequence_viewer/conservation_painter.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/sequence_viewer/conservation_painter.hh b/modules/gui/src/sequence_viewer/conservation_painter.hh
index 849c09c63221e89b8d3cfc8f1109098e85f74b67..ee7c0f8845e6a715ba2cc2fc556ad9aa66dbc8ba 100644
--- a/modules/gui/src/sequence_viewer/conservation_painter.hh
+++ b/modules/gui/src/sequence_viewer/conservation_painter.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/sequence_viewer/painter.hh b/modules/gui/src/sequence_viewer/painter.hh
index 26303e0cff363c0f4696f05113821ccc81487498..a6aac62db65ef7b0392b13fde9c77221a70c1842 100644
--- a/modules/gui/src/sequence_viewer/painter.hh
+++ b/modules/gui/src/sequence_viewer/painter.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/sequence_viewer/secstr_row.cc b/modules/gui/src/sequence_viewer/secstr_row.cc
index 50239343426ec233a0641ed5958a9a1d2e1ef7fd..5d9c73f8b8bf3482594708c8e6530ac696c1396b 100644
--- a/modules/gui/src/sequence_viewer/secstr_row.cc
+++ b/modules/gui/src/sequence_viewer/secstr_row.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/sequence_viewer/secstr_row.hh b/modules/gui/src/sequence_viewer/secstr_row.hh
index cdfebf14812d99dc90d29214e6b2f014acfa4a22..48ffaea337020e5d6d00c62bfe93e5472ac661e6 100644
--- a/modules/gui/src/sequence_viewer/secstr_row.hh
+++ b/modules/gui/src/sequence_viewer/secstr_row.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/sequence_viewer/seq_secstr_painter.cc b/modules/gui/src/sequence_viewer/seq_secstr_painter.cc
index 8d07b4dd0f0145f2a2bf8fb5010d9a6f6c95c2e7..25ebf9254f8a84b493f545d40d05f138526db877 100644
--- a/modules/gui/src/sequence_viewer/seq_secstr_painter.cc
+++ b/modules/gui/src/sequence_viewer/seq_secstr_painter.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/sequence_viewer/seq_secstr_painter.hh b/modules/gui/src/sequence_viewer/seq_secstr_painter.hh
index 0d9e36a3bdbba5d0b71ecbb2c68bac76b349ea09..c65b72603e929e65bce111342feb7c5442d35033 100644
--- a/modules/gui/src/sequence_viewer/seq_secstr_painter.hh
+++ b/modules/gui/src/sequence_viewer/seq_secstr_painter.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/sequence_viewer/seq_selection_painter.cc b/modules/gui/src/sequence_viewer/seq_selection_painter.cc
index 2ca4ad9ceeef345407a8525724b0f6e883030b1e..e483809384eb157cb9b87339a8596f92bd73dd30 100644
--- a/modules/gui/src/sequence_viewer/seq_selection_painter.cc
+++ b/modules/gui/src/sequence_viewer/seq_selection_painter.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/sequence_viewer/seq_selection_painter.hh b/modules/gui/src/sequence_viewer/seq_selection_painter.hh
index bef7ab1da29597b97c79a512eccec765ed07dbff..b52926bf03e47b91ecd4f90fb56eb44a913eeba5 100644
--- a/modules/gui/src/sequence_viewer/seq_selection_painter.hh
+++ b/modules/gui/src/sequence_viewer/seq_selection_painter.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/sequence_viewer/seq_text_painter.cc b/modules/gui/src/sequence_viewer/seq_text_painter.cc
index 157c97a04ad976ab76f5200a34c9c5f0643eeecc..8ebe532bdc53b0f86f3499642ffb17d58ac37615 100644
--- a/modules/gui/src/sequence_viewer/seq_text_painter.cc
+++ b/modules/gui/src/sequence_viewer/seq_text_painter.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/sequence_viewer/seq_text_painter.hh b/modules/gui/src/sequence_viewer/seq_text_painter.hh
index 771acdc6a3289a762103feff060bccd7c8510236..63b68dbf8be87d95f6fc07b918817fa085368436 100644
--- a/modules/gui/src/sequence_viewer/seq_text_painter.hh
+++ b/modules/gui/src/sequence_viewer/seq_text_painter.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/sequence_viewer/sequence_delegate.cc b/modules/gui/src/sequence_viewer/sequence_delegate.cc
index 46cfbe05e826f59a4b99cecb0a5e1776f49bd36c..77e9603dad9d4ccfb9897ec463e570c9a0c8ac46 100644
--- a/modules/gui/src/sequence_viewer/sequence_delegate.cc
+++ b/modules/gui/src/sequence_viewer/sequence_delegate.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/sequence_viewer/sequence_delegate.hh b/modules/gui/src/sequence_viewer/sequence_delegate.hh
index 491669d4777d822f84053a9bc815dad5704cf5cd..09727b32cd83aaaa1f0f862d1965c1433674caac 100644
--- a/modules/gui/src/sequence_viewer/sequence_delegate.hh
+++ b/modules/gui/src/sequence_viewer/sequence_delegate.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/sequence_viewer/sequence_model.cc b/modules/gui/src/sequence_viewer/sequence_model.cc
index d64020ad925ca9307ca3fafd423f7de027d4684c..dad4e1c660b1e49aa461400667d083d6a8f85380 100644
--- a/modules/gui/src/sequence_viewer/sequence_model.cc
+++ b/modules/gui/src/sequence_viewer/sequence_model.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/sequence_viewer/sequence_model.hh b/modules/gui/src/sequence_viewer/sequence_model.hh
index ce605c8f4dab661672bd2b089872e954871bdcd1..de2f1256d0959d80211f161f4e3afee7c4097848 100644
--- a/modules/gui/src/sequence_viewer/sequence_model.hh
+++ b/modules/gui/src/sequence_viewer/sequence_model.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/sequence_viewer/sequence_row.cc b/modules/gui/src/sequence_viewer/sequence_row.cc
index 1d431cbae8bc0998d00e0e3281429aaf8bbaacbf..21f741943d9b4ee794780e3ebb5a2e01d710d68f 100644
--- a/modules/gui/src/sequence_viewer/sequence_row.cc
+++ b/modules/gui/src/sequence_viewer/sequence_row.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/sequence_viewer/sequence_row.hh b/modules/gui/src/sequence_viewer/sequence_row.hh
index cbe6e285567b95c8e8c799ad5e875eb27c49b80b..fd903dbc490a5df21415cc163772c4c7eb772ffc 100644
--- a/modules/gui/src/sequence_viewer/sequence_row.hh
+++ b/modules/gui/src/sequence_viewer/sequence_row.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/sequence_viewer/sequence_search_bar.cc b/modules/gui/src/sequence_viewer/sequence_search_bar.cc
index d367b56edcd721c480f1bb752fd3902b0461a4cd..0feab0cf75957936b78a48ff855f6c32a1f5fd97 100644
--- a/modules/gui/src/sequence_viewer/sequence_search_bar.cc
+++ b/modules/gui/src/sequence_viewer/sequence_search_bar.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/sequence_viewer/sequence_search_bar.hh b/modules/gui/src/sequence_viewer/sequence_search_bar.hh
index 13e4f0fd0a8874d4dadb1b0f89719f6fc3189284..197e59eacc554063494aa7265039151fe80d3fe1 100644
--- a/modules/gui/src/sequence_viewer/sequence_search_bar.hh
+++ b/modules/gui/src/sequence_viewer/sequence_search_bar.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/sequence_viewer/sequence_table_view.cc b/modules/gui/src/sequence_viewer/sequence_table_view.cc
index 9a7020ff92915b4d74f2d62922f73218da24f793..2a8868582f4bd63f996c9e4ac5af41d00215f812 100644
--- a/modules/gui/src/sequence_viewer/sequence_table_view.cc
+++ b/modules/gui/src/sequence_viewer/sequence_table_view.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/sequence_viewer/sequence_table_view.hh b/modules/gui/src/sequence_viewer/sequence_table_view.hh
index 24c743b64cbd8e318a22091cb2032904ff98196b..d7f4354af7c64795974678e0cb322d63fba065c9 100644
--- a/modules/gui/src/sequence_viewer/sequence_table_view.hh
+++ b/modules/gui/src/sequence_viewer/sequence_table_view.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/sequence_viewer/sequence_view_object.cc b/modules/gui/src/sequence_viewer/sequence_view_object.cc
index 97993f0cdf11d45967377249f0793cf01e37ea50..16a39a7dd6633f64ad47f2aff609a0b890c30e13 100644
--- a/modules/gui/src/sequence_viewer/sequence_view_object.cc
+++ b/modules/gui/src/sequence_viewer/sequence_view_object.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/sequence_viewer/sequence_view_object.hh b/modules/gui/src/sequence_viewer/sequence_view_object.hh
index c3addfe409bb7926dd972f3a3a79b64ba3ddbb9b..e3e043abaa80aca1be155d2178e806597f9ee55c 100644
--- a/modules/gui/src/sequence_viewer/sequence_view_object.hh
+++ b/modules/gui/src/sequence_viewer/sequence_view_object.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/sequence_viewer/sequence_viewer.cc b/modules/gui/src/sequence_viewer/sequence_viewer.cc
index 85ff6ece69a9ab57da281a0b310233d6cf3a17dc..b04299a13ad75934f155382035fdf1f16e74d996 100644
--- a/modules/gui/src/sequence_viewer/sequence_viewer.cc
+++ b/modules/gui/src/sequence_viewer/sequence_viewer.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/sequence_viewer/sequence_viewer.hh b/modules/gui/src/sequence_viewer/sequence_viewer.hh
index bd780a3b9cd157000fec19fe0779134979eb9666..d8bb59c8b7ca54ee84ce48ed004da68f734dedee 100644
--- a/modules/gui/src/sequence_viewer/sequence_viewer.hh
+++ b/modules/gui/src/sequence_viewer/sequence_viewer.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/sequence_viewer/tick_painter.cc b/modules/gui/src/sequence_viewer/tick_painter.cc
index 4c1558a5a5c02469670cddeaf8c31e77aa67d2ba..13658f81959dbbac29252e968361bfb62e635095 100644
--- a/modules/gui/src/sequence_viewer/tick_painter.cc
+++ b/modules/gui/src/sequence_viewer/tick_painter.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/sequence_viewer/tick_painter.hh b/modules/gui/src/sequence_viewer/tick_painter.hh
index e2c84261652f1ea46cc4381d969f3c2b48cf5484..26615cecf1a95cf7ab0cfeb205e2d44ce431366d 100644
--- a/modules/gui/src/sequence_viewer/tick_painter.hh
+++ b/modules/gui/src/sequence_viewer/tick_painter.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/sequence_viewer/title_row.cc b/modules/gui/src/sequence_viewer/title_row.cc
index d4dd16fa5757f5ea4f43e1d5a971f1802c4381e4..9e38897b12065eb3c9a07191a8a05282ef1ada36 100644
--- a/modules/gui/src/sequence_viewer/title_row.cc
+++ b/modules/gui/src/sequence_viewer/title_row.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/sequence_viewer/title_row.hh b/modules/gui/src/sequence_viewer/title_row.hh
index 8cc3d9abbbc37068590c9b2c13088a2c331aa620..0a805765c19cf12f76f3d3290839a8cd85e1573a 100644
--- a/modules/gui/src/sequence_viewer/title_row.hh
+++ b/modules/gui/src/sequence_viewer/title_row.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/thin_splitter.cc b/modules/gui/src/thin_splitter.cc
index ba425ffa85bb7114f27f4e3655ff77c458650540..74860e2a6304ac9b81725b5fe5503cf731d7a0cf 100644
--- a/modules/gui/src/thin_splitter.cc
+++ b/modules/gui/src/thin_splitter.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/thin_splitter.hh b/modules/gui/src/thin_splitter.hh
index 2014121b672891e8db91d0f9d833b74072dea359..3f940ea96682a1c662c7b391f160c7e347131f42 100644
--- a/modules/gui/src/thin_splitter.hh
+++ b/modules/gui/src/thin_splitter.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/tools/manipulator.cc b/modules/gui/src/tools/manipulator.cc
index ee663099d35393bb0ea9698f87256fbc90056bd0..1144c06463b55e6f5fcf4e6fcdee7396e1281ded 100644
--- a/modules/gui/src/tools/manipulator.cc
+++ b/modules/gui/src/tools/manipulator.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/tools/manipulator.hh b/modules/gui/src/tools/manipulator.hh
index 78a6f88dc19a4e1e3ab6b8c143a86e5b06cce95d..baa17d250de738b472bbab84ecabeefbf241dc0b 100644
--- a/modules/gui/src/tools/manipulator.hh
+++ b/modules/gui/src/tools/manipulator.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/tools/map_tool.cc b/modules/gui/src/tools/map_tool.cc
index 96e622a3d39b914a37f6e2c87a9ec0ddcfeb72ee..b9dd7f1ecb955926f032462a4419db9910925cb5 100644
--- a/modules/gui/src/tools/map_tool.cc
+++ b/modules/gui/src/tools/map_tool.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/tools/map_tool.hh b/modules/gui/src/tools/map_tool.hh
index e7ed5b61e614534be7db853ff955f018c14b6492..bed8c99f8ce295cdaa32aac9dc333668c4539bc9 100644
--- a/modules/gui/src/tools/map_tool.hh
+++ b/modules/gui/src/tools/map_tool.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/tools/measure_tool.cc b/modules/gui/src/tools/measure_tool.cc
index 730fffa94a086a7d789570d71446ecb0f7b06ad4..b3329bf6b16c7f205605549cf8f6d8623e9417e4 100644
--- a/modules/gui/src/tools/measure_tool.cc
+++ b/modules/gui/src/tools/measure_tool.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/tools/measure_tool.hh b/modules/gui/src/tools/measure_tool.hh
index 86effde21b3dc3defb64912e2143b6c828e7d67b..98ebd79f3b2cf6fc40a8e8c9506a4df8c9b441e8 100644
--- a/modules/gui/src/tools/measure_tool.hh
+++ b/modules/gui/src/tools/measure_tool.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/tools/mouse_event.cc b/modules/gui/src/tools/mouse_event.cc
index 8c620c8a75d37ef06eb5fccf291c4ae0d3b400da..7fd2accc47a6e0e3aa06b465cdc11ca743475b26 100644
--- a/modules/gui/src/tools/mouse_event.cc
+++ b/modules/gui/src/tools/mouse_event.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/tools/mouse_event.hh b/modules/gui/src/tools/mouse_event.hh
index c46f179160ebb2ac81034c1bf633525e7df2cd01..bd08115d50d3bd241c59a2cbf23b6ec158c13dc4 100644
--- a/modules/gui/src/tools/mouse_event.hh
+++ b/modules/gui/src/tools/mouse_event.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/tools/selection_tool.cc b/modules/gui/src/tools/selection_tool.cc
index 348b308c4a56929743dd7e40c63a216614bb976f..d03216871ca203a40148067f1c11f335dadb2230 100644
--- a/modules/gui/src/tools/selection_tool.cc
+++ b/modules/gui/src/tools/selection_tool.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/tools/selection_tool.hh b/modules/gui/src/tools/selection_tool.hh
index faa68093651f92db64f65487f32ce7f88426d74b..9c8e8e83cdf4c86f2a31ef88bd3459a4105d5b47 100644
--- a/modules/gui/src/tools/selection_tool.hh
+++ b/modules/gui/src/tools/selection_tool.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/tools/tool.cc b/modules/gui/src/tools/tool.cc
index 4792763f3b2ee347de049b6408e631e0146d4bdf..cd8a12dfc7ce4a8f5329b0ce2e6ee1e00487abc2 100644
--- a/modules/gui/src/tools/tool.cc
+++ b/modules/gui/src/tools/tool.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/tools/tool.hh b/modules/gui/src/tools/tool.hh
index 945855cca912d657573e8a1d236da68712e26cdc..975889779498694e7b3c6f2ffb4f21896d549515 100644
--- a/modules/gui/src/tools/tool.hh
+++ b/modules/gui/src/tools/tool.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/tools/tool_bar.cc b/modules/gui/src/tools/tool_bar.cc
index aeac798a420653ce3b785f356a5645a5887b2661..72948ee93e76d2db5dffc0575043ee26cfbf6baa 100644
--- a/modules/gui/src/tools/tool_bar.cc
+++ b/modules/gui/src/tools/tool_bar.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/tools/tool_bar.hh b/modules/gui/src/tools/tool_bar.hh
index e904821c90d3ea766184e30ebf75b129b009ca31..67b5873edfbc1b68c638fa00c6d804c4e46ef38f 100644
--- a/modules/gui/src/tools/tool_bar.hh
+++ b/modules/gui/src/tools/tool_bar.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/tools/tool_manager.cc b/modules/gui/src/tools/tool_manager.cc
index 55cd23137718132713e340713dff29f1fc89d8ab..9c9faaa8625717a60b1fb6b0d9249127fa827822 100644
--- a/modules/gui/src/tools/tool_manager.cc
+++ b/modules/gui/src/tools/tool_manager.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/tools/tool_manager.hh b/modules/gui/src/tools/tool_manager.hh
index 85e051a9c10981da42a24e70d8f254cb6b70fa95..a404eb7a5f60aaf678f07b522beb5443315d99ef 100644
--- a/modules/gui/src/tools/tool_manager.hh
+++ b/modules/gui/src/tools/tool_manager.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/tools/tool_option.cc b/modules/gui/src/tools/tool_option.cc
index 542c99ccdd36adde5ffb5c762c9ff5c67b3056dd..219abf4abf0069ec4ac627ceffbd86c1df367f31 100644
--- a/modules/gui/src/tools/tool_option.cc
+++ b/modules/gui/src/tools/tool_option.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/tools/tool_option.hh b/modules/gui/src/tools/tool_option.hh
index 7851000cdb97264a1a92ceddb352622e5079e058..013c11200666eb5b22286bd3e5d09ac872c78963 100644
--- a/modules/gui/src/tools/tool_option.hh
+++ b/modules/gui/src/tools/tool_option.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/tools/tool_option_group.cc b/modules/gui/src/tools/tool_option_group.cc
index df5d8dcd5def7a80044a237caab4af8497df44e8..156d817ca2e5ee5fe189a26ef722e8727b4d68d3 100644
--- a/modules/gui/src/tools/tool_option_group.cc
+++ b/modules/gui/src/tools/tool_option_group.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/tools/tool_option_group.hh b/modules/gui/src/tools/tool_option_group.hh
index 3be9a7681260818f4fb8f3a8ac0f9c50aa353222..6f2660761d3e53213332d2fc36d083644c2ce07e 100644
--- a/modules/gui/src/tools/tool_option_group.hh
+++ b/modules/gui/src/tools/tool_option_group.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/tools/tool_options.cc b/modules/gui/src/tools/tool_options.cc
index a8b1557dc4d6f151d1ea76fa5c498fec78c366b0..5b1e3b35d8bf4cca4c180663ae8a6a79e4c9083f 100644
--- a/modules/gui/src/tools/tool_options.cc
+++ b/modules/gui/src/tools/tool_options.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/tools/tool_options.hh b/modules/gui/src/tools/tool_options.hh
index 47e1783246c9128c497750c7d6344d7165f9095d..83c255164c9c36443fdf90b9ed9baf70bf26ac12 100644
--- a/modules/gui/src/tools/tool_options.hh
+++ b/modules/gui/src/tools/tool_options.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/tools/tool_options_widget.cc b/modules/gui/src/tools/tool_options_widget.cc
index 8798685556a4f455140cc32780e8456911cb2dbb..6438831bf4304e72abd84aaf6a04c30b070c307e 100644
--- a/modules/gui/src/tools/tool_options_widget.cc
+++ b/modules/gui/src/tools/tool_options_widget.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/tools/tool_options_widget.hh b/modules/gui/src/tools/tool_options_widget.hh
index 24e309f566d54fe2c6ffc7ff317f197e8a0dce50..132835611d21ff28960a6bf53dc600d87e828c61 100644
--- a/modules/gui/src/tools/tool_options_widget.hh
+++ b/modules/gui/src/tools/tool_options_widget.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/tools/tool_options_win.cc b/modules/gui/src/tools/tool_options_win.cc
index 61fa450c8ba15ccbc72ae8fc050146c13fca252d..e2e7d6f1c448b76a0ff88efa7e71503092191e5e 100644
--- a/modules/gui/src/tools/tool_options_win.cc
+++ b/modules/gui/src/tools/tool_options_win.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/tools/tool_options_win.hh b/modules/gui/src/tools/tool_options_win.hh
index eb90f5f9aef17cf96b3e4e0b3190caa59b69b264..74729397d2758e242108a6af4e5df88fe4633078 100644
--- a/modules/gui/src/tools/tool_options_win.hh
+++ b/modules/gui/src/tools/tool_options_win.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/widget.cc b/modules/gui/src/widget.cc
index 809dc477b3a7a5c940b30859133e7b721364da7a..5473f01d83b853b16ffed885ae1d75ea104e4fc7 100644
--- a/modules/gui/src/widget.cc
+++ b/modules/gui/src/widget.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/widget.hh b/modules/gui/src/widget.hh
index c52d396c98b72b0d66a86ad0addddecc7e15bd7e..5399c6692e1ac36301518d23bc14fd9b17191184 100644
--- a/modules/gui/src/widget.hh
+++ b/modules/gui/src/widget.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/widget_geom_handler.cc b/modules/gui/src/widget_geom_handler.cc
index efb6d752a83c802fd6339e1be26c338d9242f8d0..b68f8f79322f595bdcc5d4a75dc4eb5682684421 100644
--- a/modules/gui/src/widget_geom_handler.cc
+++ b/modules/gui/src/widget_geom_handler.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/widget_geom_handler.hh b/modules/gui/src/widget_geom_handler.hh
index e1f664c0888f98e5212d49dbfe5743872dbe7f0f..524f68dd3fb049003e5c70e159c35fcd9634b830 100644
--- a/modules/gui/src/widget_geom_handler.hh
+++ b/modules/gui/src/widget_geom_handler.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/widget_pool.cc b/modules/gui/src/widget_pool.cc
index f19735efe2e2bf8c8f49b040843c44f4ba9d6844..50b3b3371716e4fbbb7ec7c8b851b0589db7bb22 100644
--- a/modules/gui/src/widget_pool.cc
+++ b/modules/gui/src/widget_pool.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/widget_pool.hh b/modules/gui/src/widget_pool.hh
index bc480825af91ba7f4c2172a8d47caf78d532a23f..8b04a6e0b7d33803d216b2d7f78f5e7268d20f60 100644
--- a/modules/gui/src/widget_pool.hh
+++ b/modules/gui/src/widget_pool.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/widget_registry.cc b/modules/gui/src/widget_registry.cc
index b9c20757d90591b95362a7706c32b2e4c66ec562..f567bf7f8b56703b8e20059491a715bf1afe284d 100644
--- a/modules/gui/src/widget_registry.cc
+++ b/modules/gui/src/widget_registry.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/widget_registry.hh b/modules/gui/src/widget_registry.hh
index 643e5fa54d38779657cdb087a965cfb02d37e340..035b5352ecdcfeb55445df2c34060d5119d801d0 100644
--- a/modules/gui/src/widget_registry.hh
+++ b/modules/gui/src/widget_registry.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/widget_state_saver.cc b/modules/gui/src/widget_state_saver.cc
index a02863f59d7713e5160066f3363a6d0d98ca0611..75b6dc5414c8240d341fc1ab7c9ffcc9c2dc8b4b 100644
--- a/modules/gui/src/widget_state_saver.cc
+++ b/modules/gui/src/widget_state_saver.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/gui/src/widget_state_saver.hh b/modules/gui/src/widget_state_saver.hh
index cf5e0a8f5dc989811e87fe70a53260cdd7f767b7..fb10f73d73b577a68df9858f4a426137c7142dea 100644
--- a/modules/gui/src/widget_state_saver.hh
+++ b/modules/gui/src/widget_state_saver.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/img/alg/pymod/__init__.py b/modules/img/alg/pymod/__init__.py
index d67a8675466744d97ac320e88ed67c5cf455b079..2ec19a67924b25667f922023522dcee86ce27d4a 100644
--- a/modules/img/alg/pymod/__init__.py
+++ b/modules/img/alg/pymod/__init__.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
@@ -16,4 +16,4 @@
# along with this library; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
#------------------------------------------------------------------------------
-from _ost_img_alg import *
+from ._ost_img_alg import *
diff --git a/modules/img/alg/pymod/export_filter.cc b/modules/img/alg/pymod/export_filter.cc
index f1bf0f779a13575a19b2ec94ccab6bb1f225a774..06a0ecfda02146e23674c8e485fbdf3d3c1d5797 100644
--- a/modules/img/alg/pymod/export_filter.cc
+++ b/modules/img/alg/pymod/export_filter.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/pymod/export_normalizer.cc b/modules/img/alg/pymod/export_normalizer.cc
index de8a3f016d1bb398990e4f3945e175b108567de6..1e7d334db8df0f9691506c01ffb8b0dd810c6cae 100644
--- a/modules/img/alg/pymod/export_normalizer.cc
+++ b/modules/img/alg/pymod/export_normalizer.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/pymod/export_polar.cc b/modules/img/alg/pymod/export_polar.cc
index f41aae1209629cf6a536f0f2ac8cdf075db43540..f7c53bdf4fd26ed65018c56b7999b3ec3826fe36 100644
--- a/modules/img/alg/pymod/export_polar.cc
+++ b/modules/img/alg/pymod/export_polar.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/pymod/export_transcendentals.cc b/modules/img/alg/pymod/export_transcendentals.cc
index 3f0a638c2de6a2f551434fecb8c847724cd6b56b..ca6d56d38aef7d4bfc9c4258b01c6efa9c7ed3ad 100644
--- a/modules/img/alg/pymod/export_transcendentals.cc
+++ b/modules/img/alg/pymod/export_transcendentals.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/pymod/wrap_alg.cc b/modules/img/alg/pymod/wrap_alg.cc
index b024609d30df25346d118fbfaa133b1526908a6a..a4c9e2d61212c86831f7c868d79b3b2612555752 100644
--- a/modules/img/alg/pymod/wrap_alg.cc
+++ b/modules/img/alg/pymod/wrap_alg.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/pymod/wrap_tf.cc b/modules/img/alg/pymod/wrap_tf.cc
index cee27ebf1c6b4df06df579c68c078692863de536..4778e020b427fe4b241728d602376eebc9596d76 100644
--- a/modules/img/alg/pymod/wrap_tf.cc
+++ b/modules/img/alg/pymod/wrap_tf.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/alg_mirror.cc b/modules/img/alg/src/alg_mirror.cc
index 8b92849a6219d2c61aed29bb4b46635076b3748f..1a8e216ecda305c584fe68ee3b7ece931487ad8b 100644
--- a/modules/img/alg/src/alg_mirror.cc
+++ b/modules/img/alg/src/alg_mirror.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/alg_mirror.hh b/modules/img/alg/src/alg_mirror.hh
index b2a0cb0990ad5b38c43a2cc265e941410b205570..040ed827e21aa23658df5ec24ab2d52a56f6b96d 100644
--- a/modules/img/alg/src/alg_mirror.hh
+++ b/modules/img/alg/src/alg_mirror.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/alg_shift.cc b/modules/img/alg/src/alg_shift.cc
index f39a5b4ef52cdd3c9f4405af142b344602cd86a2..35af089530c2023230540863996fc1f07bf8d890 100644
--- a/modules/img/alg/src/alg_shift.cc
+++ b/modules/img/alg/src/alg_shift.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/alg_shift.hh b/modules/img/alg/src/alg_shift.hh
index dc47beb77718254bd375886fda7eae2f7853db3a..428d8382ac4e1e4581050047362157f5e69496d9 100644
--- a/modules/img/alg/src/alg_shift.hh
+++ b/modules/img/alg/src/alg_shift.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
@@ -25,8 +25,6 @@
#include <ost/img/value_util.hh>
#include <ost/img/alg/module_config.hh>
-namespace ost { namespace img { namespace alg {
-
namespace {
unsigned int absmod(int x, unsigned int y)
@@ -36,6 +34,8 @@ unsigned int absmod(int x, unsigned int y)
} // anon ns
+namespace ost { namespace img { namespace alg {
+
class DLLEXPORT_IMG_ALG ShiftFnc {
public:
ShiftFnc(): shift_() {}
@@ -49,9 +49,9 @@ public:
unsigned int height=in_state.GetExtent().GetHeight();
unsigned int width=in_state.GetExtent().GetWidth();
- unsigned int p0=absmod(shift_[0],width);
- unsigned int p1=absmod(shift_[1],height);
- unsigned int p2=absmod(shift_[2],depth);
+ unsigned int p0=::absmod(shift_[0],width);
+ unsigned int p1=::absmod(shift_[1],height);
+ unsigned int p2=::absmod(shift_[2],depth);
for(unsigned int u=0;u<width;++u) {
for(unsigned int v=0;v<height;++v) {
diff --git a/modules/img/alg/src/alg_transform.cc b/modules/img/alg/src/alg_transform.cc
index f0dadad3d28aa4fae4e04d2644fccf00c9ce93bc..36b76edd3b34b088ec4119e29e00fa58d4bc6606 100644
--- a/modules/img/alg/src/alg_transform.cc
+++ b/modules/img/alg/src/alg_transform.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/alg_transform.hh b/modules/img/alg/src/alg_transform.hh
index 3729437992ad56c8d94cf1a0615a857db370d6ce..3c52caf1bd7f51e4eed841e01944d50543f1ae87 100644
--- a/modules/img/alg/src/alg_transform.hh
+++ b/modules/img/alg/src/alg_transform.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/anisotropic.cc b/modules/img/alg/src/anisotropic.cc
index 3ed2d1f47434a604530516f407ea9b7f3a8bc888..8fe67ae8be5cb6f4eeb489d4cda129a32efdb92b 100644
--- a/modules/img/alg/src/anisotropic.cc
+++ b/modules/img/alg/src/anisotropic.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/anisotropic.hh b/modules/img/alg/src/anisotropic.hh
index 53b6e1ca068cbf55915b7413c315563530295d86..30498be68b89b21a02d02b7afff32837ac3deb6d 100644
--- a/modules/img/alg/src/anisotropic.hh
+++ b/modules/img/alg/src/anisotropic.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/auto_correlate.cc b/modules/img/alg/src/auto_correlate.cc
index 5256ff36825a2bfb2757f523ccffba4523216ec1..6e61f90d1663c19ee92be2887c89dac75f17f78e 100644
--- a/modules/img/alg/src/auto_correlate.cc
+++ b/modules/img/alg/src/auto_correlate.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/auto_correlate.hh b/modules/img/alg/src/auto_correlate.hh
index 420d98297f6cffb6a7304cbc4ad02e445910d750..5b72520f7dd38ef8b226545e54b2eba9bd0afff5 100644
--- a/modules/img/alg/src/auto_correlate.hh
+++ b/modules/img/alg/src/auto_correlate.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/clear.hh b/modules/img/alg/src/clear.hh
index bf05037fe6e2a79081477bdb3f88678728259d37..76e4e53a1fa653bd26ba4c71e36b2296dfd72bb3 100644
--- a/modules/img/alg/src/clear.hh
+++ b/modules/img/alg/src/clear.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/clip_min_max.hh b/modules/img/alg/src/clip_min_max.hh
index e44a3e4c3ec9d83639ff4a8e5c3b77c6de00ddeb..73e52e74bff3425040c926fc0b1a363a891ccf45 100644
--- a/modules/img/alg/src/clip_min_max.hh
+++ b/modules/img/alg/src/clip_min_max.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/conjugate.hh b/modules/img/alg/src/conjugate.hh
index 9a8e4a225982aa2df2b9f18132fcfc2ea4df234c..79409ecf57946d39c0095e3ec3e2fe8ce8f2279b 100644
--- a/modules/img/alg/src/conjugate.hh
+++ b/modules/img/alg/src/conjugate.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/convolute.cc b/modules/img/alg/src/convolute.cc
index 70543151bce9f741588e9253a7af00e7a60cc8b2..51deeb2002aa21daab22db34051c5ccbd38f7b80 100644
--- a/modules/img/alg/src/convolute.cc
+++ b/modules/img/alg/src/convolute.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/convolute.hh b/modules/img/alg/src/convolute.hh
index a55a292e304ae4a6aefaef4d87e134f6c3822594..54ab0a7c0324fe5a0a1dffea5ae2d305f69558f5 100644
--- a/modules/img/alg/src/convolute.hh
+++ b/modules/img/alg/src/convolute.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/correlate.cc b/modules/img/alg/src/correlate.cc
index b473e20c09f1aa089709c53a555846631e740303..d7f8a4b15e05b3a2c4649969607dba57b60264bc 100644
--- a/modules/img/alg/src/correlate.cc
+++ b/modules/img/alg/src/correlate.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/correlate.hh b/modules/img/alg/src/correlate.hh
index a88ea566484dadd077bb20b1272c2d7e602c33ee..ccd96d534ed3debf8bfe8d426aa7cafa641e1ece 100644
--- a/modules/img/alg/src/correlate.hh
+++ b/modules/img/alg/src/correlate.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/cross_correlate.cc b/modules/img/alg/src/cross_correlate.cc
index 7df974ebe4e3a772658b78ba318687349a422a9c..e2adc5827875a506fedd32360636909b6dad9815 100644
--- a/modules/img/alg/src/cross_correlate.cc
+++ b/modules/img/alg/src/cross_correlate.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/cross_correlate.hh b/modules/img/alg/src/cross_correlate.hh
index 17a2a7b9425fd798b752829248155253eea30bdd..3b06863922dcca6c3a28762b76410fedd7a54003 100644
--- a/modules/img/alg/src/cross_correlate.hh
+++ b/modules/img/alg/src/cross_correlate.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/custom_transformer.cc b/modules/img/alg/src/custom_transformer.cc
index 6f783e83a81dd58c3fe1e5e2a511ebc74152eecd..cd8451f685e9210192464419459a15cdec79a2cd 100644
--- a/modules/img/alg/src/custom_transformer.cc
+++ b/modules/img/alg/src/custom_transformer.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/custom_transformer.hh b/modules/img/alg/src/custom_transformer.hh
index 8e2798d6c623a8fb76d8e4e0927d36d91ec1400e..9ec3ab424963348d8037d2bd1eb0f426148ecd3b 100644
--- a/modules/img/alg/src/custom_transformer.hh
+++ b/modules/img/alg/src/custom_transformer.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/density_slice.cc b/modules/img/alg/src/density_slice.cc
index dc5cedf7f53c903a8c8bea23f2670c1e052cadb0..48c45a53ede15f7433cf2c1283d3226a3404ef5c 100644
--- a/modules/img/alg/src/density_slice.cc
+++ b/modules/img/alg/src/density_slice.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/density_slice.hh b/modules/img/alg/src/density_slice.hh
index ef2d077145eaaf2404f3eee9b44aa35bb6ff36cd..3d5559431fb8153ad42c0a0dac34f45d95757bf3 100644
--- a/modules/img/alg/src/density_slice.hh
+++ b/modules/img/alg/src/density_slice.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/dft.cc b/modules/img/alg/src/dft.cc
index b5ca096d0732feae433c28f56cc4c8c2e07757cb..783ae8c4985d3734842a0a69a4bf2e242f74e361 100644
--- a/modules/img/alg/src/dft.cc
+++ b/modules/img/alg/src/dft.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/dft.hh b/modules/img/alg/src/dft.hh
index 8265dcc102c961595c428ae2b65ebd6a3ab65cb4..299c9de6577948d4d524365653beca303d0a6d57 100644
--- a/modules/img/alg/src/dft.hh
+++ b/modules/img/alg/src/dft.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/discrete_shrink.cc b/modules/img/alg/src/discrete_shrink.cc
index 6aef59bcfa03c4c6bbd1332d1254916b73a3e465..c592937c58ded820b40806d6a82ae0e4e684a805 100644
--- a/modules/img/alg/src/discrete_shrink.cc
+++ b/modules/img/alg/src/discrete_shrink.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/discrete_shrink.hh b/modules/img/alg/src/discrete_shrink.hh
index 29bbfe5615830a6d3d7830168273d0a90cab776e..6772f9c95792116b93bea765886b64b80310a00e 100644
--- a/modules/img/alg/src/discrete_shrink.hh
+++ b/modules/img/alg/src/discrete_shrink.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/fft.cc b/modules/img/alg/src/fft.cc
index 61cc3199c645e37f8d17a9daab0b9fd8c286858d..1c88ab34d7610960b7f81c4fed04c266da94281a 100644
--- a/modules/img/alg/src/fft.cc
+++ b/modules/img/alg/src/fft.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/fft.hh b/modules/img/alg/src/fft.hh
index c8b3ccfc97cdba8aa430f0d927e50a018f67e06e..e4772404906ad344d95f7e0fcebc4f31b60ef251 100644
--- a/modules/img/alg/src/fft.hh
+++ b/modules/img/alg/src/fft.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/fftw_helper.hh b/modules/img/alg/src/fftw_helper.hh
index b1b6066aaf71d91282cf8bde70d8201b7bde2456..8f01fc4adf47b16e0f96d07b0a2eac173d2c5fd8 100644
--- a/modules/img/alg/src/fftw_helper.hh
+++ b/modules/img/alg/src/fftw_helper.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/img/alg/src/fill.hh b/modules/img/alg/src/fill.hh
index b023d70f5b33c87dda614049655c5e7177455931..60a88116196178b311974e8915edd6c638dc8b80 100644
--- a/modules/img/alg/src/fill.hh
+++ b/modules/img/alg/src/fill.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
@@ -32,11 +32,17 @@ namespace {
template<typename T>
void set_val(T& v, Real rv, const Complex& cv);
+/* While the functions below are employed by the OST unit tests, GCC does not
+ notice this and complains about "unused functions".
+*/
+#pragma GCC diagnostic push
+#pragma GCC diagnostic ignored "-Wunused-function"
template<>
void set_val<Real>(Real& v, Real rv, const Complex& cv) {v=rv;}
template<>
void set_val<Complex>(Complex& v, Real rv, const Complex& cv) {v=cv;}
+#pragma GCC diagnostic pop
template<typename T>
void set_val(T& v, Real rv, const Complex& cv)
diff --git a/modules/img/alg/src/filter.hh b/modules/img/alg/src/filter.hh
index 3cd7399de409dc6ac1668fff5452aff12b6c3eae..bbeddccbd7e3b815ea10c81f8e176f36b61b5b31 100644
--- a/modules/img/alg/src/filter.hh
+++ b/modules/img/alg/src/filter.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/fourier_filters.cc b/modules/img/alg/src/fourier_filters.cc
index a130b6f4cf27275aee648e9aa1974e5fc1ef64b7..a0c98cdeae80b001d0879ec617ef310ef59306ad 100644
--- a/modules/img/alg/src/fourier_filters.cc
+++ b/modules/img/alg/src/fourier_filters.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/fourier_filters.hh b/modules/img/alg/src/fourier_filters.hh
index 3f3fa9303abbfa66f058ee6a97361c68626e17af..a38bde19db39e57a8d2641ddc4ed1723b4e6b005 100644
--- a/modules/img/alg/src/fourier_filters.hh
+++ b/modules/img/alg/src/fourier_filters.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/fractional_shift.cc b/modules/img/alg/src/fractional_shift.cc
index c9ac40bc9e06ba14524670e3c3d7c71d0ea9c787..7e39fc6553bc8677e7d805f3f78d574d11c50012 100644
--- a/modules/img/alg/src/fractional_shift.cc
+++ b/modules/img/alg/src/fractional_shift.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/fractional_shift.hh b/modules/img/alg/src/fractional_shift.hh
index ad787c1dd94020b4e91ebd06746bd8dbb41fcd07..780e59d02980eca7f96b0b52e3dfc4973908e5e4 100644
--- a/modules/img/alg/src/fractional_shift.hh
+++ b/modules/img/alg/src/fractional_shift.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/gaussian.cc b/modules/img/alg/src/gaussian.cc
index 9c8e7880ff1ba720c8cbd36429922c54a0826f34..474a8b4f5b7890ddca11f81cb432cefc6e81fa60 100644
--- a/modules/img/alg/src/gaussian.cc
+++ b/modules/img/alg/src/gaussian.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/gaussian.hh b/modules/img/alg/src/gaussian.hh
index cad9f81d628fd1ea6d84f9441e5df6b2241b0dde..0c1214de8f2ced18a2e41bfe0f899780c9d18394 100644
--- a/modules/img/alg/src/gaussian.hh
+++ b/modules/img/alg/src/gaussian.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/gaussian_gradient_magnitude.cc b/modules/img/alg/src/gaussian_gradient_magnitude.cc
index b8c760be613d5627e416c2d25bd24d622adb8a59..6c3f45fd13f7b2e9343196cec64bd264b605b567 100644
--- a/modules/img/alg/src/gaussian_gradient_magnitude.cc
+++ b/modules/img/alg/src/gaussian_gradient_magnitude.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/gaussian_gradient_magnitude.hh b/modules/img/alg/src/gaussian_gradient_magnitude.hh
index f366b07eb69ea6419a240acb7d0bffbdff3cd53b..51af3ae6c1ee893257baa251728f8ad45969aeb3 100644
--- a/modules/img/alg/src/gaussian_gradient_magnitude.hh
+++ b/modules/img/alg/src/gaussian_gradient_magnitude.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/gaussian_laplacian.cc b/modules/img/alg/src/gaussian_laplacian.cc
index fbe0426448d4d3a7e8fbf6cdd4348304cfb32105..bd3675d291e561eef47c87d26ad7ee13bba33b68 100644
--- a/modules/img/alg/src/gaussian_laplacian.cc
+++ b/modules/img/alg/src/gaussian_laplacian.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/gaussian_laplacian.hh b/modules/img/alg/src/gaussian_laplacian.hh
index 5efe73b4fd3d6e68a77bffb9a4c43f7ef572bd4f..2b7efb1f943fa3e6b60afb979aa3be196e4d9cd8 100644
--- a/modules/img/alg/src/gaussian_laplacian.hh
+++ b/modules/img/alg/src/gaussian_laplacian.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/histogram.cc b/modules/img/alg/src/histogram.cc
index 16d90f3518f722ca71afc402659292715eef08eb..ba11a81ad8a983842d708e20f0f1ddc139543a3e 100644
--- a/modules/img/alg/src/histogram.cc
+++ b/modules/img/alg/src/histogram.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/histogram.hh b/modules/img/alg/src/histogram.hh
index c930ba43a20e118bcd2cbbe953a3c1932fbca052..619a9f845cfc4b825cb55758c24a32e10eb7ac96 100644
--- a/modules/img/alg/src/histogram.hh
+++ b/modules/img/alg/src/histogram.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/line_average.cc b/modules/img/alg/src/line_average.cc
index 45e38d7a7870eda6ba021317154301d9273b89bd..50223addf9f50cd9bf6308749e9e02ccfb8f512d 100644
--- a/modules/img/alg/src/line_average.cc
+++ b/modules/img/alg/src/line_average.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/line_average.hh b/modules/img/alg/src/line_average.hh
index fece6ef10eb2464579f546de69434fe04e4faf43..281134b58bd24fd1a053482d03bf101f57cb25a4 100644
--- a/modules/img/alg/src/line_average.hh
+++ b/modules/img/alg/src/line_average.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/line_iterator.cc b/modules/img/alg/src/line_iterator.cc
index 782b2fc3e07ab04e6e1bb960060015bf5fa2a28d..d271e1e3f256b3c9ecf6732cc4752f34070f6e63 100644
--- a/modules/img/alg/src/line_iterator.cc
+++ b/modules/img/alg/src/line_iterator.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/line_iterator.hh b/modules/img/alg/src/line_iterator.hh
index a42a5d822bceb6ff667ee8d7d5ac7f13afc16ad3..9d787dd0277109895e15b4c2706d20b6561da016 100644
--- a/modules/img/alg/src/line_iterator.hh
+++ b/modules/img/alg/src/line_iterator.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/local_sigma_threshold.cc b/modules/img/alg/src/local_sigma_threshold.cc
index 062d60d55b779a1de45a827fa0a03542673ce122..1c8e1910244c62678124c73fbe24c3cbb939a55f 100644
--- a/modules/img/alg/src/local_sigma_threshold.cc
+++ b/modules/img/alg/src/local_sigma_threshold.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/local_sigma_threshold.hh b/modules/img/alg/src/local_sigma_threshold.hh
index f66cea6ec16cacf02b42a67bc4367caf2a07b01b..ef72f460d0d002458f791273ac18c61c200a1b52 100644
--- a/modules/img/alg/src/local_sigma_threshold.hh
+++ b/modules/img/alg/src/local_sigma_threshold.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/mask_image.cc b/modules/img/alg/src/mask_image.cc
index 44e8637bad1514629a41803d7a0fe42bd7e1e35b..9c2ebeb2e85cb7e8aba561b4a7ad1be5d6b5d79a 100644
--- a/modules/img/alg/src/mask_image.cc
+++ b/modules/img/alg/src/mask_image.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/mask_image.hh b/modules/img/alg/src/mask_image.hh
index de1d8ca446f2768b8c246a51f506f14b427e4817..9804712837aa5037d9e05292902653f62bb5be10 100644
--- a/modules/img/alg/src/mask_image.hh
+++ b/modules/img/alg/src/mask_image.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/module_config.hh b/modules/img/alg/src/module_config.hh
index 9749440520b0870acd089847662f5f5fd77a43a8..0aae3d3b1d0c0fba9795892cf1b33f8442dedd5c 100644
--- a/modules/img/alg/src/module_config.hh
+++ b/modules/img/alg/src/module_config.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/img/alg/src/negate.hh b/modules/img/alg/src/negate.hh
index b61642fc59fb783bfe0d572a849b6aa5a206cf42..6d888333e15d90b5d56cc8ddcfbabcbb45b000d1 100644
--- a/modules/img/alg/src/negate.hh
+++ b/modules/img/alg/src/negate.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/norm.hh b/modules/img/alg/src/norm.hh
index 6e4c54980f5d06eefcf7be5395b9abc00b1d95b2..b62bd5d863fe26b6d235a636a6a117b2d2375e36 100644
--- a/modules/img/alg/src/norm.hh
+++ b/modules/img/alg/src/norm.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/norm_linear.cc b/modules/img/alg/src/norm_linear.cc
index 4619ab86ba1067b6b808d51b0251367f500da908..ab2562b2d6b008093571d9480ffa8f0344961565 100644
--- a/modules/img/alg/src/norm_linear.cc
+++ b/modules/img/alg/src/norm_linear.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/norm_linear.hh b/modules/img/alg/src/norm_linear.hh
index 9f7c1dbf8615a8efaa0cc6650ac1e4085866c7f1..0dcf7f0adcde60e996935eea898f944c0855585e 100644
--- a/modules/img/alg/src/norm_linear.hh
+++ b/modules/img/alg/src/norm_linear.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/norm_log.cc b/modules/img/alg/src/norm_log.cc
index 739d3a6d17aa7bca583ba375d6dec737b8438300..755885ec6f8e6f6c28d244f03429d7621bac7fbd 100644
--- a/modules/img/alg/src/norm_log.cc
+++ b/modules/img/alg/src/norm_log.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/norm_log.hh b/modules/img/alg/src/norm_log.hh
index 4452404c2331fba627e595ee70b111b3f2065aa1..6d45b6cad35cb172612e4dcaec7dc42cea3b22d3 100644
--- a/modules/img/alg/src/norm_log.hh
+++ b/modules/img/alg/src/norm_log.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/norm_od.cc b/modules/img/alg/src/norm_od.cc
index 75b1a27708adaa968761bb14424cff0b667e5e6b..63ff35bd7fc7f36ad8f4b1ec3532121760e393da 100644
--- a/modules/img/alg/src/norm_od.cc
+++ b/modules/img/alg/src/norm_od.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/norm_od.hh b/modules/img/alg/src/norm_od.hh
index 21c22d45c2a9de55e2fc349f24469e5e9372a97a..5ce238421f7870f6ddac312f991e821004d80528 100644
--- a/modules/img/alg/src/norm_od.hh
+++ b/modules/img/alg/src/norm_od.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/normalizer.cc b/modules/img/alg/src/normalizer.cc
index 0aab1c74d0a7514d18080d3e2408900c85fbfa2e..a9d9d17373546863d6b024d644b61c33b8fc0a8c 100644
--- a/modules/img/alg/src/normalizer.cc
+++ b/modules/img/alg/src/normalizer.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/normalizer.hh b/modules/img/alg/src/normalizer.hh
index ab4ba6a1632529a6913405aa4020cdbf44060367..a46f8655482ccb69d17d6b749ae21f94de4c9986 100644
--- a/modules/img/alg/src/normalizer.hh
+++ b/modules/img/alg/src/normalizer.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/normalizer_factory.cc b/modules/img/alg/src/normalizer_factory.cc
index 0fef98f0fadcd9ea5a30b2a2b588e42ff4015bf7..f56eee43167f4593e5204ebd5f805ad61eec0acd 100644
--- a/modules/img/alg/src/normalizer_factory.cc
+++ b/modules/img/alg/src/normalizer_factory.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/normalizer_factory.hh b/modules/img/alg/src/normalizer_factory.hh
index e830ed0de6f3ff13157a34be41aa346723694d7e..8e3201f5db7708e3f28b244eaa33b2f1897b03c9 100644
--- a/modules/img/alg/src/normalizer_factory.hh
+++ b/modules/img/alg/src/normalizer_factory.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/polar.cc b/modules/img/alg/src/polar.cc
index aa5fa3745ddb80a6db9b932d573d4444304d0ffc..366f3928062815c4d0f138df5fd1760449a4457f 100644
--- a/modules/img/alg/src/polar.cc
+++ b/modules/img/alg/src/polar.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/polar.hh b/modules/img/alg/src/polar.hh
index c24b3f670e08c7f1eafec27883a33f5042731255..8f01d972d594882013188382fa6fc7eb27b13d17 100644
--- a/modules/img/alg/src/polar.hh
+++ b/modules/img/alg/src/polar.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/power_spectrum.cc b/modules/img/alg/src/power_spectrum.cc
index 488a188d7f295e9e2b43364ff4ab2f1fd1d0dfbf..42deac2aa6ca9bf7f586c243ea764a816e189479 100644
--- a/modules/img/alg/src/power_spectrum.cc
+++ b/modules/img/alg/src/power_spectrum.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/power_spectrum.hh b/modules/img/alg/src/power_spectrum.hh
index fd86965812b0b99edb958b9324ac6a2fac9c5965..1bb5674ef6b3dde27bd54168b1f9fe212c1e63de 100644
--- a/modules/img/alg/src/power_spectrum.hh
+++ b/modules/img/alg/src/power_spectrum.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/randomize.cc b/modules/img/alg/src/randomize.cc
index e23dc471db585d167485a322c2618d61da337e65..6af6bbb70ce70929de62ac728d9109f41e688760 100644
--- a/modules/img/alg/src/randomize.cc
+++ b/modules/img/alg/src/randomize.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/randomize.hh b/modules/img/alg/src/randomize.hh
index cc3fc20d641f211449a54f8cf2fef80bc54efd89..a37fadfa5bfe71c66d389edc71c599b56b13d3dd 100644
--- a/modules/img/alg/src/randomize.hh
+++ b/modules/img/alg/src/randomize.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/rscrosscorr.cc b/modules/img/alg/src/rscrosscorr.cc
index 037c0f6edc9b11f18047ef9af44d4814b5c58f42..bf2e32db989dcbefa42a54996f6ea50b5633ea81 100644
--- a/modules/img/alg/src/rscrosscorr.cc
+++ b/modules/img/alg/src/rscrosscorr.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/img/alg/src/rscrosscorr.hh b/modules/img/alg/src/rscrosscorr.hh
index cc8eaddb5ae6e43357d513aa5f9e06f1e7955499..d5f425ab6045e11890238e5cf6edc64dce6a328e 100644
--- a/modules/img/alg/src/rscrosscorr.hh
+++ b/modules/img/alg/src/rscrosscorr.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/img/alg/src/smooth_mask_image.cc b/modules/img/alg/src/smooth_mask_image.cc
index f4c8a506cb1100abd409ae55ff20dafbe0259269..1384b524228ad285091576b33a39c0501e3ea6a0 100644
--- a/modules/img/alg/src/smooth_mask_image.cc
+++ b/modules/img/alg/src/smooth_mask_image.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/smooth_mask_image.hh b/modules/img/alg/src/smooth_mask_image.hh
index d2c7f59cc02325966775b7c36548f3b282c27879..bf0ef9fc333d19a069b187d6e8ce58d8fea90e15 100644
--- a/modules/img/alg/src/smooth_mask_image.hh
+++ b/modules/img/alg/src/smooth_mask_image.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/stat.cc b/modules/img/alg/src/stat.cc
index 2623149985969502481659c094ffc6192a43385e..ec030d9afdfa49684fdd54c771dcf91cdc804ccd 100644
--- a/modules/img/alg/src/stat.cc
+++ b/modules/img/alg/src/stat.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/stat.hh b/modules/img/alg/src/stat.hh
index ba1861621612f2dd9fd6cb2900bda916c843b450..080c5adbb796639c020828e7d30d3217fa6359b2 100644
--- a/modules/img/alg/src/stat.hh
+++ b/modules/img/alg/src/stat.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/stat_accumulator.hh b/modules/img/alg/src/stat_accumulator.hh
index cb4530eac56c0c133d58581359b19540d25c685d..07712707276880d9233e969c55847dfab49ea9e9 100644
--- a/modules/img/alg/src/stat_accumulator.hh
+++ b/modules/img/alg/src/stat_accumulator.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/img/alg/src/stat_min_max.cc b/modules/img/alg/src/stat_min_max.cc
index c6963864462aa53fad855adede023496333fe016..177806049301586c58580a26460862a37ab31c12 100644
--- a/modules/img/alg/src/stat_min_max.cc
+++ b/modules/img/alg/src/stat_min_max.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/stat_min_max.hh b/modules/img/alg/src/stat_min_max.hh
index 15d7300bc335a7930d67dcc2f09bb76c72903ff6..b62d0069ac5cec8eb667b2c811d5cea18fe8a129 100644
--- a/modules/img/alg/src/stat_min_max.hh
+++ b/modules/img/alg/src/stat_min_max.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/threshold.cc b/modules/img/alg/src/threshold.cc
index 1437c53deff782ae3500649104bb2e3bc010038a..cba8f11dfe2cffcd4102bdc7816ff6e4baa26ba8 100644
--- a/modules/img/alg/src/threshold.cc
+++ b/modules/img/alg/src/threshold.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/threshold.hh b/modules/img/alg/src/threshold.hh
index 490fd514e032491dfbad238f2d26b71f9ba0f2f2..4a66c4d52c54cf9480174141595ac95bd43fb2a8 100644
--- a/modules/img/alg/src/threshold.hh
+++ b/modules/img/alg/src/threshold.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/transcendentals.hh b/modules/img/alg/src/transcendentals.hh
index 60c1f6bcfd24bc7f759090c4c62d48c926745308..cc936d1317fb01fca14117d404d550a2e589795a 100644
--- a/modules/img/alg/src/transcendentals.hh
+++ b/modules/img/alg/src/transcendentals.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/transform.hh b/modules/img/alg/src/transform.hh
index e2603bd6e5090aed28904f4540ffc35fa02e9d03..b538283d83ed9eada330849fc721581bf7cdfb21 100644
--- a/modules/img/alg/src/transform.hh
+++ b/modules/img/alg/src/transform.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/transform_fw.hh b/modules/img/alg/src/transform_fw.hh
index b4c780402e9720c374d5aae5c8d5923cee7eb23f..d786e411cf9b1c60644c33c309f24785fa0cb876 100644
--- a/modules/img/alg/src/transform_fw.hh
+++ b/modules/img/alg/src/transform_fw.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/transformation_base.cc b/modules/img/alg/src/transformation_base.cc
index 2aa29ed4f42b34bedbb622426d69eddf287f87f2..2c311287e248e96163cd7a77128679291f812e81 100644
--- a/modules/img/alg/src/transformation_base.cc
+++ b/modules/img/alg/src/transformation_base.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/transformation_base.hh b/modules/img/alg/src/transformation_base.hh
index 3adf0c1bace3c7f779f051b73ad5fb943a5764f7..20dbe18f82ee535f7fd26795adabaa6ef34d0c3c 100644
--- a/modules/img/alg/src/transformation_base.hh
+++ b/modules/img/alg/src/transformation_base.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/transformations.cc b/modules/img/alg/src/transformations.cc
index a99805445af08221949d15205eeb9a603912b46a..8304bc5ca86423dc701ab67ced179e692a5d5a32 100644
--- a/modules/img/alg/src/transformations.cc
+++ b/modules/img/alg/src/transformations.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/src/transformations.hh b/modules/img/alg/src/transformations.hh
index 83c17ed7eaa92259ab21ff949af2b0632a73f853..9021a4cf23897a9c65ad2acf59e8c96b652ed750 100644
--- a/modules/img/alg/src/transformations.hh
+++ b/modules/img/alg/src/transformations.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/tests/test_clear.cc b/modules/img/alg/tests/test_clear.cc
index 8a2fed0b8a7e6e31633d255444748965c4c88e36..2c78e31d1a7bac3c4cae9a01ccbd71abb87e49f7 100644
--- a/modules/img/alg/tests/test_clear.cc
+++ b/modules/img/alg/tests/test_clear.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/tests/test_conj.cc b/modules/img/alg/tests/test_conj.cc
index d5df2f79c550a60b2f187a57dba64ca331de60c6..2eedb2ec99b54a93f16d8e6348c6eef6e6f60b06 100644
--- a/modules/img/alg/tests/test_conj.cc
+++ b/modules/img/alg/tests/test_conj.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/tests/test_convolute.cc b/modules/img/alg/tests/test_convolute.cc
index 6ed68a2772c6343302c9dace61b6e3e79bfec2a3..4d87b0442cddba372ededde78d1091febd5ca648 100644
--- a/modules/img/alg/tests/test_convolute.cc
+++ b/modules/img/alg/tests/test_convolute.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/tests/test_discrete_shrink.cc b/modules/img/alg/tests/test_discrete_shrink.cc
index ce85c2d9114e32fcbd21206e777a765d04c93e91..60e071a930665e1eca4e752dc3b602f32e9fe219 100644
--- a/modules/img/alg/tests/test_discrete_shrink.cc
+++ b/modules/img/alg/tests/test_discrete_shrink.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/tests/test_fft.cc b/modules/img/alg/tests/test_fft.cc
index 7d8d0a1d125b91424af099b77db3c6f1a53d3a13..18f25b236effdd8df370dcc804f998f8e745270e 100644
--- a/modules/img/alg/tests/test_fft.cc
+++ b/modules/img/alg/tests/test_fft.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/tests/test_fill.cc b/modules/img/alg/tests/test_fill.cc
index c476a32db44afabb5ccf473359a9ad2c2a352fd8..77b2bfd9c1c21d4dc4a755ec7ab8bfb396ff7463 100644
--- a/modules/img/alg/tests/test_fill.cc
+++ b/modules/img/alg/tests/test_fill.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/tests/test_filter.cc b/modules/img/alg/tests/test_filter.cc
index af9ca66cdbbfc763dc18876a872eda56284ad061..aef7f63c8f16ab8272df98a96f1ed159b0739d5d 100644
--- a/modules/img/alg/tests/test_filter.cc
+++ b/modules/img/alg/tests/test_filter.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/tests/test_histogram.cc b/modules/img/alg/tests/test_histogram.cc
index c5382ce88745c390ebd3a988feeeb4b8b076f202..71e08ceef6697d7c02a87d30d4d596c38550c5d8 100644
--- a/modules/img/alg/tests/test_histogram.cc
+++ b/modules/img/alg/tests/test_histogram.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/tests/test_mirror.cc b/modules/img/alg/tests/test_mirror.cc
index ed6a9ff42893cccde4d25149e8f59f33bab09451..c94b9fa0e38f53558fb8e5c67e9ec5b9010fb286 100644
--- a/modules/img/alg/tests/test_mirror.cc
+++ b/modules/img/alg/tests/test_mirror.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/tests/test_negate.cc b/modules/img/alg/tests/test_negate.cc
index fe05460048d272b7955d7ae4b3d38d9475519cc6..12840d64c207d1c368917d4e98c766cff9642540 100644
--- a/modules/img/alg/tests/test_negate.cc
+++ b/modules/img/alg/tests/test_negate.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/tests/test_normalizer.cc b/modules/img/alg/tests/test_normalizer.cc
index 2b13c649f5441cc99fc7c6fa7d49ab0da05f8a7d..14534d06bbb2a57c8cde631c992a1b20856f9303 100644
--- a/modules/img/alg/tests/test_normalizer.cc
+++ b/modules/img/alg/tests/test_normalizer.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/tests/test_power_spectrum.cc b/modules/img/alg/tests/test_power_spectrum.cc
index 21108200df5994e3452b3334f0b8385040a3d3a1..a5e71cd482c4eb6f8da7d4d2f3bee704fafe5ebe 100644
--- a/modules/img/alg/tests/test_power_spectrum.cc
+++ b/modules/img/alg/tests/test_power_spectrum.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/tests/test_shift.cc b/modules/img/alg/tests/test_shift.cc
index 70a51626e9a9f63a88b35d0cf1f8a5ba489ae0e2..3c32046dccf30cbe693c1ce58fd0aa0ae1fb4ed9 100644
--- a/modules/img/alg/tests/test_shift.cc
+++ b/modules/img/alg/tests/test_shift.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/tests/test_stat.cc b/modules/img/alg/tests/test_stat.cc
index 7e202193f37dcc42a6929a777dc9e37a26c4fca0..1ea0963431c62d468c1ef7aa1f27446e45907b77 100644
--- a/modules/img/alg/tests/test_stat.cc
+++ b/modules/img/alg/tests/test_stat.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/tests/test_transform.cc b/modules/img/alg/tests/test_transform.cc
index 62a12549d8e66ea390c61ca8535f474d348d8af0..6087074e4b1b1416fc083d1ec3d0042222a3247f 100644
--- a/modules/img/alg/tests/test_transform.cc
+++ b/modules/img/alg/tests/test_transform.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/tests/test_utils.hh b/modules/img/alg/tests/test_utils.hh
index 98b617900ce75457156f20a85f96384657082bae..577a73a7a5ac28fb6ff0b5cfae33af8155776e99 100644
--- a/modules/img/alg/tests/test_utils.hh
+++ b/modules/img/alg/tests/test_utils.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/tests/tests.cc b/modules/img/alg/tests/tests.cc
index d3db88c2f29c5c3bbb19517e4d0800f9488f4ea3..d7d4d25087145e3c5e3efd8ebcc316b02a91593b 100644
--- a/modules/img/alg/tests/tests.cc
+++ b/modules/img/alg/tests/tests.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/alg/tests/tests.hh b/modules/img/alg/tests/tests.hh
index 698e7a515767d051ceac409852d8b9f28c4fbc98..e9d4b8054810c3004ac1c01cc90d4fc3115b8cdd 100644
--- a/modules/img/alg/tests/tests.hh
+++ b/modules/img/alg/tests/tests.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/doc/point-size-extent.rst b/modules/img/base/doc/point-size-extent.rst
index af2731adb21d7ffae75bb859d78f16835b392965..344f0ea288ea09c7be22544a230a2735b8d4a1a1 100644
--- a/modules/img/base/doc/point-size-extent.rst
+++ b/modules/img/base/doc/point-size-extent.rst
@@ -39,7 +39,7 @@ Point
..code-block:: python
p=img.Point(1,2,3)
- print p
+ print(p)
p[1]=5
.. method:: ToVec3()
@@ -140,4 +140,4 @@ Extent
# visits all the pixels in the extent and
# prints out their values
for pixel in ei:
- print i.GetReal(pixel)
\ No newline at end of file
+ print(i.GetReal(pixel))
diff --git a/modules/img/base/pymod/__init__.py b/modules/img/base/pymod/__init__.py
index 82a290219a5d9f3097ef53ff3f0dc1a7fdd4af51..f78f0f7ad48a367738ed6c8f22a12c0bf7d8cc6b 100644
--- a/modules/img/base/pymod/__init__.py
+++ b/modules/img/base/pymod/__init__.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
@@ -16,6 +16,6 @@
# along with this library; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
#------------------------------------------------------------------------------
-from _ost_img import *
+from ._ost_img import *
MapHandle=ImageHandle
from ost.img import alg
diff --git a/modules/img/base/pymod/export_data.cc b/modules/img/base/pymod/export_data.cc
index 24f72acb373b3b49e081f40a0c8764eac49d51d2..f96e6932aa1736b5ff5d1662eefa002754043f27 100644
--- a/modules/img/base/pymod/export_data.cc
+++ b/modules/img/base/pymod/export_data.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/pymod/export_data_algorithm.cc b/modules/img/base/pymod/export_data_algorithm.cc
index 4fe222395eb9da2c1772c8e79cce852d927fca94..167f5c78964deb231f4c9aee3550d9e815e0abec 100644
--- a/modules/img/base/pymod/export_data_algorithm.cc
+++ b/modules/img/base/pymod/export_data_algorithm.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/pymod/export_extent.cc b/modules/img/base/pymod/export_extent.cc
index 421fa2f89c9241b6126a97b52ae69a5ac32acda3..ae0a14bbb688a548a013dfc4896c1cae2ee15d1c 100644
--- a/modules/img/base/pymod/export_extent.cc
+++ b/modules/img/base/pymod/export_extent.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
@@ -72,6 +72,7 @@ void export_Extent()
.def("__iter__",&WrapExtentIterator::Iter,
return_internal_reference<>() )
.def("next",&WrapExtentIterator::Next)
+ .def("__next__",&WrapExtentIterator::Next)
;
class_<ExtentIterator>("ExtentIterator", init<const Extent&,optional<unsigned int> >() )
diff --git a/modules/img/base/pymod/export_image_handle.cc b/modules/img/base/pymod/export_image_handle.cc
index 1c6481b8750bbcd411444d2630b712a050057de5..fe9c08250fce654f6cf7ea9cd4b0a20d7ed0e27d 100644
--- a/modules/img/base/pymod/export_image_handle.cc
+++ b/modules/img/base/pymod/export_image_handle.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/pymod/export_image_list.cc b/modules/img/base/pymod/export_image_list.cc
index f1fb6a6cfa26dc251f03887b89998f2101a00003..a725befd8ec54f233db973691070e909a87f2cc5 100644
--- a/modules/img/base/pymod/export_image_list.cc
+++ b/modules/img/base/pymod/export_image_list.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/pymod/export_map.cc b/modules/img/base/pymod/export_map.cc
index f7b46a93d45ec651e36219dd7d511d955bbf6d30..64bcd01a387eeb82a4a6d2d6e914240316ea2d9e 100644
--- a/modules/img/base/pymod/export_map.cc
+++ b/modules/img/base/pymod/export_map.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/pymod/export_mask.cc b/modules/img/base/pymod/export_mask.cc
index 40f42e9b0f00e1ca5ac20021e8e544e72bc9fd7f..add09cd7c0e9494a7ad4cdc36754267d7a3b4a76 100644
--- a/modules/img/base/pymod/export_mask.cc
+++ b/modules/img/base/pymod/export_mask.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/pymod/export_peak.cc b/modules/img/base/pymod/export_peak.cc
index 540745ca547b56e1e514d106a863481aa8f62c47..74e1bf13b901a4fe47cbc8573c7d099aa00b1a8d 100644
--- a/modules/img/base/pymod/export_peak.cc
+++ b/modules/img/base/pymod/export_peak.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/pymod/export_phase.cc b/modules/img/base/pymod/export_phase.cc
index 147f22c925697b0ff04188a779546acd14aaf299..d65b817370f8e5ff34acb6fe18b1487db9ac2ab5 100644
--- a/modules/img/base/pymod/export_phase.cc
+++ b/modules/img/base/pymod/export_phase.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/pymod/export_point.cc b/modules/img/base/pymod/export_point.cc
index 53047e6e8c53041591e334806f48169a3b26ab76..10a0e838c0e63eb11d38d346669cf8111c1a3be0 100644
--- a/modules/img/base/pymod/export_point.cc
+++ b/modules/img/base/pymod/export_point.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/pymod/export_progress.cc b/modules/img/base/pymod/export_progress.cc
index ecb187e815f6bec54e8446362087c889fbd92148..9bd7d75e03d339e8131d5ae32a50bbeddfbc0d85 100644
--- a/modules/img/base/pymod/export_progress.cc
+++ b/modules/img/base/pymod/export_progress.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/pymod/export_raster_image.cc b/modules/img/base/pymod/export_raster_image.cc
index 0c4604767683a96768461fa20a68b73620d241b6..8e4f561a2380b56d984162bc1c57f60083b0243d 100644
--- a/modules/img/base/pymod/export_raster_image.cc
+++ b/modules/img/base/pymod/export_raster_image.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/pymod/export_size.cc b/modules/img/base/pymod/export_size.cc
index 8206e36a77c2cbcb0ffa0b26f258f5904070fc37..7fdd4f79140b5c75adebc42c50eb1d110c617161 100644
--- a/modules/img/base/pymod/export_size.cc
+++ b/modules/img/base/pymod/export_size.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/pymod/wrap_extent_iterator.hh b/modules/img/base/pymod/wrap_extent_iterator.hh
index fb782d51368cd76fdb125ad9df7f9e60a4a5ddcf..805ce646816227ccc25bc36ec8e9b04a9c3894f6 100644
--- a/modules/img/base/pymod/wrap_extent_iterator.hh
+++ b/modules/img/base/pymod/wrap_extent_iterator.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/pymod/wrap_img.cc b/modules/img/base/pymod/wrap_img.cc
index f89f14e95eda56af6de0be53a27bca8db4a6ffbd..26c1608c29e84acf824375e4b59e1a5c48dc01c4 100644
--- a/modules/img/base/pymod/wrap_img.cc
+++ b/modules/img/base/pymod/wrap_img.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/algorithm.hh b/modules/img/base/src/algorithm.hh
index 4b00bc04465f48f62dc2764dfbccb670f9b54840..e19024a8a885d76a5b9e681e6c5dc0d024ccf358 100644
--- a/modules/img/base/src/algorithm.hh
+++ b/modules/img/base/src/algorithm.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/base.hh b/modules/img/base/src/base.hh
index f5d73f5f4f1aa18f897d6e4710d5108ae7380bbc..eb08e7e2a3fec9dd177f27755fa60272b4c589aa 100644
--- a/modules/img/base/src/base.hh
+++ b/modules/img/base/src/base.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/circle_mask.cc b/modules/img/base/src/circle_mask.cc
index 501177b936f1a222786a72e9eeac572ce7846b5f..8ec006054506fe2bf1ac931901c0da35cc6e2ba9 100644
--- a/modules/img/base/src/circle_mask.cc
+++ b/modules/img/base/src/circle_mask.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/circle_mask.hh b/modules/img/base/src/circle_mask.hh
index 922920079290ce907860df5759f2ac4691b0f230..36e8c74b6b57e9dbc6fa5cf912391769c520e8a1 100644
--- a/modules/img/base/src/circle_mask.hh
+++ b/modules/img/base/src/circle_mask.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/composite_mask.cc b/modules/img/base/src/composite_mask.cc
index 80a0a57cd8c19635825510399d63ca6f7a795ec7..eeb3553b9dc75f4b54f2674aa5917eddea027f29 100644
--- a/modules/img/base/src/composite_mask.cc
+++ b/modules/img/base/src/composite_mask.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/composite_mask.hh b/modules/img/base/src/composite_mask.hh
index 64d04fd13d23ae22496537ae292a96b5b2959015..fc67a847b18142c209385a97a7264b174f82cc11 100644
--- a/modules/img/base/src/composite_mask.hh
+++ b/modules/img/base/src/composite_mask.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/data.cc b/modules/img/base/src/data.cc
index 47c00ba80919a443a6e4f1cf0d928fc496e1e893..65bdea8c0d62678f8ea6d5538c49780166e7fc41 100644
--- a/modules/img/base/src/data.cc
+++ b/modules/img/base/src/data.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/data.hh b/modules/img/base/src/data.hh
index 3ab5d6063a93e997ff1f94981ffd236f7a3ba2a6..8c7f492d30e16598b43670bf29514be6058aa3c5 100644
--- a/modules/img/base/src/data.hh
+++ b/modules/img/base/src/data.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/data_algorithm.cc b/modules/img/base/src/data_algorithm.cc
index cb581c5f6abf53ea324fe27dece0139977a2ee5d..3cfe86026e6a11e9af44adf9a9136d010efa2b08 100644
--- a/modules/img/base/src/data_algorithm.cc
+++ b/modules/img/base/src/data_algorithm.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/data_algorithm.hh b/modules/img/base/src/data_algorithm.hh
index 02e05ff4cb1ba198c63ee2b134594f526cd40600..0509b9893dcc61c852e048c207cd9df12481bc27 100644
--- a/modules/img/base/src/data_algorithm.hh
+++ b/modules/img/base/src/data_algorithm.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/data_observer.cc b/modules/img/base/src/data_observer.cc
index 4d42d66213ae5e60f4ae131f76229576c0caa957..c8854576b9f8e8c89b58ce8edfa79179931f5079 100644
--- a/modules/img/base/src/data_observer.cc
+++ b/modules/img/base/src/data_observer.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/data_observer.hh b/modules/img/base/src/data_observer.hh
index 0d369a2bdadf2597c60a12e06922b65d91d57cc3..c061a97c3158b5e3facd4c37b2eb65ed0440a6cc 100644
--- a/modules/img/base/src/data_observer.hh
+++ b/modules/img/base/src/data_observer.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/data_types.hh b/modules/img/base/src/data_types.hh
index 234cfaade6a3a28b65450b757968e7886f437ac0..ae1563cc51af3813f4ac9d21b292a04fa047e9a0 100644
--- a/modules/img/base/src/data_types.hh
+++ b/modules/img/base/src/data_types.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/debug.hh b/modules/img/base/src/debug.hh
index 13b90f4d311abe58f0f7c3cfa2c6e97f05049856..b6ee88dd1626169cde887de8bad0a44cb7a0e6b6 100644
--- a/modules/img/base/src/debug.hh
+++ b/modules/img/base/src/debug.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/dllexport.hh b/modules/img/base/src/dllexport.hh
index 3f32d13d89dbb9138b6259699b766de11d1bbd10..f6ceff5da74c2d3d3d85b3d2006d9a8572b61398 100644
--- a/modules/img/base/src/dllexport.hh
+++ b/modules/img/base/src/dllexport.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/extent.cc b/modules/img/base/src/extent.cc
index 492c4ccb0f69bcc7281983581253f0a9d86cc0b7..608c9892f0e8555a03e4bfbe5e7415e169b14031 100644
--- a/modules/img/base/src/extent.cc
+++ b/modules/img/base/src/extent.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/extent.hh b/modules/img/base/src/extent.hh
index 7d6d0afad475ec3fa9729d8ec372f75de5727a32..16978d96ef627ce10328c20f68448549e90844c1 100644
--- a/modules/img/base/src/extent.hh
+++ b/modules/img/base/src/extent.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/extent_iterator.cc b/modules/img/base/src/extent_iterator.cc
index 238b680b823933e5052fd4e5cd22f4c8fea2e87e..e1e566bfaf19e992df79b4d982cd32ad6780be6c 100644
--- a/modules/img/base/src/extent_iterator.cc
+++ b/modules/img/base/src/extent_iterator.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/extent_iterator.hh b/modules/img/base/src/extent_iterator.hh
index 56b2f68b936765a900feef0f0de449ff627eef60..e2349c1c3cb2173836d5832e168419b3b9d1a2e1 100644
--- a/modules/img/base/src/extent_iterator.hh
+++ b/modules/img/base/src/extent_iterator.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/extent_mask.cc b/modules/img/base/src/extent_mask.cc
index bf8fbb45383bf37219eed374807be2f043de0c7b..b3674bf652791ade2c47fae422f7cc4ddb54d3ef 100644
--- a/modules/img/base/src/extent_mask.cc
+++ b/modules/img/base/src/extent_mask.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/extent_mask.hh b/modules/img/base/src/extent_mask.hh
index bbc17548c2e80002871b39fc5184c47ff2365ab6..1e6220e7037fb16c2be68456006813c586e48886 100644
--- a/modules/img/base/src/extent_mask.hh
+++ b/modules/img/base/src/extent_mask.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/image.hh b/modules/img/base/src/image.hh
index dba4fd7585a43de0aaa351c85faa73eb3e49555f..79bdc308a57a6a0a2815efd9aae410647693b478 100644
--- a/modules/img/base/src/image.hh
+++ b/modules/img/base/src/image.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/image_factory.cc b/modules/img/base/src/image_factory.cc
index e3838fd6b6a5e8042d136bfa16bc015773ff11ea..6e15920b224e8b35bdb8512b5833e6d5c96e5fc4 100644
--- a/modules/img/base/src/image_factory.cc
+++ b/modules/img/base/src/image_factory.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/image_factory.hh b/modules/img/base/src/image_factory.hh
index 101a562a21ded7c8100d597cbaef5f6a2e7776f7..ad921f7d99d65f14abefc1f9737efb8f059d4d31 100644
--- a/modules/img/base/src/image_factory.hh
+++ b/modules/img/base/src/image_factory.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/image_fw.hh b/modules/img/base/src/image_fw.hh
index 03b877c117b8c083223799f62a2998dae33ca256..6bbf1bda63e473161ceb702381dda29c7d81748b 100644
--- a/modules/img/base/src/image_fw.hh
+++ b/modules/img/base/src/image_fw.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/image_handle.cc b/modules/img/base/src/image_handle.cc
index fe84239cd624c3c3e6584151ddff9ecf1dffca3d..9303835bfb50dff7c01713dd7971d41635dfb022 100644
--- a/modules/img/base/src/image_handle.cc
+++ b/modules/img/base/src/image_handle.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/image_handle.hh b/modules/img/base/src/image_handle.hh
index 847d897c40b88b7ed3bf0c31516e048c922c967c..3d7261f9ceafc45b6cdb8b3b044d6ed52bb53fff 100644
--- a/modules/img/base/src/image_handle.hh
+++ b/modules/img/base/src/image_handle.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/image_handle_fw.hh b/modules/img/base/src/image_handle_fw.hh
index f91784055a6fe443fab9ac6f15576888ac18188f..3e88fbbdd5e8a3ce3714aaa2e4bffee1bcf649b1 100644
--- a/modules/img/base/src/image_handle_fw.hh
+++ b/modules/img/base/src/image_handle_fw.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/image_impl.cc b/modules/img/base/src/image_impl.cc
index 6feb304b19fa88fa7b6787acb192466105e829d1..f1e4bd278a2229ea61787290c676d262ac364dd1 100644
--- a/modules/img/base/src/image_impl.cc
+++ b/modules/img/base/src/image_impl.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/image_impl.hh b/modules/img/base/src/image_impl.hh
index 3b885a0fb93c07cbf76bfa4f6ef5f7c6af27d62f..6cd6f15c65290995942eef98c438d1396d0f19c8 100644
--- a/modules/img/base/src/image_impl.hh
+++ b/modules/img/base/src/image_impl.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/image_list.cc b/modules/img/base/src/image_list.cc
index 522e5f7af76c67f2b171ec5ad6f07e9782adef4c..74fe70e1a0bd89694c85bbeeda8073fb2d642ae9 100644
--- a/modules/img/base/src/image_list.cc
+++ b/modules/img/base/src/image_list.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/image_list.hh b/modules/img/base/src/image_list.hh
index 43314701376a1a550918eebb83c2c5f2f97df99e..1b2248f04ef2e61dbe4f3963b4ccf03bbb1c1a4d 100644
--- a/modules/img/base/src/image_list.hh
+++ b/modules/img/base/src/image_list.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/image_state.hh b/modules/img/base/src/image_state.hh
index 6a519b9bf8fdd8747462596fad0c8f7b15e9a81f..1bcecb2bd46a40bd6ce5565249e0ea46b90dfb4b 100644
--- a/modules/img/base/src/image_state.hh
+++ b/modules/img/base/src/image_state.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/image_state/dispatch.hh b/modules/img/base/src/image_state/dispatch.hh
index c0dd863036a28158f6bb582a914f72c1d07b6316..3e6fcb3a3fc3b2badffb8c3b1096a8dc841ec299 100644
--- a/modules/img/base/src/image_state/dispatch.hh
+++ b/modules/img/base/src/image_state/dispatch.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/image_state/image_state.hh b/modules/img/base/src/image_state/image_state.hh
index 28dab6fdfba5a9160423a45ac032beb59986aa7b..0dc05b585b07b3d276e1e87b465bb8cd3508d847 100644
--- a/modules/img/base/src/image_state/image_state.hh
+++ b/modules/img/base/src/image_state/image_state.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/image_state/image_state_algorithm.cc b/modules/img/base/src/image_state/image_state_algorithm.cc
index 12da6444f63e082ea37e983d1a43430564f762d0..cdcde6836908d9517aa5e88b973e8701b74fc606 100644
--- a/modules/img/base/src/image_state/image_state_algorithm.cc
+++ b/modules/img/base/src/image_state/image_state_algorithm.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/image_state/image_state_algorithm.hh b/modules/img/base/src/image_state/image_state_algorithm.hh
index 54a4b939ebb48e56b1abd32c24e090a77aac4418..3b3027d1f5148a2dceaec92c25edd917ef05946e 100644
--- a/modules/img/base/src/image_state/image_state_algorithm.hh
+++ b/modules/img/base/src/image_state/image_state_algorithm.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/image_state/image_state_base.cc b/modules/img/base/src/image_state/image_state_base.cc
index 2c96b2f868a3101fe92aadf637c176e7c6138434..c829d841d4ca6ff80256e434144ce1853eb0b8b4 100644
--- a/modules/img/base/src/image_state/image_state_base.cc
+++ b/modules/img/base/src/image_state/image_state_base.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/image_state/image_state_base.hh b/modules/img/base/src/image_state/image_state_base.hh
index 34fc74e61d9a531807763a5b2f633f4c486ff3bf..394fb0d6423e418956b0ceb4613a3d84ac861e02 100644
--- a/modules/img/base/src/image_state/image_state_base.hh
+++ b/modules/img/base/src/image_state/image_state_base.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/image_state/image_state_base_fw.hh b/modules/img/base/src/image_state/image_state_base_fw.hh
index d32edb98d29a219c4cf24de2192f82e92b887cd3..5be50dc6097137dcfe86b374e8c59bdc110bb8a3 100644
--- a/modules/img/base/src/image_state/image_state_base_fw.hh
+++ b/modules/img/base/src/image_state/image_state_base_fw.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/image_state/image_state_def.hh b/modules/img/base/src/image_state/image_state_def.hh
index 0749e4be2f8cb14d94c178b0428efc7e3f135932..f4c291e485909c7f7a7f13f18c01e94738050a80 100644
--- a/modules/img/base/src/image_state/image_state_def.hh
+++ b/modules/img/base/src/image_state/image_state_def.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/image_state/image_state_factory.cc b/modules/img/base/src/image_state/image_state_factory.cc
index 32d00ed40c8bd50d40757c835d6e99f5696bb5ae..60b4cc96794b9ac833ed5d3e623146c54b35574d 100644
--- a/modules/img/base/src/image_state/image_state_factory.cc
+++ b/modules/img/base/src/image_state/image_state_factory.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/image_state/image_state_factory.hh b/modules/img/base/src/image_state/image_state_factory.hh
index 67e72957474d6c9b81edba9ff70e262fe0a6fee9..15bdd7a2f41d3bc740f1796fb008b8fd7df4bd71 100644
--- a/modules/img/base/src/image_state/image_state_factory.hh
+++ b/modules/img/base/src/image_state/image_state_factory.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/image_state/image_state_fft.cc b/modules/img/base/src/image_state/image_state_fft.cc
index 37120dd31e252bd63a92512702e7a5a03d8af3a6..b7b774e075ef354bace0b8a29a8e6e55a663ba97 100644
--- a/modules/img/base/src/image_state/image_state_fft.cc
+++ b/modules/img/base/src/image_state/image_state_fft.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/image_state/image_state_fft.hh b/modules/img/base/src/image_state/image_state_fft.hh
index 50ef49fed209a53120ce3897f40cb11b16243ef2..d77a3cd3652a8f01ad6f03afc8d482f47b04d72a 100644
--- a/modules/img/base/src/image_state/image_state_fft.hh
+++ b/modules/img/base/src/image_state/image_state_fft.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/image_state/image_state_frequency_domain.hh b/modules/img/base/src/image_state/image_state_frequency_domain.hh
index 0b5e4e6018b3c12697ddede6e2b57d63c61ebb9a..5faf04b6478e392963aee8bbaac2a33defe54960 100644
--- a/modules/img/base/src/image_state/image_state_frequency_domain.hh
+++ b/modules/img/base/src/image_state/image_state_frequency_domain.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/image_state/image_state_fw.hh b/modules/img/base/src/image_state/image_state_fw.hh
index 3783caec51af0e7dbdea8ed6dbc86768be6c20c9..7f6b2af98cc79ba2711a207cf8d56b85338b7d72 100644
--- a/modules/img/base/src/image_state/image_state_fw.hh
+++ b/modules/img/base/src/image_state/image_state_fw.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/image_state/image_state_half_frequency_domain.hh b/modules/img/base/src/image_state/image_state_half_frequency_domain.hh
index 2726358d6d05540262d6c7eb6d924f91bf0cb48d..2628e7695a1bac094c8ece9736fc1b9676b68ac8 100644
--- a/modules/img/base/src/image_state/image_state_half_frequency_domain.hh
+++ b/modules/img/base/src/image_state/image_state_half_frequency_domain.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/image_state/image_state_impl.cc b/modules/img/base/src/image_state/image_state_impl.cc
index 352d710f6d35ccf4a2c1a2ae3231c8031067eea6..d743f923599be7c98fdfdc94e85a939c49062d3c 100644
--- a/modules/img/base/src/image_state/image_state_impl.cc
+++ b/modules/img/base/src/image_state/image_state_impl.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/image_state/image_state_impl.hh b/modules/img/base/src/image_state/image_state_impl.hh
index 0f8dad75bd378675423715c293d7dcdac4378949..ca5eb571732c6ffd01e806b23b9641294d87ec65 100644
--- a/modules/img/base/src/image_state/image_state_impl.hh
+++ b/modules/img/base/src/image_state/image_state_impl.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/image_state/image_state_inst.hh b/modules/img/base/src/image_state/image_state_inst.hh
index 3d0a8472bab7b3fda21a9f89c8f9a0426b83a544..a00d58da2a8ed4bf949197975053b75eb360e042 100644
--- a/modules/img/base/src/image_state/image_state_inst.hh
+++ b/modules/img/base/src/image_state/image_state_inst.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/image_state/image_state_spatial_domain.hh b/modules/img/base/src/image_state/image_state_spatial_domain.hh
index a8b22ff5e3905faf3ddd67deff511694f9ce914b..3d70607d9f4423640e9dff165ad5857b6f593c1c 100644
--- a/modules/img/base/src/image_state/image_state_spatial_domain.hh
+++ b/modules/img/base/src/image_state/image_state_spatial_domain.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/image_state/image_state_visitor.hh b/modules/img/base/src/image_state/image_state_visitor.hh
index 64fdadb3f29cb2344f02b689bd113f80eeac48ab..c5a74904d7e797c52515774354a4d30341951dd3 100644
--- a/modules/img/base/src/image_state/image_state_visitor.hh
+++ b/modules/img/base/src/image_state/image_state_visitor.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/image_state/image_state_visitor_fw.hh b/modules/img/base/src/image_state/image_state_visitor_fw.hh
index a83820aa162450c1b1b88b9b89e5e2593fb0a0ae..3607590afa91d5ac9a8d7ce18005be16de3e9716 100644
--- a/modules/img/base/src/image_state/image_state_visitor_fw.hh
+++ b/modules/img/base/src/image_state/image_state_visitor_fw.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/image_state/index.cc b/modules/img/base/src/image_state/index.cc
index 27974200e4671e3c5f5b0ff11b80ebd176ad26b8..13fdb9ac90a1f38e1dbf22c7263561369d27620f 100644
--- a/modules/img/base/src/image_state/index.cc
+++ b/modules/img/base/src/image_state/index.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/image_state/index.hh b/modules/img/base/src/image_state/index.hh
index 8f7e8c6ee62acd1d219613036fd8668a8930c6d1..a33e9d350c32c33e2caa9168fe7a0d10d0fc89ca 100644
--- a/modules/img/base/src/image_state/index.hh
+++ b/modules/img/base/src/image_state/index.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/image_state/test_inst.cc b/modules/img/base/src/image_state/test_inst.cc
index 37a3cbd909fd88685ab41e2f601f5091dd9a455a..4544b49dc4ce79b7a7555a48957eec19a14e7c88 100644
--- a/modules/img/base/src/image_state/test_inst.cc
+++ b/modules/img/base/src/image_state/test_inst.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/image_state/type_fw.hh b/modules/img/base/src/image_state/type_fw.hh
index 2e59892bd8d4d2e4f088773e08b54a4cd27eab57..81e082340d47c86973151a1db0370e57852592ff 100644
--- a/modules/img/base/src/image_state/type_fw.hh
+++ b/modules/img/base/src/image_state/type_fw.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/image_state/value_holder.cc b/modules/img/base/src/image_state/value_holder.cc
index 1eaf3c77a1b7f7eba18343eeeada4206d4537e54..003b68470aea5d38644a4cb3f818cef16022c449 100644
--- a/modules/img/base/src/image_state/value_holder.cc
+++ b/modules/img/base/src/image_state/value_holder.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/image_state/value_holder.hh b/modules/img/base/src/image_state/value_holder.hh
index 05f9cb384313df8ac39e765472643e1d869f5e8a..22c7023bb47598d57901230e04c6afa0d82edac4 100644
--- a/modules/img/base/src/image_state/value_holder.hh
+++ b/modules/img/base/src/image_state/value_holder.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/image_state_fw.hh b/modules/img/base/src/image_state_fw.hh
index 12be417eef96e3eea3549253292e889da6d84196..3c5492f084a6eb5f15d275820e43b2049e279637 100644
--- a/modules/img/base/src/image_state_fw.hh
+++ b/modules/img/base/src/image_state_fw.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/inverted_mask.cc b/modules/img/base/src/inverted_mask.cc
index b38bfe57f2b7726c83a815668997efd42316598e..a680121a536e7da54b217ff4c6ee50c8a0cd48d5 100644
--- a/modules/img/base/src/inverted_mask.cc
+++ b/modules/img/base/src/inverted_mask.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/inverted_mask.hh b/modules/img/base/src/inverted_mask.hh
index a4dfd4774b785ae8f323051850b02eb763f4a3f7..6401257ea66964fe9e4cadd4acbd41d57da11661 100644
--- a/modules/img/base/src/inverted_mask.hh
+++ b/modules/img/base/src/inverted_mask.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/map.cc b/modules/img/base/src/map.cc
index 8f1a0a087aab54e0cf77636e32887c4e1788f8d5..1a946efb266fe0965557931a4e3f2c861cd57619 100644
--- a/modules/img/base/src/map.cc
+++ b/modules/img/base/src/map.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/img/base/src/map.hh b/modules/img/base/src/map.hh
index 231a4d1d14dd42e69b98b50365964d3adfc7bbd4..8a8959a0daded1cc97dfdb439d1775fd82b141c8 100644
--- a/modules/img/base/src/map.hh
+++ b/modules/img/base/src/map.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/img/base/src/mask.cc b/modules/img/base/src/mask.cc
index feb22bacb613080e916008412d4dc187c90b7691..1f5278f0cad60586d2a0f77de66ac0f4617f0a68 100644
--- a/modules/img/base/src/mask.cc
+++ b/modules/img/base/src/mask.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/mask.hh b/modules/img/base/src/mask.hh
index 6d96125c2d546b91857b28f14202c6aabdf3cabc..45822e1638c85d87c4451cde10504502aae99a63 100644
--- a/modules/img/base/src/mask.hh
+++ b/modules/img/base/src/mask.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/mask_base.cc b/modules/img/base/src/mask_base.cc
index 5f26dc7299e0c44e1069a3b563781d5d86de81f9..9e7c294104c5085892c354ea848afab74b535d34 100644
--- a/modules/img/base/src/mask_base.cc
+++ b/modules/img/base/src/mask_base.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/mask_base.hh b/modules/img/base/src/mask_base.hh
index 4cd5287ea51456760a3ffed1d703b1cb9680ecf1..d13d9a7731e48104dfc31fcc5222d1af24fbe833 100644
--- a/modules/img/base/src/mask_base.hh
+++ b/modules/img/base/src/mask_base.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/mask_base_fw.hh b/modules/img/base/src/mask_base_fw.hh
index cf3879f8746eb30f1f02fbca9b87a8987eea9b86..21d7effdcde4a7d381446a7438dc52f5b87961a0 100644
--- a/modules/img/base/src/mask_base_fw.hh
+++ b/modules/img/base/src/mask_base_fw.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/mask_info_convert.cc b/modules/img/base/src/mask_info_convert.cc
index 847c47d800f76f62bd9b74dbe00d4bbfc6c4b24b..e6e2746cad2aff38bc57cfc385d0a96b7f8f88c5 100644
--- a/modules/img/base/src/mask_info_convert.cc
+++ b/modules/img/base/src/mask_info_convert.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/mask_info_convert.hh b/modules/img/base/src/mask_info_convert.hh
index f25b37a2248133b840ddd29c1dadcd75c4a3da5c..2c1b3f37e16311ab8bdfa311d6e191ab07606209 100644
--- a/modules/img/base/src/mask_info_convert.hh
+++ b/modules/img/base/src/mask_info_convert.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/mask_op.cc b/modules/img/base/src/mask_op.cc
index 434f2abb6b938a5f8b24fc853da80a6c4f01e39f..1cfdbdad88b7f84efee27bbcc3fceb01cc81171a 100644
--- a/modules/img/base/src/mask_op.cc
+++ b/modules/img/base/src/mask_op.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/mask_op.hh b/modules/img/base/src/mask_op.hh
index 5de7c61e4c92d60713a9a9885144d88b7a58e6e6..9342cc52ae8b8b18a7ff91d24db7fc23d82bb419 100644
--- a/modules/img/base/src/mask_op.hh
+++ b/modules/img/base/src/mask_op.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/mask_visitor.hh b/modules/img/base/src/mask_visitor.hh
index 76f6ad8f1f59adf2d32d796c2658574549d61582..8b2214a003b62329e275b60a12605becb87b637b 100644
--- a/modules/img/base/src/mask_visitor.hh
+++ b/modules/img/base/src/mask_visitor.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/module_config.hh b/modules/img/base/src/module_config.hh
index 0387491ff13e659826912886934e73fbbb67de99..db482e1949a8b8c945297ab2f42308d39a729a42 100644
--- a/modules/img/base/src/module_config.hh
+++ b/modules/img/base/src/module_config.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/img/base/src/normalizer_fw.hh b/modules/img/base/src/normalizer_fw.hh
index e602ede1b6e20443962704412cf8a7a955a2a223..510c9cd08274d0f3ffa93eb3aeefb43a58541b96 100644
--- a/modules/img/base/src/normalizer_fw.hh
+++ b/modules/img/base/src/normalizer_fw.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/normalizer_impl.hh b/modules/img/base/src/normalizer_impl.hh
index 0a68b3851f29eab9165ce2b48630dd9b5d1190f8..ca0655a185807a3f6908b40e2b1a78d67939221f 100644
--- a/modules/img/base/src/normalizer_impl.hh
+++ b/modules/img/base/src/normalizer_impl.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/null_data.hh b/modules/img/base/src/null_data.hh
index 3a2d3a86490b858452562f3e048bb177e17b1ba4..4099a9ea8206120c1ff894d8b70b905b5df92db3 100644
--- a/modules/img/base/src/null_data.hh
+++ b/modules/img/base/src/null_data.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/observable.cc b/modules/img/base/src/observable.cc
index 36d52009408a2d470d97cc3edfcf4396ba92ffb2..ef8ad6bec766f273538ddf8ab19e4f28d6a650e4 100644
--- a/modules/img/base/src/observable.cc
+++ b/modules/img/base/src/observable.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/observable.hh b/modules/img/base/src/observable.hh
index 7b8ca63b81b135c88e5d4f9d42a4f6f35a06de55..6329873ffdf50c03a13e7b961054d16a35ec9ee4 100644
--- a/modules/img/base/src/observable.hh
+++ b/modules/img/base/src/observable.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/paste_impl.cc b/modules/img/base/src/paste_impl.cc
index c3f5840b7ad2999cedfe4b89848f8d504328ec0a..c7b7e9c818dcad8a78afd571b1719100e649b30a 100644
--- a/modules/img/base/src/paste_impl.cc
+++ b/modules/img/base/src/paste_impl.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/paste_impl.hh b/modules/img/base/src/paste_impl.hh
index 700a786cd5c2592a09967e44563dfcf276f375bb..865d72e0408a1ccd9876f5b1ed2cae592382dcb9 100644
--- a/modules/img/base/src/paste_impl.hh
+++ b/modules/img/base/src/paste_impl.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/peak.cc b/modules/img/base/src/peak.cc
index 329bd9c7cc280da6032fb0cbbb83a3d7a0cc07e9..417fdc342e0257fae9a096788be3d39962cc3e03 100644
--- a/modules/img/base/src/peak.cc
+++ b/modules/img/base/src/peak.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/peak.hh b/modules/img/base/src/peak.hh
index fd1131ec620f4260c59e47072c76906b15368722..42e25b7a8bda4722518cf7523c8975d805200560 100644
--- a/modules/img/base/src/peak.hh
+++ b/modules/img/base/src/peak.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/phase.cc b/modules/img/base/src/phase.cc
index b50eab4407a61d751b3b24b0acee5b1a0fe68835..8c61d6e3420791c87db78299dc7be58b2804ecc9 100644
--- a/modules/img/base/src/phase.cc
+++ b/modules/img/base/src/phase.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/phase.hh b/modules/img/base/src/phase.hh
index 73bb6a409dac3abfd2b422c5f38942a7b61d8208..94ad9d50ccd50185e7cd374317f3a86cf7ebe3f5 100644
--- a/modules/img/base/src/phase.hh
+++ b/modules/img/base/src/phase.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/physical_units.cc b/modules/img/base/src/physical_units.cc
index 01d0f22cdd54d65d51050d3b964c8838ca1c2638..82671d20605ef9480661376dd142c6ff00947afc 100644
--- a/modules/img/base/src/physical_units.cc
+++ b/modules/img/base/src/physical_units.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/physical_units.hh b/modules/img/base/src/physical_units.hh
index caf0fdda20597ac8ec824733b3d3b2e6b744fcd7..ee3a6c1fa0529ac6ba0eb624f99a2a335647a89f 100644
--- a/modules/img/base/src/physical_units.hh
+++ b/modules/img/base/src/physical_units.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/pixel_sampling.cc b/modules/img/base/src/pixel_sampling.cc
index 2c790e421d05be5f59daae33290fc5dd313205bc..08eda0161b342b0a0d19913abd75d1ac9b17ce10 100644
--- a/modules/img/base/src/pixel_sampling.cc
+++ b/modules/img/base/src/pixel_sampling.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/pixel_sampling.hh b/modules/img/base/src/pixel_sampling.hh
index 73187545039ecb4d3f60708adc76b9668b5f005b..7101fd04f5e0298151fd298dfefb614a8d021b44 100644
--- a/modules/img/base/src/pixel_sampling.hh
+++ b/modules/img/base/src/pixel_sampling.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/point.cc b/modules/img/base/src/point.cc
index 94d1d2914b90dfff950525a5be4cae5070b69c52..2de59687ddb00704875474560a2cb02a272f91e8 100644
--- a/modules/img/base/src/point.cc
+++ b/modules/img/base/src/point.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/point.hh b/modules/img/base/src/point.hh
index 0d9f307e7c5f48d7170ebdece6e07e17f38cc868..757a2d18bd9b09b87bc98389a805ca0770ce4d83 100644
--- a/modules/img/base/src/point.hh
+++ b/modules/img/base/src/point.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/point_list.cc b/modules/img/base/src/point_list.cc
index 559f787b6953cb938389d628f9c0975b711e419b..3fcde1f7a185255804c443644380cc47bfa81cba 100644
--- a/modules/img/base/src/point_list.cc
+++ b/modules/img/base/src/point_list.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/point_list.hh b/modules/img/base/src/point_list.hh
index ca287cb8887c471eff054b777c5ebc92e2188607..d4aa34bea17805a0c6bb2dec99de4db2ea7b64bb 100644
--- a/modules/img/base/src/point_list.hh
+++ b/modules/img/base/src/point_list.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/polygon_mask.cc b/modules/img/base/src/polygon_mask.cc
index 72b9be47e07cbe1d4cb73d8f1473be1e28d205d1..917694895aab6e09892bc638de5ef3234a7b7927 100644
--- a/modules/img/base/src/polygon_mask.cc
+++ b/modules/img/base/src/polygon_mask.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/polygon_mask.hh b/modules/img/base/src/polygon_mask.hh
index 8b8d6827fe2ad49928bcc7b762490e26f6912933..3d5b0eda0d71b9a334ea1dab00f4bd79a4c016a0 100644
--- a/modules/img/base/src/polygon_mask.hh
+++ b/modules/img/base/src/polygon_mask.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/progress.cc b/modules/img/base/src/progress.cc
index 380f93ea13d360ce1ef943f8103693d0d11dbc5a..7eebf7651d2ebc7adf67c62f316180a4fba7081e 100644
--- a/modules/img/base/src/progress.cc
+++ b/modules/img/base/src/progress.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/progress.hh b/modules/img/base/src/progress.hh
index 4af9cfc6b3f2db6ecaf96aa7b67ea2e9bd317ea4..0342b50fd8d7b62a6a9bbacad7af38adddf31430 100644
--- a/modules/img/base/src/progress.hh
+++ b/modules/img/base/src/progress.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/raster_image/raster_image.cc b/modules/img/base/src/raster_image/raster_image.cc
index 44cfdf1a9e2eeb71e2062db5ea1ac5eed3974581..b516838482cb41166fd561848dba83c3e5bde138 100644
--- a/modules/img/base/src/raster_image/raster_image.cc
+++ b/modules/img/base/src/raster_image/raster_image.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/raster_image/raster_image.hh b/modules/img/base/src/raster_image/raster_image.hh
index f27ad4c2a7ee94c716fc79f161fba705996b467a..9c99d6af8fc28365faabda473c51176871dfbe9d 100644
--- a/modules/img/base/src/raster_image/raster_image.hh
+++ b/modules/img/base/src/raster_image/raster_image.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/size.cc b/modules/img/base/src/size.cc
index 97e1fa46001e1365d21fb3b9e2ed67d9c49f6252..09b609dc8639cff8c0923c8ffbe9d720bcc8cd71 100644
--- a/modules/img/base/src/size.cc
+++ b/modules/img/base/src/size.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/size.hh b/modules/img/base/src/size.hh
index e648d11f252990c7345fd95094aae7a440e51743..ef44bca55be875c31a2b86cad91aa22c7f91ec3f 100644
--- a/modules/img/base/src/size.hh
+++ b/modules/img/base/src/size.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/spherical_mask.cc b/modules/img/base/src/spherical_mask.cc
index 26258de7438b0d07561e3b91026c46a34b706cc8..0790879d6977cc14ee4b2828d4de6b9918aef93f 100644
--- a/modules/img/base/src/spherical_mask.cc
+++ b/modules/img/base/src/spherical_mask.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/spherical_mask.hh b/modules/img/base/src/spherical_mask.hh
index fae8e01835aa23a8f65efd3ba19b7062bcfb7231..5785cc5aa7ce48a87021eb0474de269f4b3403db 100644
--- a/modules/img/base/src/spherical_mask.hh
+++ b/modules/img/base/src/spherical_mask.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/util.cc b/modules/img/base/src/util.cc
index bbe25ac0cc11248155f6756ee29c11358f61e763..b8a08132674bd68ce04827e43e001d8e32f5a57f 100644
--- a/modules/img/base/src/util.cc
+++ b/modules/img/base/src/util.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/util.hh b/modules/img/base/src/util.hh
index 8436553fced8c570bda7747493ae8a93c45c4085..0e10a2e3e72a1511d870320e43a670501320db35 100644
--- a/modules/img/base/src/util.hh
+++ b/modules/img/base/src/util.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/value_util.hh b/modules/img/base/src/value_util.hh
index 045ccf97f3148ce55e906625076108d0a27e08b7..a475cc1cb7b720af46e5ad63e1ee7f2808500175 100644
--- a/modules/img/base/src/value_util.hh
+++ b/modules/img/base/src/value_util.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/src/vecmat.hh b/modules/img/base/src/vecmat.hh
index 92815608be5386cae18add3570913f994fab2a2a..b7508ce9093251e28b14cd297d873fe2523e336d 100644
--- a/modules/img/base/src/vecmat.hh
+++ b/modules/img/base/src/vecmat.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/tests/simple_test.cc b/modules/img/base/tests/simple_test.cc
index fc659113385f4a10ccb52e0dad9c85ae76724520..066e033bb23d1b0e6381629016f480c817f61fa4 100644
--- a/modules/img/base/tests/simple_test.cc
+++ b/modules/img/base/tests/simple_test.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/tests/single_test_image_handle_mem.cc b/modules/img/base/tests/single_test_image_handle_mem.cc
index 4ae6cb1b26319a985739ebd4945b2ba87f4f56a6..64456854b8a99d1ed2e2cb5aeb4906625a66866e 100644
--- a/modules/img/base/tests/single_test_image_handle_mem.cc
+++ b/modules/img/base/tests/single_test_image_handle_mem.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/tests/test_data.cc b/modules/img/base/tests/test_data.cc
index b9700fc814beda8dd3f71c54bde4cbd4f3acc74d..af7313be4754dc8b7507cebd8ff1165d05a95d30 100644
--- a/modules/img/base/tests/test_data.cc
+++ b/modules/img/base/tests/test_data.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/tests/test_data.hh b/modules/img/base/tests/test_data.hh
index cd87ed0e7e0de8f5240f76bc2397ae08c2b5cbc4..c8adeae849e4c7970c69b63d43c14000a57bfb61 100644
--- a/modules/img/base/tests/test_data.hh
+++ b/modules/img/base/tests/test_data.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/tests/test_domains.cc b/modules/img/base/tests/test_domains.cc
index 00357322ca3141f212d7e94f261c32235098527f..099fec5c61cde93b0724995344f637951c2142bd 100644
--- a/modules/img/base/tests/test_domains.cc
+++ b/modules/img/base/tests/test_domains.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/tests/test_extent.cc b/modules/img/base/tests/test_extent.cc
index c6430782f2e9fa23e38e77b8a246fbe972d9b0bc..78cbafb45c22a2fcd7147f3b2ff76269047cf8b2 100644
--- a/modules/img/base/tests/test_extent.cc
+++ b/modules/img/base/tests/test_extent.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/tests/test_extent.hh b/modules/img/base/tests/test_extent.hh
index 2018095cccfe98f17613582bfb63cbce3086147a..5bbe985fe79df32adf376bab40733628439a57d8 100644
--- a/modules/img/base/tests/test_extent.hh
+++ b/modules/img/base/tests/test_extent.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/tests/test_image.cc b/modules/img/base/tests/test_image.cc
index 8d5d2e1db1fdc0c7c9bac2e524dbebcdbfd29195..a038c2b6e60414e1f75bb554d5450129dca53108 100644
--- a/modules/img/base/tests/test_image.cc
+++ b/modules/img/base/tests/test_image.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/tests/test_image.hh b/modules/img/base/tests/test_image.hh
index 9dcc187e3d4fe65d5613345b7c6e91f66852c6b0..e7533359d2f6a7f837102523d2e7d6778e344695 100644
--- a/modules/img/base/tests/test_image.hh
+++ b/modules/img/base/tests/test_image.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/tests/test_image_impl.cc b/modules/img/base/tests/test_image_impl.cc
index 07324c71c6baf02cd262f1f1ab535ceb11a3593a..c62385413b44a3403699c37f1063c9ae27d2e36b 100644
--- a/modules/img/base/tests/test_image_impl.cc
+++ b/modules/img/base/tests/test_image_impl.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/tests/test_image_impl.hh b/modules/img/base/tests/test_image_impl.hh
index 053a7ecfab5213f0926c7bd6bc30139c3fbb93f6..9a1489dc2b26b5ef50b64596aebae247550f12a4 100644
--- a/modules/img/base/tests/test_image_impl.hh
+++ b/modules/img/base/tests/test_image_impl.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/tests/test_image_state.cc b/modules/img/base/tests/test_image_state.cc
index 47a290b7e53ed50176a3316748dd18803fddca01..979758618523b1c959eff219123e74f2e5159a99 100644
--- a/modules/img/base/tests/test_image_state.cc
+++ b/modules/img/base/tests/test_image_state.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/tests/test_image_state.hh b/modules/img/base/tests/test_image_state.hh
index 0a8f9962242f1e0f58ca74bbe1d3baf444384596..3f4d1b4e8e7c95f6ae5f74fd8066dc5cf980256c 100644
--- a/modules/img/base/tests/test_image_state.hh
+++ b/modules/img/base/tests/test_image_state.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/tests/test_image_state_visitor.cc b/modules/img/base/tests/test_image_state_visitor.cc
index a093c3efa161e3c992d4708b0292180d835fd748..57cd30af3885290cd53ade710541418faad325da 100644
--- a/modules/img/base/tests/test_image_state_visitor.cc
+++ b/modules/img/base/tests/test_image_state_visitor.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/tests/test_image_state_visitor.hh b/modules/img/base/tests/test_image_state_visitor.hh
index 4ae162a7b8c0e632630a15aaf9bea9105cc3c4cc..1581c59077f01cabc758a056bc8f90de36402204 100644
--- a/modules/img/base/tests/test_image_state_visitor.hh
+++ b/modules/img/base/tests/test_image_state_visitor.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/tests/test_index.cc b/modules/img/base/tests/test_index.cc
index 3fa1490c4d8522bd19ed0f1bcb0889eda3b6b64b..dab46136ae97a5f4f3a701c5bbbf2c3cb4069db6 100644
--- a/modules/img/base/tests/test_index.cc
+++ b/modules/img/base/tests/test_index.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/tests/test_index.hh b/modules/img/base/tests/test_index.hh
index dced5481d12079f0d1547fd250276434d1d11147..001bfb4d4e70f9c563c8e208366f3e20fd7f35f7 100644
--- a/modules/img/base/tests/test_index.hh
+++ b/modules/img/base/tests/test_index.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/tests/test_point.cc b/modules/img/base/tests/test_point.cc
index 2a7891c3209a9f2dc6c58f9972b4d4b44a1db365..6ad97d530bd0b13b1ea3dc6226e347371d55e770 100644
--- a/modules/img/base/tests/test_point.cc
+++ b/modules/img/base/tests/test_point.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/tests/test_point.hh b/modules/img/base/tests/test_point.hh
index f7aca6252d5bd4a47ca6572de8f187c62de6a17e..743c1acf7f6ef28c6629f989bbb3b8dc95986c80 100644
--- a/modules/img/base/tests/test_point.hh
+++ b/modules/img/base/tests/test_point.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/tests/test_sampling.cc b/modules/img/base/tests/test_sampling.cc
index 9da2212591f7a8114d8d029c1300389811e224a7..7d85b2cd1418394431c8d49906b1637e45169454 100644
--- a/modules/img/base/tests/test_sampling.cc
+++ b/modules/img/base/tests/test_sampling.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/tests/test_sampling.hh b/modules/img/base/tests/test_sampling.hh
index dea44e1d6be82becb3654b7ce03efc9a09687c85..9774715f154638706334815cc392d6efe861a201 100644
--- a/modules/img/base/tests/test_sampling.hh
+++ b/modules/img/base/tests/test_sampling.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/tests/test_size.cc b/modules/img/base/tests/test_size.cc
index 6ad36ac838bb79d1d42131928ee1e36ca4c41ea2..2269a5d28e78a2af76ba29270fa60c1b3b0ca82e 100644
--- a/modules/img/base/tests/test_size.cc
+++ b/modules/img/base/tests/test_size.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/tests/test_size.hh b/modules/img/base/tests/test_size.hh
index 9840cee0cf0c9271082497414f9dc7bf4727c47c..25d2d0c867734074fb6b85184bfa59a623cf9469 100644
--- a/modules/img/base/tests/test_size.hh
+++ b/modules/img/base/tests/test_size.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/tests/test_transform.hh b/modules/img/base/tests/test_transform.hh
index 9f76073d49dd73e16ae60e7f830cd6f5dbfba95f..fa41d86524236ddac87efc85cf54831cf7c1f968 100644
--- a/modules/img/base/tests/test_transform.hh
+++ b/modules/img/base/tests/test_transform.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/tests/test_utils.hh b/modules/img/base/tests/test_utils.hh
index 6af2dd3c0ea2b10e2988c3966d1dce27dc74b778..465c6bae015636770f24743ac0aa55f2d998f208 100644
--- a/modules/img/base/tests/test_utils.hh
+++ b/modules/img/base/tests/test_utils.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/tests/test_value_holder.cc b/modules/img/base/tests/test_value_holder.cc
index bd0cacbd6ba76084ea7933717ff47a308dc15136..36ed0c9e3dc0f72b1140d6a33f763ed480a966f2 100644
--- a/modules/img/base/tests/test_value_holder.cc
+++ b/modules/img/base/tests/test_value_holder.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/tests/test_value_holder.hh b/modules/img/base/tests/test_value_holder.hh
index ab1e6d879ff73bfeb6410a6ce4fbf9b9e71ce3b6..eb422652d02aa3e2dba74f8979a5de8320f0cb66 100644
--- a/modules/img/base/tests/test_value_holder.hh
+++ b/modules/img/base/tests/test_value_holder.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/img/base/tests/tests.cc b/modules/img/base/tests/tests.cc
index 161687ebee631fcabb08218358556c594363862c..2040417cb1a0b15d59702b6cbaf08b53cddc0726 100644
--- a/modules/img/base/tests/tests.cc
+++ b/modules/img/base/tests/tests.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/info/pymod/__init__.py b/modules/info/pymod/__init__.py
index 4243e15ac1f0a1f129535918388d15e1c58d1b11..a46082e98e3d0fc22aeb43f4b198653ec05285ed 100644
--- a/modules/info/pymod/__init__.py
+++ b/modules/info/pymod/__init__.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
@@ -16,7 +16,7 @@
# along with this library; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
#------------------------------------------------------------------------------
-from _ost_info import *
+from ._ost_info import *
def LoadOrCreateInfo(name):
import os.path
diff --git a/modules/info/pymod/wrap_info.cc b/modules/info/pymod/wrap_info.cc
index cf15c736d937cccbd6f910e3646aba3c8448d97a..1a6bf12488845f3194b9fcd8373373981668c142 100644
--- a/modules/info/pymod/wrap_info.cc
+++ b/modules/info/pymod/wrap_info.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/info/src/geom_info_conversion.cc b/modules/info/src/geom_info_conversion.cc
index 8e5711904bb103d9ce0237b051e7c799bb0071e9..e73b9e6524f1010f65e75b6e92add3308ec7e806 100644
--- a/modules/info/src/geom_info_conversion.cc
+++ b/modules/info/src/geom_info_conversion.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/info/src/geom_info_conversion.hh b/modules/info/src/geom_info_conversion.hh
index bab90abec02b82cfbf701a75dcd258db88b9bbaa..83584eda973673f91d1b376b635b2c8e53f57df8 100644
--- a/modules/info/src/geom_info_conversion.hh
+++ b/modules/info/src/geom_info_conversion.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/info/src/info.hh b/modules/info/src/info.hh
index fdb365a7ff3523758d6eef777bf84d6036efa1d9..1981f7a6cfda1089c823594ade75fb19ffa9c44f 100644
--- a/modules/info/src/info.hh
+++ b/modules/info/src/info.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/info/src/info_error.hh b/modules/info/src/info_error.hh
index 6464cbb3895e232a29b32ba12746b5a7beac7a59..7d74b3f86d4ec2aa1c21264f1a1291e835fcfe2b 100644
--- a/modules/info/src/info_error.hh
+++ b/modules/info/src/info_error.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/info/src/info_fw.hh b/modules/info/src/info_fw.hh
index 2483d6487f4f125b9e276e003255705e6306fe88..8250d8afd034a0e7996f7ac9819b3e398ab1a084 100644
--- a/modules/info/src/info_fw.hh
+++ b/modules/info/src/info_fw.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/info/src/info_group.cc b/modules/info/src/info_group.cc
index 2ed933084b985e53d920bddba28acf42ee00c286..023cef9109f5ef1f5a09af3592f7cea4a0dcc8c9 100644
--- a/modules/info/src/info_group.cc
+++ b/modules/info/src/info_group.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/info/src/info_group.hh b/modules/info/src/info_group.hh
index d0823edf85fbee95a3d0b9c09df378388b1cc429..449ce728d947791793428e411cec4b5734ff3168 100644
--- a/modules/info/src/info_group.hh
+++ b/modules/info/src/info_group.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/info/src/info_handle.cc b/modules/info/src/info_handle.cc
index 263ae222c9ed261b0de6061631dfb94e98753bee..cc7ce71888e95bef799678d1d5481ea37a74b874 100644
--- a/modules/info/src/info_handle.cc
+++ b/modules/info/src/info_handle.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/info/src/info_handle.hh b/modules/info/src/info_handle.hh
index 30aeda5622715d4892746d2d5be1939074ac1a9b..99dc7e6713b16c4904dc5bc984c74983544ca368 100644
--- a/modules/info/src/info_handle.hh
+++ b/modules/info/src/info_handle.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/info/src/info_impl.cc b/modules/info/src/info_impl.cc
index e556e79ba9bb76cbfb4b1f3ce141fde9833b6e20..d91552d4a00f4ba9525a2b0e1f5700aa19200c56 100644
--- a/modules/info/src/info_impl.cc
+++ b/modules/info/src/info_impl.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/info/src/info_impl.hh b/modules/info/src/info_impl.hh
index 4b3c46be3be1953f79812b0ce892a3f7eb6468fc..40aa9f7ed0ce89e52a1bd05091a2bea462b20c75 100644
--- a/modules/info/src/info_impl.hh
+++ b/modules/info/src/info_impl.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/info/src/info_impl_fw.hh b/modules/info/src/info_impl_fw.hh
index 9e24085f0b03aec9217eca3b8e8751306879beac..95155280d9561633f906cde36015432fb6f5cdcd 100644
--- a/modules/info/src/info_impl_fw.hh
+++ b/modules/info/src/info_impl_fw.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/info/src/info_item.cc b/modules/info/src/info_item.cc
index d3317eb001d9a8a092a056c79b03bfe60435ecf8..8eb5d393feb03ad424047d91bd759e64dc54509d 100644
--- a/modules/info/src/info_item.cc
+++ b/modules/info/src/info_item.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/info/src/info_item.hh b/modules/info/src/info_item.hh
index 9036727c55ab23c7b2b0cb05ad7ed464ba342112..2a1e25514c776ee375cb6adc72a72fe4cf2aa095 100644
--- a/modules/info/src/info_item.hh
+++ b/modules/info/src/info_item.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/info/src/info_path.cc b/modules/info/src/info_path.cc
index 24e862d72c6ebc31e6d09eee2f666182b6b43e3d..1091a106fc6210c2e5e8f4d74df460d846fea7db 100644
--- a/modules/info/src/info_path.cc
+++ b/modules/info/src/info_path.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/info/src/info_path.hh b/modules/info/src/info_path.hh
index 2cca7e5fd9d32d1905050681135136547066fc6a..78a12b06ea224f2669481d297fcf1c73b326512d 100644
--- a/modules/info/src/info_path.hh
+++ b/modules/info/src/info_path.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/info/src/info_set.cc b/modules/info/src/info_set.cc
index 9cfd9d6ac1db02be7dca20354a6d819fe7f03f3e..573aa8c6bb49f50e6fe6803d52e3cfd68c1c7c10 100644
--- a/modules/info/src/info_set.cc
+++ b/modules/info/src/info_set.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/info/src/info_set.hh b/modules/info/src/info_set.hh
index fe8421a8f1e4e3f71ba32b253b7990ad6ae23dfb..1a985760a8c593b2b43e076937048105ab944ef5 100644
--- a/modules/info/src/info_set.hh
+++ b/modules/info/src/info_set.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/info/src/info_verbose_visitor.cc b/modules/info/src/info_verbose_visitor.cc
index cf778aae9f134f6dda6a30decf94676a3a140b24..a94e2b984b1c4193319bb6f5c491cc99b6bb362f 100644
--- a/modules/info/src/info_verbose_visitor.cc
+++ b/modules/info/src/info_verbose_visitor.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/info/src/info_verbose_visitor.hh b/modules/info/src/info_verbose_visitor.hh
index 6e68fde8f7d06fad5aecbc69329d38b473527386..a7b34d206824b1a89bc2ba99911e6be6185ee871 100644
--- a/modules/info/src/info_verbose_visitor.hh
+++ b/modules/info/src/info_verbose_visitor.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/info/src/info_visitor.cc b/modules/info/src/info_visitor.cc
index 1646812706d38feb803c72989c90b0c1066fbba0..84c071f29efcf6a57c827775fcdc95c6fbd79354 100644
--- a/modules/info/src/info_visitor.cc
+++ b/modules/info/src/info_visitor.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/info/src/info_visitor.hh b/modules/info/src/info_visitor.hh
index 2db76766702aee2a3b11eb6686b9f4c1174272b7..a78bf4911c93295c0230570904d4b2d046b9a4dc 100644
--- a/modules/info/src/info_visitor.hh
+++ b/modules/info/src/info_visitor.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/info/src/item_type.hh b/modules/info/src/item_type.hh
index 132034406fa599fe869230d2e44206e8b7d2df27..509f22fbd4d6f44dbf7ef1fe6066bfb556474f2b 100644
--- a/modules/info/src/item_type.hh
+++ b/modules/info/src/item_type.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/info/src/item_type_cast.hh b/modules/info/src/item_type_cast.hh
index 0b364d575a31737eec8e0f6fa775d5b1a14956dd..605b5a11509866e9c017db20f22d9cf87a4b0548 100644
--- a/modules/info/src/item_type_cast.hh
+++ b/modules/info/src/item_type_cast.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/info/src/module_config.hh b/modules/info/src/module_config.hh
index ec6c38ef1c8d5566b32675bc5ad37140af7bac3b..c52301847873d462a94ddff658bae4c9171411c8 100644
--- a/modules/info/src/module_config.hh
+++ b/modules/info/src/module_config.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/doc/io.rst b/modules/io/doc/io.rst
index 995950ed29fcf6a4c0d22a8606f64463f841ca01..10be9a05532493ccaf23afa06cd49be89a8887a1 100644
--- a/modules/io/doc/io.rst
+++ b/modules/io/doc/io.rst
@@ -478,28 +478,6 @@ Saving Density Maps
io.SaveImage(image, 'new_map.map', CCP4())
-
-
-
-.. testsetup:: io
- from ost import io
-
-.. testcode:: io
- :hide:
-
- from ost import io,seq
- ent = io.LoadPDB('./examples/entity/fragment.pdb')
- print ent.atom_count
- myseq = seq.SequenceFromChain('t',ent.chains[0])
- print myseq.GetLength()
-
-.. testoutput:: io
- :hide:
-
- 81
- 12
-
-
Stereochemical Parameters
--------------------------------------------------------------------------------
diff --git a/modules/io/pymod/__init__.py b/modules/io/pymod/__init__.py
index f6aff418323d96e2636e39d631958aa2ec8215c8..a71fe0d186936e0fe0114afec9180a469e3341a2 100644
--- a/modules/io/pymod/__init__.py
+++ b/modules/io/pymod/__init__.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
@@ -16,9 +16,9 @@
# along with this library; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
#------------------------------------------------------------------------------
-import os, tempfile, ftplib, httplib
+import os, tempfile, ftplib, http.client
-from _ost_io import *
+from ._ost_io import *
from ost import mol, geom, conop, seq
profiles=None
@@ -404,7 +404,7 @@ def _PDBize(biounit, asu, seqres=None, min_polymer_size=10,
pdbizer.Add(assu, trans_matrices, ss)
pdb_bu = pdbizer.Finish(transformation)
if transformation:
- return pdb_bu, pdb_bu.GetTransformationMatrix()
+ return pdb_bu, pdb_bu.GetTransform().GetMatrix()
return pdb_bu
MMCifInfoBioUnit.PDBize = _PDBize
diff --git a/modules/io/pymod/export_map_io.cc b/modules/io/pymod/export_map_io.cc
index ab195ef2dc25f8323f27f08de82e31b4f8363980..0b730140d0b3b67605eff5795e3e8baf9c970b3d 100644
--- a/modules/io/pymod/export_map_io.cc
+++ b/modules/io/pymod/export_map_io.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/pymod/export_mmcif_io.cc b/modules/io/pymod/export_mmcif_io.cc
index 0252c553278b46717c1539d635897e818fdcf8cb..fa63ed2448bf4fad6dc88fb9751bb74ec0ebf9aa 100644
--- a/modules/io/pymod/export_mmcif_io.cc
+++ b/modules/io/pymod/export_mmcif_io.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/pymod/export_pdb_io.cc b/modules/io/pymod/export_pdb_io.cc
index 6aa26d96fba8a4fdd0c3052b22f3e3aa7d04a6e6..addb94f3bbd0d8f101da1b846af2a5b90c042592 100644
--- a/modules/io/pymod/export_pdb_io.cc
+++ b/modules/io/pymod/export_pdb_io.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/pymod/remote.py b/modules/io/pymod/remote.py
index 1f593060f1f0b583996253be6e8015db11bc4aa0..42fee8bc76b9fe5a04e9ddac45f6f0fc071128cf 100644
--- a/modules/io/pymod/remote.py
+++ b/modules/io/pymod/remote.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
@@ -17,7 +17,7 @@
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
#------------------------------------------------------------------------------
-import urllib2
+import urllib.request, urllib.error, urllib.parse
import tempfile
from ost.io import LoadPDB, LoadMMCIF
@@ -49,19 +49,18 @@ class RemoteRepository:
tmp_file_suffix+='.gz'
try:
- connection = urllib2.urlopen(remote_url)
+ connection = urllib.request.urlopen(remote_url)
if hasattr(connection, 'code'):
status = connection.code
else:
status = connection.getcode()
- except urllib2.HTTPError, e:
+ except urllib.error.HTTPError as e:
status = e.code
if status != 200:
raise IOError('Could not load %s from %s (status code %d, url %s)' \
% (id, self.name, status, remote_url))
tmp_file = tempfile.NamedTemporaryFile(suffix=tmp_file_suffix)
- contents = ''.join(connection)
- tmp_file.write(contents)
+ tmp_file.write(connection.read())
tmp_file.flush()
return tmp_file
diff --git a/modules/io/pymod/wrap_io.cc b/modules/io/pymod/wrap_io.cc
index 55e0dd61c3c2a0646bc63c4e810cf05a3fc50343..0cf910a439ac54ea4c15d1f867c92fc2664a606c 100644
--- a/modules/io/pymod/wrap_io.cc
+++ b/modules/io/pymod/wrap_io.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/io/src/binary_data_sink.hh b/modules/io/src/binary_data_sink.hh
index 3062fa1db2c9f34a225bd8d4b900ceb7e6fe4c0d..00d57b6c7ff2372db04eeafa3d8e4bf817bd9706 100644
--- a/modules/io/src/binary_data_sink.hh
+++ b/modules/io/src/binary_data_sink.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/binary_data_source.hh b/modules/io/src/binary_data_source.hh
index f610f376dd3e2e71b62e2462cc86ffc1f3515238..7a417dc3ae3162297cbeaff9be79240da3f51545 100644
--- a/modules/io/src/binary_data_source.hh
+++ b/modules/io/src/binary_data_source.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/container_serialization.hh b/modules/io/src/container_serialization.hh
index 88cbb7e71ddea8bdf6de00eb77eaccf5458d4283..ffe36c6f4645dc590169b6b515305d876bcfbcf1 100644
--- a/modules/io/src/container_serialization.hh
+++ b/modules/io/src/container_serialization.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/convert.cc b/modules/io/src/convert.cc
index cc42070f078818c30e28aa7f328d8364b837dd37..19a7bfe6590b81cd572ff7e448592aa84d1c17fb 100644
--- a/modules/io/src/convert.cc
+++ b/modules/io/src/convert.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
@@ -150,6 +150,9 @@ public:
// specialization for source!=target vax conversion integer types
+// NOTE: the VAX conversion is based on the libvaxdata code by L. M. Baker
+// -> a copy of Baker's code was included until OST 1.11 and removed as unused
+
// byte swapping for int types if local is big endian
template<class VALUETYPE>
class ConvertHelper<OST_BIG_ENDIAN,OST_VAX_DATA,VALUETYPE>{
diff --git a/modules/io/src/convert.hh b/modules/io/src/convert.hh
index c5002ea0b30e1662e5bfc575c00546e21cc16560..7224f6986116fc0ce513ba7c5eed899a83915b06 100644
--- a/modules/io/src/convert.hh
+++ b/modules/io/src/convert.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/converting_streams.hh b/modules/io/src/converting_streams.hh
index b451769185cd823c7f66cd465242b935dfd24078..47ee2a5af63a320baed64a6509b1e4d57d958c04 100644
--- a/modules/io/src/converting_streams.hh
+++ b/modules/io/src/converting_streams.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/img/CMakeLists.txt b/modules/io/src/img/CMakeLists.txt
index d17f46e8ec5e043b1a74c67ee900e5e01271ccd7..d3fea543a184ec80f1f847580de07c10856aa631 100644
--- a/modules/io/src/img/CMakeLists.txt
+++ b/modules/io/src/img/CMakeLists.txt
@@ -12,7 +12,6 @@ map_io_jpk_handler.cc
map_io_nanoscope_handler.cc
map_io_png_handler.cc
map_io_df3_handler.cc
-convert_vax_data.c
image_format.cc
tiff_util.cc
PARENT_SCOPE
@@ -22,7 +21,6 @@ set(OST_IO_IMG_HEADERS
load_map.hh
map_io_df3_handler.hh
image_format.hh
-image_format_conversion.cc
map_io_dx_handler.hh
map_io_spi_handler.hh
map_io_situs_handler.hh
@@ -35,7 +33,6 @@ map_io_nanoscope_handler.hh
map_io_png_handler.hh
map_io_dm3_handler.hh
map_io_tiff_handler.hh
-convert_vax_data.h
tiff_util.hh
jpk_util.hh
PARENT_SCOPE
diff --git a/modules/io/src/img/convert_vax_data.c b/modules/io/src/img/convert_vax_data.c
deleted file mode 100755
index cab50f2aef7915a9932cf5450644aa9feb58135e..0000000000000000000000000000000000000000
--- a/modules/io/src/img/convert_vax_data.c
+++ /dev/null
@@ -1,1408 +0,0 @@
-/******************************************************************************
- * *
- * convert_vax_data.c - Convert VAX-format data to/from Unix (IEEE) format. *
- * *
- * from_vax_i2() - Byte swap Integer*2 *
- * from_vax_i4() - Byte reverse Integer*4 *
- * from_vax_r4() - 32-bit VAX F_floating to IEEE S_floating *
- * from_vax_d8() - 64-bit VAX D_floating to IEEE T_floating *
- * from_vax_g8() - 64-bit VAX G_floating to IEEE T_floating *
- * from_vax_h16() - 128-bit VAX H_floating to Alpha X_floating *
- * *
- * to_vax_i2() - Byte swap Integer*2 *
- * to_vax_i4() - Byte reverse Integer*4 *
- * to_vax_r4() - 32-bit IEEE S_floating to VAX F_floating *
- * to_vax_d8() - 64-bit IEEE T_floating to VAX D_floating *
- * to_vax_g8() - 64-bit IEEE T_floating to VAX G_floating *
- * to_vax_h16() - 128-bit Alpha X_floating to VAX H_floating *
- * *
- * All calls take 3 arguments: *
- * *
- * C declaration: #include "convert_vax_data.h" *
- * usage: name( in_array, out_array, &count ); *
- * *
- * Fortran usage: Call NAME( in_array, out_array, count ) *
- * *
- * The in_array and out_array parameters may refer to the same object. *
- * *
- * *
- * See convert_vax_data.h for a description of the VAX and Unix (IEEE) data *
- * formats and the compilation options available. *
- * *
- * *
- * References: ANSI/IEEE Std 754-1985, IEEE Standard for Binary Floating- *
- * Point Arithmetic, Institute of Electrical and Electronics *
- * Engineers *
- * Brunner, Richard A., Ed., 1991, VAX Architecture Reference *
- * Manual, Second Edition, Digital Press *
- * Sites, Richard L., and Witek, Richard T., 1995, Alpha AXP *
- * Architecture Reference Manual, Second Edition, Digital *
- * Press *
- * *
- * Author: Lawrence M. Baker *
- * U.S. Geological Survey *
- * 345 Middlefield Road MS977 *
- * Menlo Park, CA 94025 *
- * baker@usgs.gov *
- * *
- * Citation: Baker, L.M., 2005, libvaxdata: VAX Data Format Conversion *
- * Routines: U.S. Geological Survey Open-File Report 2005- *
- * 1424 (http://pubs.usgs.gov/of/2005/1424/). *
- * *
- * *
- * Disclaimer *
- * *
- * Although this program has been used by the USGS, no warranty, expressed or *
- * implied, is made by the USGS or the United States Government as to the *
- * accuracy and functioning of the program and related program material, nor *
- * shall the fact of distribution constitute any such warranty, and no *
- * responsibility is assumed by the USGS in connection therewith. *
- * *
- * *
- * Modification History: *
- * *
- * 8-Sep-1992 L. M. Baker Original version. *
- * 12-Jan-1993 L. M. Baker Convert Fortran data conversion routines to *
- * C. *
- * Force underflows to 0 (as the VAX hardware *
- * does) to avoid IEEE Not-a-Numbers (NaNs). *
- * 14-Jan-1993 L. M. Baker Define forward and backward conversions for *
- * all numeric data types (not all implemen- *
- * ted yet). *
- * 20-Jan-1993 L. M. Baker Convert VAX extrema to subnormal/infinities. *
- * 22-Jan-1993 L. M. Baker Allow for little-endian and big-endian *
- * machines. *
- * Define register variables for Microsoft C (2 *
- * max). *
- * 25-Jan-1993 L. M. Baker Provide for Fortran naming with underscores. *
- * Provide for separate compilation for librar- *
- * ies. *
- * 27-Jan-1993 L. M. Baker Swap (16-bit) words in floating-point for- *
- * mats for little-endian machines. *
- * 16-May-2000 L. M. Baker Add conditionals for DEC C, Microsoft Visual *
- * C++. *
- * Convert VAX dirty zero (s=e=0, m<>0) to true *
- * zero. *
- * raise( SIGFPE ) for VAX reserved operands. *
- * Implement to_vax_r4(), to_vax_d8(), *
- * to_vax_g8(). *
- * Add const specifier where appropriate. *
- * 1-Feb-2001 L. M. Baker Change long to int (long's are 64 bits on *
- * Compaq's Tru64 UNIX). *
- * Add __alpha to the list of predefined macros *
- * that set IS_LITTLE_ENDIAN to 1. *
- * 5-Feb-2001 L. M. Baker Add prototypes for all functions (Matlab's *
- * MrC command on Macintosh requires them). *
- * 9-Mar-2001 L. M. Baker #include "convert_vax_data.h". *
- * 12-Aug-2005 L. M. Baker Add conditionals for GNU C and Portland *
- * Group C on AMD Opteron/Intel EM64T 64-bit *
- * x86 machines. *
- * 16-Sep-2005 L. M. Baker IEEE X_floating exponent is 15 bits, not 11 *
- * bits (fix from_vax_h16()). *
- * Correct recognition of +-0, +-Inf and +-NaN *
- * in to_vax_d8(), to_vax_g8(). *
- * Implement to_vax_h16(). *
- * 17-Sep-2005 L. M. Baker Add macro definitions for every float type. *
- * 19-Sep-2005 L. M. Baker Add fixups for IEEE-to-VAX conversion *
- * faults (+-infinity, +-NaN, overflow). *
- * 22-Sep-2005 L. M. Baker Change LITTLE_ENDIAN to IS_LITTLE_ENDIAN to *
- * avoid conflict with GCC/BSD predefined *
- * macro named LITTLE_ENDIAN. *
- * 12-Oct-2005 L. M. Baker Remove unreferenced variables. *
- * 8-Nov-2005 L. M. Baker Move #define const if not __STDC__ to *
- * convert_vax_data.h *
- * *
- ******************************************************************************/
-
-/*
- adapted for IPLT: removed SIGFPE signal
-*/
-
-#include "convert_vax_data.h" /* UPCASE, APPEND_UNDERSCORE, FORTRAN_LINKAGE */
-
-#ifndef IS_LITTLE_ENDIAN
-
-/* VAX C, GNU C on a VAX or an Alpha, or DEC C */
-
-#if defined( vax ) || defined( __vax ) || defined( vms ) || \
- defined( __vms ) || defined( __alpha )
-#define IS_LITTLE_ENDIAN 1
-#endif
-
-/* Microsoft 80x86 C or Microsoft Visual C++ on an 80x86 or an Alpha */
-
-#if defined( M_I86 ) || defined( _M_IX86 ) || defined( __M_ALPHA )
-#define IS_LITTLE_ENDIAN 1
-#endif
-
-/* Sun C, GNU C, or Intel C on an 80x86 */
-
-#if defined( i386 ) || defined( __i386 )
-#define IS_LITTLE_ENDIAN 1
-#endif
-
-/* GNU C or Portland Group C on an AMD Opteron or Intel EM64T */
-
-#if defined( __x86_64 ) || defined( __x86_64__ )
-#define IS_LITTLE_ENDIAN 1
-#endif
-
-/* Otherwise, assume big-endian machine */
-
-#ifndef IS_LITTLE_ENDIAN
-#define IS_LITTLE_ENDIAN 0
-#endif
-
-#endif
-
-#if !defined( MAKE_FROM_VAX_I2 ) && !defined( MAKE_FROM_VAX_I4 ) && \
- !defined( MAKE_FROM_VAX_R4 ) && !defined( MAKE_FROM_VAX_D8 ) && \
- !defined( MAKE_FROM_VAX_G8 ) && !defined( MAKE_FROM_VAX_H16 ) && \
- !defined( MAKE_TO_VAX_I2 ) && !defined( MAKE_TO_VAX_I4 ) && \
- !defined( MAKE_TO_VAX_R4 ) && !defined( MAKE_TO_VAX_D8 ) && \
- !defined( MAKE_TO_VAX_G8 ) && !defined( MAKE_TO_VAX_H16 )
-
-#define MAKE_FROM_VAX_I2
-#define MAKE_FROM_VAX_I4
-#define MAKE_FROM_VAX_R4
-#define MAKE_FROM_VAX_D8
-#define MAKE_FROM_VAX_G8
-#define MAKE_FROM_VAX_H16
-
-#define MAKE_TO_VAX_I2
-#define MAKE_TO_VAX_I4
-#define MAKE_TO_VAX_R4
-#define MAKE_TO_VAX_D8
-#define MAKE_TO_VAX_G8
-#define MAKE_TO_VAX_H16
-
-#endif
-
-#include <limits.h> /* UCHAR_MAX, USHRT_MAX, UINT_MAX */
-
-#if UCHAR_MAX != 255U || USHRT_MAX != 65535U || UINT_MAX != 4294967295U
-#error convert_vax_data.c requires 8-bit chars, 16-bit shorts, and 32-bit ints
-#endif
-
-#if defined( MAKE_FROM_VAX_R4 ) || defined( MAKE_FROM_VAX_D8 ) || \
- defined( MAKE_FROM_VAX_G8 ) || defined( MAKE_FROM_VAX_H16 ) || \
- defined( MAKE_TO_VAX_R4 ) || defined( MAKE_TO_VAX_D8 ) || \
- defined( MAKE_TO_VAX_G8 ) || defined( MAKE_TO_VAX_H16 )
-#include <signal.h> /* SIGFPE, raise() */
-#endif
-
-/* FLoating point data format invariants */
-
-#define SIGN_BIT 0x80000000
-
-/* VAX floating point data formats (see VAX Architecture Reference Manual) */
-
-#define VAX_F_SIGN_BIT SIGN_BIT
-#define VAX_F_EXPONENT_MASK 0x7F800000
-#define VAX_F_EXPONENT_SIZE 8
-#define VAX_F_EXPONENT_BIAS ( 1 << ( VAX_F_EXPONENT_SIZE - 1 ) )
-#define VAX_F_MANTISSA_MASK 0x007FFFFF
-#define VAX_F_MANTISSA_SIZE 23
-#define VAX_F_HIDDEN_BIT ( 1 << VAX_F_MANTISSA_SIZE )
-
-#define VAX_D_SIGN_BIT SIGN_BIT
-#define VAX_D_EXPONENT_MASK 0x7F800000
-#define VAX_D_EXPONENT_SIZE 8
-#define VAX_D_EXPONENT_BIAS ( 1 << ( VAX_D_EXPONENT_SIZE - 1 ) )
-#define VAX_D_MANTISSA_MASK 0x007FFFFF
-#define VAX_D_MANTISSA_SIZE 23
-#define VAX_D_HIDDEN_BIT ( 1 << VAX_D_MANTISSA_SIZE )
-
-#define VAX_G_SIGN_BIT SIGN_BIT
-#define VAX_G_EXPONENT_MASK 0x7FF00000
-#define VAX_G_EXPONENT_SIZE 11
-#define VAX_G_EXPONENT_BIAS ( 1 << ( VAX_G_EXPONENT_SIZE - 1 ) )
-#define VAX_G_MANTISSA_MASK 0x000FFFFF
-#define VAX_G_MANTISSA_SIZE 20
-#define VAX_G_HIDDEN_BIT ( 1 << VAX_G_MANTISSA_SIZE )
-
-#define VAX_H_SIGN_BIT SIGN_BIT
-#define VAX_H_EXPONENT_MASK 0x7FFF0000
-#define VAX_H_EXPONENT_SIZE 15
-#define VAX_H_EXPONENT_BIAS ( 1 << ( VAX_H_EXPONENT_SIZE - 1 ) )
-#define VAX_H_MANTISSA_MASK 0x0000FFFF
-#define VAX_H_MANTISSA_SIZE 16
-#define VAX_H_HIDDEN_BIT ( 1 << VAX_H_MANTISSA_SIZE )
-
-/* IEEE floating point data formats (see Alpha Architecture Reference Manual) */
-
-#define IEEE_S_SIGN_BIT SIGN_BIT
-#define IEEE_S_EXPONENT_MASK 0x7F800000
-#define IEEE_S_EXPONENT_SIZE 8
-#define IEEE_S_EXPONENT_BIAS ( ( 1 << ( IEEE_S_EXPONENT_SIZE - 1 ) ) - 1 )
-#define IEEE_S_MANTISSA_MASK 0x007FFFFF
-#define IEEE_S_MANTISSA_SIZE 23
-#define IEEE_S_HIDDEN_BIT ( 1 << IEEE_S_MANTISSA_SIZE )
-
-#define IEEE_T_SIGN_BIT SIGN_BIT
-#define IEEE_T_EXPONENT_MASK 0x7FF00000
-#define IEEE_T_EXPONENT_SIZE 11
-#define IEEE_T_EXPONENT_BIAS ( ( 1 << ( IEEE_T_EXPONENT_SIZE - 1 ) ) - 1 )
-#define IEEE_T_MANTISSA_MASK 0x000FFFFF
-#define IEEE_T_MANTISSA_SIZE 20
-#define IEEE_T_HIDDEN_BIT ( 1 << IEEE_T_MANTISSA_SIZE )
-
-#define IEEE_X_SIGN_BIT SIGN_BIT
-#define IEEE_X_EXPONENT_MASK 0x7FFF0000
-#define IEEE_X_EXPONENT_SIZE 15
-#define IEEE_X_EXPONENT_BIAS ( ( 1 << ( IEEE_X_EXPONENT_SIZE - 1 ) ) - 1 )
-#define IEEE_X_MANTISSA_MASK 0x0000FFFF
-#define IEEE_X_MANTISSA_SIZE 16
-#define IEEE_X_HIDDEN_BIT ( 1 << IEEE_X_MANTISSA_SIZE )
-
-/************************************************************** from_vax_i2() */
-
-#ifdef MAKE_FROM_VAX_I2
-
-void FORTRAN_LINKAGE from_vax_i2( const void *inbuf, void *outbuf,
- const int *count ) {
-
-#if IS_LITTLE_ENDIAN
-
- register const unsigned short *in; /* Microsoft C: up to 2 register vars */
- register unsigned short *out; /* Microsoft C: up to 2 register vars */
- int n;
-
-
- in = (const unsigned short *) inbuf;
- out = (unsigned short *) outbuf;
-
- if ( in != out ) {
- for ( n = *count; n > 0; n-- ) {
- *out++ = *in++;
- }
- }
-
-#else
-
- const unsigned char *in;
- unsigned char *out;
- int n;
- unsigned char c1;
-
-
- in = (const unsigned char *) inbuf;
- out = (unsigned char *) outbuf;
-
- for ( n = *count; n > 0; n-- ) {
- c1 = *in++;
- *out++ = *in++;
- *out++ = c1;
- }
-
-#endif
-
-}
-
-#endif /* #ifdef MAKE_FROM_VAX_I2 */
-
-/************************************************************** from_vax_i4() */
-
-#ifdef MAKE_FROM_VAX_I4
-
-void FORTRAN_LINKAGE from_vax_i4( const void *inbuf, void *outbuf,
- const int *count ) {
-
-#if IS_LITTLE_ENDIAN
-
- register const unsigned int *in; /* Microsoft C: up to 2 register vars */
- register unsigned int *out; /* Microsoft C: up to 2 register vars */
- int n;
-
-
- in = (const unsigned int *) inbuf;
- out = (unsigned int *) outbuf;
-
- if ( in != out ) {
- for ( n = *count; n > 0; n-- ) {
- *out++ = *in++;
- }
- }
-
-#else
-
- const unsigned char *in;
- unsigned char *out;
- int n;
- unsigned char c1, c2, c3;
-
-
- in = (unsigned char *) inbuf;
- out = (unsigned char *) outbuf;
-
- for ( n = *count; n > 0; n-- ) {
- c1 = *in++;
- c2 = *in++;
- c3 = *in++;
- *out++ = *in++;
- *out++ = c3;
- *out++ = c2;
- *out++ = c1;
- }
-
-#endif
-
-}
-
-#endif /* #ifdef MAKE_FROM_VAX_I4 */
-
-/************************************************************** from_vax_r4() */
-
-#ifdef MAKE_FROM_VAX_R4
-
-/* Assert the mantissa in a VAX F_float is the same as in an IEEE S_float */
-#if VAX_F_MANTISSA_MASK != IEEE_S_MANTISSA_MASK
-#error MANTISSA_MASK mismatch in from_vax_r4()
-#endif
-#define MANTISSA_MASK VAX_F_MANTISSA_MASK
-/* If the mantissas are the same, then so are the no. of bits and the hidden */
-/* normalization bit */
-#define MANTISSA_SIZE VAX_F_MANTISSA_SIZE
-#define HIDDEN_BIT VAX_F_HIDDEN_BIT
-
-/* Assert the VAX F_float exponent bias is greater than the IEEE S_float */
-/* exponent bias (overflow is not possible) */
-#define EXPONENT_ADJUSTMENT ( 1 + VAX_F_EXPONENT_BIAS - IEEE_S_EXPONENT_BIAS )
-#if EXPONENT_ADJUSTMENT < 2
-#error EXPONENT_ADJUSTMENT assertion failure in from_vax_r4()
-#endif
-#define IN_PLACE_EXPONENT_ADJUSTMENT \
- ( EXPONENT_ADJUSTMENT << IEEE_S_MANTISSA_SIZE )
-
-void FORTRAN_LINKAGE from_vax_r4( const void *inbuf, void *outbuf,
- const int *count ) {
-
-#if IS_LITTLE_ENDIAN
- register const unsigned short *in; /* Microsoft C: up to 2 register vars */
- union { unsigned short i[2]; unsigned int l; } part;
-#else
- const unsigned char *in;
- union { unsigned char c[4]; unsigned int l; } part;
-#endif
- register unsigned int *out; /* Microsoft C: up to 2 register vars */
- unsigned int part1;
- int n;
- int e;
-
-
-#if IS_LITTLE_ENDIAN
- in = (const unsigned short *) inbuf;
-#else
- in = (const unsigned char *) inbuf;
-#endif
- out = (unsigned int *) outbuf;
-
- for ( n = *count; n > 0; n-- ) {
-#if IS_LITTLE_ENDIAN
- part.i[1] = *in++;
- part.i[0] = *in++;
- part1 = part.l;
-#else
- part.c[1] = *in++;
- part.c[0] = *in++;
- part.c[3] = *in++;
- part.c[2] = *in++;
- part1 = part.l;
-#endif
- if ( ( e = ( part1 & VAX_F_EXPONENT_MASK ) ) == 0 ) {
- /* If the biased VAX exponent is zero [e=0] */
-
- if ( ( part1 & SIGN_BIT ) == SIGN_BIT ) { /* If negative [s=1] */
- //raise( SIGFPE );/* VAX reserved operand fault; fixup to IEEE zero */
- return;
- }
- /* Set VAX dirty [m<>0] or true [m=0] zero to IEEE +zero [s=e=m=0] */
- *out++ = 0;
-
- } else { /* The biased VAX exponent is non-zero [e<>0] */
-
- e >>= MANTISSA_SIZE; /* Obtain the biased VAX exponent */
-
- /* The biased VAX exponent has to be adjusted to account for the */
- /* right shift of the IEEE mantissa binary point and the difference */
- /* between the biases in their "excess n" exponent representations. */
- /* If the resulting biased IEEE exponent is less than or equal to */
- /* zero, the converted IEEE S_float must use subnormal form. */
-
- if ( ( e - EXPONENT_ADJUSTMENT ) > 0 ) {
- /* Use IEEE normalized form [e>0] */
-
- /* Both mantissas are 23 bits; adjust the exponent field in place */
- *out++ = part1 - IN_PLACE_EXPONENT_ADJUSTMENT;
-
- } else { /* Use IEEE subnormal form [e=0, m>0] */
-
- *out++ = ( part1 & SIGN_BIT ) |
- ( ( HIDDEN_BIT | ( part1 & MANTISSA_MASK ) ) >>
- ( 1 - e ) );
-
- }
- }
- }
-
-}
-
-#undef MANTISSA_MASK
-#undef MANTISSA_SIZE
-#undef HIDDEN_BIT
-#undef EXPONENT_ADJUSTMENT
-#undef IN_PLACE_EXPONENT_ADJUSTMENT
-
-#endif /* #ifdef MAKE_FROM_VAX_R4 */
-
-/************************************************************** from_vax_d8() */
-
-#ifdef MAKE_FROM_VAX_D8
-
-/* Assert the IEEE T_float exponent bias is so much larger than the VAX */
-/* D_float exponent bias that it is not possible for this conversion to */
-/* overflow or underflow */
-#define EXPONENT_ADJUSTMENT ( 1 + VAX_D_EXPONENT_BIAS - IEEE_T_EXPONENT_BIAS )
-#if ( EXPONENT_ADJUSTMENT + VAX_D_MANTISSA_SIZE + 1 ) > 0
-#error EXPONENT_ADJUSTMENT assertion failure in from_vax_d8()
-#endif
-#define IN_PLACE_EXPONENT_ADJUSTMENT \
- ( EXPONENT_ADJUSTMENT << IEEE_T_MANTISSA_SIZE )
-
-/* Assert the VAX D_float mantissa is wider than the IEEE T_float mantissa */
-#define EXPONENT_RIGHT_SHIFT ( VAX_D_MANTISSA_SIZE - IEEE_T_MANTISSA_SIZE )
-#if EXPONENT_RIGHT_SHIFT <= 0
-#error EXPONENT_RIGHT_SHIFT assertion failure in from_vax_d8()
-#endif
-
-void FORTRAN_LINKAGE from_vax_d8( const void *inbuf, void *outbuf,
- const int *count ) {
-
-#if IS_LITTLE_ENDIAN
- register const unsigned short *in; /* Microsoft C: up to 2 register vars */
- union { unsigned short i[2]; unsigned int l; } part;
-#else
- const unsigned char *in;
- union { unsigned char c[4]; unsigned int l; } part;
-#endif
- register unsigned int *out; /* Microsoft C: up to 2 register vars */
- unsigned int part1, part2;
- int n;
-
-
-#if IS_LITTLE_ENDIAN
- in = (const unsigned short *) inbuf;
-#else
- in = (const unsigned char *) inbuf;
-#endif
- out = (unsigned int *) outbuf;
-
- for ( n = *count; n > 0; n-- ) {
-#if IS_LITTLE_ENDIAN
- part.i[1] = *in++;
- part.i[0] = *in++;
- part1 = part.l;
- part.i[1] = *in++;
- part.i[0] = *in++;
- part2 = part.l;
-#else
- part.c[1] = *in++;
- part.c[0] = *in++;
- part.c[3] = *in++;
- part.c[2] = *in++;
- part1 = part.l;
- part.c[1] = *in++;
- part.c[0] = *in++;
- part.c[3] = *in++;
- part.c[2] = *in++;
- part2 = part.l;
-#endif
- if ( ( part1 & VAX_D_EXPONENT_MASK ) == 0 ) {
- /* If the biased VAX exponent is zero [e=0] */
-
- if ( ( part1 & SIGN_BIT ) == SIGN_BIT ) { /* If negative [s=1] */
- //raise( SIGFPE );/* VAX reserved operand fault; fixup to IEEE zero */
- return;
- }
- /* Set VAX dirty [m<>0] or true [m=0] zero to IEEE +zero [s=e=m=0] */
- *out++ = 0;
- *out++ = 0;
-
- } else { /* The biased VAX exponent is non-zero [e<>0] */
-
- /* Because the range of an IEEE T_float is so much larger than a VAX */
- /* D_float, the converted IEEE T_float will never be subnormal form. */
-
- /* Use IEEE normalized form [e>0]; truncate the mantissa from 55 to */
- /* 52 bits, then adjust the exponent field in place */
- *out++ = ( ( part1 & SIGN_BIT ) |
- ( ( part1 & ~SIGN_BIT ) >> EXPONENT_RIGHT_SHIFT ) ) -
- IN_PLACE_EXPONENT_ADJUSTMENT;
- *out++ = ( part1 << ( 32 - EXPONENT_RIGHT_SHIFT ) ) |
- ( part2 >> EXPONENT_RIGHT_SHIFT );
-
- }
- }
-
-}
-
-#undef EXPONENT_ADJUSTMENT
-#undef IN_PLACE_EXPONENT_ADJUSTMENT
-#undef EXPONENT_RIGHT_SHIFT
-
-#endif /* #ifdef MAKE_FROM_VAX_D8 */
-
-/************************************************************** from_vax_g8() */
-
-#ifdef MAKE_FROM_VAX_G8
-
-/* Assert the mantissa in a VAX G_float is the same as in an IEEE T_float */
-#if VAX_G_MANTISSA_MASK != IEEE_T_MANTISSA_MASK
-#error MANTISSA_MASK mismatch in from_vax_g8()
-#endif
-#define MANTISSA_MASK VAX_G_MANTISSA_MASK
-/* If the mantissas are the same, then so are the no. of bits and the hidden */
-/* normalization bit */
-#define MANTISSA_SIZE VAX_G_MANTISSA_SIZE
-#define HIDDEN_BIT VAX_G_HIDDEN_BIT
-
-/* Assert the VAX G_float exponent bias is greater than the IEEE T_float */
-/* exponent bias (overflow is not possible) */
-#define EXPONENT_ADJUSTMENT ( 1 + VAX_G_EXPONENT_BIAS - IEEE_T_EXPONENT_BIAS )
-#if EXPONENT_ADJUSTMENT < 2
-#error EXPONENT_ADJUSTMENT assertion failure in from_vax_g8()
-#endif
-#define IN_PLACE_EXPONENT_ADJUSTMENT \
- ( EXPONENT_ADJUSTMENT << IEEE_T_MANTISSA_SIZE )
-
-void FORTRAN_LINKAGE from_vax_g8( const void *inbuf, void *outbuf,
- const int *count ) {
-
-#if IS_LITTLE_ENDIAN
- register const unsigned short *in; /* Microsoft C: up to 2 register vars */
- union { unsigned short i[2]; unsigned int l; } part;
-#else
- const unsigned char *in;
- union { unsigned char c[4]; unsigned int l; } part;
-#endif
- register unsigned int *out; /* Microsoft C: up to 2 register vars */
- unsigned int part1, part2;
- int n;
- int e;
-
-
-#if IS_LITTLE_ENDIAN
- in = (const unsigned short *) inbuf;
-#else
- in = (const unsigned char *) inbuf;
-#endif
- out = (unsigned int *) outbuf;
-
- for ( n = *count; n > 0; n-- ) {
-#if IS_LITTLE_ENDIAN
- part.i[1] = *in++;
- part.i[0] = *in++;
- part1 = part.l;
- part.i[1] = *in++;
- part.i[0] = *in++;
- part2 = part.l;
-#else
- part.c[1] = *in++;
- part.c[0] = *in++;
- part.c[3] = *in++;
- part.c[2] = *in++;
- part1 = part.l;
- part.c[1] = *in++;
- part.c[0] = *in++;
- part.c[3] = *in++;
- part.c[2] = *in++;
- part2 = part.l;
-#endif
- if ( ( e = ( part1 & VAX_G_EXPONENT_MASK ) ) == 0 ) {
- /* If the biased VAX exponent is zero [e=0] */
-
- if ( ( part1 & SIGN_BIT ) == SIGN_BIT ) { /* If negative [s=1] */
- //raise( SIGFPE );/* VAX reserved operand fault; fixup to IEEE zero */
- return;
- }
- /* Set VAX dirty [m<>0] or true [m=0] zero to IEEE +zero [s=e=m=0] */
- *out++ = 0;
- *out++ = 0;
-
- } else { /* The biased VAX exponent is non-zero [e<>0] */
-
- e >>= MANTISSA_SIZE; /* Obtain the biased VAX exponent */
-
- /* The biased VAX exponent has to be adjusted to account for the */
- /* right shift of the IEEE mantissa binary point and the difference */
- /* between the biases in their "excess n" exponent representations. */
- /* If the resulting biased IEEE exponent is less than or equal to */
- /* zero, the converted IEEE T_float must use subnormal form. */
-
- if ( ( e - EXPONENT_ADJUSTMENT ) > 0 ) {
- /* Use IEEE normalized form [e>0] */
-
- /* Both mantissas are 52 bits; adjust the exponent field in place */
- *out++ = part1 - IN_PLACE_EXPONENT_ADJUSTMENT;
- *out++ = part2;
-
- } else { /* Use IEEE subnormal form [e=0, m>0] */
-
- part1 = ( part1 & ( SIGN_BIT | MANTISSA_MASK ) ) | HIDDEN_BIT;
- *out++ = ( part1 & SIGN_BIT ) |
- ( ( part1 & ( HIDDEN_BIT | MANTISSA_MASK ) ) >>
- ( 1 - e ) );
- *out++ = ( part1 << ( 31 + e ) ) | ( part2 >> ( 1 - e ) );
-
- }
- }
- }
-
-}
-
-#undef MANTISSA_MASK
-#undef MANTISSA_SIZE
-#undef HIDDEN_BIT
-#undef EXPONENT_ADJUSTMENT
-#undef IN_PLACE_EXPONENT_ADJUSTMENT
-
-#endif /* #ifdef MAKE_FROM_VAX_G8 */
-
-/************************************************************* from_vax_h16() */
-
-#ifdef MAKE_FROM_VAX_H16
-
-/* Assert the mantissa in a VAX H_float is the same as in an IEEE X_float */
-#if VAX_H_MANTISSA_MASK != IEEE_X_MANTISSA_MASK
-#error MANTISSA_MASK mismatch in from_vax_h16()
-#endif
-#define MANTISSA_MASK VAX_H_MANTISSA_MASK
-/* If the mantissas are the same, then so are the no. of bits and the hidden */
-/* normalization bit */
-#define MANTISSA_SIZE VAX_H_MANTISSA_SIZE
-#define HIDDEN_BIT VAX_H_HIDDEN_BIT
-
-/* Assert the VAX H_float exponent bias is greater than the IEEE X_float */
-/* exponent bias (overflow is not possible) */
-#define EXPONENT_ADJUSTMENT ( 1 + VAX_H_EXPONENT_BIAS - IEEE_X_EXPONENT_BIAS )
-#if EXPONENT_ADJUSTMENT < 2
-#error EXPONENT_ADJUSTMENT assertion failure in from_vax_H16()
-#endif
-#define IN_PLACE_EXPONENT_ADJUSTMENT \
- ( EXPONENT_ADJUSTMENT << IEEE_X_MANTISSA_SIZE )
-
-void FORTRAN_LINKAGE from_vax_h16( const void *inbuf, void *outbuf,
- const int *count ) {
-
-#if IS_LITTLE_ENDIAN
- register const unsigned short *in; /* Microsoft C: up to 2 register vars */
- union { unsigned short i[2]; unsigned int l; } part;
-#else
- const unsigned char *in;
- union { unsigned char c[4]; unsigned int l; } part;
-#endif
- register unsigned int *out; /* Microsoft C: up to 2 register vars */
- unsigned int part1, part2, part3, part4;
- int n;
- int e;
-
-
-#if IS_LITTLE_ENDIAN
- in = (const unsigned short *) inbuf;
-#else
- in = (const unsigned char *) inbuf;
-#endif
- out = (unsigned int *) outbuf;
-
- for ( n = *count; n > 0; n-- ) {
-#if IS_LITTLE_ENDIAN
- part.i[1] = *in++;
- part.i[0] = *in++;
- part1 = part.l;
- part.i[1] = *in++;
- part.i[0] = *in++;
- part2 = part.l;
- part.i[1] = *in++;
- part.i[0] = *in++;
- part3 = part.l;
- part.i[1] = *in++;
- part.i[0] = *in++;
- part4 = part.l;
-#else
- part.c[1] = *in++;
- part.c[0] = *in++;
- part.c[3] = *in++;
- part.c[2] = *in++;
- part1 = part.l;
- part.c[1] = *in++;
- part.c[0] = *in++;
- part.c[3] = *in++;
- part.c[2] = *in++;
- part2 = part.l;
- part.c[1] = *in++;
- part.c[0] = *in++;
- part.c[3] = *in++;
- part.c[2] = *in++;
- part3 = part.l;
- part.c[1] = *in++;
- part.c[0] = *in++;
- part.c[3] = *in++;
- part.c[2] = *in++;
- part4 = part.l;
-#endif
- if ( ( e = ( part1 & VAX_H_EXPONENT_MASK ) ) == 0 ) {
- /* If the biased VAX exponent is zero [e=0] */
-
- if ( ( part1 & SIGN_BIT ) == SIGN_BIT ) { /* If negative [s=1] */
- //raise( SIGFPE );/* VAX reserved operand fault; fixup to IEEE zero */
- return;
- }
- /* Set VAX dirty [m<>0] or true [m=0] zero to IEEE +zero [s=e=m=0] */
- *out++ = 0;
- *out++ = 0;
- *out++ = 0;
- *out++ = 0;
-
- } else { /* The biased VAX exponent is non-zero [e<>0] */
-
- e >>= MANTISSA_SIZE; /* Obtain the biased VAX exponent */
-
- /* The biased VAX exponent has to be adjusted to account for the */
- /* right shift of the IEEE mantissa binary point and the difference */
- /* between the biases in their "excess n" exponent representations. */
- /* If the resulting biased IEEE exponent is less than or equal to */
- /* zero, the converted IEEE X_float must use subnormal form. */
-
- if ( ( e - EXPONENT_ADJUSTMENT ) > 0 ) {
- /* Use IEEE normalized form [e>0] */
-
- /* Both mantissas are 112 bits; adjust the exponent field in place */
- *out++ = part1 - IN_PLACE_EXPONENT_ADJUSTMENT;
- *out++ = part2;
- *out++ = part3;
- *out++ = part4;
-
- } else { /* Use IEEE subnormal form [e=0, m>0] */
-
- part1 = ( part1 & ( SIGN_BIT | MANTISSA_MASK ) ) | HIDDEN_BIT;
- *out++ = ( part1 & SIGN_BIT ) |
- ( ( part1 & ( HIDDEN_BIT | MANTISSA_MASK ) ) >>
- ( 1 - e ) );
- *out++ = ( part1 << ( 31 + e ) ) | ( part2 >> ( 1 - e ) );
- *out++ = ( part2 << ( 31 + e ) ) | ( part3 >> ( 1 - e ) );
- *out++ = ( part3 << ( 31 + e ) ) | ( part4 >> ( 1 - e ) );
-
- }
- }
- }
-
-}
-
-#undef MANTISSA_MASK
-#undef MANTISSA_SIZE
-#undef HIDDEN_BIT
-#undef EXPONENT_ADJUSTMENT
-#undef IN_PLACE_EXPONENT_ADJUSTMENT
-
-#endif /* #ifdef MAKE_FROM_VAX_H16 */
-
-/**************************************************************** to_vax_i2() */
-
-#ifdef MAKE_TO_VAX_I2
-
-void FORTRAN_LINKAGE to_vax_i2( const void *inbuf, void *outbuf,
- const int *count ) {
-
-#if IS_LITTLE_ENDIAN
-
- register const unsigned short *in; /* Microsoft C: up to 2 register vars */
- register unsigned short *out; /* Microsoft C: up to 2 register vars */
- int n;
-
-
- in = (const unsigned short *) inbuf;
- out = (unsigned short *) outbuf;
-
- if ( in != out ) {
- for ( n = *count; n > 0; n-- ) {
- *out++ = *in++;
- }
- }
-
-#else
-
- const unsigned char *in;
- unsigned char *out;
- int n;
- unsigned char c1;
-
-
- in = (const unsigned char *) inbuf;
- out = (unsigned char *) outbuf;
-
- for ( n = *count; n > 0; n-- ) {
- c1 = *in++;
- *out++ = *in++;
- *out++ = c1;
- }
-
-#endif
-
-}
-
-#endif /* #ifdef MAKE_TO_VAX_I2 */
-
-/**************************************************************** to_vax_i4() */
-
-#ifdef MAKE_TO_VAX_I4
-
-void FORTRAN_LINKAGE to_vax_i4( const void *inbuf, void *outbuf,
- const int *count ) {
-
-#if IS_LITTLE_ENDIAN
-
- register const unsigned int *in; /* Microsoft C: up to 2 register vars */
- register unsigned int *out; /* Microsoft C: up to 2 register vars */
- int n;
-
-
- in = (const unsigned int *) inbuf;
- out = (unsigned int *) outbuf;
-
- if ( in != out ) {
- for ( n = *count; n > 0; n-- ) {
- *out++ = *in++;
- }
- }
-
-#else
-
- const unsigned char *in;
- unsigned char *out;
- int n;
- unsigned char c1, c2, c3;
-
-
- in = (const unsigned char *) inbuf;
- out = (unsigned char *) outbuf;
-
- for ( n = *count; n > 0; n-- ) {
- c1 = *in++;
- c2 = *in++;
- c3 = *in++;
- *out++ = *in++;
- *out++ = c3;
- *out++ = c2;
- *out++ = c1;
- }
-
-#endif
-
-}
-
-#endif /* #ifdef MAKE_TO_VAX_I4 */
-
-/**************************************************************** to_vax_r4() */
-
-#ifdef MAKE_TO_VAX_R4
-
-/* Assert the mantissa in a VAX F_float is the same as in an IEEE S_float */
-#if VAX_F_MANTISSA_MASK != IEEE_S_MANTISSA_MASK
-#error MANTISSA_MASK mismatch in to_vax_r4()
-#endif
-#define MANTISSA_MASK VAX_F_MANTISSA_MASK
-/* If the mantissas are the same, then so are the no. of bits and the hidden */
-/* normalization bit */
-#define MANTISSA_SIZE VAX_F_MANTISSA_SIZE
-#define HIDDEN_BIT VAX_F_HIDDEN_BIT
-
-#define EXPONENT_ADJUSTMENT ( 1 + VAX_F_EXPONENT_BIAS - IEEE_S_EXPONENT_BIAS )
-
-void FORTRAN_LINKAGE to_vax_r4( const void *inbuf, void *outbuf,
- const int *count ) {
-
- register const unsigned int *in; /* Microsoft C: up to 2 register vars */
-#if IS_LITTLE_ENDIAN
- register unsigned short *out; /* Microsoft C: up to 2 register vars */
- union { unsigned short i[2]; unsigned int l; } part;
-#else
- unsigned char *out;
- union { unsigned char c[4]; unsigned int l; } part;
-#endif
- unsigned int part1;
- unsigned int m;
- int n;
- int e;
-
-
- in = (const unsigned int *) inbuf;
-#if IS_LITTLE_ENDIAN
- out = (unsigned short *) outbuf;
-#else
- out = (unsigned char *) outbuf;
-#endif
-
- for ( n = *count; n > 0; n-- ) {
- part1 = *in++;
- if ( ( part1 & ~SIGN_BIT ) == 0 ) {
-
- part.l = 0; /* Set IEEE +-zero [e=m=0] to VAX zero [s=e=m=0] */
-
- } else if ( ( e = ( part1 & IEEE_S_EXPONENT_MASK ) ) ==
- IEEE_S_EXPONENT_MASK ) {
-
- /* VAX's have no equivalents for IEEE +-Infinity and +-NaN [e=all-1's] */
- //raise( SIGFPE );
- return;
-
- /* Fixup to VAX +-extrema [e=all-1's] with zero mantissa [m=0] */
- part.l = ( part1 & SIGN_BIT ) | VAX_F_EXPONENT_MASK;
-
- } else {
-
- e >>= MANTISSA_SIZE; /* Obtain the biased IEEE exponent */
- m = part1 & MANTISSA_MASK; /* Obtain the IEEE mantissa */
-
- if ( e == 0 ) { /* Denormalized [e=0, m<>0] */
- m <<= 1; /* Adjust representation from 2**(1-bias) to 2**(e-bias) */
- while ( ( m & HIDDEN_BIT ) == 0 ) {
- m <<= 1;
- e -= 1; /* Adjust exponent */
- }
- m &= MANTISSA_MASK; /* Adjust mantissa to hidden-bit form */
- }
-
- if ( ( e += EXPONENT_ADJUSTMENT ) <= 0 ) {
-
- part.l = 0; /* Silent underflow */
-
- } else if ( e > ( 2 * VAX_F_EXPONENT_BIAS - 1 ) ) {
-
- //raise( SIGFPE );/* Overflow; fixup to VAX +-extrema [e=m=all-1's] */
- return;
- part.l = ( part1 & SIGN_BIT ) | ~SIGN_BIT;
-
- } else {
-
- /* VAX normalized form [e>0] (both mantissas are 23 bits) */
- part.l = ( part1 & SIGN_BIT ) | ( e << MANTISSA_SIZE ) | m;
-
- }
-
- }
-#if IS_LITTLE_ENDIAN
- *out++ = part.i[1];
- *out++ = part.i[0];
-#else
- *out++ = part.c[1];
- *out++ = part.c[0];
- *out++ = part.c[3];
- *out++ = part.c[2];
-#endif
- }
-
-}
-
-#undef MANTISSA_MASK
-#undef MANTISSA_SIZE
-#undef HIDDEN_BIT
-#undef EXPONENT_ADJUSTMENT
-
-#endif /* #ifdef MAKE_TO_VAX_R4 */
-
-/**************************************************************** to_vax_d8() */
-
-#ifdef MAKE_TO_VAX_D8
-
-#define EXPONENT_ADJUSTMENT ( 1 + VAX_D_EXPONENT_BIAS - IEEE_T_EXPONENT_BIAS )
-
-/* Assert the VAX D_float mantissa is wider than the IEEE T_float mantissa */
-#define EXPONENT_LEFT_SHIFT ( VAX_D_MANTISSA_SIZE - IEEE_T_MANTISSA_SIZE )
-#if EXPONENT_LEFT_SHIFT <= 0
-#error EXPONENT_LEFT_SHIFT assertion failure in to_vax_d8()
-#endif
-
-void FORTRAN_LINKAGE to_vax_d8( const void *inbuf, void *outbuf,
- const int *count ) {
-
- register const unsigned int *in; /* Microsoft C: up to 2 register vars */
-#if IS_LITTLE_ENDIAN
- register unsigned short *out; /* Microsoft C: up to 2 register vars */
- union { unsigned short i[2]; unsigned int l; } part;
-#else
- unsigned char *out;
- union { unsigned char c[4]; unsigned int l; } part;
-#endif
- unsigned int part1, part2;
- unsigned int m;
- int n;
- int e;
-
-
- in = (const unsigned int *) inbuf;
-#if IS_LITTLE_ENDIAN
- out = (unsigned short *) outbuf;
-#else
- out = (unsigned char *) outbuf;
-#endif
-
- for ( n = *count; n > 0; n-- ) {
- part1 = *in++;
- part2 = *in++;
- if ( ( ( part1 & ~SIGN_BIT ) | part2 ) == 0 ) {
-
- part.l = 0; /* Set IEEE +-zero [e=m=0] to VAX zero [s=e=m=0] */
- /* part2 = 0; */ /* part2 is already zero */
-
- } else if ( ( e = ( part1 & IEEE_T_EXPONENT_MASK ) ) ==
- IEEE_T_EXPONENT_MASK ) {
-
- /* VAX's have no equivalents for IEEE +-Infinity and +-NaN [e=all-1's] */
- //raise( SIGFPE );
- return;
- /* Fixup to VAX +-extrema [e=all-1's] with zero mantissa [m=0] */
- part.l = ( part1 & SIGN_BIT ) | VAX_D_EXPONENT_MASK;
- part2 = 0;
-
- } else {
-
- e >>= IEEE_T_MANTISSA_SIZE; /* Obtain the biased IEEE exponent */
- m = part1 & IEEE_T_MANTISSA_MASK; /* Obtain the IEEE mantissa */
-
- if ( e == 0 ) { /* Denormalized [e=0, m<>0] */
- /* Adjust representation from 2**(1-bias) to 2**(e-bias) */
- m = ( m << 1 ) | ( part2 >> 31 );
- part2 <<= 1;
- while ( ( m & IEEE_T_HIDDEN_BIT ) == 0 ) {
- m = ( m << 1 ) | ( part2 >> 31 );
- part2 <<= 1;
- e -= 1; /* Adjust exponent */
- }
- m &= IEEE_T_MANTISSA_MASK; /* Adjust mantissa to hidden-bit form */
- }
-
- if ( ( e += EXPONENT_ADJUSTMENT ) <= 0 ) {
-
- part.l = 0; /* Silent underflow */
- part2 = 0;
-
- } else if ( e > ( 2 * VAX_D_EXPONENT_BIAS - 1 ) ) {
-
- //raise( SIGFPE );/* Overflow; fixup to VAX +-extrema [e=m=all-1's] */
- return;
- part.l = ( part1 & SIGN_BIT ) | ~SIGN_BIT;
- part2 = ~0;
-
- } else {
-
- /* VAX normalized form [e>0]; zero pad mantissa from 52 to 55 bits */
- part.l = ( part1 & SIGN_BIT ) |
- ( e << ( VAX_D_MANTISSA_SIZE + EXPONENT_LEFT_SHIFT ) ) |
- ( m << EXPONENT_LEFT_SHIFT ) |
- ( part2 >> ( 32 - EXPONENT_LEFT_SHIFT ) );
- part2 <<= EXPONENT_LEFT_SHIFT;
-
- }
-
- }
-#if IS_LITTLE_ENDIAN
- *out++ = part.i[1];
- *out++ = part.i[0];
- part.l = part2;
- *out++ = part.i[1];
- *out++ = part.i[0];
-#else
- *out++ = part.c[1];
- *out++ = part.c[0];
- *out++ = part.c[3];
- *out++ = part.c[2];
- part.l = part2;
- *out++ = part.c[1];
- *out++ = part.c[0];
- *out++ = part.c[3];
- *out++ = part.c[2];
-#endif
- }
-
-}
-
-#undef EXPONENT_ADJUSTMENT
-#undef EXPONENT_RIGHT_SHIFT
-
-#endif /* #ifdef MAKE_TO_VAX_D8 */
-
-/**************************************************************** to_vax_g8() */
-
-#ifdef MAKE_TO_VAX_G8
-
-/* Assert the mantissa in a VAX G_float is the same as in an IEEE T_float */
-#if VAX_G_MANTISSA_MASK != IEEE_T_MANTISSA_MASK
-#error MANTISSA_MASK mismatch in to_vax_g8()
-#endif
-#define MANTISSA_MASK VAX_G_MANTISSA_MASK
-/* If the mantissas are the same, then so are the no. of bits and the hidden */
-/* normalization bit */
-#define MANTISSA_SIZE VAX_G_MANTISSA_SIZE
-#define HIDDEN_BIT VAX_G_HIDDEN_BIT
-
-#define EXPONENT_ADJUSTMENT ( 1 + VAX_G_EXPONENT_BIAS - IEEE_T_EXPONENT_BIAS )
-
-void FORTRAN_LINKAGE to_vax_g8( const void *inbuf, void *outbuf,
- const int *count ) {
-
- register const unsigned int *in; /* Microsoft C: up to 2 register vars */
-#if IS_LITTLE_ENDIAN
- register unsigned short *out; /* Microsoft C: up to 2 register vars */
- union { unsigned short i[2]; unsigned int l; } part;
-#else
- unsigned char *out;
- union { unsigned char c[4]; unsigned int l; } part;
-#endif
- unsigned int part1, part2;
- unsigned int m;
- int n;
- int e;
-
-
- in = (const unsigned int *) inbuf;
-#if IS_LITTLE_ENDIAN
- out = (unsigned short *) outbuf;
-#else
- out = (unsigned char *) outbuf;
-#endif
-
- for ( n = *count; n > 0; n-- ) {
- part1 = *in++;
- part2 = *in++;
- if ( ( ( part1 & ~SIGN_BIT ) | part2 ) == 0 ) {
-
- part.l = 0; /* Set IEEE +-zero [e=m=0] to VAX zero [s=e=m=0] */
- /* part2 = 0; */ /* part2 is already zero */
-
- } else if ( ( e = ( part1 & IEEE_T_EXPONENT_MASK ) ) ==
- IEEE_T_EXPONENT_MASK ) {
-
- /* VAX's have no equivalents for IEEE +-Infinity and +-NaN [e=all-1's] */
- //raise( SIGFPE );
- return;
- /* Fixup to VAX +-extrema [e=all-1's] with zero mantissa [m=0] */
- part.l = ( part1 & SIGN_BIT ) | VAX_G_EXPONENT_MASK;
- part2 = 0;
-
- } else {
-
- e >>= MANTISSA_SIZE; /* Obtain the biased IEEE exponent */
- m = part1 & MANTISSA_MASK; /* Obtain the IEEE mantissa */
-
- if ( e == 0 ) { /* Denormalized [e=0, m<>0] */
- /* Adjust representation from 2**(1-bias) to 2**(e-bias) */
- m = ( m << 1 ) | ( part2 >> 31 );
- part2 <<= 1;
- while ( ( m & HIDDEN_BIT ) == 0 ) {
- m = ( m << 1 ) | ( part2 >> 31 );
- part2 <<= 1;
- e -= 1; /* Adjust exponent */
- }
- m &= MANTISSA_MASK; /* Adjust mantissa to hidden-bit form */
- }
-
- if ( ( e += EXPONENT_ADJUSTMENT ) <= 0 ) {
-
- part.l = 0; /* Silent underflow */
- part2 = 0;
-
- } else if ( e > ( 2 * VAX_D_EXPONENT_BIAS - 1 ) ) {
-
- //raise( SIGFPE );/* Overflow; fixup to VAX +-extrema [e=m=all-1's] */
- return;
- part.l = ( part1 & SIGN_BIT ) | ~SIGN_BIT;
- part2 = ~0;
-
- } else {
-
- /* VAX normalized form [e>0] (both mantissas are 52 bits) */
- part.l = ( part1 & SIGN_BIT ) | ( e << MANTISSA_SIZE ) | m;
- /* part2 is already correct */
-
- }
-
- }
-#if IS_LITTLE_ENDIAN
- *out++ = part.i[1];
- *out++ = part.i[0];
- part.l = part2;
- *out++ = part.i[1];
- *out++ = part.i[0];
-#else
- *out++ = part.c[1];
- *out++ = part.c[0];
- *out++ = part.c[3];
- *out++ = part.c[2];
- part.l = part2;
- *out++ = part.c[1];
- *out++ = part.c[0];
- *out++ = part.c[3];
- *out++ = part.c[2];
-#endif
- }
-
-}
-
-#undef MANTISSA_MASK
-#undef MANTISSA_SIZE
-#undef HIDDEN_BIT
-#undef EXPONENT_ADJUSTMENT
-
-#endif /* #ifdef MAKE_TO_VAX_G8 */
-
-/*************************************************************** to_vax_h16() */
-
-#ifdef MAKE_TO_VAX_H16
-
-/* Assert the mantissa in a VAX H_float is the same as in an IEEE X_float */
-#if VAX_H_MANTISSA_MASK != IEEE_X_MANTISSA_MASK
-#error MANTISSA_MASK mismatch in to_vax_h16()
-#endif
-#define MANTISSA_MASK VAX_H_MANTISSA_MASK
-/* If the mantissas are the same, then so are the no. of bits and the hidden */
-/* normalization bit */
-#define MANTISSA_SIZE VAX_H_MANTISSA_SIZE
-#define HIDDEN_BIT VAX_H_HIDDEN_BIT
-
-#define EXPONENT_ADJUSTMENT ( 1 + VAX_H_EXPONENT_BIAS - IEEE_X_EXPONENT_BIAS )
-
-void FORTRAN_LINKAGE to_vax_h16( const void *inbuf, void *outbuf,
- const int *count ) {
-
- register const unsigned int *in; /* Microsoft C: up to 2 register vars */
-#if IS_LITTLE_ENDIAN
- register unsigned short *out; /* Microsoft C: up to 2 register vars */
- union { unsigned short i[2]; unsigned int l; } part;
-#else
- unsigned char *out;
- union { unsigned char c[4]; unsigned int l; } part;
-#endif
- unsigned int part1, part2, part3, part4;
- unsigned int m;
- int n;
- int e;
-
-
- in = (const unsigned int *) inbuf;
-#if IS_LITTLE_ENDIAN
- out = (unsigned short *) outbuf;
-#else
- out = (unsigned char *) outbuf;
-#endif
-
- for ( n = *count; n > 0; n-- ) {
- part1 = *in++;
- part2 = *in++;
- part3 = *in++;
- part4 = *in++;
- if ( ( ( part1 & ~SIGN_BIT ) | part2 | part3 | part4 ) == 0 ) {
-
- part.l = 0; /* Set IEEE +-zero [e=m=0] to VAX zero [s=e=m=0] */
- /* part2 = 0; */ /* part2, part3, and part4 are already zero */
- /* part3 = 0; */
- /* part4 = 0; */
-
- } else if ( ( e = ( part1 & IEEE_X_EXPONENT_MASK ) ) ==
- IEEE_X_EXPONENT_MASK ) {
-
- /* VAX's have no equivalents for IEEE +-Infinity and +-NaN [e=all-1's] */
- //raise( SIGFPE );
- return;
- /* Fixup to VAX +-extrema [e=all-1's] with zero mantissa [m=0] */
- part.l = ( part1 & SIGN_BIT ) | VAX_H_EXPONENT_MASK;
- part2 = 0;
- part3 = 0;
- part4 = 0;
-
- } else {
-
- e >>= MANTISSA_SIZE; /* Obtain the biased IEEE exponent */
- m = part1 & MANTISSA_MASK; /* Obtain the IEEE mantissa */
-
- if ( e == 0 ) { /* Denormalized [e=0, m<>0] */
- /* Adjust representation from 2**(1-bias) to 2**(e-bias) */
- m = ( m << 1 ) | ( part2 >> 31 );
- part2 <<= 1;
- while ( ( m & HIDDEN_BIT ) == 0 ) {
- m = ( m << 1 ) | ( part2 >> 31 );
- part2 = ( part2 << 1 ) | ( part3 >> 31 );
- part3 = ( part3 << 1 ) | ( part4 >> 31 );
- part4 <<= 1;
- e -= 1; /* Adjust exponent */
- }
- m &= MANTISSA_MASK; /* Adjust mantissa to hidden-bit form */
- }
-
- if ( ( e += EXPONENT_ADJUSTMENT ) <= 0 ) {
-
- part.l = 0; /* Silent underflow */
- part2 = 0;
- part3 = 0;
- part4 = 0;
-
- } else if ( e > ( 2 * VAX_H_EXPONENT_BIAS - 1 ) ) {
-
- //raise( SIGFPE );/* Overflow; fixup to VAX +-extrema [e=m=all-1's] */
- return;
- part.l = ( part1 & SIGN_BIT ) | ~SIGN_BIT;
- part2 = ~0;
- part3 = ~0;
- part4 = ~0;
-
- } else {
-
- /* VAX normalized form [e>0] (both mantissas are 112 bits) */
- part.l = ( part1 & SIGN_BIT ) | ( e << MANTISSA_SIZE ) | m;
- /* part2, part3, and part4 are already correct */
-
- }
-
- }
-#if IS_LITTLE_ENDIAN
- *out++ = part.i[1];
- *out++ = part.i[0];
- part.l = part2;
- *out++ = part.i[1];
- *out++ = part.i[0];
- part.l = part3;
- *out++ = part.i[1];
- *out++ = part.i[0];
- part.l = part4;
- *out++ = part.i[1];
- *out++ = part.i[0];
-#else
- *out++ = part.c[1];
- *out++ = part.c[0];
- *out++ = part.c[3];
- *out++ = part.c[2];
- part.l = part2;
- *out++ = part.c[1];
- *out++ = part.c[0];
- *out++ = part.c[3];
- *out++ = part.c[2];
- part.l = part3;
- *out++ = part.c[1];
- *out++ = part.c[0];
- *out++ = part.c[3];
- *out++ = part.c[2];
- part.l = part4;
- *out++ = part.c[1];
- *out++ = part.c[0];
- *out++ = part.c[3];
- *out++ = part.c[2];
-#endif
- }
-
-}
-
-#undef MANTISSA_MASK
-#undef MANTISSA_SIZE
-#undef HIDDEN_BIT
-#undef EXPONENT_ADJUSTMENT
-
-#endif /* #ifdef MAKE_TO_VAX_H16 */
diff --git a/modules/io/src/img/convert_vax_data.h b/modules/io/src/img/convert_vax_data.h
deleted file mode 100755
index e8e0577808ea4656c94bbe17ff7481831d80e3e4..0000000000000000000000000000000000000000
--- a/modules/io/src/img/convert_vax_data.h
+++ /dev/null
@@ -1,263 +0,0 @@
-/******************************************************************************
- * *
- * convert_vax_data.h - Convert VAX-format data to/from Unix (IEEE) format. *
- * *
- * from_vax_i2() - Byte swap Integer*2 *
- * from_vax_i4() - Byte reverse Integer*4 *
- * from_vax_r4() - 32-bit VAX F_floating to IEEE S_floating *
- * from_vax_d8() - 64-bit VAX D_floating to IEEE T_floating *
- * from_vax_g8() - 64-bit VAX G_floating to IEEE T_floating *
- * from_vax_h16() - 128-bit VAX H_floating to Alpha X_floating *
- * *
- * to_vax_i2() - Byte swap Integer*2 *
- * to_vax_i4() - Byte reverse Integer*4 *
- * to_vax_r4() - 32-bit IEEE S_floating to VAX F_floating *
- * to_vax_d8() - 64-bit IEEE T_floating to VAX D_floating *
- * to_vax_g8() - 64-bit IEEE T_floating to VAX G_floating *
- * to_vax_h16() - 128-bit Alpha X_floating to VAX H_floating *
- * *
- * All calls take 3 arguments: *
- * *
- * C declaration: #include "convert_vax_data.h" *
- * usage: name( in_array, out_array, &count ); *
- * *
- * Fortran usage: Call NAME( in_array, out_array, count ) *
- * *
- * The in_array and out_array parameters may refer to the same object. *
- * *
- * *
- * VAXes (as well as the Intel 80x86 family) store integers in 2's complement *
- * format, ordering the bytes in memory from low-order to high-order (collo- *
- * quially called little-endian format). Most Unix machines (Sun, IBM, HP) *
- * also store integers in 2's complement format, but use the opposite (so *
- * called big-endian) byte ordering. *
- * *
- * A VAX integer is converted to (big-endian) Unix format by reversing the *
- * byte order. *
- * *
- * Most Unix machines implement the ANSI/IEEE 754-1985 floating-point arith- *
- * metic standard. VAX and IEEE formats are similar (after byte-swapping). *
- * The high-order bit is a sign bit (s). This is followed by a biased expo- *
- * nent (e), and a (usually) hidden-bit normalized mantissa (m). They differ *
- * in the number used to bias the exponent, the location of the implicit bi- *
- * nary point for the mantissa, and the representation of exceptional numbers *
- * (e.g., +/-infinity). *
- * *
- * VAX floating-point formats: (-1)^s * 2^(e-bias) * 0.1m *
- * *
- * 31 15 0 *
- * | | | *
- * F_floating mmmmmmmmmmmmmmmmseeeeeeeemmmmmmm bias = 128 *
- * D_floating mmmmmmmmmmmmmmmmseeeeeeeemmmmmmm bias = 128 *
- * mmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmm *
- * G_floating mmmmmmmmmmmmmmmmseeeeeeeeeeemmmm bias = 1024 *
- * mmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmm *
- * H_floating mmmmmmmmmmmmmmmmseeeeeeeeeeeeeee bias = 16384 *
- * mmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmm *
- * mmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmm *
- * mmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmm *
- * *
- * IEEE floating-point formats: (-1)^s * 2^(e-bias) * 1.m *
- * *
- * 31 15 0 *
- * | | | *
- * S_floating seeeeeeeemmmmmmmmmmmmmmmmmmmmmmm bias = 127 *
- * T_floating seeeeeeeeeeemmmmmmmmmmmmmmmmmmmm bias = 1023 *
- * mmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmm *
- * X_floating seeeeeeeeeeeeeeemmmmmmmmmmmmmmmm bias = 16383 *
- * mmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmm *
- * mmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmm *
- * mmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmm *
- * *
- * A VAX floating-point number is converted to IEEE floating-point format by *
- * subtracting (1+VAX_bias-IEEE_bias) from the exponent field to (1) adjust *
- * from VAX 0.1m hidden-bit normalization to IEEE 1.m hidden-bit normaliza- *
- * tion and (2) adjust the bias from VAX format to IEEE format. True zero *
- * [s=e=m=0] and dirty zero [s=e=0, m<>0] are special cases which must be *
- * recognized and handled separately. *
- * *
- * Numbers whose absolute value is too small to represent in the normalized *
- * IEEE format illustrated above are converted to subnormal form [e=0, m>0]: *
- * (-1)^s * 2^(1-bias) * 0.m. Numbers whose absolute value is too small to *
- * represent in subnormal form are set to 0.0 (silent underflow). *
- * *
- * Note: If the fractional part of the VAX floating-point number is too large *
- * for the corresponding IEEE floating-point format, bits are simply *
- * discarded from the right. Thus, the remaining fractional part is *
- * chopped, not rounded to the lowest-order bit. This can only occur *
- * when the conversion requires IEEE subnormal form. *
- * *
- * A VAX floating-point reserved operand [s=1, e=0, m=any] causes a SIGFPE *
- * exception to be raised. The converted result is set to zero. *
- * *
- * Conversely, an IEEE floating-point number is converted to VAX floating- *
- * point format by adding (1+VAX_bias-IEEE_bias) to the exponent field. *
- * +zero [s=e=m=0], -zero [s=1, e=m=0], infinities [s=X, e=all-1's, m=0], and *
- * NaNs [s=X, e=all-1's, m<>0] are special cases which must be recognized and *
- * handled separately. Infinities and NaNs cause a SIGFPE exception to be *
- * raised. The result returned has the largest VAX exponent [e=all-1's] and *
- * zero mantissa [m=0] with the same sign as the original. *
- * *
- * Numbers whose absolute value is too small to represent in the normalized *
- * VAX format illustrated above are set to 0.0 (silent underflow). (VAX *
- * floating-point format does not support subnormal numbers.) Numbers whose *
- * absolute value exceeds the largest representable VAX-format number cause a *
- * SIGFPE exception to be raised (overflow). (VAX floating-point format does *
- * not have reserved bit patterns for infinities and not-a-numbers [NaNs].) *
- * The result returned has the largest VAX exponent and mantissa [e=m= *
- * all-1's] with the same sign as the original. *
- * *
- * *
- * Two variants of convert_vax_data.c are available using IS_LITTLE_ENDIAN *
- * and APPEND_UNDERSCORE. If IS_LITTLE_ENDIAN is defined as 0 (false), then *
- * the conversions are performed for a big-endian machine, i.e., byte reor- *
- * dering is performed for all data types. If IS_LITTLE_ENDIAN is defined as *
- * 1 (true), then no reordering is performed. (Integers are identical to VAX *
- * format.) *
- * *
- * If IS_LITTLE_ENDIAN is not defined, then it is defined as 1 (true) if any *
- * of the following macros are defined: *
- * *
- * vax __vax vms __vms __alpha DEC VAX C, GNU C on a DEC VAX or a DEC *
- * Alpha, DEC C *
- * M_I86 _M_IX86 __M_ALPHA Microsoft 80x86 C or Microsoft Visual C++ *
- * on an Intel x86 or a DEC Alpha *
- * i386 __i386 Sun C, GNU C, or Intel C on an Intel x86 *
- * __x86_64 __x86_64__ GNU C or Portland Group C on an AMD *
- * Opteron or an Intel EM64T *
- * *
- * If APPEND_UNDERSCORE is defined, the entry point names are compiled with *
- * an underscore appended. This is required so that they can be called by *
- * Fortran in cases where the Fortran compiler appends an underscore to *
- * externally called routines (e.g., Sun Fortran). *
- * *
- * Normally, all routines are compiled into a single object module. To com- *
- * pile a single routine into its own module, define MAKE_routine_name, sub- *
- * stituting the upper-case name of the routine for routine_name. For exam- *
- * ple, MAKE_TO_VAX_I2. (This is useful, for example, to insert the routines *
- * into a library such that a linker may extract only the routines actually *
- * needed by a particular program.) *
- * *
- * convert_vax_data.c assumes an ANSI C compiler, 8-bit chars, 16-bit shorts, *
- * and 32-bit ints. *
- * *
- * *
- * References: ANSI/IEEE Std 754-1985, IEEE Standard for Binary Floating- *
- * Point Arithmetic, Institute of Electrical and Electronics *
- * Engineers *
- * Brunner, Richard A., Ed., 1991, VAX Architecture Reference *
- * Manual, Second Edition, Digital Press *
- * Sites, Richard L., and Witek, Richard T., 1995, Alpha AXP *
- * Architecture Reference Manual, Second Edition, Digital *
- * Press *
- * *
- * Author: Lawrence M. Baker *
- * U.S. Geological Survey *
- * 345 Middlefield Road MS977 *
- * Menlo Park, CA 94025 *
- * baker@usgs.gov *
- * *
- * Citation: Baker, L.M., 2005, libvaxdata: VAX Data Format Conversion *
- * Routines: U.S. Geological Survey Open-File Report 2005- *
- * 1424 (http://pubs.usgs.gov/of/2005/1424/). *
- * *
- * *
- * Disclaimer *
- * *
- * Although this program has been used by the USGS, no warranty, expressed or *
- * implied, is made by the USGS or the United States Government as to the *
- * accuracy and functioning of the program and related program material, nor *
- * shall the fact of distribution constitute any such warranty, and no *
- * responsibility is assumed by the USGS in connection therewith. *
- * *
- * *
- * Modification History: *
- * *
- * 8-Mar-2001 L. M. Baker Original version. *
- * Define upcased and underscore-appended *
- * variants. *
- * 9-Mar-2001 L. M. Baker Add #ifndef _CONVERT_VAX_DATA guard. *
- * 16-Sep-2005 L. M. Baker Correct the diagram of IEEE X_floating *
- * (exponent is 15 bits, not 11 bits). *
- * 19-Sep-2005 L. M. Baker Add fixups for IEEE-to-VAX conversion *
- * faults (+-infinity, +-NaN, overflow). *
- * 8-Nov-2005 L. M. Baker Move #define const if not __STDC__ from *
- * convert_vax_data.c *
- * *
- ******************************************************************************/
-
-#ifndef _CONVERT_VAX_DATA
-#define _CONVERT_VAX_DATA
-
-#ifndef FORTRAN_LINKAGE
-#define FORTRAN_LINKAGE
-#endif
-
-#ifdef UPCASE
-
-#define from_vax_i2 FROM_VAX_I2
-#define from_vax_i4 FROM_VAX_I4
-#define from_vax_r4 FROM_VAX_R4
-#define from_vax_d8 FROM_VAX_D8
-#define from_vax_g8 FROM_VAX_G8
-#define from_vax_h16 FROM_VAX_H16
-
-#define to_vax_i2 TO_VAX_I2
-#define to_vax_i4 TO_VAX_I4
-#define to_vax_r4 TO_VAX_R4
-#define to_vax_d8 TO_VAX_D8
-#define to_vax_g8 TO_VAX_G8
-#define to_vax_h16 TO_VAX_H16
-
-#endif
-
-#ifdef APPEND_UNDERSCORE
-
-#define from_vax_i2 from_vax_i2##_
-#define from_vax_i4 from_vax_i4##_
-#define from_vax_r4 from_vax_r4##_
-#define from_vax_d8 from_vax_d8##_
-#define from_vax_g8 from_vax_g8##_
-#define from_vax_h16 from_vax_h16##_
-
-#define to_vax_i2 to_vax_i2##_
-#define to_vax_i4 to_vax_i4##_
-#define to_vax_r4 to_vax_r4##_
-#define to_vax_d8 to_vax_d8##_
-#define to_vax_g8 to_vax_g8##_
-#define to_vax_h16 to_vax_h16##_
-
-#endif
-
-/* const is ANSI C, C++ only */
-#if !defined( __STDC__ ) && !defined( __cplusplus )
-#define const
-#endif
-
-void FORTRAN_LINKAGE from_vax_i2( const void *inbuf, void *outbuf,
- const int *count );
-void FORTRAN_LINKAGE from_vax_i4( const void *inbuf, void *outbuf,
- const int *count );
-void FORTRAN_LINKAGE from_vax_r4( const void *inbuf, void *outbuf,
- const int *count );
-void FORTRAN_LINKAGE from_vax_d8( const void *inbuf, void *outbuf,
- const int *count );
-void FORTRAN_LINKAGE from_vax_g8( const void *inbuf, void *outbuf,
- const int *count );
-void FORTRAN_LINKAGE from_vax_h16( const void *inbuf, void *outbuf,
- const int *count );
-
-void FORTRAN_LINKAGE to_vax_i2( const void *inbuf, void *outbuf,
- const int *count );
-void FORTRAN_LINKAGE to_vax_i4( const void *inbuf, void *outbuf,
- const int *count );
-void FORTRAN_LINKAGE to_vax_r4( const void *inbuf, void *outbuf,
- const int *count );
-void FORTRAN_LINKAGE to_vax_d8( const void *inbuf, void *outbuf,
- const int *count );
-void FORTRAN_LINKAGE to_vax_g8( const void *inbuf, void *outbuf,
- const int *count );
-void FORTRAN_LINKAGE to_vax_h16( const void *inbuf, void *outbuf,
- const int *count );
-
-#endif /* #ifndef _CONVERT_VAX_DATA */
diff --git a/modules/io/src/img/image_format.hh b/modules/io/src/img/image_format.hh
index 95a6113677385c708adb1241ea47804169bffa59..97603f9181095a3c33b83c47998edf50fc0463df 100644
--- a/modules/io/src/img/image_format.hh
+++ b/modules/io/src/img/image_format.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/io/src/img/image_format_conversion.cc b/modules/io/src/img/image_format_conversion.cc
deleted file mode 100644
index 2fa3ddc99168b02bce3b86f7013daac438bd8e87..0000000000000000000000000000000000000000
--- a/modules/io/src/img/image_format_conversion.cc
+++ /dev/null
@@ -1,110 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2011 by the OpenStructure authors
-// Copyright (C) 2003-2010 by the IPLT authors
-//
-// This library 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 3.0 of the License, or (at your option)
-// any later version.
-// This library 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 Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
-//------------------------------------------------------------------------------
-
-/*
- wrapper around Lawrence Baker's vax conversion routines
-
- Author: Ansgar Philippsen
-*/
-
-#ifndef IMG_IMAGE_FORMAT_H
-#error "image_format_conversion.cc must be included from image_format.hh"
-#endif
-
-#include <ost/message.hh>
-#include <ost/io/io_exception.hh>
-
-extern "C" {
-#include "convert_vax_data.h"
-}
-
-namespace ost { namespace io {
-
-template<typename T>
-inline
-void VaxToIEEE(T* t,unsigned int n);
-
-template<>
-inline
-void VaxToIEEE(char* t,unsigned int n)
-{
- // noop
-}
-
-template<>
-inline
-void VaxToIEEE(unsigned char* t,unsigned int n)
-{
- // noop
-}
-
-template<>
-inline
-void VaxToIEEE(float* t,unsigned int n)
-{
- static int count[]={0};
- count[0]=n;
- from_vax_r4(t,t,count);
-}
-
-template<>
-inline
-void VaxToIEEE(int* t,unsigned int n)
-{
- static int count[]={0};
- count[0]=n;
- from_vax_i4(t,t,count);
-}
-
-template<>
-inline
-void VaxToIEEE(unsigned int* t,unsigned int n)
-{
- static int count[]={0};
- count[0]=n;
- from_vax_i4(t,t,count);
-}
-
-template<>
-inline
-void VaxToIEEE(short* t,unsigned int n)
-{
- static int count[]={0};
- count[0]=n;
- from_vax_i2(t,t,count);
-}
-
-template<>
-inline
-void VaxToIEEE(unsigned short* t,unsigned int n)
-{
- static int count[]={0};
- count[0]=n;
- from_vax_i2(t,t,count);
-}
-
-template<typename T>
-inline
-void VaxToIEEE(T* t,unsigned int n)
-{
- throw IOException("unsupported VaxToIEEE conversion");
-}
-
-}} // ns
diff --git a/modules/io/src/img/image_io_plugin.hh b/modules/io/src/img/image_io_plugin.hh
index 2700d45096758c042324c3dc6d5ece09821f72e0..0fcc421fb5f6ec5b58d146be4ce33cc00c8fd3d0 100644
--- a/modules/io/src/img/image_io_plugin.hh
+++ b/modules/io/src/img/image_io_plugin.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/io/src/img/jpk_util.hh b/modules/io/src/img/jpk_util.hh
index b0bcf89da599aae831adadfb18528dd8f2038448..f704ba4213c107873af7eed582f01c81dfb8954c 100644
--- a/modules/io/src/img/jpk_util.hh
+++ b/modules/io/src/img/jpk_util.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
//
diff --git a/modules/io/src/img/load_map.cc b/modules/io/src/img/load_map.cc
index dfb61702b0aefcdbba6e29b33623d91e19c0dc6f..4256e2bf0bb289eb8d58d3dd4da84497ba52d6a0 100644
--- a/modules/io/src/img/load_map.cc
+++ b/modules/io/src/img/load_map.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
//
diff --git a/modules/io/src/img/load_map.hh b/modules/io/src/img/load_map.hh
index 5f012919fffe8143175107ed6956e4fc40588450..0a7e60c5995aea5f7fcdf1ef83ee01dd9d2c72db 100644
--- a/modules/io/src/img/load_map.hh
+++ b/modules/io/src/img/load_map.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/io/src/img/map_io_dat_handler.cc b/modules/io/src/img/map_io_dat_handler.cc
index 4fdd6e285c2dc8fd0e2bbc2fd39f596b6edf2fa9..e599bf51c144b4f40974776130e77c5bdb08b2e3 100644
--- a/modules/io/src/img/map_io_dat_handler.cc
+++ b/modules/io/src/img/map_io_dat_handler.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/io/src/img/map_io_dat_handler.hh b/modules/io/src/img/map_io_dat_handler.hh
index 4bc8ce268649c65cc45ebd6ae5d9eb4139b2c615..9061495033db61f0b4b1d4985a2efe5785e1699e 100644
--- a/modules/io/src/img/map_io_dat_handler.hh
+++ b/modules/io/src/img/map_io_dat_handler.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/io/src/img/map_io_df3_handler.cc b/modules/io/src/img/map_io_df3_handler.cc
index f035b5cccb0be47aa8cab8fc5baf1bdb4356d258..2f49ab4616cb355b85beaab5003770c28a228888 100644
--- a/modules/io/src/img/map_io_df3_handler.cc
+++ b/modules/io/src/img/map_io_df3_handler.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/io/src/img/map_io_df3_handler.hh b/modules/io/src/img/map_io_df3_handler.hh
index 53fb9bfd15555241c101a7581d1764887178135f..48d7e6f4143f0624cedfce899b16f114be250411 100644
--- a/modules/io/src/img/map_io_df3_handler.hh
+++ b/modules/io/src/img/map_io_df3_handler.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/io/src/img/map_io_dm3_handler.cc b/modules/io/src/img/map_io_dm3_handler.cc
index 6e7e5681637c4115224fa0e35ca29ec5f91b0992..c7b3351ec81e7eb84f3e58a373dbe653e417d8e8 100644
--- a/modules/io/src/img/map_io_dm3_handler.cc
+++ b/modules/io/src/img/map_io_dm3_handler.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/io/src/img/map_io_dm3_handler.hh b/modules/io/src/img/map_io_dm3_handler.hh
index 97191f67ef9456c3c3d5e804ec9a8011454daea2..0d48a32650571167dda673e0ee630f445411dbce 100644
--- a/modules/io/src/img/map_io_dm3_handler.hh
+++ b/modules/io/src/img/map_io_dm3_handler.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/io/src/img/map_io_dx_handler.cc b/modules/io/src/img/map_io_dx_handler.cc
index 4c823edc1497e80a156ab273cafd3eaa67af9357..ef43ef502ef7092ecbf97a12930366ac3a80e58a 100644
--- a/modules/io/src/img/map_io_dx_handler.cc
+++ b/modules/io/src/img/map_io_dx_handler.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/io/src/img/map_io_dx_handler.hh b/modules/io/src/img/map_io_dx_handler.hh
index ca4ee55c2c71066b80c22d5a2dcab987b04492e2..2c3883d8dd1ab4f59a8ffe4258f4d22d659477a8 100644
--- a/modules/io/src/img/map_io_dx_handler.hh
+++ b/modules/io/src/img/map_io_dx_handler.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
//
diff --git a/modules/io/src/img/map_io_handler.hh b/modules/io/src/img/map_io_handler.hh
index 163d0241399d94ee06061a5a844602b9b3c8f971..4cab4e891e717ffe3556764b35367b033b369b4b 100644
--- a/modules/io/src/img/map_io_handler.hh
+++ b/modules/io/src/img/map_io_handler.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/io/src/img/map_io_ipl_handler.cc b/modules/io/src/img/map_io_ipl_handler.cc
index a61715908fba718173e7af9b347e7ca7a5f3eaa7..13749047f019fcc23abd8f250fdba73d1eaa647f 100644
--- a/modules/io/src/img/map_io_ipl_handler.cc
+++ b/modules/io/src/img/map_io_ipl_handler.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/io/src/img/map_io_ipl_handler.hh b/modules/io/src/img/map_io_ipl_handler.hh
index 3e76ac9895c0689defe002d0399359e03f3e09aa..97de7c67c78b9f02291f87b66107d2543b5772ba 100644
--- a/modules/io/src/img/map_io_ipl_handler.hh
+++ b/modules/io/src/img/map_io_ipl_handler.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/io/src/img/map_io_jpk_handler.cc b/modules/io/src/img/map_io_jpk_handler.cc
index 6092503496f63c37bb7b8c688d9edab95015700d..3225ef8717b78fde842aa9df778b65e4c5349e46 100644
--- a/modules/io/src/img/map_io_jpk_handler.cc
+++ b/modules/io/src/img/map_io_jpk_handler.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/io/src/img/map_io_jpk_handler.hh b/modules/io/src/img/map_io_jpk_handler.hh
index aeaf2c54e960896b74e9a3cf056a8d69fa5beb76..7ee93968f9928a29603f43709c2daee9221e3819 100644
--- a/modules/io/src/img/map_io_jpk_handler.hh
+++ b/modules/io/src/img/map_io_jpk_handler.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/io/src/img/map_io_mrc_handler.cc b/modules/io/src/img/map_io_mrc_handler.cc
index 9d1740abbd6a1b0b20e463ee166514af472d477a..65ce4691a279a483aa6d1b58603718d32130b865 100644
--- a/modules/io/src/img/map_io_mrc_handler.cc
+++ b/modules/io/src/img/map_io_mrc_handler.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/io/src/img/map_io_mrc_handler.hh b/modules/io/src/img/map_io_mrc_handler.hh
index d8e2e9710dfa15eb688bd8594fb055923e3d1c11..9c5f90a9634791bd5062584db89fa5b3eec891a6 100644
--- a/modules/io/src/img/map_io_mrc_handler.hh
+++ b/modules/io/src/img/map_io_mrc_handler.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/io/src/img/map_io_nanoscope_handler.cc b/modules/io/src/img/map_io_nanoscope_handler.cc
index 64f7c17af2d251455e14fb36d35b4a874a8eb9c2..f0abdd7127c8c74897e54542532ae0367a23a4d1 100644
--- a/modules/io/src/img/map_io_nanoscope_handler.cc
+++ b/modules/io/src/img/map_io_nanoscope_handler.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/io/src/img/map_io_nanoscope_handler.hh b/modules/io/src/img/map_io_nanoscope_handler.hh
index 35bfea6115fae2742e9c37f522dbc32a5ad49b96..f4bae5260615280db6957b0f8a0fb6810a3a1ff1 100644
--- a/modules/io/src/img/map_io_nanoscope_handler.hh
+++ b/modules/io/src/img/map_io_nanoscope_handler.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/io/src/img/map_io_png_handler.cc b/modules/io/src/img/map_io_png_handler.cc
index 61156a58b2121bb00b698455906a9733125f3907..345796c075d1b69c4ff886ae81dbe8a42389f84b 100644
--- a/modules/io/src/img/map_io_png_handler.cc
+++ b/modules/io/src/img/map_io_png_handler.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/io/src/img/map_io_png_handler.hh b/modules/io/src/img/map_io_png_handler.hh
index 337ccc1dfdd00d9c8b085f8e7b90518487fb57e1..dac33489acbdc61939123b8176fc80f6fb925a2c 100644
--- a/modules/io/src/img/map_io_png_handler.hh
+++ b/modules/io/src/img/map_io_png_handler.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/io/src/img/map_io_situs_handler.cc b/modules/io/src/img/map_io_situs_handler.cc
index 5de368e2a77698723e5dfb4dda0221c634e84880..1ff47c99f66fa99668eaacaa4f7ea89684b6424e 100644
--- a/modules/io/src/img/map_io_situs_handler.cc
+++ b/modules/io/src/img/map_io_situs_handler.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/io/src/img/map_io_situs_handler.hh b/modules/io/src/img/map_io_situs_handler.hh
index 4b5a1a360d225505ec7b9e0e1065f656a5f2f76e..77ab77640300b65e293586479b872ec879fcb311 100644
--- a/modules/io/src/img/map_io_situs_handler.hh
+++ b/modules/io/src/img/map_io_situs_handler.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/io/src/img/map_io_spi_handler.cc b/modules/io/src/img/map_io_spi_handler.cc
index ad261daf908ec2bc0294f9b52e56a0d345d8553f..36a08bb3ae383ec53999f9878ff795ca5d36f3c2 100644
--- a/modules/io/src/img/map_io_spi_handler.cc
+++ b/modules/io/src/img/map_io_spi_handler.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/io/src/img/map_io_spi_handler.hh b/modules/io/src/img/map_io_spi_handler.hh
index aa6f9a438251da75e2699e40d944ea1a7c9f0750..e0170d8519c9e5eb81db84520ff97f266d24ed5b 100644
--- a/modules/io/src/img/map_io_spi_handler.hh
+++ b/modules/io/src/img/map_io_spi_handler.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/io/src/img/map_io_tiff_handler.cc b/modules/io/src/img/map_io_tiff_handler.cc
index cd0ad364c112f65118498e292194cc1749f9e422..5de5b240fb5d0293508ea850044783084bfde6c3 100644
--- a/modules/io/src/img/map_io_tiff_handler.cc
+++ b/modules/io/src/img/map_io_tiff_handler.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/io/src/img/map_io_tiff_handler.hh b/modules/io/src/img/map_io_tiff_handler.hh
index c3efe901796fbd45b285d48eb2eacbd7768cd90c..715743c057513e106e327cf37472b3f484c33e2f 100644
--- a/modules/io/src/img/map_io_tiff_handler.hh
+++ b/modules/io/src/img/map_io_tiff_handler.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/io/src/img/tiff_util.cc b/modules/io/src/img/tiff_util.cc
index 053f179766865a3cdb3d4a64553c55f59b7268e0..701b94e496bd37aca4596897d56a9767808ea8c5 100644
--- a/modules/io/src/img/tiff_util.cc
+++ b/modules/io/src/img/tiff_util.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/io/src/img/tiff_util.hh b/modules/io/src/img/tiff_util.hh
index 76de383f7c2e227fea4bd4acd6d5f6e800417fc7..81b72d2d7e4b852e0b5469ce085676676d4e09cf 100644
--- a/modules/io/src/img/tiff_util.hh
+++ b/modules/io/src/img/tiff_util.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/io/src/io_exception.hh b/modules/io/src/io_exception.hh
index 782565d2c5561b7067a5b280a3dff45738b74efc..0547519a62fb858682d869a59fb947cfa91ca28b 100644
--- a/modules/io/src/io_exception.hh
+++ b/modules/io/src/io_exception.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/io_manager.cc b/modules/io/src/io_manager.cc
index cfd288c75ea302e8c6ece75af15593c92a74dad8..61f880d46d4a63e4061334cbf796db8eb99c48f1 100644
--- a/modules/io/src/io_manager.cc
+++ b/modules/io/src/io_manager.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/io_manager.hh b/modules/io/src/io_manager.hh
index 18297af6d03fda77784aca5593c2d6a0d2f63012..4a6e9d26664fca61b7eae266b57becd809137bd7 100644
--- a/modules/io/src/io_manager.hh
+++ b/modules/io/src/io_manager.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/io_utils.cc b/modules/io/src/io_utils.cc
index d47cc94fdec360c99c0385e64bbfb677bcb46a4f..7db9a10c370e2e9538c814e9a6dfc16412b58228 100644
--- a/modules/io/src/io_utils.cc
+++ b/modules/io/src/io_utils.cc
@@ -2,7 +2,7 @@
// This file is part of the OpenStructure project <www.openstructure.org>
//
// Copyright (C) 2003-2010 by the IPLT authors
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/io_utils.hh b/modules/io/src/io_utils.hh
index aafd33a7920a3404cec46dfbad7c87153ff4ba99..af15c1235766415699c773cc26ceb776808e501d 100644
--- a/modules/io/src/io_utils.hh
+++ b/modules/io/src/io_utils.hh
@@ -2,7 +2,7 @@
// This file is part of the OpenStructure project <www.openstructure.org>
//
// Copyright (C) 2003-2010 by the IPLT authors
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/module_config.hh b/modules/io/src/module_config.hh
index 83f2f1a1bf768336a7426199c978878504a96f66..1d12e0b52feaca7a6c330a96a9dc2f325f24ab70 100644
--- a/modules/io/src/module_config.hh
+++ b/modules/io/src/module_config.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/mol/chemdict_parser.hh b/modules/io/src/mol/chemdict_parser.hh
index 16c968252faf07a0dc9ba3efcde81e9ef18d2dcc..d42fe9a223f39b4805991e017ff1e7df34e7809e 100644
--- a/modules/io/src/mol/chemdict_parser.hh
+++ b/modules/io/src/mol/chemdict_parser.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/mol/dcd_io.cc b/modules/io/src/mol/dcd_io.cc
index e81d3135144fd4c9aef7439b0f482726a72c8cd1..ec31b4bbf88694f714854645845557c42485a1e2 100644
--- a/modules/io/src/mol/dcd_io.cc
+++ b/modules/io/src/mol/dcd_io.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/mol/dcd_io.hh b/modules/io/src/mol/dcd_io.hh
index dded28a462727caeffb9d396092c2334819d667a..2afd163e3ac4dd13aecd07414ff6747ec9331792 100644
--- a/modules/io/src/mol/dcd_io.hh
+++ b/modules/io/src/mol/dcd_io.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/mol/entity_io_crd_handler.cc b/modules/io/src/mol/entity_io_crd_handler.cc
index 3d858fcc6243f21e7125234548e43e297892763c..1c2c2327e5b3079eb9a9394d67d47f08bf96eb5f 100644
--- a/modules/io/src/mol/entity_io_crd_handler.cc
+++ b/modules/io/src/mol/entity_io_crd_handler.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/mol/entity_io_crd_handler.hh b/modules/io/src/mol/entity_io_crd_handler.hh
index 3781fcda4e3305307c7bf61b6fb65f38ed27736a..b12cb5187e357db221eaa319686fb968492c5e1f 100644
--- a/modules/io/src/mol/entity_io_crd_handler.hh
+++ b/modules/io/src/mol/entity_io_crd_handler.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/mol/entity_io_handler.hh b/modules/io/src/mol/entity_io_handler.hh
index 709b0762317192d4c6488534b1a52d03f3c6fd56..78116c81b024588cb59c81083a70de2b6172785a 100644
--- a/modules/io/src/mol/entity_io_handler.hh
+++ b/modules/io/src/mol/entity_io_handler.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/mol/entity_io_mae_handler.cc b/modules/io/src/mol/entity_io_mae_handler.cc
index ca9590169c4b69e2399183a6fade389665789184..98e4a830f0ca4ffd672b4d69464ca49bf8edac25 100644
--- a/modules/io/src/mol/entity_io_mae_handler.cc
+++ b/modules/io/src/mol/entity_io_mae_handler.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/mol/entity_io_mae_handler.hh b/modules/io/src/mol/entity_io_mae_handler.hh
index 7f923d3453ed60090a615b14fa2d44c20996d817..6c032dc32effb5b63d973157bc38f26f839ed28e 100644
--- a/modules/io/src/mol/entity_io_mae_handler.hh
+++ b/modules/io/src/mol/entity_io_mae_handler.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/mol/entity_io_mmcif_handler.cc b/modules/io/src/mol/entity_io_mmcif_handler.cc
index a86d1dcebda7cc5ec73791d706b482bd6ecdb9e7..68955f3fd85d1aa2034cc415c59fd7404bfdd6e8 100644
--- a/modules/io/src/mol/entity_io_mmcif_handler.cc
+++ b/modules/io/src/mol/entity_io_mmcif_handler.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/mol/entity_io_mmcif_handler.hh b/modules/io/src/mol/entity_io_mmcif_handler.hh
index e55a409b850f5ceae92f3b62830a8e895c0f4930..7fefdc8902fd1511c4144f6f664642c54bd8b0cd 100644
--- a/modules/io/src/mol/entity_io_mmcif_handler.hh
+++ b/modules/io/src/mol/entity_io_mmcif_handler.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/mol/entity_io_pdb_handler.cc b/modules/io/src/mol/entity_io_pdb_handler.cc
index 69e466a23b0c092aef483c7e1c62e18b719d2a2b..f9f76eca6706058943041430322bc5c96b85255b 100644
--- a/modules/io/src/mol/entity_io_pdb_handler.cc
+++ b/modules/io/src/mol/entity_io_pdb_handler.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/mol/entity_io_pdb_handler.hh b/modules/io/src/mol/entity_io_pdb_handler.hh
index 07bfca81e49714d6aaa5b5440820b30815baf1f0..f1fbfbb00521fa89bed2affa908241ed1579716a 100644
--- a/modules/io/src/mol/entity_io_pdb_handler.hh
+++ b/modules/io/src/mol/entity_io_pdb_handler.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/mol/entity_io_pqr_handler.cc b/modules/io/src/mol/entity_io_pqr_handler.cc
index f1efaee3cc9da176584382cee45d26b2d530ed45..ada62fb928b0c23605c2f9703c3f738c6e1bfcc0 100644
--- a/modules/io/src/mol/entity_io_pqr_handler.cc
+++ b/modules/io/src/mol/entity_io_pqr_handler.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/mol/entity_io_pqr_handler.hh b/modules/io/src/mol/entity_io_pqr_handler.hh
index 0b48e50be3a448d0ec2d7069b74e953a4b11c0cb..ff2512b123062b02085798d72bedaf3f01691c4d 100644
--- a/modules/io/src/mol/entity_io_pqr_handler.hh
+++ b/modules/io/src/mol/entity_io_pqr_handler.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/mol/entity_io_sdf_handler.cc b/modules/io/src/mol/entity_io_sdf_handler.cc
index e99933ec3044f97dbcc2715f66bb2a411a168e95..a9dced835da7097a7a0804f979f4a24ab818fd15 100644
--- a/modules/io/src/mol/entity_io_sdf_handler.cc
+++ b/modules/io/src/mol/entity_io_sdf_handler.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/mol/entity_io_sdf_handler.hh b/modules/io/src/mol/entity_io_sdf_handler.hh
index 55c20fc9675ed0df36494b11c456e7e8e4b49e0b..d5b4aef15d2a3b241f605685303a2487c30cee42 100644
--- a/modules/io/src/mol/entity_io_sdf_handler.hh
+++ b/modules/io/src/mol/entity_io_sdf_handler.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/mol/io_profile.hh b/modules/io/src/mol/io_profile.hh
index 4f14b35e31aa4fe501cd7abe04ae042aca2710ec..22060e8c6514d0597d0e3d17113f6941e67c6d93 100644
--- a/modules/io/src/mol/io_profile.hh
+++ b/modules/io/src/mol/io_profile.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/mol/load_entity.cc b/modules/io/src/mol/load_entity.cc
index 4ce5f94b7e7a2aad92bef022b44463881242641a..a9d34c3eb26030bd00a7facf485d70423056af8d 100644
--- a/modules/io/src/mol/load_entity.cc
+++ b/modules/io/src/mol/load_entity.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/mol/load_entity.hh b/modules/io/src/mol/load_entity.hh
index 80ff0bb492923ed94de7db92b7766bccc37efa8c..b6e18a132cf20b463a80785fff379d5f2f5eea7b 100644
--- a/modules/io/src/mol/load_entity.hh
+++ b/modules/io/src/mol/load_entity.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/mol/load_surface.cc b/modules/io/src/mol/load_surface.cc
index 5312ae7166d45f201f8899a6e0fe1ade8f729df3..838f24a3c7e1d3f36903d0552ddb73a2f427ca26 100644
--- a/modules/io/src/mol/load_surface.cc
+++ b/modules/io/src/mol/load_surface.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/mol/load_surface.hh b/modules/io/src/mol/load_surface.hh
index 5b3a9388a29b17ff7c043d46886da9f38314d8c1..e27761948bf5d12f5e06b6ed410094594ebb5579 100644
--- a/modules/io/src/mol/load_surface.hh
+++ b/modules/io/src/mol/load_surface.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/mol/mmcif_info.cc b/modules/io/src/mol/mmcif_info.cc
index 3e0fa35370df8d80480920e3f14f5d0f95ddd7ff..25c58ff9ced52ae52170239f132ccdc57c946674 100644
--- a/modules/io/src/mol/mmcif_info.cc
+++ b/modules/io/src/mol/mmcif_info.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/mol/mmcif_info.hh b/modules/io/src/mol/mmcif_info.hh
index 22e3e33a8be233e92a4dc118aa059f6b24581cbe..c152229ef838e7ce1d0abb4d39688112d3662def 100644
--- a/modules/io/src/mol/mmcif_info.hh
+++ b/modules/io/src/mol/mmcif_info.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/mol/mmcif_reader.cc b/modules/io/src/mol/mmcif_reader.cc
index 9e84138535372ada46053525af406dcf7f64731d..6392ef4b11cc5f3eaff1fbd23536f0ffe03586b5 100644
--- a/modules/io/src/mol/mmcif_reader.cc
+++ b/modules/io/src/mol/mmcif_reader.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/mol/mmcif_reader.hh b/modules/io/src/mol/mmcif_reader.hh
index e7d0e6bcb5d4df7b777712a7265915da9dd1d0d7..925dfde23b3362612a3fe63d5e0f04e6ff6c2df7 100644
--- a/modules/io/src/mol/mmcif_reader.hh
+++ b/modules/io/src/mol/mmcif_reader.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/mol/pdb_reader.cc b/modules/io/src/mol/pdb_reader.cc
index bf0a3a8a004835440cc5da73fa99302041eef262..14acca8cab1784a18b7770f4b1fde7fb242a5933 100644
--- a/modules/io/src/mol/pdb_reader.cc
+++ b/modules/io/src/mol/pdb_reader.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/mol/pdb_reader.hh b/modules/io/src/mol/pdb_reader.hh
index f360b974e7205766fb9d08191a4aca8256dfa8f7..df98fa2dd6bdc7a39e646c88b18bda7ab14e3b1c 100644
--- a/modules/io/src/mol/pdb_reader.hh
+++ b/modules/io/src/mol/pdb_reader.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/mol/pdb_str.cc b/modules/io/src/mol/pdb_str.cc
index 3884fb268124445bd2eef11ebbb7ad10ce1864a8..a0dfa38ec38db40aa5ec349b79113ce31a4110cc 100644
--- a/modules/io/src/mol/pdb_str.cc
+++ b/modules/io/src/mol/pdb_str.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/mol/pdb_str.hh b/modules/io/src/mol/pdb_str.hh
index a2f070850c9f4e0378a7f5220e3a3429ea7791f1..2bab0097e66c4e52221872be7d76fe254c46d922 100644
--- a/modules/io/src/mol/pdb_str.hh
+++ b/modules/io/src/mol/pdb_str.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/mol/pdb_writer.cc b/modules/io/src/mol/pdb_writer.cc
index 181c2ad8ad618941e775118269ee92661e53d74b..7b28c8b2a5da8b5a840ea437fffc55ab8a92cd26 100644
--- a/modules/io/src/mol/pdb_writer.cc
+++ b/modules/io/src/mol/pdb_writer.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/mol/pdb_writer.hh b/modules/io/src/mol/pdb_writer.hh
index d12b3219f5cd509cebefea9f1444cdd028ae7b60..ed7bea103873b00b1bcfba47a6dd3244d6a3f5b5 100644
--- a/modules/io/src/mol/pdb_writer.hh
+++ b/modules/io/src/mol/pdb_writer.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/mol/save_entity.cc b/modules/io/src/mol/save_entity.cc
index 23aa1978209d4a241f0b539e05f3376292a252aa..5e0e1c529041aa7c36ebb98c88234f7eb92da133 100644
--- a/modules/io/src/mol/save_entity.cc
+++ b/modules/io/src/mol/save_entity.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/mol/save_entity.hh b/modules/io/src/mol/save_entity.hh
index 033890c9617f83ffd4edafea98f5769302a145f4..7ac15b69471ae87b841e38bd7181b7458a6346cc 100644
--- a/modules/io/src/mol/save_entity.hh
+++ b/modules/io/src/mol/save_entity.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/mol/sdf_reader.cc b/modules/io/src/mol/sdf_reader.cc
index 6a2603d0d2f877ad1004dc8701c5d6c4d358829c..f402fc3c0b0d1cd96c4469252666715e746e930d 100644
--- a/modules/io/src/mol/sdf_reader.cc
+++ b/modules/io/src/mol/sdf_reader.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/mol/sdf_reader.hh b/modules/io/src/mol/sdf_reader.hh
index d90bb9d1abba33672eb76860cb68de9416c8d32d..e7a478b7a295e0c60c0957a171fd8c0633544591 100644
--- a/modules/io/src/mol/sdf_reader.hh
+++ b/modules/io/src/mol/sdf_reader.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/mol/sdf_writer.cc b/modules/io/src/mol/sdf_writer.cc
index 45bc1867a1d6083601189c2c149ff75c9eaebf64..8089d7ac146db63b4c603f60ad6be668f1827e15 100644
--- a/modules/io/src/mol/sdf_writer.cc
+++ b/modules/io/src/mol/sdf_writer.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/mol/sdf_writer.hh b/modules/io/src/mol/sdf_writer.hh
index 02e29464974f4e3c21726c4e5f2cce35b764ff9d..8ca166d97b50c7d635ed285ccf11b0840ff97a71 100644
--- a/modules/io/src/mol/sdf_writer.hh
+++ b/modules/io/src/mol/sdf_writer.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/mol/star_parser.cc b/modules/io/src/mol/star_parser.cc
index 214eb626c9f743a1cbbb218bede0ad7f795b2f73..da9c087c6f1df5cdf97d5c2132924e25d657515f 100644
--- a/modules/io/src/mol/star_parser.cc
+++ b/modules/io/src/mol/star_parser.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/mol/star_parser.hh b/modules/io/src/mol/star_parser.hh
index 139c39a840c9703345fff61489165c09ed6bfb14..bc6a3947a6694ec83e8e3fd699d30223cc87359f 100644
--- a/modules/io/src/mol/star_parser.hh
+++ b/modules/io/src/mol/star_parser.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/mol/stereochemical_params_reader.cc b/modules/io/src/mol/stereochemical_params_reader.cc
index 0201caf573168a860ae10190cef51ec526238ed2..3737b6adee853b971f37d3f5eb23e85ea302aeb3 100644
--- a/modules/io/src/mol/stereochemical_params_reader.cc
+++ b/modules/io/src/mol/stereochemical_params_reader.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/mol/stereochemical_params_reader.hh b/modules/io/src/mol/stereochemical_params_reader.hh
index a5d33acce7888bdcd88b74ec0aecd38a120eb9d6..6ef348fbc59bbdeea1912c02a1340be091d9f69e 100644
--- a/modules/io/src/mol/stereochemical_params_reader.hh
+++ b/modules/io/src/mol/stereochemical_params_reader.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/mol/surface_io_handler.hh b/modules/io/src/mol/surface_io_handler.hh
index 6f198b7f3ef136134ac251ccbe7c3a21a2abf567..a63ab720c89bc2b6f8c387fd8e62cad47d3af37c 100644
--- a/modules/io/src/mol/surface_io_handler.hh
+++ b/modules/io/src/mol/surface_io_handler.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/mol/surface_io_msms_handler.cc b/modules/io/src/mol/surface_io_msms_handler.cc
index 5ed6ceb3982ff143d9d8eb9d788be35cf74f0d24..25c45b92576e8c35ffc241d6e0021b58becb601f 100644
--- a/modules/io/src/mol/surface_io_msms_handler.cc
+++ b/modules/io/src/mol/surface_io_msms_handler.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/mol/surface_io_msms_handler.hh b/modules/io/src/mol/surface_io_msms_handler.hh
index 8053a0c1a522a4480e81d1806c9396a24d20264b..4f11b5967057612d254578a2e63f29d94784f801 100644
--- a/modules/io/src/mol/surface_io_msms_handler.hh
+++ b/modules/io/src/mol/surface_io_msms_handler.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/seq/clustal_io_handler.cc b/modules/io/src/seq/clustal_io_handler.cc
index 309ab98f2414593e0a91b45ac996392e732730fe..8eb8eb650d518c2433472be106082b022429f66c 100644
--- a/modules/io/src/seq/clustal_io_handler.cc
+++ b/modules/io/src/seq/clustal_io_handler.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/seq/clustal_io_handler.hh b/modules/io/src/seq/clustal_io_handler.hh
index 81a6acb2ceee3bd79f28314649241fe5be136945..69fb8907c8bf4dec9b5828a64e68e9d36256bfc3 100644
--- a/modules/io/src/seq/clustal_io_handler.hh
+++ b/modules/io/src/seq/clustal_io_handler.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/seq/fasta_io_handler.cc b/modules/io/src/seq/fasta_io_handler.cc
index 0b55a73f1f895b4e818b9bd1137462bcee10428e..c15f6debb4f49b4c182a62201c6695677a628ba2 100644
--- a/modules/io/src/seq/fasta_io_handler.cc
+++ b/modules/io/src/seq/fasta_io_handler.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/seq/fasta_io_handler.hh b/modules/io/src/seq/fasta_io_handler.hh
index e89a0dc6dad8e0324d798af6d72ad8ecbedbb365..6926421c5c56a02c14890e9d80ff9680e1686eb9 100644
--- a/modules/io/src/seq/fasta_io_handler.hh
+++ b/modules/io/src/seq/fasta_io_handler.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/seq/hhm_io_handler.cc b/modules/io/src/seq/hhm_io_handler.cc
index b524f3161bae3a85f541ad2213d7fcb9cf07b138..d8f7403b9fbb7bf7a686a08bc55cc3593eaf0e34 100644
--- a/modules/io/src/seq/hhm_io_handler.cc
+++ b/modules/io/src/seq/hhm_io_handler.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/seq/hhm_io_handler.hh b/modules/io/src/seq/hhm_io_handler.hh
index a3acd275c1e7feff6ca57692efa2bbaddcc02532..97fe449cf6bdc451f41336c36b989af7720c40fc 100644
--- a/modules/io/src/seq/hhm_io_handler.hh
+++ b/modules/io/src/seq/hhm_io_handler.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/seq/load.cc b/modules/io/src/seq/load.cc
index 9bca49efef18b341e107f0653ca1506af7e401ab..e652b845a53bd98840ee48909a9f1ba5aa173658 100644
--- a/modules/io/src/seq/load.cc
+++ b/modules/io/src/seq/load.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/seq/load.hh b/modules/io/src/seq/load.hh
index a72cee4b297615fbf8900fc7bdf9df8e0285d810..6c623241ad7c46f60ce2281498927b5996ec0036 100644
--- a/modules/io/src/seq/load.hh
+++ b/modules/io/src/seq/load.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/seq/pir_io_handler.cc b/modules/io/src/seq/pir_io_handler.cc
index be4798d76e5044e10c4bf67ce4d73bb61ae9f5f7..a84710b7cf6ef872dc2d47f744e5a5c37a4b361a 100644
--- a/modules/io/src/seq/pir_io_handler.cc
+++ b/modules/io/src/seq/pir_io_handler.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/seq/pir_io_handler.hh b/modules/io/src/seq/pir_io_handler.hh
index 90ed88622a573b83148d3e8760bdab835a7268ae..41841329528b45ed424f3b043ec971760db55cc1 100644
--- a/modules/io/src/seq/pir_io_handler.hh
+++ b/modules/io/src/seq/pir_io_handler.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/seq/profile_io_handler.hh b/modules/io/src/seq/profile_io_handler.hh
index 783d697620164263cc71af8bddfc3bd029accd87..19c78de8b1c78e7b7c09222ff61f1b3d4412e104 100644
--- a/modules/io/src/seq/profile_io_handler.hh
+++ b/modules/io/src/seq/profile_io_handler.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/seq/promod_io_handler.cc b/modules/io/src/seq/promod_io_handler.cc
index 9312ed0c409940b28f643b2e01ca26980ac0710b..612ca2b1099857005bd4419e52ecc1c08ff1050d 100644
--- a/modules/io/src/seq/promod_io_handler.cc
+++ b/modules/io/src/seq/promod_io_handler.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/seq/promod_io_handler.hh b/modules/io/src/seq/promod_io_handler.hh
index 1be00a1e25e09c2b18cb08dc86e6f2e3dba6e90d..74aa87f98ef4d442a978c99da6e0bb6363432128 100644
--- a/modules/io/src/seq/promod_io_handler.hh
+++ b/modules/io/src/seq/promod_io_handler.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/seq/pssm_io_handler.cc b/modules/io/src/seq/pssm_io_handler.cc
index 746bae3223149b065b61b4a3eb432bf5aff4a8b5..2dff01015975b28e86944cd0eb63c14a39a95742 100644
--- a/modules/io/src/seq/pssm_io_handler.cc
+++ b/modules/io/src/seq/pssm_io_handler.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/seq/pssm_io_handler.hh b/modules/io/src/seq/pssm_io_handler.hh
index 87a00673bdab1f8ad242b43c3c6818b0f7b8e7a5..ae83507310ce3da4e4405baf06d9d25867bdf344 100644
--- a/modules/io/src/seq/pssm_io_handler.hh
+++ b/modules/io/src/seq/pssm_io_handler.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/seq/save.cc b/modules/io/src/seq/save.cc
index d023c1361e1f2ea1500be23b35295063916a809d..461d457cb0d02b0f0d22d0dd27a910b0067163c2 100644
--- a/modules/io/src/seq/save.cc
+++ b/modules/io/src/seq/save.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/seq/save.hh b/modules/io/src/seq/save.hh
index 843e7eeba91706ea6334619ea102dc06a4a676e2..4ca0c06f04ff5caeb3e05f18851a062b194593ca 100644
--- a/modules/io/src/seq/save.hh
+++ b/modules/io/src/seq/save.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/seq/sequence_io_handler.hh b/modules/io/src/seq/sequence_io_handler.hh
index 5fb188ad363d33bcc019ddc01e7d97601227c04f..564ffe488e3b5d73db04c122e733e0812750a18d 100644
--- a/modules/io/src/seq/sequence_io_handler.hh
+++ b/modules/io/src/seq/sequence_io_handler.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/src/swap_util.hh b/modules/io/src/swap_util.hh
index 915a45e6024e9fda61011c0bcd57be1ec0ef6b77..de540f6beb1de9f9adb93057dc083b3b540c138a 100755
--- a/modules/io/src/swap_util.hh
+++ b/modules/io/src/swap_util.hh
@@ -2,7 +2,7 @@
// This file is part of the OpenStructure project <www.openstructure.org>
//
// Copyright (C) 2003-2010 by the IPLT authors
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/tests/test_clustal.cc b/modules/io/tests/test_clustal.cc
index c6cb21c58e51d927510d2b572d7753fcbd61a3a8..93d4ccb13a3ce9c8afaafef0567e3d735ffc14a0 100644
--- a/modules/io/tests/test_clustal.cc
+++ b/modules/io/tests/test_clustal.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/tests/test_exceptions.cc b/modules/io/tests/test_exceptions.cc
index 1a2befe054a8a8f7214e4bb12016f247b3bb8377..4d1a139b7f94c42bd1c76b5ab66b7d7673538bdb 100644
--- a/modules/io/tests/test_exceptions.cc
+++ b/modules/io/tests/test_exceptions.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/tests/test_io_crd.cc b/modules/io/tests/test_io_crd.cc
index f51d67af15a68defa531106acef59f72cdaf3e7d..4f229bed14fb6217fba178256e6c4df21b418bd3 100644
--- a/modules/io/tests/test_io_crd.cc
+++ b/modules/io/tests/test_io_crd.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/tests/test_io_dcd.cc b/modules/io/tests/test_io_dcd.cc
index 270d371e8034c6edea2a6e2a7ec37984e304b682..73b8f24c8a81f4874f11479d0c6686d309fb349f 100644
--- a/modules/io/tests/test_io_dcd.cc
+++ b/modules/io/tests/test_io_dcd.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
@@ -76,13 +76,13 @@ BOOST_AUTO_TEST_CASE(test_io_dcd_charmm_frames)
BOOST_CHECK_EQUAL(cg2.GetFrameCount(),uint(1));
mol::CoordFramePtr cf2 = cg2.GetFrame(0);
- BOOST_CHECK(geom::Distance(cf2->GetCellSize(),cell_size)<1e-6);
- BOOST_CHECK(geom::Distance(cf2->GetCellAngles(),cell_angles)<1e-6);
+ BOOST_CHECK(geom::Distance(cf2->GetCellSize(),cell_size)<1e-5);
+ BOOST_CHECK(geom::Distance(cf2->GetCellAngles(),cell_angles)<1e-5);
geom::Vec3List atom_pos2=cg2.GetFramePositions(0);
for(size_t i=0;i<natoms;++i) {
- BOOST_CHECK(geom::Distance(atom_pos[i],atom_pos2[i])<1e-6);
+ BOOST_CHECK(geom::Distance(atom_pos[i],atom_pos2[i])<1e-5);
}
}
diff --git a/modules/io/tests/test_io_img.cc b/modules/io/tests/test_io_img.cc
index 11821e11f06ec1560abe8036c90ef1da2c981850..bb7f541b1b0682575c5d79df7117d6502b0fa561 100644
--- a/modules/io/tests/test_io_img.cc
+++ b/modules/io/tests/test_io_img.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/tests/test_io_mmcif.py b/modules/io/tests/test_io_mmcif.py
index e0672fc39e30c87f07288cef61c6ba321d9d3971..cfa10798c248f5d58385fcee070088ea138f0566 100644
--- a/modules/io/tests/test_io_mmcif.py
+++ b/modules/io/tests/test_io_mmcif.py
@@ -1,4 +1,5 @@
import unittest
+import subprocess
import ost
from ost import *
@@ -10,51 +11,51 @@ class TestMMCifInfo(unittest.TestCase):
c = io.MMCifInfoCitation()
# test ID setting/ getting
c.SetID('ID')
- self.assertEquals(c.GetID(), 'ID')
+ self.assertEqual(c.GetID(), 'ID')
# test CAS setting/ getting
c.SetCAS('FOO')
- self.assertEquals(c.GetCAS(), 'FOO')
+ self.assertEqual(c.GetCAS(), 'FOO')
# test ISBN setting/ getting
c.SetISBN('0-0-0-0-0-0')
- self.assertEquals(c.GetISBN(), '0-0-0-0-0-0')
+ self.assertEqual(c.GetISBN(), '0-0-0-0-0-0')
# test published_in setting/ getting
c.SetPublishedIn('Best Book Ever')
- self.assertEquals(c.GetPublishedIn(), 'Best Book Ever')
+ self.assertEqual(c.GetPublishedIn(), 'Best Book Ever')
# test volume setting/ getting
c.SetVolume('3')
- self.assertEquals(c.GetVolume(), '3')
+ self.assertEqual(c.GetVolume(), '3')
# test page setting/ getting
c.SetPageFirst('1')
- self.assertEquals(c.GetPageFirst(), '1')
+ self.assertEqual(c.GetPageFirst(), '1')
c.SetPageLast('10')
- self.assertEquals(c.GetPageLast(), '10')
+ self.assertEqual(c.GetPageLast(), '10')
# test doi setting/ getting
c.SetDOI('HERE')
- self.assertEquals(c.GetDOI(), 'HERE')
+ self.assertEqual(c.GetDOI(), 'HERE')
# test PubMed setting/ getting
c.SetPubMed(815)
- self.assertEquals(c.GetPubMed(), 815)
+ self.assertEqual(c.GetPubMed(), 815)
# test year setting/ getting
c.SetYear(815)
- self.assertEquals(c.GetYear(), 815)
+ self.assertEqual(c.GetYear(), 815)
# test title setting/ getting
c.SetTitle('Foo')
- self.assertEquals(c.GetTitle(), 'Foo')
+ self.assertEqual(c.GetTitle(), 'Foo')
# test book_publisher set & get
c.SetBookPublisher("Hugo")
- self.assertEquals(c.GetBookPublisher(), "Hugo")
+ self.assertEqual(c.GetBookPublisher(), "Hugo")
# test book_publisher_city set & get
c.SetBookPublisherCity("Basel")
- self.assertEquals(c.book_publisher_city, "Basel")
+ self.assertEqual(c.book_publisher_city, "Basel")
# test citation type
self.assertTrue(c.IsCitationTypeUnknown())
- self.assertEquals(c.citation_type, io.MMCifInfoCType.Unknown)
+ self.assertEqual(c.citation_type, io.MMCifInfoCType.Unknown)
# test auhtors setting/ getting
s = ost.StringList()
s.append('Foo')
c.SetAuthorList(s)
s2 = c.GetAuthorList()
- self.assertEquals(s2[0], 'Foo')
+ self.assertEqual(s2[0], 'Foo')
i = io.MMCifInfo()
i.SetMethod('Deep-Fry')
@@ -64,31 +65,31 @@ class TestMMCifInfo(unittest.TestCase):
i.AddAuthorsToCitation('ID', s)
cl = i.GetCitations()
- self.assertEquals(len(cl), 1)
+ self.assertEqual(len(cl), 1)
al = cl[0].GetAuthorList()
- self.assertEquals(len(al), 2)
- self.assertEquals(al[0], 'Foo')
- self.assertEquals(al[1], 'Bar')
+ self.assertEqual(len(al), 2)
+ self.assertEqual(al[0], 'Foo')
+ self.assertEqual(al[1], 'Bar')
- self.assertEquals(i.GetMethod(), 'Deep-Fry')
- self.assertEquals(i.GetResolution(), 2.0)
+ self.assertEqual(i.GetMethod(), 'Deep-Fry')
+ self.assertEqual(i.GetResolution(), 2.0)
def test_mmcifinfo_biounit(self):
b = io.MMCifInfoBioUnit()
b.SetDetails('Details')
b.SetMethodDetails('MethodDetails')
- self.assertEquals(b.GetDetails(), 'Details')
- self.assertEquals(b.GetMethodDetails(), 'MethodDetails')
+ self.assertEqual(b.GetDetails(), 'Details')
+ self.assertEqual(b.GetMethodDetails(), 'MethodDetails')
b.method_details = 'AttrMethodDetails'
- self.assertEquals(b.method_details, 'AttrMethodDetails')
+ self.assertEqual(b.method_details, 'AttrMethodDetails')
b.AddChain('A')
b.AddChain('B')
cl = b.GetChainList()
il = b.GetChainIntervalList()
- self.assertEquals(cl[0], 'A')
- self.assertEquals(il[0][0], 0)
- self.assertEquals(il[0][1], 2)
+ self.assertEqual(cl[0], 'A')
+ self.assertEqual(il[0][0], 0)
+ self.assertEqual(il[0][1], 2)
s = ost.StringList()
s.append('B')
s.append('C')
@@ -96,11 +97,11 @@ class TestMMCifInfo(unittest.TestCase):
b.SetChainList(s)
cl = b.GetChainList()
il = b.GetChainIntervalList()
- self.assertEquals(il[0][0], 0)
- self.assertEquals(il[0][1], 3)
- self.assertEquals(cl[0], 'B')
- self.assertEquals(cl[1], 'C')
- self.assertEquals(cl[2], 'D')
+ self.assertEqual(il[0][0], 0)
+ self.assertEqual(il[0][1], 3)
+ self.assertEqual(cl[0], 'B')
+ self.assertEqual(cl[1], 'C')
+ self.assertEqual(cl[2], 'D')
i = io.MMCifInfo()
i.AddBioUnit(b)
@@ -110,40 +111,40 @@ class TestMMCifInfo(unittest.TestCase):
bl = i.GetBioUnits()
il = bl[0].GetChainIntervalList()
- self.assertEquals(il[0][0], 0)
- self.assertEquals(il[0][1], 3)
- self.assertEquals(il[1][0], 3)
- self.assertEquals(il[1][1], 6)
- self.assertEquals(len(bl), 2)
+ self.assertEqual(il[0][0], 0)
+ self.assertEqual(il[0][1], 3)
+ self.assertEqual(il[1][0], 3)
+ self.assertEqual(il[1][1], 6)
+ self.assertEqual(len(bl), 2)
def test_mmcifinfo_transoperation(self):
o = io.MMCifInfoTransOp()
o.SetID("1")
- self.assertEquals(o.GetID(), '1')
+ self.assertEqual(o.GetID(), '1')
o.SetType("identity operation")
- self.assertEquals(o.GetType(), 'identity operation')
+ self.assertEqual(o.GetType(), 'identity operation')
o.SetVector(1.0, 2.0, 3.0)
- self.assertEquals(o.GetVector().x, 1.0)
- self.assertEquals(o.GetVector().y, 2.0)
- self.assertEquals(o.GetVector().z, 3.0)
+ self.assertEqual(o.GetVector().x, 1.0)
+ self.assertEqual(o.GetVector().y, 2.0)
+ self.assertEqual(o.GetVector().z, 3.0)
o.SetMatrix(1, 2, 3, 4, 5, 6, 7, 8, 9)
- self.assertEquals(geom.Equal(o.GetMatrix(),
+ self.assertEqual(geom.Equal(o.GetMatrix(),
geom.Mat3(1, 2, 3, 4, 5, 6, 7, 8, 9)), True)
i = io.MMCifInfo()
i.AddOperation(o)
ol = i.GetOperations()
- self.assertEquals(ol[0].GetID(), '1')
+ self.assertEqual(ol[0].GetID(), '1')
b = io.MMCifInfoBioUnit()
b.AddOperations(ol)
oll = b.GetOperations()
- self.assertEquals(oll[0][0].GetID(), '1')
+ self.assertEqual(oll[0][0].GetID(), '1')
tr_ol = b.GetOperationsIntervalList()
- self.assertEquals(len(tr_ol), 1)
- self.assertEquals(tr_ol[0][0], 0)
- self.assertEquals(tr_ol[0][1], 1)
+ self.assertEqual(len(tr_ol), 1)
+ self.assertEqual(tr_ol[0][0], 0)
+ self.assertEqual(tr_ol[0][1], 1)
def test_mmcifinfo_biounit_pdbize_with_multiple_transforms(self):
ent, seqres, info = io.LoadMMCIF("testfiles/mmcif/multiple_transforms.cif.gz",
@@ -151,11 +152,11 @@ class TestMMCifInfo(unittest.TestCase):
info=True)
pdb_ent = info.GetBioUnits()[0].PDBize(ent)
chains = pdb_ent.chains
- self.assertEquals(''.join([c.name for c in chains]),
+ self.assertEqual(''.join([c.name for c in chains]),
'A_-BCD')
ligand_chain = chains[1]
ligand_residues = ligand_chain.residues
- self.assertEquals([r.number for r in ligand_residues],
+ self.assertEqual([r.number for r in ligand_residues],
[mol.ResNum(1), mol.ResNum(2), mol.ResNum(3), mol.ResNum(4)])
def test_mmcifinfo_biounit_pdbize(self):
@@ -165,22 +166,22 @@ class TestMMCifInfo(unittest.TestCase):
pdb_ent = info.GetBioUnits()[0].PDBize(ent)
pdb_seqres_ent = info.GetBioUnits()[0].PDBize(ent, seqres)
- self.assertEquals(''.join([c.name for c in pdb_ent.chains]),
+ self.assertEqual(''.join([c.name for c in pdb_ent.chains]),
'AB_-CDEFGH')
- self.assertEquals([c.residue_count for c in pdb_ent.chains],
+ self.assertEqual([c.residue_count for c in pdb_ent.chains],
[415, 414, 64, 3816, 415, 414, 415, 414, 415, 414])
- self.assertEquals([c.atom_count for c in pdb_ent.chains],
+ self.assertEqual([c.atom_count for c in pdb_ent.chains],
[3231, 3223, 268, 3816, 3231, 3223, 3231, 3223, 3231, 3223])
- self.assertEquals([c.GetBondCount() for c in pdb_ent.chains],
+ self.assertEqual([c.GetBondCount() for c in pdb_ent.chains],
[3311, 3303, 204, 0, 3311, 3303, 3311, 3303, 3311, 3303])
- self.assertEquals(''.join([c.name for c in pdb_seqres_ent.chains]),
+ self.assertEqual(''.join([c.name for c in pdb_seqres_ent.chains]),
''.join([c.name for c in pdb_ent.chains]))
- self.assertEquals([c.residue_count for c in pdb_seqres_ent.chains],
+ self.assertEqual([c.residue_count for c in pdb_seqres_ent.chains],
[c.residue_count for c in pdb_ent.chains])
- self.assertEquals([c.atom_count for c in pdb_seqres_ent.chains],
+ self.assertEqual([c.atom_count for c in pdb_seqres_ent.chains],
[c.atom_count for c in pdb_ent.chains])
- self.assertEquals([c.GetBondCount() for c in pdb_seqres_ent.chains],
+ self.assertEqual([c.GetBondCount() for c in pdb_seqres_ent.chains],
[c.GetBondCount() for c in pdb_ent.chains])
def test_mmcifinfo_biounit_pdbize_transformation(self):
@@ -188,10 +189,10 @@ class TestMMCifInfo(unittest.TestCase):
seqres=True,
info=True)
pdb_ent, t = info.GetBioUnits()[0].PDBize(ent, transformation=True)
- self.assertAlmostEquals(pdb_ent.GetCenterOfAtoms()[0], -915.759, 1)
- self.assertAlmostEquals(pdb_ent.GetCenterOfAtoms()[1], -952.345, 1)
- self.assertAlmostEquals(pdb_ent.GetCenterOfAtoms()[2], 3221.75, 1)
- self.assertEquals(geom.Equal(t,
+ self.assertAlmostEqual(pdb_ent.GetCenterOfAtoms()[0], -915.759, 1)
+ self.assertAlmostEqual(pdb_ent.GetCenterOfAtoms()[1], -952.345, 1)
+ self.assertAlmostEqual(pdb_ent.GetCenterOfAtoms()[2], 3221.75, 1)
+ self.assertEqual(geom.Equal(t,
geom.Mat4(1,0,0,-920.462,
0,1,0,-966.654,
0,0,1,1703,
@@ -209,26 +210,26 @@ class TestMMCifInfo(unittest.TestCase):
d.SetMassMethod('Good Guess')
d.SetModelDetails('Created with SwissModel')
d.SetModelTypeDetails('Average')
- self.assertEquals(d.GetEntryID(), '1BAR')
- self.assertEquals(d.GetTitle(), 'A Title')
- self.assertEquals(d.GetCASPFlag(), 'N')
- self.assertEquals(d.GetDescriptor(), 'FooBar')
- self.assertEquals(d.GetMass(), 1.0)
- self.assertEquals(d.GetMassMethod(), 'Good Guess')
- self.assertEquals(d.GetModelDetails(), 'Created with SwissModel')
- self.assertEquals(d.GetModelTypeDetails(), 'Average')
+ self.assertEqual(d.GetEntryID(), '1BAR')
+ self.assertEqual(d.GetTitle(), 'A Title')
+ self.assertEqual(d.GetCASPFlag(), 'N')
+ self.assertEqual(d.GetDescriptor(), 'FooBar')
+ self.assertEqual(d.GetMass(), 1.0)
+ self.assertEqual(d.GetMassMethod(), 'Good Guess')
+ self.assertEqual(d.GetModelDetails(), 'Created with SwissModel')
+ self.assertEqual(d.GetModelTypeDetails(), 'Average')
i = io.MMCifInfo()
i.SetStructDetails(d)
- self.assertEquals(i.GetStructDetails().GetEntryID(), '1BAR')
- self.assertEquals(i.GetStructDetails().GetTitle(), 'A Title')
- self.assertEquals(i.GetStructDetails().GetCASPFlag(), 'N')
- self.assertEquals(i.GetStructDetails().GetDescriptor(), 'FooBar')
- self.assertEquals(i.GetStructDetails().GetMass(), 1.0)
- self.assertEquals(i.GetStructDetails().GetMassMethod(), 'Good Guess')
- self.assertEquals(i.GetStructDetails().GetModelDetails(),
+ self.assertEqual(i.GetStructDetails().GetEntryID(), '1BAR')
+ self.assertEqual(i.GetStructDetails().GetTitle(), 'A Title')
+ self.assertEqual(i.GetStructDetails().GetCASPFlag(), 'N')
+ self.assertEqual(i.GetStructDetails().GetDescriptor(), 'FooBar')
+ self.assertEqual(i.GetStructDetails().GetMass(), 1.0)
+ self.assertEqual(i.GetStructDetails().GetMassMethod(), 'Good Guess')
+ self.assertEqual(i.GetStructDetails().GetModelDetails(),
'Created with SwissModel')
- self.assertEquals(i.GetStructDetails().GetModelTypeDetails(), 'Average')
+ self.assertEqual(i.GetStructDetails().GetModelTypeDetails(), 'Average')
def test_mmcifinfo_obsolete(self):
obs = io.MMCifInfoObsolete()
@@ -236,18 +237,31 @@ class TestMMCifInfo(unittest.TestCase):
obs.SetID('SPRSDE')
obs.SetPDBID('1FOO')
obs.SetReplacedPDBID('2BAR')
- self.assertEquals(obs.GetDate(), '2011-08-31')
- self.assertEquals(obs.GetID(), 'Supersede')
- self.assertEquals(obs.GetPDBID(), '1FOO')
- self.assertEquals(obs.GetReplacedPDBID(), '2BAR')
+ self.assertEqual(obs.GetDate(), '2011-08-31')
+ self.assertEqual(obs.GetID(), 'Supersede')
+ self.assertEqual(obs.GetPDBID(), '1FOO')
+ self.assertEqual(obs.GetReplacedPDBID(), '2BAR')
i = io.MMCifInfo()
obs.id = 'OBSLTE'
i.SetObsoleteInfo(obs)
- self.assertEquals(i.GetObsoleteInfo().GetDate(), '2011-08-31')
- self.assertEquals(i.GetObsoleteInfo().GetID(), 'Obsolete')
- self.assertEquals(i.GetObsoleteInfo().GetPDBID(), '1FOO')
- self.assertEquals(i.GetObsoleteInfo().GetReplacedPDBID(), '2BAR')
+ self.assertEqual(i.GetObsoleteInfo().GetDate(), '2011-08-31')
+ self.assertEqual(i.GetObsoleteInfo().GetID(), 'Obsolete')
+ self.assertEqual(i.GetObsoleteInfo().GetPDBID(), '1FOO')
+ self.assertEqual(i.GetObsoleteInfo().GetReplacedPDBID(), '2BAR')
+
+ def test_remote_loading(self):
+
+ if subprocess.call(['ping google.com -c 1'], shell=True,
+ stdout=subprocess.PIPE, stderr=subprocess.PIPE) != 0:
+ print("No internet connection (or wrong OS) to test remote loading in "
+ "io.LoadMMCIF: ignoring unit test")
+ return
+
+ # let's hope that crambin stays the same forever
+ crambin_pdb = io.LoadMMCIF('1crn', remote=True)
+ self.assertEqual(len(crambin_pdb.residues), 46)
+ self.assertEqual(len(crambin_pdb.atoms), 327)
if __name__== '__main__':
from ost import testutils
diff --git a/modules/io/tests/test_io_pdb.cc b/modules/io/tests/test_io_pdb.cc
index 4cfc224927c64c7bc04799fc131a30536489c178..400034f9b8cf25a93d9953607e058881b7e4ee37 100644
--- a/modules/io/tests/test_io_pdb.cc
+++ b/modules/io/tests/test_io_pdb.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/tests/test_io_pdb.py b/modules/io/tests/test_io_pdb.py
index f3f3acbdf8593fe6c238b0ef2da1636840291d0b..77a504fd8ff650f4ef26ca3a3477b38328c9f7aa 100644
--- a/modules/io/tests/test_io_pdb.py
+++ b/modules/io/tests/test_io_pdb.py
@@ -1,5 +1,6 @@
import unittest
from ost import *
+import subprocess
class TestPDB(unittest.TestCase):
def setUp(self):
@@ -7,9 +8,9 @@ class TestPDB(unittest.TestCase):
def test_compnd_parser(self):
e=io.LoadPDB('testfiles/pdb/compnd.pdb', restrict_chains="A")
- self.assertEquals(e.GetChainCount(), 1)
+ self.assertEqual(e.GetChainCount(), 1)
ch = e.FindChain("A");
- self.assertEquals(ch.GetIntProp("mol_id"), 1)
+ self.assertEqual(ch.GetIntProp("mol_id"), 1)
def test_properly_assigns_profile_properties(self):
io.profiles['TEST'] = io.IOProfile()
@@ -34,6 +35,22 @@ class TestPDB(unittest.TestCase):
self.assertFalse(mol.BondExists(res1.FindAtom("CA"),res1.FindAtom("CB")))
self.assertTrue(mol.BondExists(res2.FindAtom("CA"),res2.FindAtom("CB")))
self.assertTrue(mol.BondExists(resd.FindAtom("CA"),resd.FindAtom("CB")))
+
+ def test_remote_loading(self):
+
+ if subprocess.call(['ping google.com -c 1'], shell=True,
+ stdout=subprocess.PIPE, stderr=subprocess.PIPE) != 0:
+ print("No internet connection (or wrong OS) to test remote loading in "
+ "io.LoadPDB: ignoring unit test")
+ return
+
+ with self.assertRaises(IOError):
+ io.LoadPDB('1ake', remote=True, remote_repo="cheeseisgoodforyou")
+
+ # let's hope that crambin stays the same forever
+ crambin_pdb = io.LoadPDB('1crn', remote=True, remote_repo='pdb')
+ self.assertEqual(len(crambin_pdb.residues), 46)
+ self.assertEqual(len(crambin_pdb.atoms), 327)
if __name__== '__main__':
from ost import testutils
diff --git a/modules/io/tests/test_io_sdf.cc b/modules/io/tests/test_io_sdf.cc
index 1aa5faf282ca170dc948a0ae2950331e2ce1623f..0dcbf5fd688dd876ccb3df8335053b42492de7b9 100644
--- a/modules/io/tests/test_io_sdf.cc
+++ b/modules/io/tests/test_io_sdf.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/tests/test_io_sequence_profile.cc b/modules/io/tests/test_io_sequence_profile.cc
index a99b93c9cc8dcf7c11c51ec8ab2d67149646d8f0..b866c394928efb2fbe68315e4caee2add0629fa9 100644
--- a/modules/io/tests/test_io_sequence_profile.cc
+++ b/modules/io/tests/test_io_sequence_profile.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/tests/test_iomanager.cc b/modules/io/tests/test_iomanager.cc
index 7cc80671bb2eb6b4c824e08370b65008df47c869..a6c1b543ab44a7ba6cd42a966bff20cc85468b1d 100644
--- a/modules/io/tests/test_iomanager.cc
+++ b/modules/io/tests/test_iomanager.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/tests/test_mmcif_info.cc b/modules/io/tests/test_mmcif_info.cc
index ecd3e3f6706700225a686e6036021461ce6aa5f3..efb35d54ff84a5772b7193ba0a0c2382880585c2 100644
--- a/modules/io/tests/test_mmcif_info.cc
+++ b/modules/io/tests/test_mmcif_info.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/tests/test_mmcif_reader.cc b/modules/io/tests/test_mmcif_reader.cc
index b3c9d7c238b3d9b9fd0e1e5b852f19e683181c80..21efd569f65aa472f69954a19d96ffc683cc4d16 100644
--- a/modules/io/tests/test_mmcif_reader.cc
+++ b/modules/io/tests/test_mmcif_reader.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/tests/test_pir.cc b/modules/io/tests/test_pir.cc
index 7c4c67d97148436d7174cffbef97339220e254b2..10961781c0a456576e53b0dd8fdb8763134fb8f3 100644
--- a/modules/io/tests/test_pir.cc
+++ b/modules/io/tests/test_pir.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/tests/test_star_parser.cc b/modules/io/tests/test_star_parser.cc
index 86edfe272ad6ed327d5c222baaff51743f1ffe71..c97140079f0b0bb4f569cc8261d941a1fdb31b4a 100644
--- a/modules/io/tests/test_star_parser.cc
+++ b/modules/io/tests/test_star_parser.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/io/tests/tests.cc b/modules/io/tests/tests.cc
index faa6774fc478a3bf696a7105461792447f9fff7a..f06c51adb573a6df1df32a6f2bb641277c83a2bc 100644
--- a/modules/io/tests/tests.cc
+++ b/modules/io/tests/tests.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/alg/doc/lddt.rst b/modules/mol/alg/doc/lddt.rst
index 3201243bdaa59551cc73e543e16100c161bfb5f4..711c06f9f89a39ff1d8f9a394270756d6dcd1eb2 100644
--- a/modules/mol/alg/doc/lddt.rst
+++ b/modules/mol/alg/doc/lddt.rst
@@ -240,7 +240,7 @@ One can replicate the binary using simple python script:
#
# Check consistency
is_cons = ResidueNamesMatch(model_view, references[0], True)
- print "Consistency check: ", "OK" if is_cons else "ERROR"
+ print("Consistency check: ", "OK" if is_cons else "ERROR")
#
# Calculate lDDT
LocalDistDiffTest(model_view,
diff --git a/modules/mol/alg/doc/molalg.rst b/modules/mol/alg/doc/molalg.rst
index 300852d954f6869c02ed7d2410ba9d3f8f958bf7..d1957af348352fef64244f099abd962f7e29d2fe 100644
--- a/modules/mol/alg/doc/molalg.rst
+++ b/modules/mol/alg/doc/molalg.rst
@@ -576,7 +576,7 @@ Local Distance Test scores (lDDT, DRMSD)
#
# Calculate lDDT
scorer = lDDTScorer(references=references, model=model_view, settings=settings)
- print "Global score:", scorer.global_score
+ print("Global score:", scorer.global_score)
scorer.PrintPerResidueStats()
:param references: Sets :attr:`references`
@@ -1075,7 +1075,7 @@ The following function detects steric clashes in atomic structures. Two atoms ar
The function requires a reference structure and a probe structure. The
function checks that all the residues in the reference structure that appear
in the probe structure (i.e., that have the same ResNum) are of the same
- residue type. Chains are comapred by order, not by chain name (i.e.: the first
+ residue type. Chains are compared by order, not by chain name (i.e.: the first
chain of the reference will be compared with the first chain of the probe
structure, etc.)
@@ -1656,17 +1656,22 @@ to standard amino acids.
Copies the atoms of ``src_res`` to ``dst_res`` using the residue names
as guide to decide which of the atoms should be copied. If ``src_res`` and
``dst_res`` have the same name, or ``src_res`` is a modified version of
- ``dst_res`` (i.e. have the same single letter code), CopyConserved will be
- called, otherwise CopyNonConserved will be called.
+ ``dst_res`` (i.e. have the same single letter code), :func:`CopyConserved`
+ will be called, otherwise :func:`CopyNonConserved`.
+
+ If a CBeta atom wasn't already copied from ``src_res``, a new one at a
+ reconstructed position will be added to ``dst_res`` if it is not ``GLY`` and
+ all backbone positions are available to do it.
:param src_res: The source residue
:type src_res: :class:`~ost.mol.ResidueHandle`
- :param dst_res: The destination residue
+ :param dst_res: The destination residue (expected to be a standard amino acid)
:type dst_res: :class:`~ost.mol.ResidueHandle`
:param editor: Editor used to modify *dst_res*.
:type editor: :class:`~ost.mol.XCSEditor`
- :returns: True if the residue could be copied, False if not.
+ :returns: True if the residue could be copied as a conserved residue,
+ False if it had to fallback to :func:`CopyNonConserved`.
.. function:: CopyConserved(src_res, dst_res, editor)
@@ -1677,35 +1682,37 @@ to standard amino acids.
to ``dst_res``. If ``src_res`` is a modified version of ``dst_res`` and the
modification is a pure addition (e.g. the phosphate group of phosphoserine),
the modification is stripped off and all other heavy atoms are copied to
- ``dst_res``. If the modification is not a pure addition, only the backbone
- heavy atoms are copied to ``dst_res``.
+ ``dst_res``. If the modification is not a pure addition, it falls back to
+ :func:`CopyNonConserved`.
- Additionally, the selenium atom of ``MSE`` is converted to sulphur.
+ Additionally, the selenium atom of ``MSE`` is converted to sulphur to map
+ ``MSE`` to ``MET``.
:param src_res: The source residue
:type src_res: :class:`~ost.mol.ResidueHandle`
- :param dst_res: The destination residue
+ :param dst_res: The destination residue (expected to be a standard amino acid)
:type dst_res: :class:`~ost.mol.ResidueHandle`
:param editor: Editor used to modify *dst_res*.
:type editor: :class:`~ost.mol.XCSEditor`
- :returns: A tuple of bools stating whether the residue could be copied and
- whether the Cbeta atom was inserted into the ``dst_res``.
+ :returns: A tuple of bools stating whether the residue could be copied without
+ falling back to :func:`CopyNonConserved` and whether the CBeta atom
+ was copied from ``src_res`` to ``dst_res``.
.. function:: CopyNonConserved(src_res, dst_res, editor)
- Copies the heavy backbone atoms and Cbeta (except for ``GLY``) of ``src_res``
+ Copies the heavy backbone atoms and CBeta (except for ``GLY``) of ``src_res``
to ``dst_res``.
:param src_res: The source residue
:type src_res: :class:`~ost.mol.ResidueHandle`
- :param dst_res: The destination residue
+ :param dst_res: The destination residue (expected to be a standard amino acid)
:type dst_res: :class:`~ost.mol.ResidueHandle`
:param editor: Editor used to modify *dst_res*.
:type editor: :class:`~ost.mol.XCSEditor`
- :returns: A tuple of bools stating whether the residue could be copied and
- whether the Cbeta atom was inserted into the ``dst_res``.
+ :returns: A tuple of bools as in :func:`CopyConserved` with the first bool
+ always being False.
Molecular Checker (Molck)
diff --git a/modules/mol/alg/doc/molck.rst b/modules/mol/alg/doc/molck.rst
index 7ffd414ae95c5f2f10c6cb739398dd164718792b..7c4d9ee6300a7076e32dd9c81161fde444f35d67 100644
--- a/modules/mol/alg/doc/molck.rst
+++ b/modules/mol/alg/doc/molck.rst
@@ -37,29 +37,33 @@ All Options
The molck executable supports several other command line options,
please find them following:
-.. code-block:: bash
+.. 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:
+ 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)
- --rm=<a>,<b> remove atoms and residues matching some criteria:
+ 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
- --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
- --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.
+ - nonstd - Remove all residues not one of the
+ 20 standard amino acids
+ - unk - Remove unknown atoms not following
+ the nomenclature
+ Default: hyd
+ --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
+ --color=auto|on|off Whether output should be colored. Delault: auto
+ --map-nonstd Maps modified residues back to the parent amino acid,
+ for example: MSE -> MET, SEP -> SER.
================
Molck Python API
diff --git a/modules/mol/alg/pymod/__init__.py b/modules/mol/alg/pymod/__init__.py
index 73d5bd802ce28765d309e65b7eed4f65374abdfb..16127a16603e93e5f3f1c19f79dfb74bdd4031a7 100644
--- a/modules/mol/alg/pymod/__init__.py
+++ b/modules/mol/alg/pymod/__init__.py
@@ -1,5 +1,5 @@
import os.path
-from _ost_mol_alg import *
+from ._ost_mol_alg import *
from ost.mol.alg.superpose import *
import ost.mol.alg.trajectory_analysis
import ost.mol.alg.structure_analysis
diff --git a/modules/mol/alg/pymod/export_accessibility.cc b/modules/mol/alg/pymod/export_accessibility.cc
index 789c8f8da6c8ff2fabdba8ba13b1f7754c0f3347..ebafe3635774bf0a729fce77e11c6247abdde729 100644
--- a/modules/mol/alg/pymod/export_accessibility.cc
+++ b/modules/mol/alg/pymod/export_accessibility.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2017 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/alg/pymod/export_clash.cc b/modules/mol/alg/pymod/export_clash.cc
index 0720999be1cf7e65eb42ddb256768f3072f9f2f1..5e78f6cbc64dfc7812afdd5856e09880d17f9d71 100644
--- a/modules/mol/alg/pymod/export_clash.cc
+++ b/modules/mol/alg/pymod/export_clash.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/alg/pymod/export_entity_to_density.cc b/modules/mol/alg/pymod/export_entity_to_density.cc
index ee122d2da81899b32009bbe6ecb41224a95293fd..256c3e21999241c00c409259cfa9d230fa109994 100644
--- a/modules/mol/alg/pymod/export_entity_to_density.cc
+++ b/modules/mol/alg/pymod/export_entity_to_density.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/alg/pymod/export_membrane.cc b/modules/mol/alg/pymod/export_membrane.cc
index fe8ebe52de9e43c2a98499718f1951015794453f..51f6b7510ea26343aa39174eebacf9f1bb4b6d1c 100644
--- a/modules/mol/alg/pymod/export_membrane.cc
+++ b/modules/mol/alg/pymod/export_membrane.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2017 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/alg/pymod/export_molck.cc b/modules/mol/alg/pymod/export_molck.cc
index c626a6ce306f96ed9cbbcb24fe8b05aa4385b9ce..5578bd0504cf39c91f1eab59388be03ac1b92ffb 100644
--- a/modules/mol/alg/pymod/export_molck.cc
+++ b/modules/mol/alg/pymod/export_molck.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/alg/pymod/export_non_standard.cc b/modules/mol/alg/pymod/export_non_standard.cc
index 8d485b169ecbd290483daf5f0ab5ca3e06e8da80..ccb6053abc5040373694da1e047c9ccfce2b091e 100644
--- a/modules/mol/alg/pymod/export_non_standard.cc
+++ b/modules/mol/alg/pymod/export_non_standard.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/alg/pymod/export_sec_structure.cc b/modules/mol/alg/pymod/export_sec_structure.cc
index 6191b6921b026c3d6d7d4096fa4bb60b9bc5822a..d79dea60c5fc7e2fa7753fecb531951244b7cf49 100644
--- a/modules/mol/alg/pymod/export_sec_structure.cc
+++ b/modules/mol/alg/pymod/export_sec_structure.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2017 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/alg/pymod/export_structure_analysis.cc b/modules/mol/alg/pymod/export_structure_analysis.cc
index 2714f5847ea4e40bd1ec5c63faec3ea317b57336..a819658899a5e17a3a2ab5f83058bb456ce036d7 100644
--- a/modules/mol/alg/pymod/export_structure_analysis.cc
+++ b/modules/mol/alg/pymod/export_structure_analysis.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/alg/pymod/export_superpose_frames.cc b/modules/mol/alg/pymod/export_superpose_frames.cc
index 8f03153e54bb8823435461d7e69924444daa9a1e..0dcfd0e5eb93261ac3e347cf15590c2d92d85076 100644
--- a/modules/mol/alg/pymod/export_superpose_frames.cc
+++ b/modules/mol/alg/pymod/export_superpose_frames.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/alg/pymod/export_svd_superpose.cc b/modules/mol/alg/pymod/export_svd_superpose.cc
index 87e4cbbc76af199a357155261c729676528b7b29..ffe803a0a7368822cc1e706ef30bb766e6ddbd21 100644
--- a/modules/mol/alg/pymod/export_svd_superpose.cc
+++ b/modules/mol/alg/pymod/export_svd_superpose.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/alg/pymod/export_trajectory_analysis.cc b/modules/mol/alg/pymod/export_trajectory_analysis.cc
index 4db2668e91832d72952b12b637ad7141a7117ff3..d006ca09d4e79bb11c0c63b48bf4e41249477473 100644
--- a/modules/mol/alg/pymod/export_trajectory_analysis.cc
+++ b/modules/mol/alg/pymod/export_trajectory_analysis.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/alg/pymod/hbond.py b/modules/mol/alg/pymod/hbond.py
index 33545bd2f5430aac82e65cbb9023bece29608634..0807fe833801de466a66460b2ff35b649993bd47 100644
--- a/modules/mol/alg/pymod/hbond.py
+++ b/modules/mol/alg/pymod/hbond.py
@@ -139,10 +139,10 @@ class HBondDonor:
_donor=res.FindAtom(donor_name).handle
_hydrogen=res.FindAtom(hydrogen_name).handle
if not _donor.IsValid():
- if verbose:print 'Could not find '+donor_name+' in residue '+str(res)
+ if verbose:print('Could not find '+donor_name+' in residue '+str(res))
return
if not _hydrogen.IsValid():
- if verbose:print 'Could not find '+hydrogen_name+' in residue '+str(res)
+ if verbose:print('Could not find '+hydrogen_name+' in residue '+str(res))
return
return cls(_donor,_hydrogen)
@@ -164,11 +164,11 @@ class HBondAcceptor:
_acceptor=res.FindAtom(acceptor_name).handle
_antecedent_list=_ost.mol.AtomHandleList([res.FindAtom(name).handle for name in antecedent_name_list])
if not _acceptor.IsValid():
- if verbose:print 'Could not find '+acceptor_name+' in residue '+str(res)
+ if verbose:print('Could not find '+acceptor_name+' in residue '+str(res))
return
for i,a in enumerate(_antecedent_list):
if not a.IsValid():
- if verbose:print 'Could not find '+antecedent_name_list[i]+' in residue '+str(res)
+ if verbose:print('Could not find '+antecedent_name_list[i]+' in residue '+str(res))
return
return cls(_acceptor,_antecedent_list)
@@ -223,13 +223,13 @@ def GetHbondDonorAcceptorList(eh,hbond_donor_acceptor_dict={},verbose=True):
These names are given in a dictionary, which defaults to CHARMM.
"""
if not hbond_donor_acceptor_dict:
- print 'Using default CHARMM atom namings'
+ print('Using default CHARMM atom namings')
hbond_donor_acceptor_dict=BuildCHARMMHBondDonorAcceptorDict()
donor_list=[]
acceptor_list=[]
for r in eh.residues:
if not r.name in hbond_donor_acceptor_dict:
- print 'donors and acceptors for',r,'are not defined in the dictionary and will not be included'
+ print('donors and acceptors for',r,'are not defined in the dictionary and will not be included')
continue
res_da_dict=hbond_donor_acceptor_dict[r.name]
for acceptor in res_da_dict.acceptors:
@@ -274,10 +274,10 @@ def GetHbondListFromTraj(t,eh,cutoff=0.7,stride=1,swap=False,donor_swap_dict={},
"""
if swap:
if not donor_swap_dict:
- print 'use of standard CHARMM HBond donor swap dictionary'
+ print('use of standard CHARMM HBond donor swap dictionary')
donor_swap_dict=BuildCHARMMHBondDonorEquivalenceDict()
if not acceptor_swap_dict:
- print 'use of standard CHARMM HBond acceptor swap dictionary'
+ print('use of standard CHARMM HBond acceptor swap dictionary')
acceptor_swap_dict=BuildCHARMMHBondAcceptorEquivalenceDict()
[donor_list,acceptor_list]=GetHbondDonorAcceptorList(eh,hbond_donor_acceptor_dict,verbose)
hb_list=[]
@@ -339,10 +339,10 @@ def GetEquivalentHBonds(ref_hbond_list,eh,swap=False,donor_swap_dict={},acceptor
hbond_list.append(set([HBond(donor,acceptor)]))
else:
if not donor_swap_dict:
- print 'use of standard CHARMM HBond donor swap dictionary'
+ print('use of standard CHARMM HBond donor swap dictionary')
donor_swap_dict=BuildCHARMMHBondDonorEquivalenceDict()
if not acceptor_swap_dict:
- print 'use of standard CHARMM HBond acceptor swap dictionary'
+ print('use of standard CHARMM HBond acceptor swap dictionary')
acceptor_swap_dict=BuildCHARMMHBondAcceptorEquivalenceDict()
for hbond in ref_hbond_list:
res1=eh.FindResidue(hbond.donor.heavy_atom.chain.name,hbond.donor.heavy_atom.residue.number.num)
@@ -374,7 +374,7 @@ def CalculateHBondScore(ref_eh,eh2,ref_eh2=None,hbond_donor_acceptor_dict={},swa
else:hbond_list1=GetHbondListFromView(ref_eh,hbond_donor_acceptor_dict,verbose)
nbonds=float(len(hbond_list1))
if nbonds==0:
- print 'No HBonds in reference view'
+ print('No HBonds in reference view')
return None
hbond_list2=GetEquivalentHBonds(hbond_list1,eh2,swap,donor_swap_dict,acceptor_swap_dict,verbose)
c=0
@@ -392,19 +392,19 @@ def AnalyzeHBondScore(ref_eh,t,eh2,ref_eh2=None,hbond_donor_acceptor_dict={},swa
"""
if swap:
if not donor_swap_dict:
- print 'use of standard CHARMM HBond donor swap dictionary'
+ print('use of standard CHARMM HBond donor swap dictionary')
donor_swap_dict=BuildCHARMMHBondDonorEquivalenceDict()
if not acceptor_swap_dict:
- print 'use of standard CHARMM HBond acceptor swap dictionary'
+ print('use of standard CHARMM HBond acceptor swap dictionary')
acceptor_swap_dict=BuildCHARMMHBondAcceptorEquivalenceDict()
if ref_eh2:hbond_list1=GetHbondListBetweenViews(ref_eh,ref_eh2,hbond_donor_acceptor_dict,verbose)
elif type(ref_eh)==list:hbond_list1=ref_eh
else:hbond_list1=GetHbondListFromView(ref_eh,hbond_donor_acceptor_dict,verbose)
nbonds=float(len(hbond_list1))
if nbonds==0:
- print 'No HBonds in reference view'
+ print('No HBonds in reference view')
return None
- print 'number of hbonds in ref_eh:',nbonds
+ print('number of hbonds in ref_eh:',nbonds)
hbond_list2=GetEquivalentHBonds(hbond_list1,eh2,swap,donor_swap_dict,acceptor_swap_dict,verbose)
if last==-1:last=t.GetFrameCount()
score=FloatList()
@@ -423,10 +423,10 @@ def AnalyzeHBondScore(ref_eh,t,eh2,ref_eh2=None,hbond_donor_acceptor_dict={},swa
def GetHBondListIntersection(ref_hbond_list,ref_eh,hbond_list,swap=False,donor_swap_dict={},acceptor_swap_dict={}):
if swap:
if not donor_swap_dict:
- print 'use of standard CHARMM HBond donor swap dictionary'
+ print('use of standard CHARMM HBond donor swap dictionary')
donor_swap_dict=BuildCHARMMHBondDonorEquivalenceDict()
if not acceptor_swap_dict:
- print 'use of standard CHARMM HBond acceptor swap dictionary'
+ print('use of standard CHARMM HBond acceptor swap dictionary')
acceptor_swap_dict=BuildCHARMMHBondAcceptorEquivalenceDict()
hbond_list=GetEquivalentHBonds(hbond_list,ref_eh,swap,donor_swap_dict,acceptor_swap_dict)
ref_hbond_list=GetEquivalentHBonds(ref_hbond_list,ref_eh,swap,donor_swap_dict,acceptor_swap_dict)
diff --git a/modules/mol/alg/pymod/helix_kinks.py b/modules/mol/alg/pymod/helix_kinks.py
index 3bfb86047ef167f3824b6f1e4e78c75e7f374f52..7d9de7da00f3092f7b03de229367163306a2417b 100644
--- a/modules/mol/alg/pymod/helix_kinks.py
+++ b/modules/mol/alg/pymod/helix_kinks.py
@@ -9,17 +9,17 @@ import ost
def __FindProline(sele,proline):
if not sele.IsValid():
- print 'selection is not valid'
+ print('selection is not valid')
raise RuntimeError
if proline==False:
proline=sele.Select('rname=PRO')
if not proline.GetResidueCount()==1:
- print proline.GetResidueCount(),'prolines in the selection. One proline is needed'
+ print(proline.GetResidueCount(),'prolines in the selection. One proline is needed')
raise RuntimeError
proline=proline.residues[0]
proline_ca=proline.FindAtom('CA')
if not proline_ca.IsValid():
- print 'proline has no CA atom'
+ print('proline has no CA atom')
raise RuntimeError
return (proline,proline_ca)
proline.GetNumber().num
@@ -27,14 +27,14 @@ def __FindProline(sele,proline):
def __SelectPreAndPostProline(sele,proline_num):
pre_proline=sele.Select('rnum<'+str(proline_num))
post_proline=sele.Select('rnum>'+str(proline_num))
- print 'pre-proline residues'
+ print('pre-proline residues')
for res in pre_proline.residues:
- print res
- print 'post-proline residues'
+ print(res)
+ print('post-proline residues')
for res in post_proline.residues:
- print res
+ print(res)
if pre_proline.GetResidueCount()<4 or post_proline.GetResidueCount()<4:
- print 'pre and post proline helices should be at least 4 residues long, 7 for better stability'
+ print('pre and post proline helices should be at least 4 residues long, 7 for better stability')
raise RuntimeError
return (pre_proline,post_proline)
@@ -42,7 +42,7 @@ def __FindCa3AndCa4(sele,proline_ca,proline_num):
ca_3=sele.FindAtom(proline_ca.GetHandle().GetChain().GetName(),proline_num-3,'CA')
ca_4=sele.FindAtom(proline_ca.GetHandle().GetChain().GetName(),proline_num-4,'CA')
if not (ca_3.IsValid() and ca_4.IsValid()):
- print 'CA not found in (i-4) or (i-3) residue'
+ print('CA not found in (i-4) or (i-3) residue')
raise RuntimeError
return (ca_3,ca_4)
diff --git a/modules/mol/alg/pymod/qsscoring.py b/modules/mol/alg/pymod/qsscoring.py
index 3a793310a3c6deb4116c6033c6e443f2283997e0..fa838faabb18405849f0d0dc55110716c4c077b0 100644
--- a/modules/mol/alg/pymod/qsscoring.py
+++ b/modules/mol/alg/pymod/qsscoring.py
@@ -22,7 +22,7 @@ from ost.bindings.clustalw import ClustalW
from ost.mol.alg import lDDTScorer
from ost.seq.alg.renumber import Renumber
import numpy as np
-from scipy.misc import factorial
+from scipy.special import factorial
from scipy.special import binom
from scipy.cluster.hierarchy import fclusterdata
import itertools
@@ -228,6 +228,10 @@ class QSscorer:
self._chem_mapping = _GetChemGroupsMapping(self.qs_ent_1, self.qs_ent_2)
return self._chem_mapping
+ @chem_mapping.setter
+ def chem_mapping(self, chem_mapping):
+ self._chem_mapping = chem_mapping
+
@property
def ent_to_cm_1(self):
"""Subset of :attr:`qs_ent_1` used to compute chain mapping and symmetries.
@@ -255,6 +259,10 @@ class QSscorer:
self._ComputeAlignedEntities()
return self._ent_to_cm_1
+ @ent_to_cm_1.setter
+ def ent_to_cm_1(self, ent_to_cm_1):
+ self._ent_to_cm_1 = ent_to_cm_1
+
@property
def ent_to_cm_2(self):
"""Subset of :attr:`qs_ent_1` used to compute chain mapping and symmetries
@@ -264,6 +272,10 @@ class QSscorer:
self._ComputeAlignedEntities()
return self._ent_to_cm_2
+ @ent_to_cm_2.setter
+ def ent_to_cm_2(self, ent_to_cm_2):
+ self._ent_to_cm_2 = ent_to_cm_2
+
@property
def symm_1(self):
"""Symmetry groups for :attr:`qs_ent_1` used to speed up chain mapping.
@@ -384,6 +396,10 @@ class QSscorer:
LogInfo('Mapping found: %s' % str(self._chain_mapping))
return self._chain_mapping
+ @chain_mapping.setter
+ def chain_mapping(self, chain_mapping):
+ self._chain_mapping = chain_mapping
+
@property
def chain_mapping_scheme(self):
"""Mapping scheme used to get :attr:`chain_mapping`.
@@ -440,6 +456,10 @@ class QSscorer:
self.res_num_alignment)
return self._alignments
+ @alignments.setter
+ def alignments(self, alignments):
+ self._alignments = alignments
+
@property
def mapped_residues(self):
"""Mapping of shared residues in :attr:`alignments`.
@@ -454,6 +474,10 @@ class QSscorer:
self._mapped_residues = _GetMappedResidues(self.alignments)
return self._mapped_residues
+ @mapped_residues.setter
+ def mapped_residues(self, mapped_residues):
+ self._mapped_residues = mapped_residues
+
@property
def global_score(self):
"""QS-score with penalties.
@@ -522,6 +546,10 @@ class QSscorer:
self._clustalw_bin = settings.Locate(('clustalw', 'clustalw2'))
return self._clustalw_bin
+ @clustalw_bin.setter
+ def clustalw_bin(self, clustalw_bin):
+ self._clustalw_bin = clustalw_bin
+
def GetOligoLDDTScorer(self, settings, penalize_extra_chains=True):
"""
:return: :class:`OligoLDDTScorer` object, setup for this QS scoring problem.
@@ -1100,7 +1128,7 @@ class OligoLDDTScorer(object):
nominator = sum([s * w for s, w in zip(scores, weights)])
if self.penalize_extra_chains:
ref_scorers = self._GetRefScorers()
- denominator = sum(s.total_contacts for s in ref_scorers.values())
+ denominator = sum(s.total_contacts for s in list(ref_scorers.values()))
denominator += self._GetModelPenalty()
else:
denominator = sum(weights)
@@ -1261,7 +1289,7 @@ class OligoLDDTScorer(object):
for ch_name_mdl in sorted(unmapped_mdl_chains):
# get penalty for chain
cur_penalty = None
- for cm_ref, cm_mdl in self.chem_mapping.iteritems():
+ for cm_ref, cm_mdl in self.chem_mapping.items():
if ch_name_mdl in cm_mdl:
# penalize by an average of the chem. mapped ref. chains
cur_penalty = 0
@@ -1590,7 +1618,7 @@ def _GetAngles(Rt):
:type Rt: :class:`ost.geom.Mat4`
:return: A :class:`tuple` of angles for each axis (x,y,z)
"""
- rot = np.asmatrix(Rt.ExtractRotation().data).reshape(3,3)
+ rot = np.asarray(Rt.ExtractRotation().data).reshape(3,3)
tx = np.arctan2(rot[2,1], rot[2,2])
if tx < 0:
tx += 2*np.pi
@@ -1635,8 +1663,8 @@ def _GetChemGroupsMapping(qs_ent_1, qs_ent_2):
chain_pairs = []
ca_chains_1 = qs_ent_1.ca_chains
ca_chains_2 = qs_ent_2.ca_chains
- for ch_1 in repr_chains_1.keys():
- for ch_2 in repr_chains_2.keys():
+ for ch_1 in list(repr_chains_1.keys()):
+ for ch_2 in list(repr_chains_2.keys()):
aln = _AlignAtomSeqs(ca_chains_1[ch_1], ca_chains_2[ch_2])
if aln:
chains_seqid = seq.alg.SequenceIdentity(aln)
@@ -1648,24 +1676,24 @@ def _GetChemGroupsMapping(qs_ent_1, qs_ent_2):
chem_mapping = {}
for _, c1, c2 in chain_pairs:
skip = False
- for a,b in chem_mapping.iteritems():
+ for a,b in chem_mapping.items():
if repr_chains_1[c1] == a or repr_chains_2[c2] == b:
skip = True
break
if not skip:
chem_mapping[repr_chains_1[c1]] = repr_chains_2[c2]
if swapped:
- chem_mapping = {y: x for x, y in chem_mapping.iteritems()}
+ chem_mapping = {y: x for x, y in chem_mapping.items()}
qs_ent_1, qs_ent_2 = qs_ent_2, qs_ent_1
# notify chains without partner
- mapped_1 = set([i for s in chem_mapping.keys() for i in s])
+ mapped_1 = set([i for s in list(chem_mapping.keys()) for i in s])
chains_1 = set([c.name for c in qs_ent_1.ent.chains])
if chains_1 - mapped_1:
LogWarning('Unmapped Chains in %s: %s'
% (qs_ent_1.GetName(), ','.join(list(chains_1 - mapped_1))))
- mapped_2 = set([i for s in chem_mapping.values() for i in s])
+ mapped_2 = set([i for s in list(chem_mapping.values()) for i in s])
chains_2 = set([c.name for c in qs_ent_2.ent.chains])
if chains_2 - mapped_2:
LogWarning('Unmapped Chains in %s: %s'
@@ -1716,7 +1744,7 @@ def _GetAlignedResidues(qs_ent_1, qs_ent_2, chem_mapping, max_ca_per_chain,
ca_chains_1 = qs_ent_1.ca_chains
ca_chains_2 = qs_ent_2.ca_chains
# go through all mapped chemical groups
- for group_1, group_2 in chem_mapping.iteritems():
+ for group_1, group_2 in chem_mapping.items():
# MSA with ClustalW
seq_list = seq.CreateSequenceList()
# keep sequence-name (must be unique) to view mapping
@@ -1772,9 +1800,9 @@ def _FindSymmetry(qs_ent_1, qs_ent_2, ent_to_cm_1, ent_to_cm_2, chem_mapping):
# get possible symmetry groups
symm_subg_1 = _GetSymmetrySubgroups(qs_ent_1, ent_to_cm_1,
- chem_mapping.keys())
+ list(chem_mapping.keys()))
symm_subg_2 = _GetSymmetrySubgroups(qs_ent_2, ent_to_cm_2,
- chem_mapping.values())
+ list(chem_mapping.values()))
# check combination of groups
LogInfo('Selecting Symmetry Groups...')
@@ -1880,7 +1908,7 @@ def _GetChainMapping(ent_1, ent_2, symm_1, symm_2, chem_mapping,
ref_symm_2 = symm_2[0]
asu_chem_mapping = _LimitChemMapping(chem_mapping, ref_symm_1, ref_symm_2)
# for each chemically identical group
- for g1, g2 in asu_chem_mapping.iteritems():
+ for g1, g2 in asu_chem_mapping.items():
# try to superpose all possible pairs
for c1, c2 in itertools.product(g1, g2):
# get superposition transformation
@@ -1908,7 +1936,7 @@ def _GetChainMapping(ent_1, ent_2, symm_1, symm_2, chem_mapping,
index_asu_c1 = ref_symm_1.index(intra_asu_c1)
index_asu_c2 = ref_symm_2.index(intra_asu_c2)
index_mapp = {ref_symm_1.index(s1): ref_symm_2.index(s2) \
- for s1, s2 in intra_asu_mapp.iteritems()}
+ for s1, s2 in intra_asu_mapp.items()}
LogInfo('Intra symmetry-group mapping: %s' % str(intra_asu_mapp))
# get INTER symmetry group chain mapping
@@ -1930,8 +1958,8 @@ def _GetChainMapping(ent_1, ent_2, symm_1, symm_2, chem_mapping,
check += 1
# need to extract full chain mapping (use indexing)
mapping = {}
- for a, b in asu_mapp.iteritems():
- for id_a, id_b in index_mapp.iteritems():
+ for a, b in asu_mapp.items():
+ for id_a, id_b in index_mapp.items():
mapping[a[id_a]] = b[id_b]
chains_rmsd = cached_rmsd.GetMappedRMSD(mapping, res.transformation)
full_mappings.append((chains_rmsd, mapping))
@@ -2037,16 +2065,16 @@ def _GetDihedralSubgroups(ent, chem_groups, angles, angle_thr):
# get those which are non redundant and covering all chains
symm_groups = []
- for clst in same_angles.values():
- group = clst.keys()
+ for clst in list(same_angles.values()):
+ group = list(clst.keys())
if _ValidChainGroup(group, ent):
if len(chem_groups) > 1:
# if hetero, we want to group toghether different chains only
- symm_groups.append(zip(*group))
+ symm_groups.append(list(zip(*group)))
else:
# if homo, we also want pairs
symm_groups.append(group)
- symm_groups.append(zip(*group))
+ symm_groups.append(list(zip(*group)))
return symm_groups
def _GetCyclicSubgroups(ent, chem_groups, axis, axis_thr):
@@ -2068,8 +2096,8 @@ def _GetCyclicSubgroups(ent, chem_groups, axis, axis_thr):
# use to get grouping
symm_groups = []
- for clst in same_axis.values():
- all_chain = [item for sublist in clst.keys() for item in sublist]
+ for clst in list(same_axis.values()):
+ all_chain = [item for sublist in list(clst.keys()) for item in sublist]
if len(set(all_chain)) == ent.chain_count:
# if we have an hetero we can exploit cyclic symmetry for grouping
if len(chem_groups) > 1:
@@ -2106,14 +2134,14 @@ def _ClusterData(data, thr, metric):
"""
# special case length 1
if len(data) == 1:
- return {0: {data.keys()[0]: data.values()[0]} }
+ return {0: {list(data.keys())[0]: list(data.values())[0]} }
# do the clustering
- cluster_indices = fclusterdata(np.asarray(data.values()), thr,
+ cluster_indices = fclusterdata(np.asarray(list(data.values())), thr,
method='complete', criterion='distance',
metric=metric)
# fclusterdata output is cluster ids -> put into dict of clusters
res = {}
- for cluster_idx, data_key in zip(cluster_indices, data.keys()):
+ for cluster_idx, data_key in zip(cluster_indices, list(data.keys())):
if not cluster_idx in res:
res[cluster_idx] = {}
res[cluster_idx][data_key] = data[data_key]
@@ -2217,7 +2245,7 @@ def _LimitChemMapping(chem_mapping, limit_1, limit_2):
limit_1_set = set(limit_1)
limit_2_set = set(limit_2)
asu_chem_mapping = dict()
- for key, value in chem_mapping.iteritems():
+ for key, value in chem_mapping.items():
new_key = tuple(set(key) & limit_1_set)
if new_key:
asu_chem_mapping[new_key] = tuple(set(value) & limit_2_set)
@@ -2249,7 +2277,7 @@ def _CountSuperpositionsAndMappings(symm_1, symm_2, chem_mapping):
ref_symm_1 = symm_1[0]
ref_symm_2 = symm_2[0]
asu_chem_mapping = _LimitChemMapping(chem_mapping, ref_symm_1, ref_symm_2)
- for g1, g2 in asu_chem_mapping.iteritems():
+ for g1, g2 in asu_chem_mapping.items():
chain_superpositions = len(g1) * len(g2)
c['intra']['superpositions'] += chain_superpositions
map_per_sup = _PermutationOrCombinations(g1[0], g2[0], asu_chem_mapping)
@@ -2268,12 +2296,12 @@ def _PermutationOrCombinations(sup1, sup2, chem_mapping):
"""Should match len(_ListPossibleMappings(sup1, sup2, chem_mapping))."""
# remove superposed elements, put smallest complex as key
chem_map = {}
- for a,b in chem_mapping.iteritems():
+ for a,b in chem_mapping.items():
new_a = tuple([x for x in a if x != sup1])
new_b = tuple([x for x in b if x != sup2])
chem_map[new_a] = new_b
mapp_nr = 1.0
- for a, b in chem_map.iteritems():
+ for a, b in chem_map.items():
if len(a) == len(b):
mapp_nr *= factorial(len(a))
elif len(a) < len(b):
@@ -2308,14 +2336,14 @@ def _ListPossibleMappings(sup1, sup2, chem_mapping):
less elements) has more elements for any given mapped group.
"""
# find smallest complex
- chain1 = [i for s in chem_mapping.keys() for i in s]
- chain2 = [i for s in chem_mapping.values() for i in s]
+ chain1 = [i for s in list(chem_mapping.keys()) for i in s]
+ chain2 = [i for s in list(chem_mapping.values()) for i in s]
swap = False
if len(chain1) > len(chain2):
swap = True
# remove superposed elements, put smallest complex as key
chem_map = {}
- for a, b in chem_mapping.iteritems():
+ for a, b in chem_mapping.items():
new_a = tuple([x for x in a if x != sup1])
new_b = tuple([x for x in b if x != sup2])
if swap:
@@ -2326,7 +2354,7 @@ def _ListPossibleMappings(sup1, sup2, chem_mapping):
# equivalent chains
chem_perm = []
chem_ref = []
- for a, b in chem_map.iteritems():
+ for a, b in chem_map.items():
if len(a) == len(b):
chem_perm.append(list(itertools.permutations(b)))
chem_ref.append(a)
@@ -2343,7 +2371,7 @@ def _ListPossibleMappings(sup1, sup2, chem_mapping):
flat_perm = [i for s in perm for i in s]
d = {c1: c2 for c1, c2 in zip(flat_ref, flat_perm)}
if swap:
- d = {v: k for k, v in d.items()}
+ d = {v: k for k, v in list(d.items())}
d.update({sup1: sup2})
mappings.append(d)
return mappings
@@ -2389,7 +2417,7 @@ def _CheckClosedSymmetry(ent_1, ent_2, symm_1, symm_2, chem_mapping,
asu_chem_mapping = _LimitChemMapping(chem_mapping, ref_symm_1, ref_symm_2)
# for each chemically identical group
rmsd_mappings = []
- for g1, g2 in asu_chem_mapping.iteritems():
+ for g1, g2 in asu_chem_mapping.items():
# try to superpose all possible pairs
# -> note that some chain-chain combinations may work better than others
# to superpose the full oligomer (e.g. if some chains are open/closed)
@@ -2438,10 +2466,10 @@ def _GetSuperpositionMapping(ent_1, ent_2, chem_mapping, transformation,
swap = True
ent_1, ent_2 = ent_2, ent_1
transformation = geom.Invert(transformation)
- chem_pairs = zip(chem_mapping.values(), chem_mapping.keys())
+ chem_pairs = list(zip(list(chem_mapping.values()), list(chem_mapping.keys())))
else:
swap = False
- chem_pairs = chem_mapping.iteritems()
+ chem_pairs = iter(chem_mapping.items())
# sanity check
if ent_1.chain_count == 0:
return None
@@ -2463,7 +2491,7 @@ def _GetSuperpositionMapping(ent_1, ent_2, chem_mapping, transformation,
ch_atoms[a_2.chain.name].add(a_2.hash_code)
# get one with most atoms in overlap
max_num, max_name = max((len(atoms), name)
- for name, atoms in ch_atoms.iteritems())
+ for name, atoms in ch_atoms.items())
# early abort if overlap fraction not good enough
ch_2 = ent_2.FindChain(max_name)
if max_num == 0 or max_num / float(ch_2.handle.atom_count) < sup_fract:
@@ -2482,7 +2510,7 @@ def _GetSuperpositionMapping(ent_1, ent_2, chem_mapping, transformation,
mapped_chains.add(max_name)
# unswap if needed and return
if swap:
- mapping = {v: k for k, v in mapping.iteritems()}
+ mapping = {v: k for k, v in mapping.items()}
return mapping
def _GetMappedRMSD(ent_1, ent_2, chain_mapping, transformation):
@@ -2498,7 +2526,7 @@ def _GetMappedRMSD(ent_1, ent_2, chain_mapping, transformation):
# collect RMSDs and atom counts chain by chain and combine afterwards
rmsds = []
atoms = []
- for c1, c2 in chain_mapping.iteritems():
+ for c1, c2 in chain_mapping.items():
# get views and atom counts
chain_1 = ent_1.Select('cname="%s"' % c1)
chain_2 = ent_2.Select('cname="%s"' % c2)
@@ -2568,7 +2596,7 @@ class _CachedRMSD:
# collect RMSDs and atom counts chain by chain and combine afterwards
rmsds = []
atoms = []
- for c1, c2 in chain_mapping.iteritems():
+ for c1, c2 in chain_mapping.items():
# cached?
if (c1, c2) in self._pair_rmsd:
atom_count, rmsd = self._pair_rmsd[(c1, c2)]
diff --git a/modules/mol/alg/pymod/structure_analysis.py b/modules/mol/alg/pymod/structure_analysis.py
index 75ae223e1203e6116bccc487341d00e7d52d80a0..2103b14a71aa4ebd0be528df66d3fe21d6782313 100644
--- a/modules/mol/alg/pymod/structure_analysis.py
+++ b/modules/mol/alg/pymod/structure_analysis.py
@@ -30,11 +30,11 @@ def GetDistanceBetwCenterOfMass(sele1,sele2):
:return: :class:`float`
"""
if not sele1.IsValid() and sele2.IsValid():
- print 'invalid view'
+ print('invalid view')
return
eh=sele1.GetHandle()
if not eh==sele2.GetHandle():
- print 'The two views must be from the same entity'
+ print('The two views must be from the same entity')
return
f=GetFrameFromEntity(eh)
return f.GetDistanceBetwCenterOfMass(sele1,sele2)
@@ -52,11 +52,11 @@ def GetMinDistanceBetweenViews(sele1,sele2):
:return: :class:`float`
"""
if not sele1.IsValid() and sele2.IsValid():
- print 'invalid view'
+ print('invalid view')
return
eh=sele1.GetHandle()
if not eh==sele2.GetHandle():
- print 'The two views must be from the same entity'
+ print('The two views must be from the same entity')
return
f=GetFrameFromEntity(eh)
return f.GetMinDistance(sele1,sele2)
@@ -74,11 +74,11 @@ def GetMinDistBetwCenterOfMassAndView(sele1,sele2):
:return: distance (\ :class:`float`\ )
"""
if not sele1.IsValid() and sele2.IsValid():
- print 'invalid view'
+ print('invalid view')
return
eh=sele1.GetHandle()
if not eh==sele2.GetHandle():
- print 'The two views must be from the same entity'
+ print('The two views must be from the same entity')
return
f=GetFrameFromEntity(eh)
return f.GetMinDistBetwCenterOfMassAndView(sele1,sele2)
@@ -95,7 +95,7 @@ def GetAlphaHelixContent(sele1):
:return: :class:`float`
"""
if not sele1.IsValid():
- print 'invalid view'
+ print('invalid view')
return
eh=sele1.GetHandle()
f=GetFrameFromEntity(eh)
@@ -112,7 +112,7 @@ def CalculateBestFitLine(sele1):
:return: :class:`~ost.geom.Line3`
"""
if not sele1.IsValid():
- print 'invalid view'
+ print('invalid view')
return
eh=sele1.GetHandle()
f=GetFrameFromEntity(eh)
@@ -128,7 +128,7 @@ def CalculateBestFitPlane(sele1):
:return: :class:`~ost.geom.Plane`
"""
if not sele1.IsValid():
- print 'invalid view'
+ print('invalid view')
return
eh=sele1.GetHandle()
f=GetFrameFromEntity(eh)
@@ -146,7 +146,7 @@ def CalculateHelixAxis(sele1):
:return: :class:`~ost.geom.Line3`
"""
if not sele1.IsValid():
- print 'invalid view'
+ print('invalid view')
return
eh=sele1.GetHandle()
f=GetFrameFromEntity(eh)
@@ -172,10 +172,10 @@ def CalculateDistanceDifferenceMatrix(sele1,sele2):
LogError("Function needs numpy, but I could not import it.")
raise
if not sele1.IsValid() and sele2.IsValid():
- print 'invalid view'
+ print('invalid view')
return
if not sele1.GetAtomCount()==sele2.GetAtomCount():
- print 'The two views must have the same number of atoms'
+ print('The two views must have the same number of atoms')
return
n_atoms=sele1.GetAtomCount()
M=npy.zeros([n_atoms,n_atoms])
diff --git a/modules/mol/alg/pymod/superpose.py b/modules/mol/alg/pymod/superpose.py
index 546d71c4611c01a5dc64bb07f27dfbe062bb3392..515a4970363980ec3a9c2bad7ed8756831262af6 100644
--- a/modules/mol/alg/pymod/superpose.py
+++ b/modules/mol/alg/pymod/superpose.py
@@ -110,13 +110,13 @@ def MatchResidueByNum(ent_a, ent_b, atoms='all'):
## check residues & copy to views
try:
while True:
- r_a=residues_a.next()
- r_b=residues_b.next()
+ r_a=next(residues_a)
+ r_b=next(residues_b)
while r_a.number!=r_b.number:
while r_a.number<r_b.number:
- r_a=residues_a.next()
+ r_a=next(residues_a)
while r_b.number<r_a.number:
- r_b=residues_b.next()
+ r_b=next(residues_b)
assert r_a.number==r_b.number
result_a,result_b=_fetch_atoms(r_a, r_b, result_a, result_b, atmset)
except StopIteration:
@@ -125,7 +125,7 @@ def MatchResidueByNum(ent_a, ent_b, atoms='all'):
## iterate one list of residues, search in other list
try:
while True:
- r_a=residues_a.next()
+ r_a=next(residues_a)
r_b=chain_b.FindResidue(r_a.number)
if r_b.IsValid():
result_a,result_b=_fetch_atoms(r_a, r_b, result_a, result_b, atmset)
diff --git a/modules/mol/alg/pymod/trajectory_analysis.py b/modules/mol/alg/pymod/trajectory_analysis.py
index 2d71b5a4d533c8a14a066176311c2da99e5b84d5..9ff4b341ef55ebde0d3a8c966df2292793a3fa95 100644
--- a/modules/mol/alg/pymod/trajectory_analysis.py
+++ b/modules/mol/alg/pymod/trajectory_analysis.py
@@ -199,7 +199,7 @@ def DistRMSDFromTraj(t,sele,ref_sele,radius=7.0,average=False,seq_sep=4,first=0,
:return: a numpy vecor dist_rmsd(N\ :subscript:`frames`).
"""
if not sele.GetAtomCount()==ref_sele.GetAtomCount():
- print 'Not same number of atoms in the two views'
+ print('Not same number of atoms in the two views')
return
try:
import numpy as npy
diff --git a/modules/mol/alg/pymod/views.py b/modules/mol/alg/pymod/views.py
index f4a20307724c6b814183ad242637a9852f714ebb..8889538246b310b0af20e8bcf49fe826addb22b8 100644
--- a/modules/mol/alg/pymod/views.py
+++ b/modules/mol/alg/pymod/views.py
@@ -38,12 +38,12 @@ def PairResiduesByNum(view_a, view_b,
result_b=_EmptyView(view_b)
try:
while True:
- r1=residues_a.next()
- r2=residues_b.next()
+ r1=next(residues_a)
+ r2=next(residues_b)
while r1.number<r2.number:
- r1=residues_a.next()
+ r1=next(residues_a)
while r2.number<r1.number:
- r2=residues_b.next()
+ r2=next(residues_b)
assert r1.number==r2.number
result_a.AddResidue(r1, view_add_flags)
result_b.AddResidue(r2, view_add_flags)
diff --git a/modules/mol/alg/pymod/wrap_mol_alg.cc b/modules/mol/alg/pymod/wrap_mol_alg.cc
index 1c42af212a6b849d977d2afb4f43923bd042ed56..fd5b6d94de273dc57317e270d58596534fb5131f 100644
--- a/modules/mol/alg/pymod/wrap_mol_alg.cc
+++ b/modules/mol/alg/pymod/wrap_mol_alg.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
@@ -30,6 +30,7 @@
#include <ost/mol/alg/consistency_checks.hh>
#include <ost/mol/alg/pdbize.hh>
#include <ost/mol/alg/contact_overlap.hh>
+#include <ost/mol/alg/construct_cbeta.hh>
#include <ost/export_helper/pair_to_tuple_conv.hh>
#include <ost/export_helper/vec_to_list_conv.hh>
@@ -294,6 +295,15 @@ void print_lddt_per_residue_stats_wrapper(list& scores, bool structural_checks,
return mol::alg::PrintlDDTPerResidueStats(scores_vector, structural_checks, cutoffs_size);
}
+
+geom::Vec3 cbeta_vectors(const geom::Vec3& n_pos, const geom::Vec3& ca_pos,
+ const geom::Vec3& c_pos, Real l) {
+ return mol::alg::CBetaPosition(n_pos, ca_pos, c_pos, l);
+}
+
+geom::Vec3 cbeta_residue(const ost::mol::ResidueHandle& r, Real l) {
+ return mol::alg::CBetaPosition(r, l);
+}
}
@@ -529,4 +539,10 @@ BOOST_PYTHON_MODULE(_ost_mol_alg)
def("DRMSD",&mol::alg::DRMSD,(arg("view"),arg("distance_list"),
arg("cap_distance")=5.0,arg("sequence_separation")=0));
+ def("CBetaPosition", &cbeta_vectors, (arg("n_pos"), arg("ca_pos"),
+ arg("c_pos"), arg("l")=1.5));
+ def("CBetaPosition", &cbeta_residue, (arg("r"), arg("l") = 1.5));
+
+ def("ConstructCBetas", &mol::alg::ConstructCBetas, (arg("ent"),
+ arg("include_gly")=false));
}
diff --git a/modules/mol/alg/src/accessibility.hh b/modules/mol/alg/src/accessibility.hh
index 2ed83cc53493ed39b16ddc6067b5c38c1b75730b..d942ff3b4a757384b228d94b7811fd72ebc1b3aa 100644
--- a/modules/mol/alg/src/accessibility.hh
+++ b/modules/mol/alg/src/accessibility.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2017 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/alg/src/adjacency_bitmap.cc b/modules/mol/alg/src/adjacency_bitmap.cc
index e117e08645d8acad456df2b102a4650e57ea304c..d7204be01a433d0ba143c2ad56d0d5bfd7052322 100644
--- a/modules/mol/alg/src/adjacency_bitmap.cc
+++ b/modules/mol/alg/src/adjacency_bitmap.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/alg/src/clash_score.cc b/modules/mol/alg/src/clash_score.cc
index c42ca2ef67acdc9c9b3c2ddb4bbf8b60a3cd1fd4..797ac4b3fff7cce302ac55e76ac376d9f605da94 100644
--- a/modules/mol/alg/src/clash_score.cc
+++ b/modules/mol/alg/src/clash_score.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/alg/src/clash_score.hh b/modules/mol/alg/src/clash_score.hh
index ba1700295b341ded0caa6ae727f1ff2c86c5c5e6..6dbe03ca9d679c0863e6052ff74c4f8ab897364a 100644
--- a/modules/mol/alg/src/clash_score.hh
+++ b/modules/mol/alg/src/clash_score.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/alg/src/consistency_checks.cc b/modules/mol/alg/src/consistency_checks.cc
index bdc0ab646f8fb4bb42762034fa6c618b54a8ca98..f476f3ad685ba3ca02087be57c72e0bbfed44a86 100644
--- a/modules/mol/alg/src/consistency_checks.cc
+++ b/modules/mol/alg/src/consistency_checks.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
@@ -31,21 +31,29 @@ bool ResidueNamesMatch(const EntityView& probe, const EntityView& reference,
ChainViewList ref_chains = reference.GetChainList();
ChainViewList probe_chains = probe.GetChainList();
for (unsigned int rci = 0; rci < ref_chains.size(); ++rci) {
- ChainView ref_chain= ref_chains[rci];
- if (rci<probe_chains.size()) {
+ ChainView ref_chain = ref_chains[rci];
+ if (rci < probe_chains.size()) {
ChainView probe_chain = probe_chains[rci];
ResidueViewList ref_residues = ref_chain.GetResidueList();
- for (ResidueViewList::iterator rri=ref_residues.begin(), rre=ref_residues.end(); rri!=rre; ++rri) {
+ for (ResidueViewList::iterator rri = ref_residues.begin(),
+ rre = ref_residues.end(); rri != rre; ++rri) {
ResidueView probe_residue = probe_chain.FindResidue(rri->GetNumber());
if (probe_residue.IsValid()) {
if (probe_residue.GetName()!=rri->GetName()) {
return_value = false;
if (log_as_error) {
- LOG_ERROR("Name mismatch for residue " << probe_residue.GetNumber() << ": in the reference structure(s) is " << rri->GetName() << ", in the model " << probe_residue.GetName());
+ LOG_ERROR("Name mismatch for residue "
+ << probe_residue.GetNumber()
+ << ": in the reference structure(s) is "
+ << rri->GetName() << ", in the model "
+ << probe_residue.GetName());
} else {
- LOG_WARNING("Name mismatch for residue " << probe_residue.GetNumber() << ": in the reference structure(s) is " << rri->GetName() << ", in the model " << probe_residue.GetName());
+ LOG_WARNING("Name mismatch for residue "
+ << probe_residue.GetNumber()
+ << ": in the reference structure(s) is "
+ << rri->GetName() << ", in the model "
+ << probe_residue.GetName());
}
-
}
}
}
diff --git a/modules/mol/alg/src/consistency_checks.hh b/modules/mol/alg/src/consistency_checks.hh
index 34eb4568b82f54cdfba2e5b2423d176d322d9a2f..23038e366f8d053e534708605a724a88225ed063 100644
--- a/modules/mol/alg/src/consistency_checks.hh
+++ b/modules/mol/alg/src/consistency_checks.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/alg/src/construct_cbeta.hh b/modules/mol/alg/src/construct_cbeta.hh
index f67d3556dc375e85ed4bdff03444736a174ff214..7a5c7b9befa1441473c873e5405b48c58e86ff96 100644
--- a/modules/mol/alg/src/construct_cbeta.hh
+++ b/modules/mol/alg/src/construct_cbeta.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/alg/src/distance_rmsd_test.hh b/modules/mol/alg/src/distance_rmsd_test.hh
index bd583ed0210a8f3e276432ba5e75162d6f3ffc85..8a1f47c9a4902a5725a171893e071568ccee5172 100644
--- a/modules/mol/alg/src/distance_rmsd_test.hh
+++ b/modules/mol/alg/src/distance_rmsd_test.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/alg/src/distance_test_common.hh b/modules/mol/alg/src/distance_test_common.hh
index 22bc3fe8bf32d3df561ec0c0a225b54639d87ce7..53ecaba1544113a77623ccef2ddbe8ed2d49f0fd 100644
--- a/modules/mol/alg/src/distance_test_common.hh
+++ b/modules/mol/alg/src/distance_test_common.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/alg/src/filter_clashes.cc b/modules/mol/alg/src/filter_clashes.cc
index 8623d8779342b089366d6d43bf835cdc1c51377b..84df0f6657d1dd244322d676ac78a5fa75de92c9 100644
--- a/modules/mol/alg/src/filter_clashes.cc
+++ b/modules/mol/alg/src/filter_clashes.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/alg/src/filter_clashes.hh b/modules/mol/alg/src/filter_clashes.hh
index fe6d12c75a7303ec637e194d341831c1200ac4b0..0365a2826854fef2f11f44ec07d6010dd4cddf8c 100644
--- a/modules/mol/alg/src/filter_clashes.hh
+++ b/modules/mol/alg/src/filter_clashes.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/alg/src/find_membrane.hh b/modules/mol/alg/src/find_membrane.hh
index c2e00d87a9446bcf3907d35cdabae7bef248d483..f8e5331cdc76528b22052bec9deb84b44af45f42 100644
--- a/modules/mol/alg/src/find_membrane.hh
+++ b/modules/mol/alg/src/find_membrane.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/alg/src/lddt.cc b/modules/mol/alg/src/lddt.cc
index 8f592a37ff2c395fc063d13d81e6d1f1d009532c..4b913efdb6a90b111681ba8385640ff26410e261 100644
--- a/modules/mol/alg/src/lddt.cc
+++ b/modules/mol/alg/src/lddt.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/alg/src/local_dist_diff_test.hh b/modules/mol/alg/src/local_dist_diff_test.hh
index 916fe4facd4f71dbc0aa672b824e4d6c84500c00..794c671e06039c132f3f20bdeac9cc2e564a44a6 100644
--- a/modules/mol/alg/src/local_dist_diff_test.hh
+++ b/modules/mol/alg/src/local_dist_diff_test.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/alg/src/module_config.hh b/modules/mol/alg/src/module_config.hh
index 2ab0ff089013b63b86bc0a8331ddf84aaf7f992d..592eda0bfb0271106c7857a20cf83dba979736d2 100644
--- a/modules/mol/alg/src/module_config.hh
+++ b/modules/mol/alg/src/module_config.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/alg/src/molck.hh b/modules/mol/alg/src/molck.hh
index f021ef7ec9b81aaeabf5a46ceaaf8a8bfd84edee..0dae68b930a4f20da86049d471c1fca70626df14 100644
--- a/modules/mol/alg/src/molck.hh
+++ b/modules/mol/alg/src/molck.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/alg/src/nonstandard.cc b/modules/mol/alg/src/nonstandard.cc
index b51c582adcdd81fb5b02cff834c18c218b7b317d..04d05720cafe26e476169c40cda9d721cc0ae915 100644
--- a/modules/mol/alg/src/nonstandard.cc
+++ b/modules/mol/alg/src/nonstandard.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
@@ -21,6 +21,7 @@
Author: Marco Biasini, Juergen Haas
*/
+#include <ost/message.hh>
#include <ost/log.hh>
#include <ost/dyn_cast.hh>
#include <ost/conop/conop.hh>
@@ -48,18 +49,25 @@ bool CopyResidue(ResidueHandle src_res, ResidueHandle dst_res,
bool has_cbeta = false;
bool ret;
char parent_src = (comp_lib->FindCompound(src_res.GetName(),
- Compound::PDB))->GetOneLetterCode ();
+ Compound::PDB))->GetOneLetterCode();
char parent_dst = (comp_lib->FindCompound(dst_res.GetName(),
- Compound::PDB))->GetOneLetterCode ();
- if (parent_src==parent_dst) {
+ Compound::PDB))->GetOneLetterCode();
+ if (parent_src == parent_dst) {
ret = CopyConserved(src_res, dst_res, edi, has_cbeta, comp_lib);
} else {
ret = CopyNonConserved(src_res, dst_res, edi, has_cbeta);
}
// insert Cbeta, unless dst residue is glycine.
- if (!has_cbeta && dst_res.GetName()!="GLY") {
- geom::Vec3 cbeta_pos=mol::alg::CBetaPosition(dst_res);
- edi.InsertAtom(dst_res, "CB", cbeta_pos, "C");
+ if (!has_cbeta && dst_res.GetName() != "GLY") {
+ try {
+ geom::Vec3 cbeta_pos = mol::alg::CBetaPosition(dst_res);
+ edi.InsertAtom(dst_res, "CB", cbeta_pos, "C");
+ } catch (ost::Error& e) {
+ LOG_WARNING("Issue in CB reconstruction while copying residue "
+ << src_res.GetQualifiedName() << " to "
+ << dst_res.GetQualifiedName() << ": " << e.what()
+ << ". Skipped reconstruction.");
+ }
}
return ret;
}
diff --git a/modules/mol/alg/src/nonstandard.hh b/modules/mol/alg/src/nonstandard.hh
index 1dce74fd4c2cf102f985f06d22c2723e93053075..06a9149aa086401c829c695f6c3b046078db4e54 100644
--- a/modules/mol/alg/src/nonstandard.hh
+++ b/modules/mol/alg/src/nonstandard.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/alg/src/pdbize.cc b/modules/mol/alg/src/pdbize.cc
index e9265312c6f07be3752229ed4eb8348fb736df1a..0eea5cb94b5eb05f39e0d3258a08a1994b5e4ab9 100644
--- a/modules/mol/alg/src/pdbize.cc
+++ b/modules/mol/alg/src/pdbize.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/alg/src/pdbize.hh b/modules/mol/alg/src/pdbize.hh
index b344cfca415f809d39a5164396f7ae844a444945..1ddf66fc5d047d882563b5e0fe7e61dc989f8c86 100644
--- a/modules/mol/alg/src/pdbize.hh
+++ b/modules/mol/alg/src/pdbize.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/alg/src/sec_struct.hh b/modules/mol/alg/src/sec_struct.hh
index 198efee76d2d5fca91fbbcb70b000b8f6e5ec5b3..6a6b35cd8b1c578a59f0957bcba3ee6dc84a326e 100644
--- a/modules/mol/alg/src/sec_struct.hh
+++ b/modules/mol/alg/src/sec_struct.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2017 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/alg/src/sec_structure_segments.cc b/modules/mol/alg/src/sec_structure_segments.cc
index 4c156ba1fb85f564f271c1edfc103492200837ba..506ac2b7d011e15242c537e59a1541eebdc01e43 100644
--- a/modules/mol/alg/src/sec_structure_segments.cc
+++ b/modules/mol/alg/src/sec_structure_segments.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/alg/src/sec_structure_segments.hh b/modules/mol/alg/src/sec_structure_segments.hh
index 7874c245456641dc584044f6c7ae23feca95d705..958c285209dc7723ffd9aa31d4057eb9c3057c16 100644
--- a/modules/mol/alg/src/sec_structure_segments.hh
+++ b/modules/mol/alg/src/sec_structure_segments.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/alg/src/structure_analysis.cc b/modules/mol/alg/src/structure_analysis.cc
index b561b0a7fb7d7607217190317c18d643aedd62ea..e1b36a0b3ce2560c116bf58a3902d9815d013c53 100644
--- a/modules/mol/alg/src/structure_analysis.cc
+++ b/modules/mol/alg/src/structure_analysis.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/alg/src/structure_analysis.hh b/modules/mol/alg/src/structure_analysis.hh
index 2f450f6924fb9d0f50e558e2da1d54d1dce5606b..2de4d70fd06132ef3fb953197b0c524aaaa72d05 100644
--- a/modules/mol/alg/src/structure_analysis.hh
+++ b/modules/mol/alg/src/structure_analysis.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/alg/src/superpose_frames.cc b/modules/mol/alg/src/superpose_frames.cc
index ef8ebe9216de6d6cbc69b918509e6c37d044367b..b2cbbf9c06259cc4b787f63d0b08fd8c2d5b42f3 100644
--- a/modules/mol/alg/src/superpose_frames.cc
+++ b/modules/mol/alg/src/superpose_frames.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/alg/src/superpose_frames.hh b/modules/mol/alg/src/superpose_frames.hh
index 8a75ef9aa9d8469d1b55a4518adca96c0f5d80b8..3f85c5c273ccbb7fbe86b396b2c879653e81d06f 100644
--- a/modules/mol/alg/src/superpose_frames.hh
+++ b/modules/mol/alg/src/superpose_frames.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/alg/src/svd_superpose.cc b/modules/mol/alg/src/svd_superpose.cc
index b8f7759391399723eda64a3e2fb3c291c1cdbc68..6780213cf513cbd4785b50f542881570ec62b003 100644
--- a/modules/mol/alg/src/svd_superpose.cc
+++ b/modules/mol/alg/src/svd_superpose.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/alg/src/svd_superpose.hh b/modules/mol/alg/src/svd_superpose.hh
index 72719c2e66c5f49f7ae16917ef59be76f05c9334..c7c1f74ab7b6149cb2fe0c0942237723ccac34ed 100644
--- a/modules/mol/alg/src/svd_superpose.hh
+++ b/modules/mol/alg/src/svd_superpose.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/alg/src/trajectory_analysis.cc b/modules/mol/alg/src/trajectory_analysis.cc
index 359530f7cf63f18778acb40507c251df01a81567..38678d797f48839f83dbd0fbb6c0598e98caa345 100644
--- a/modules/mol/alg/src/trajectory_analysis.cc
+++ b/modules/mol/alg/src/trajectory_analysis.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/alg/src/trajectory_analysis.hh b/modules/mol/alg/src/trajectory_analysis.hh
index f32e4a85a07538d438ca25fcfba63eb8b74b5b35..623b344f6796504f51b2ae252b17c19b53092c59 100644
--- a/modules/mol/alg/src/trajectory_analysis.hh
+++ b/modules/mol/alg/src/trajectory_analysis.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/alg/tests/test_accessibility.py b/modules/mol/alg/tests/test_accessibility.py
index c3d857fd52f43dc5c30c58ebab47b763fa28da45..8a951529f41b71db43d73b6098997ccc4f699e27 100644
--- a/modules/mol/alg/tests/test_accessibility.py
+++ b/modules/mol/alg/tests/test_accessibility.py
@@ -106,7 +106,7 @@ class TestAccessibility(unittest.TestCase):
acc_naccess = AccessibilitiesRaw(ent_three, use_naccess=True)
self.assertTrue(Compare(acc_classic, acc_naccess))
except:
- print "Could not find NACCESS, could not compare Accessiblity function..."
+ print("Could not find NACCESS, could not compare Accessiblity function...")
def testAccDSSP(self):
@@ -117,7 +117,7 @@ class TestAccessibility(unittest.TestCase):
dssp_path = settings.Locate(['dsspcmbi', 'dssp', 'mkdssp'],
env_name='DSSP_EXECUTABLE')
except:
- print "Could not find DSSP, could not compare Accessibility function..."
+ print("Could not find DSSP, could not compare Accessibility function...")
return
# we assume oligo mode to be working as it is tested in
diff --git a/modules/mol/alg/tests/test_consistency_checks.cc b/modules/mol/alg/tests/test_consistency_checks.cc
index 927b9d1efacbc4d5a56a411c7ab421cec327f1bb..657c3076f47f7518f541c15af8bbe7e0e2c90fd6 100644
--- a/modules/mol/alg/tests/test_consistency_checks.cc
+++ b/modules/mol/alg/tests/test_consistency_checks.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
@@ -35,37 +35,40 @@ BOOST_AUTO_TEST_SUITE( mol_alg );
BOOST_AUTO_TEST_CASE(consistency_check)
{
- EntityHandle a=CreateEntity();
- XCSEditor eda=a.EditXCS();
- ChainHandle ca=eda.InsertChain("A");
- ResidueHandle r1a = eda.AppendResidue(ca, "ALA",1);
- ResidueHandle r2a = eda.AppendResidue(ca, "TYR",2);
- ResidueHandle r3a = eda.AppendResidue(ca, "LEU",3);
- ResidueHandle r4a = eda.AppendResidue(ca, "GLY",4);
- ChainHandle ca2=eda.InsertChain("C");
- ResidueHandle r1a2 = eda.AppendResidue(ca2, "PRO",1);
+ EntityHandle a = CreateEntity();
+ XCSEditor eda = a.EditXCS();
+ ChainHandle ca = eda.InsertChain("A");
+ ResidueHandle r1a = eda.AppendResidue(ca, "ALA", 1);
+ ResidueHandle r2a = eda.AppendResidue(ca, "TYR", 2);
+ ResidueHandle r3a = eda.AppendResidue(ca, "LEU", 3);
+ ResidueHandle r4a = eda.AppendResidue(ca, "GLY", 4);
+ ChainHandle ca2 = eda.InsertChain("C");
+ ResidueHandle r1a2 = eda.AppendResidue(ca2, "PRO", 1);
+ EntityHandle b = CreateEntity();
+ XCSEditor edb = b.EditXCS();
+ ChainHandle cb = edb.InsertChain("A");
+ ResidueHandle r1b = edb.AppendResidue(cb, "ALA", 1);
+ ResidueHandle r2b = edb.AppendResidue(cb, "TYR", 2);
+ ResidueHandle r3b = edb.AppendResidue(cb, "LEU", 3);
+ ResidueHandle r4b = edb.AppendResidue(cb, "GLY", 4);
+ ResidueHandle r5b = edb.AppendResidue(cb, "PRO", 5);
- EntityHandle b=CreateEntity();
- XCSEditor edb=b.EditXCS();
- ChainHandle cb=edb.InsertChain("A");
- ResidueHandle r1b = edb.AppendResidue(cb, "ALA",1);
- ResidueHandle r2b = edb.AppendResidue(cb, "TYR",2);
- ResidueHandle r3b = edb.AppendResidue(cb, "LEU",3);
- ResidueHandle r4b = edb.AppendResidue(cb, "GLY",4);
- ResidueHandle r5b = edb.AppendResidue(cb, "PRO",5);
-
-
- EntityHandle c=CreateEntity();
- XCSEditor edc=c.EditXCS();
- ChainHandle cc=edc.InsertChain("A");
- ResidueHandle r1c = edc.AppendResidue(cc, "ALA",1);
- ResidueHandle r2c = edc.AppendResidue(cc, "PRO",2);
- ResidueHandle r3c = edc.AppendResidue(cc, "LEU",3);
- ResidueHandle r4c = edc.AppendResidue(cc, "GLY",4);
+ EntityHandle c = CreateEntity();
+ XCSEditor edc = c.EditXCS();
+ ChainHandle cc = edc.InsertChain("A");
+ ResidueHandle r1c = edc.AppendResidue(cc, "ALA", 1);
+ ResidueHandle r2c = edc.AppendResidue(cc, "PRO", 2);
+ ResidueHandle r3c = edc.AppendResidue(cc, "LEU", 3);
+ ResidueHandle r4c = edc.AppendResidue(cc, "GLY", 4);
- BOOST_CHECK(ost::mol::alg::ResidueNamesMatch(a.CreateFullView(),b.CreateFullView())==true);
- BOOST_CHECK(ost::mol::alg::ResidueNamesMatch(c.CreateFullView(),b.CreateFullView())==false);
+ const EntityView eva = a.CreateFullView();
+ const EntityView evb = b.CreateFullView();
+ const EntityView evc = c.CreateFullView();
+ BOOST_CHECK(ResidueNamesMatch(eva, evb) == true);
+ BOOST_CHECK(ResidueNamesMatch(evb, eva) == true);
+ BOOST_CHECK(ResidueNamesMatch(evc, evb) == false);
+ BOOST_CHECK(ResidueNamesMatch(evb, evc) == false);
}
BOOST_AUTO_TEST_SUITE_END();
diff --git a/modules/mol/alg/tests/test_convenient_superpose.py b/modules/mol/alg/tests/test_convenient_superpose.py
index 30f06242931c9197c9334fc326a278e7de3b505a..8e01b4937d8fb6c45a0193ba103790e84e107a47 100644
--- a/modules/mol/alg/tests/test_convenient_superpose.py
+++ b/modules/mol/alg/tests/test_convenient_superpose.py
@@ -9,9 +9,9 @@ class TestConvenientSuperpose(unittest.TestCase):
pass
def assertEqualAtomOrder(self, view1, view2):
- self.assertEquals(len(view1.atoms),len(view2.atoms))
+ self.assertEqual(len(view1.atoms),len(view2.atoms))
for a1, a2 in zip(view1.atoms, view2.atoms):
- self.assertEquals(a1.element, a2.element)
+ self.assertEqual(a1.element, a2.element)
self.assertTrue(geom.Equal(a1.pos, a2.pos))
def testAssertion(self):
diff --git a/modules/mol/alg/tests/test_nonstandard.py b/modules/mol/alg/tests/test_nonstandard.py
index c81c92479a4150c76aa89ff92409a4dc7656e25f..c7f49215eb79b559c1c43cd71659569de5e447fb 100644
--- a/modules/mol/alg/tests/test_nonstandard.py
+++ b/modules/mol/alg/tests/test_nonstandard.py
@@ -57,11 +57,56 @@ class TestNonStandard(unittest.TestCase):
self.assertTrue(residues[3].FindAtom("CB").IsValid())
+ def test_CBetaFail(self):
+ # make sure that we can handle cases where CB reconstruction fails
+
+ # NOTES:
+ # - SNN is (since June 2011) labeled as a modified ASN but has a weird
+ # backbone structure without any overlap in atom names with ASN
+ # -> we hence expect it to a) always fall back to CopyNonConserved
+ # and b) fail to copy any atoms (and hence also fail to)
+ # - SNN also removes N of following residue which is expected to have an
+ # incomplete backbone which would make it impossible to create a CB pos.
+
+ # source of file: residues A.198 and A.199 from PDB ID 2YHW
+ tpl = io.LoadPDB('testfiles/cbeta_fail.pdb')
+ new_hdl = mol.CreateEntity();
+ ed = new_hdl.EditXCS()
+ c = ed.InsertChain('A')
+ ed.AppendResidue(c, 'GLY')
+ ed.AppendResidue(c, 'ALA')
+ ed.AppendResidue(c, 'ASN')
+ ed.AppendResidue(c, 'GLY')
+ ed.AppendResidue(c, 'ALA')
+ # SNN to GLY
+ err = mol.alg.CopyResidue(tpl.residues[0], new_hdl.residues[0], ed)
+ self.assertFalse(err)
+ self.assertEqual(new_hdl.residues[0].atom_count, 0)
+ # SNN to ALA
+ err = mol.alg.CopyResidue(tpl.residues[0], new_hdl.residues[1], ed)
+ self.assertFalse(err)
+ self.assertEqual(new_hdl.residues[1].atom_count, 0)
+ # SNN to ASN
+ err = mol.alg.CopyResidue(tpl.residues[0], new_hdl.residues[2], ed)
+ self.assertFalse(err)
+ self.assertEqual(new_hdl.residues[2].atom_count, 0)
+ # GLY to GLY
+ err = mol.alg.CopyResidue(tpl.residues[1], new_hdl.residues[3], ed)
+ self.assertTrue(err)
+ self.assertEqual(new_hdl.residues[3].atom_count, 3)
+ self.assertFalse(new_hdl.residues[3].FindAtom("CB").IsValid())
+ # GLY to ALA
+ err = mol.alg.CopyResidue(tpl.residues[1], new_hdl.residues[4], ed)
+ self.assertFalse(err)
+ self.assertEqual(new_hdl.residues[4].atom_count, 3)
+ self.assertFalse(new_hdl.residues[4].FindAtom("CB").IsValid())
+
+
def test_CopyResidue(self):
- tpl=io.LoadPDB('testfiles/cbeta.pdb')
- new_hdl=mol.CreateEntity();
- ed=new_hdl.EditXCS()
- c=ed.InsertChain('A')
+ tpl = io.LoadPDB('testfiles/cbeta.pdb')
+ new_hdl = mol.CreateEntity();
+ ed = new_hdl.EditXCS()
+ c = ed.InsertChain('A')
ed.AppendResidue(c, 'MET')
ed.AppendResidue(c, 'GLY')
ed.AppendResidue(c, 'GLY')
@@ -72,31 +117,31 @@ class TestNonStandard(unittest.TestCase):
ed.AppendResidue(c, 'MET')
# MET to MET
- err =mol.alg.CopyResidue(tpl.residues[0], new_hdl.residues[0], ed)
+ err = mol.alg.CopyResidue(tpl.residues[0], new_hdl.residues[0], ed)
self.assertTrue(err)
#GLY to GLY
- err =mol.alg.CopyResidue(tpl.residues[1], new_hdl.residues[1], ed)
+ err = mol.alg.CopyResidue(tpl.residues[1], new_hdl.residues[1], ed)
self.assertTrue(err)
# GLY to GLY
- err =mol.alg.CopyResidue(tpl.residues[2], new_hdl.residues[2], ed)
+ err = mol.alg.CopyResidue(tpl.residues[2], new_hdl.residues[2], ed)
self.assertTrue(err)
#now we copy a HIS to a HIS
- err =mol.alg.CopyResidue(tpl.residues[3], new_hdl.residues[3], ed)
+ err = mol.alg.CopyResidue(tpl.residues[3], new_hdl.residues[3], ed)
self.assertTrue(err)
# copy a GLY to a HIS
- err, has_cbeta=mol.alg.CopyNonConserved(tpl.residues[1], new_hdl.residues[4], ed)
+ err, has_cbeta = mol.alg.CopyNonConserved(tpl.residues[1], new_hdl.residues[4], ed)
self.assertFalse(has_cbeta)
- # copy a MET to a GLY
- err =mol.alg.CopyResidue(tpl.residues[0], new_hdl.residues[5], ed)
+ # copy a MET to a GLY
+ err = mol.alg.CopyResidue(tpl.residues[0], new_hdl.residues[5], ed)
self.assertFalse(err)
- # copy a MET to a HIS
- err =mol.alg.CopyResidue(tpl.residues[0], new_hdl.residues[6], ed)
+ # copy a MET to a HIS
+ err = mol.alg.CopyResidue(tpl.residues[0], new_hdl.residues[6], ed)
self.assertFalse(err)
# copy a GLY to a MET with adding CB
- err=mol.alg.CopyResidue(tpl.residues[1], new_hdl.residues[7], ed)
+ err = mol.alg.CopyResidue(tpl.residues[1], new_hdl.residues[7], ed)
self.assertFalse(err)
- residues=new_hdl.residues
+ residues = new_hdl.residues
self.assertEqual(len(residues), 8)
# MET to MET
self.assertTrue(residues[0].FindAtom("CB").IsValid())
@@ -121,4 +166,4 @@ if __name__ == "__main__":
if testutils.SetDefaultCompoundLib():
testutils.RunTests()
else:
- print 'No compound library available. Ignoring test_nonstandard.py tests.'
+ print('No compound library available. Ignoring test_nonstandard.py tests.')
diff --git a/modules/mol/alg/tests/test_partial_sec_struct_assignment.cc b/modules/mol/alg/tests/test_partial_sec_struct_assignment.cc
index 56d247515b06a0dc3e54692641f1aaa8fcc7c469..11a194b2a7827b2b120a0b74247189774d324aa7 100644
--- a/modules/mol/alg/tests/test_partial_sec_struct_assignment.cc
+++ b/modules/mol/alg/tests/test_partial_sec_struct_assignment.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2017 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/alg/tests/test_pdbize.py b/modules/mol/alg/tests/test_pdbize.py
index abf2bc892f2618aa85f37b1ffd79c93d106b4d5d..0048f9b3683c99be13f13380f1c94e4c04d7431a 100644
--- a/modules/mol/alg/tests/test_pdbize.py
+++ b/modules/mol/alg/tests/test_pdbize.py
@@ -18,13 +18,13 @@ class TestPDBize(unittest.TestCase):
seqs = seq.CreateSequenceList()
pdbizer.Add(m.Select(''), transformations, seqs)
pdbized = pdbizer.Finish()
- self.assertEquals([c.name for c in pdbized.chains], ["-"])
+ self.assertEqual([c.name for c in pdbized.chains], ["-"])
residues = pdbized.residues
for i in range(26):
- self.assertEquals(residues[i].number.num, 1)
- self.assertEquals(residues[i].number.ins_code, chr(ord('A')+i))
- self.assertEquals(residues[26].number.num, 2)
- self.assertEquals(residues[26].number.ins_code, 'A')
+ self.assertEqual(residues[i].number.num, 1)
+ self.assertEqual(residues[i].number.ins_code, chr(ord('A')+i))
+ self.assertEqual(residues[26].number.num, 2)
+ self.assertEqual(residues[26].number.ins_code, 'A')
def test_starts_from_last_water_rnum(self):
m = mol.CreateEntity()
e = m.EditXCS(mol.BUFFERED_EDIT)
@@ -38,9 +38,9 @@ class TestPDBize(unittest.TestCase):
pdbizer.Add(m.Select(''), transformations,seqs)
pdbizer.Add(m.Select(''), transformations,seqs)
pdbized = pdbizer.Finish()
- self.assertEquals([c.name for c in pdbized.chains], ["-"])
+ self.assertEqual([c.name for c in pdbized.chains], ["-"])
residues = pdbized.residues
- self.assertEquals([r.number for r in residues],
+ self.assertEqual([r.number for r in residues],
[mol.ResNum(1, 'A'), mol.ResNum(1, 'B')])
diff --git a/modules/mol/alg/tests/test_qsscoring.py b/modules/mol/alg/tests/test_qsscoring.py
index c241eea49dea794a7f620014561a482019b3507a..b8f7271205c8e21b5297e88b4e3ab537d2543467 100644
--- a/modules/mol/alg/tests/test_qsscoring.py
+++ b/modules/mol/alg/tests/test_qsscoring.py
@@ -5,8 +5,8 @@ from ost import io, mol, settings
try:
from ost.mol.alg.qsscoring import *
except ImportError:
- print "Failed to import qsscoring. Happens when numpy or scipy missing. " \
- "Ignoring test_qsscoring.py tests."
+ print("Failed to import qsscoring. Happens when numpy or scipy missing. " \
+ "Ignoring test_qsscoring.py tests.")
sys.exit(0)
from ost.mol.alg import lDDTSettings
@@ -130,8 +130,10 @@ class TestQSscore(unittest.TestCase):
# check mappings
self.assertEqual(qs_scorer.chem_mapping,
{('D', 'F'): ('B', 'D'), ('C', 'E'): ('A', 'C')})
- self.assertEqual(sorted(qs_scorer.symm_1), [('D', 'C'), ('F', 'E')])
- self.assertEqual(sorted(qs_scorer.symm_2), [('A', 'B'), ('C', 'D')])
+ self.assertEqual(len(qs_scorer.symm_1), 2)
+ self.assertEqual(len(qs_scorer.symm_1[0]), 2)
+ self.assertEqual(len(qs_scorer.symm_2), 2)
+ self.assertEqual(len(qs_scorer.symm_2[0]), 2)
self.assertEqual(qs_scorer.chain_mapping,
{'C': 'A', 'E': 'C', 'D': 'B', 'F': 'D'})
# check scoring
@@ -151,8 +153,10 @@ class TestQSscore(unittest.TestCase):
# check mappings
self.assertEqual(qs_scorer.chem_mapping,
{('C', 'E'): ('A', 'C'), ('D', 'F'): ('D', 'B')})
- self.assertEqual(sorted(qs_scorer.symm_1), [('D', 'C'), ('F', 'E')])
- self.assertEqual(sorted(qs_scorer.symm_2), [('B', 'A'), ('D', 'C')])
+ self.assertEqual(len(qs_scorer.symm_1), 2)
+ self.assertEqual(len(qs_scorer.symm_1[0]), 2)
+ self.assertEqual(len(qs_scorer.symm_2), 2)
+ self.assertEqual(len(qs_scorer.symm_2[0]), 2)
self.assertEqual(qs_scorer.chain_mapping,
{'C': 'A', 'E': 'C', 'D': 'B', 'F': 'D'})
# check scoring
@@ -190,8 +194,10 @@ class TestQSscore(unittest.TestCase):
self.assertFalse(qs_scorer.calpha_only)
self.assertEqual(qs_scorer.chem_mapping,
{('A', 'C'): ('A',), ('B', 'D'): ('B',)})
- self.assertEqual(sorted(qs_scorer.symm_1), [('A', 'B'), ('C', 'D')])
- self.assertEqual(sorted(qs_scorer.symm_2), [('A', 'B')])
+ self.assertEqual(len(qs_scorer.symm_1), 2)
+ self.assertEqual(len(qs_scorer.symm_1[0]), 2)
+ self.assertEqual(len(qs_scorer.symm_2), 1)
+ self.assertEqual(len(qs_scorer.symm_2[0]), 2)
self.assertEqual(qs_scorer.chain_mapping, {'A': 'A', 'B': 'B'})
def test_HeteroCase3(self):
@@ -207,11 +213,10 @@ class TestQSscore(unittest.TestCase):
self.assertEqual(qs_scorer.chem_mapping,
{('A', 'C', 'E', 'G', 'I', 'K'): ('A', 'C', 'E'),
('B', 'D', 'F', 'H', 'J', 'L'): ('B', 'D', 'F')})
- self.assertEqual(sorted(qs_scorer.symm_1),
- [('A', 'B'), ('C', 'D'), ('E', 'F'),
- ('G', 'H'), ('I', 'J'), ('K', 'L')])
- self.assertEqual(sorted(qs_scorer.symm_2),
- [('A', 'B'), ('C', 'D'), ('E', 'F')])
+ self.assertEqual(len(qs_scorer.symm_1), 6)
+ self.assertEqual(len(qs_scorer.symm_1[0]), 2)
+ self.assertEqual(len(qs_scorer.symm_2), 3)
+ self.assertEqual(len(qs_scorer.symm_2[0]), 2)
self.assertEqual(qs_scorer.chain_mapping,
{'A':'A', 'B':'B', 'G':'C', 'H':'D', 'I':'E', 'J':'F'})
@@ -302,8 +307,10 @@ class TestQSscore(unittest.TestCase):
# check properties
self.assertFalse(qs_scorer.calpha_only)
self.assertEqual(qs_scorer.chem_mapping, {('A', 'B'): ('B', 'C', 'D', 'A')})
- self.assertEqual(sorted(qs_scorer.symm_1), [('A', 'B')])
- self.assertEqual(sorted(qs_scorer.symm_2), [('B', 'A'), ('C', 'D')])
+ self.assertEqual(len(qs_scorer.symm_1), 1)
+ self.assertEqual(len(qs_scorer.symm_1[0]), 2)
+ self.assertEqual(len(qs_scorer.symm_2), 2)
+ self.assertEqual(len(qs_scorer.symm_2[0]), 2)
self.assertEqual(qs_scorer.chain_mapping, {'A': 'B', 'B': 'A'})
def test_HomoCase2(self):
@@ -319,8 +326,10 @@ class TestQSscore(unittest.TestCase):
self.assertFalse(qs_scorer.calpha_only)
self.assertEqual(qs_scorer.chem_mapping,
{('A', 'B', 'C', 'D', 'E', 'F'): ('A', 'B')})
- self.assertEqual(sorted(qs_scorer.symm_1), [('A', 'B', 'C', 'D', 'E', 'F')])
- self.assertEqual(sorted(qs_scorer.symm_2), [('B', 'A')])
+ self.assertEqual(len(qs_scorer.symm_1), 1)
+ self.assertEqual(len(qs_scorer.symm_1[0]), 6)
+ self.assertEqual(len(qs_scorer.symm_2), 1)
+ self.assertEqual(len(qs_scorer.symm_2[0]), 2)
self.assertEqual(qs_scorer.chain_mapping, {'A': 'A', 'B': 'B'})
self._CheckScorer(qs_scorer)
@@ -386,9 +395,17 @@ class TestQSscore(unittest.TestCase):
self.assertAlmostEqual(qs_scorer.global_score, 0.171, 2)
self.assertAlmostEqual(qs_scorer.best_score, 1.00, 2)
self.assertAlmostEqual(lddt_oligo_scorer.oligo_lddt, 1.00, 2)
+ self.assertAlmostEqual(lddt_oligo_scorer.weighted_lddt, 1.00, 2)
+ self.assertEqual(len(lddt_oligo_scorer.sc_lddt), 2)
+ self.assertAlmostEqual(lddt_oligo_scorer.sc_lddt[0], 1.00, 2)
+ self.assertAlmostEqual(lddt_oligo_scorer.sc_lddt[1], 1.00, 2)
# with penalty we account for extra model chains
lddt_oligo_scorer_pen = qs_scorer.GetOligoLDDTScorer(lddt_settings, True)
self.assertAlmostEqual(lddt_oligo_scorer_pen.oligo_lddt, 0.5213, 2)
+ self.assertAlmostEqual(lddt_oligo_scorer_pen.weighted_lddt, 0.50, 2)
+ self.assertEqual(len(lddt_oligo_scorer_pen.sc_lddt), 2)
+ self.assertAlmostEqual(lddt_oligo_scorer_pen.sc_lddt[0], 1.00, 2)
+ self.assertAlmostEqual(lddt_oligo_scorer_pen.sc_lddt[1], 1.00, 2)
# flip them (use QSscoreEntity to go faster)
qs_scorer2 = QSscorer(qs_scorer.qs_ent_2,
qs_scorer.qs_ent_1,
@@ -396,11 +413,19 @@ class TestQSscore(unittest.TestCase):
lddt_oligo_scorer2 = qs_scorer2.GetOligoLDDTScorer(lddt_settings, False)
self.assertAlmostEqual(qs_scorer2.global_score, 0.171, 2)
self.assertAlmostEqual(qs_scorer2.best_score, 1.00, 2)
+ self.assertAlmostEqual(lddt_oligo_scorer2.weighted_lddt, 1.00, 2)
+ self.assertEqual(len(lddt_oligo_scorer2.sc_lddt), 2)
+ self.assertAlmostEqual(lddt_oligo_scorer2.sc_lddt[0], 1.00, 2)
+ self.assertAlmostEqual(lddt_oligo_scorer2.sc_lddt[1], 1.00, 2)
# without penalty we don't see extra chains
self.assertAlmostEqual(lddt_oligo_scorer2.oligo_lddt, 1.00, 2)
# with penalty we account for extra reference chains
lddt_oligo_scorer2_pen = qs_scorer2.GetOligoLDDTScorer(lddt_settings, True)
self.assertAlmostEqual(lddt_oligo_scorer2_pen.oligo_lddt, 0.4496, 2)
+ self.assertAlmostEqual(lddt_oligo_scorer2_pen.weighted_lddt, 0.50, 2)
+ self.assertEqual(len(lddt_oligo_scorer2_pen.sc_lddt), 2)
+ self.assertAlmostEqual(lddt_oligo_scorer2_pen.sc_lddt[0], 1.00, 2)
+ self.assertAlmostEqual(lddt_oligo_scorer2_pen.sc_lddt[1], 1.00, 2)
# check properties
self.assertFalse(qs_scorer.calpha_only)
self.assertEqual(qs_scorer.chem_mapping, {('B', 'A'): ('B', 'C', 'D', 'A')})
@@ -424,11 +449,10 @@ class TestQSscore(unittest.TestCase):
self.assertEqual(qs_scorer.chem_mapping,
{('A', 'C', 'E', 'G', 'I', 'K', 'M', 'O'): ('A', 'C', 'E', 'G'),
('B', 'D', 'F', 'H', 'J', 'L', 'N', 'P'): ('B', 'D', 'F', 'H')})
- self.assertEqual(sorted(qs_scorer.symm_1),
- [('A', 'B'), ('C', 'D'), ('E', 'F'), ('G', 'H'),
- ('I', 'J'), ('K', 'L'), ('M', 'N'), ('O', 'P')])
- self.assertEqual(sorted(qs_scorer.symm_2),
- [('A', 'B'), ('C', 'D'), ('E', 'F'), ('G', 'H')])
+ self.assertEqual(len(qs_scorer.symm_1), 8)
+ self.assertEqual(len(qs_scorer.symm_1[0]), 2)
+ self.assertEqual(len(qs_scorer.symm_2), 4)
+ self.assertEqual(len(qs_scorer.symm_2[0]), 2)
self.assertEqual(qs_scorer.chain_mapping,
{'A': 'A', 'C': 'C', 'B': 'B', 'E': 'E',
'D': 'D', 'G': 'G', 'F': 'F', 'H': 'H'})
@@ -447,14 +471,10 @@ class TestQSscore(unittest.TestCase):
('A', 'E', 'I', 'M', 'Q'): ('A', 'E', 'I', 'M', 'Q'),
('C', 'G', 'K', 'O', 'S'): ('C', 'G', 'K', 'O', 'S'),
('B', 'F', 'J', 'N', 'R'): ('B', 'F', 'J', 'N', 'R')})
- self.assertEqual(sorted(qs_scorer.symm_1),
- [('D', 'A', 'S', 'B'), ('H', 'E', 'C', 'F'),
- ('L', 'I', 'G', 'J'), ('P', 'M', 'K', 'N'),
- ('T', 'Q', 'O', 'R')])
- self.assertEqual(sorted(qs_scorer.symm_2),
- [('D', 'A', 'S', 'B'), ('H', 'E', 'C', 'F'),
- ('L', 'I', 'G', 'J'), ('P', 'M', 'K', 'N'),
- ('T', 'Q', 'O', 'R')])
+ self.assertEqual(len(qs_scorer.symm_1), 5)
+ self.assertEqual(len(qs_scorer.symm_1[0]), 4)
+ self.assertEqual(len(qs_scorer.symm_2), 5)
+ self.assertEqual(len(qs_scorer.symm_2[0]), 4)
self.assertEqual(qs_scorer.chain_mapping,
{'A': 'A', 'C': 'C', 'B': 'B', 'E': 'E', 'D': 'D',
'G': 'G', 'F': 'F', 'I': 'I', 'H': 'H', 'K': 'K',
@@ -473,12 +493,10 @@ class TestQSscore(unittest.TestCase):
self.assertEqual(qs_scorer.chem_mapping,
{('A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J', 'K', 'L'): \
('A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J', 'K', 'L')})
- self.assertEqual(sorted(qs_scorer.symm_1),
- [('A', 'D'), ('B', 'E'), ('C', 'F'),
- ('G', 'J'), ('H', 'K'), ('I', 'L')])
- self.assertEqual(sorted(qs_scorer.symm_2),
- [('A', 'G'), ('B', 'I'), ('C', 'E'),
- ('D', 'K'), ('F', 'J'), ('H', 'L')])
+ self.assertEqual(len(qs_scorer.symm_1), 6)
+ self.assertEqual(len(qs_scorer.symm_1[0]), 2)
+ self.assertEqual(len(qs_scorer.symm_2), 6)
+ self.assertEqual(len(qs_scorer.symm_2[0]), 2)
# chain mapping is ambiguous here so we cannot check it
def test_Urease(self):
@@ -495,14 +513,10 @@ class TestQSscore(unittest.TestCase):
('B', 'D', 'F', 'H', 'J', 'L', 'N', 'P', 'R', 'T', 'V', 'X'),
('A', 'C', 'E', 'G', 'I', 'K', 'M', 'O', 'Q', 'S', 'U', 'W'): \
('A', 'C', 'E', 'G', 'I', 'K', 'M', 'O', 'Q', 'S', 'U', 'W')})
- self.assertEqual(sorted(qs_scorer.symm_1),
- [('B', 'Q'), ('D', 'G'), ('F', 'W'), ('H', 'U'),
- ('J', 'K'), ('L', 'S'), ('N', 'A'), ('P', 'E'),
- ('R', 'M'), ('T', 'I'), ('V', 'C'), ('X', 'O')])
- self.assertEqual(sorted(qs_scorer.symm_2),
- [('B', 'Q'), ('D', 'W'), ('F', 'U'), ('H', 'C'),
- ('J', 'K'), ('L', 'S'), ('N', 'A'), ('P', 'E'),
- ('R', 'M'), ('T', 'I'), ('V', 'O'), ('X', 'G')])
+ self.assertEqual(len(qs_scorer.symm_1), 12)
+ self.assertEqual(len(qs_scorer.symm_1[0]), 2)
+ self.assertEqual(len(qs_scorer.symm_2), 12)
+ self.assertEqual(len(qs_scorer.symm_2[0]), 2)
self.assertEqual(qs_scorer.chain_mapping,
{'A': 'A', 'C': 'W', 'B': 'B', 'E': 'E', 'D': 'X',
'G': 'G', 'F': 'F', 'I': 'I', 'H': 'H', 'K': 'K',
@@ -522,12 +536,10 @@ class TestQSscore(unittest.TestCase):
self.assertEqual(qs_scorer.chem_mapping,
{('A', 'B', 'C', 'D', 'E', 'F'): ('A', 'B', 'C', 'D', 'E', 'F'),
('G', 'H', 'I', 'J', 'K', 'L'): ('G', 'H', 'I', 'J', 'K', 'L')})
- self.assertEqual(sorted(qs_scorer.symm_1),
- [('A', 'G'), ('B', 'H'), ('C', 'I'),
- ('D', 'J'), ('E', 'K'), ('F', 'L')])
- self.assertEqual(sorted(qs_scorer.symm_2),
- [('A', 'G'), ('B', 'H'), ('C', 'I'),
- ('D', 'J'), ('E', 'K'), ('F', 'L')])
+ self.assertEqual(len(qs_scorer.symm_1), 6)
+ self.assertEqual(len(qs_scorer.symm_1[0]), 2)
+ self.assertEqual(len(qs_scorer.symm_2), 6)
+ self.assertEqual(len(qs_scorer.symm_2[0]), 2)
self.assertEqual(qs_scorer.chain_mapping,
{'A': 'A', 'C': 'C', 'B': 'B', 'E': 'E',
'D': 'D', 'G': 'G', 'F': 'F', 'I': 'I',
@@ -547,20 +559,22 @@ class TestQSscore(unittest.TestCase):
'J', 'K', 'L', 'N', 'O', 'P', 'R', 'S', 'T', 'V', 'W', 'X'): \
('A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J', 'K', 'L',
'M', 'N', 'O', 'P', 'Q', 'R', 'S', 'T', 'U', 'V', 'W', 'X')})
- self.assertEqual(sorted(qs_scorer.symm_1),
- [('A', 'X'), ('B', 'H'), ('C', 'P'), ('D', 'K'),
- ('E', 'I'), ('F', 'J'), ('G', 'T'), ('L', 'R'),
- ('M', 'S'), ('O', 'V'), ('Q', 'N'), ('U', 'W')])
- self.assertEqual(sorted(qs_scorer.symm_2),
- [('A', 'O'), ('B', 'M'), ('C', 'N'), ('D', 'G'),
- ('E', 'H'), ('F', 'I'), ('J', 'W'), ('K', 'X'),
- ('L', 'V'), ('P', 'T'), ('Q', 'U'), ('R', 'S')])
- self.assertEqual(qs_scorer.chain_mapping,
- {'A': 'J', 'C': 'L', 'B': 'K', 'E': 'P', 'D': 'R',
- 'G': 'O', 'F': 'Q', 'I': 'T', 'H': 'X', 'K': 'S',
- 'J': 'U', 'M': 'G', 'L': 'I', 'O': 'N', 'N': 'H',
- 'Q': 'E', 'P': 'V', 'S': 'D', 'R': 'F', 'U': 'B',
- 'T': 'A', 'W': 'M', 'V': 'C', 'X': 'W'})
+ self.assertEqual(len(qs_scorer.symm_1), 12)
+ self.assertEqual(len(qs_scorer.symm_1[0]), 2)
+ self.assertEqual(len(qs_scorer.symm_2), 12)
+ self.assertEqual(len(qs_scorer.symm_2[0]), 2)
+
+ # Don't check for exact mapping, as structures are highly symmetric.
+ # Several mappings are thus valid. Only check whether we found an
+ # automated mapping with strict (stuff must really match)
+ # chain_mapping_scheme
+ self.assertEqual(qs_scorer.chain_mapping_scheme, 'strict')
+ #self.assertEqual(qs_scorer.chain_mapping,
+ # {'A': 'J', 'C': 'L', 'B': 'K', 'E': 'P', 'D': 'R',
+ # 'G': 'O', 'F': 'Q', 'I': 'T', 'H': 'X', 'K': 'S',
+ # 'J': 'U', 'M': 'G', 'L': 'I', 'O': 'N', 'N': 'H',
+ # 'Q': 'E', 'P': 'V', 'S': 'D', 'R': 'F', 'U': 'B',
+ # 'T': 'A', 'W': 'M', 'V': 'C', 'X': 'W'})
###########################################################################
@@ -605,7 +619,7 @@ class TestQSscore(unittest.TestCase):
cn2 = set([c for cg in qs_ent_2.chem_groups for c in cg])
cm_names_1 = list()
cm_names_2 = list()
- for cg1, cg2 in qs_scorer.chem_mapping.iteritems():
+ for cg1, cg2 in qs_scorer.chem_mapping.items():
ch_ref = qs_scorer.ent_to_cm_1.FindChain(cg1[0])
self.assertEqual(ch_ref.residue_count, ch_ref.atom_count)
self.assertGreaterEqual(ch_ref.residue_count, 5)
@@ -634,24 +648,24 @@ class TestQSscore(unittest.TestCase):
cm_names_2)
# check symm_1 / symm_2
# (>= 1 symm. group, all groups same length, all chains appear)
- self.assertGreaterEqual(qs_scorer.symm_1, 1)
+ self.assertGreaterEqual(len(qs_scorer.symm_1), 1)
ref_symm_1 = qs_scorer.symm_1[0]
self.assertTrue(all(len(cg) == len(ref_symm_1) for cg in qs_scorer.symm_1))
self.assertEqual(sorted(c for cg in qs_scorer.symm_1 for c in cg),
cm_names_1)
- self.assertGreaterEqual(qs_scorer.symm_2, 1)
+ self.assertGreaterEqual(len(qs_scorer.symm_2), 1)
ref_symm_2 = qs_scorer.symm_2[0]
self.assertTrue(all(len(cg) == len(ref_symm_2) for cg in qs_scorer.symm_2))
self.assertEqual(sorted(c for cg in qs_scorer.symm_2 for c in cg),
cm_names_2)
# check chain_mapping
# (all chains of ent with less chains mapped, each only once, chem_map)
- chm_names_1 = qs_scorer.chain_mapping.keys()
- chm_names_2 = qs_scorer.chain_mapping.values()
+ chm_names_1 = list(qs_scorer.chain_mapping.keys())
+ chm_names_2 = list(qs_scorer.chain_mapping.values())
self.assertEqual(len(chm_names_1), min(len(cm_names_1), len(cm_names_2)))
self.assertEqual(len(set(chm_names_1)), len(chm_names_1))
self.assertEqual(len(set(chm_names_2)), len(chm_names_2))
- for cg1, cg2 in qs_scorer.chem_mapping.iteritems():
+ for cg1, cg2 in qs_scorer.chem_mapping.items():
for ch_name in cg1:
if ch_name in qs_scorer.chain_mapping:
self.assertTrue(qs_scorer.chain_mapping[ch_name] in cg2)
@@ -678,10 +692,10 @@ if __name__ == "__main__":
try:
settings.Locate(('clustalw', 'clustalw2'))
except:
- print "Could not find ClustalW. Ignoring test_qsscoring.py tests."
+ print("Could not find ClustalW. Ignoring test_qsscoring.py tests.")
sys.exit(0)
from ost import testutils
if testutils.SetDefaultCompoundLib():
testutils.RunTests()
else:
- print 'No compound library available. Ignoring test_qsscoring.py tests.'
+ print('No compound library available. Ignoring test_qsscoring.py tests.')
diff --git a/modules/mol/alg/tests/test_sec_struct.py b/modules/mol/alg/tests/test_sec_struct.py
index 207f8600c8f14589577fd1fabddd6ee0ebf72598..c6b6a928e20e33db23622681f70bd6c64821f54c 100644
--- a/modules/mol/alg/tests/test_sec_struct.py
+++ b/modules/mol/alg/tests/test_sec_struct.py
@@ -14,7 +14,7 @@ class TestSecStruct(unittest.TestCase):
dssp_path = settings.Locate(['dsspcmbi', 'dssp', 'mkdssp'],
env_name='DSSP_EXECUTABLE')
except:
- print "Could not find DSSP, could not compare sec struct assignment..."
+ print("Could not find DSSP, could not compare sec struct assignment...")
return
dssp_ent = io.LoadPDB(os.path.join("testfiles", "1a0s.pdb"))
diff --git a/modules/mol/alg/tests/test_superposition.cc b/modules/mol/alg/tests/test_superposition.cc
index ba35aa122831036ab00fadeca2beb469750d5ca5..1ea1edbeee18aaf4879db64525b4c99cf0525fb8 100644
--- a/modules/mol/alg/tests/test_superposition.cc
+++ b/modules/mol/alg/tests/test_superposition.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/alg/tests/testfiles/cbeta_fail.pdb b/modules/mol/alg/tests/testfiles/cbeta_fail.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..3c856297e848d7621a9d20414b336f2feec59c93
--- /dev/null
+++ b/modules/mol/alg/tests/testfiles/cbeta_fail.pdb
@@ -0,0 +1,13 @@
+ATOM 1 N1 SNN A 198 -29.170 34.390 20.593 1.00 19.36 N
+ATOM 2 C2 SNN A 198 -29.098 33.236 19.935 1.00 22.44 C
+ATOM 3 C3 SNN A 198 -30.445 32.723 19.591 1.00 22.60 C
+ATOM 4 N3 SNN A 198 -30.638 31.540 20.497 1.00 19.05 N
+ATOM 5 C4 SNN A 198 -31.361 33.870 20.080 1.00 24.77 C
+ATOM 6 C5 SNN A 198 -30.421 34.922 20.754 1.00 31.46 C
+ATOM 7 O2 SNN A 198 -28.057 32.598 19.660 1.00 21.86 O
+ATOM 8 O5 SNN A 198 -30.731 36.074 21.349 1.00 31.34 O
+ATOM 9 CA GLY A 199 -27.868 35.007 21.247 1.00 21.30 C
+ATOM 10 C GLY A 199 -27.140 35.813 20.142 1.00 19.04 C
+ATOM 11 O GLY A 199 -27.544 35.877 18.965 1.00 19.95 O
+TER 12 GLY A 199
+END
diff --git a/modules/mol/alg/tests/tests.cc b/modules/mol/alg/tests/tests.cc
index 4308786c168fa90c76c2b7e0417e86407509efe8..1631a0299b8bbd93322b2e75c397d52c174d7db7 100644
--- a/modules/mol/alg/tests/tests.cc
+++ b/modules/mol/alg/tests/tests.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/doc/entity.rst b/modules/mol/base/doc/entity.rst
index fd99d80cc0286876d056095826fe646e28e93762..1e7b008861df783c0970fbc2af4a14975f939f38 100644
--- a/modules/mol/base/doc/entity.rst
+++ b/modules/mol/base/doc/entity.rst
@@ -58,7 +58,7 @@ The Handle Classes
.. code-block:: python
for res in ent.residues:
- print res.name, res.atom_count
+ print(res.name, res.atom_count)
Also available as :meth:`GetResidueList`. To access a single residue, use
:meth:`FindResidue`.
@@ -380,7 +380,7 @@ The Handle Classes
chain=ent.FindChain("A")
for res in chain.residues:
- print res.name, res.atom_count
+ print(res.name, res.atom_count)
Also available as :meth:`GetResidueList`. To access a single residue, use
:meth:`FindResidue`.
@@ -394,12 +394,12 @@ The Handle Classes
.. code-block:: python
chain=ent.FindChain("A")
- print chain.residues # [A.GLY1, A.GLY2, A.GLY4A, A.GLY4B]
- print chain.in_sequence # prints true
+ print(chain.residues) # [A.GLY1, A.GLY2, A.GLY4A, A.GLY4B]
+ print(chain.in_sequence) # prints true
chain=ent.FindChain("B")
- print chain.residues # [B.GLY1, B.GLY4, B.GLY3]
- print chain.in_sequence # prints false
+ print(chain.residues) # [B.GLY1, B.GLY4, B.GLY3]
+ print(chain.in_sequence) # prints false
.. attribute:: residue_count
@@ -537,7 +537,7 @@ The Handle Classes
.. code-block:: python
- print ''.join([r.one_letter_code for r in chain.residues])
+ print(''.join([r.one_letter_code for r in chain.residues]))
:type: str
@@ -1063,7 +1063,7 @@ The View Classes
.. code-block:: python
for res in ent.residues:
- print res.name, res.atom_count
+ print(res.name, res.atom_count)
Also available as :meth:`GetResidueList`. To access a single residue, use
:meth:`FindResidue`.
@@ -1410,7 +1410,7 @@ The View Classes
chain=ent.FindChain("A")
for res in chain.residues:
- print res.name, res.atom_count
+ print(res.name, res.atom_count)
Also available as :meth:`GetResidueList`. To access a single residue, use
:meth:`FindResidue`.
@@ -1424,12 +1424,12 @@ The View Classes
.. code-block:: python
chain=ent.FindChain("A")
- print chain.residues # [A.GLY1, A.GLY2, A.GLY4A, A.GLY4B]
- print chain.in_sequence # prints true
+ print(chain.residues) # [A.GLY1, A.GLY2, A.GLY4A, A.GLY4B]
+ print(chain.in_sequence) # prints true
chain=ent.FindChain("B")
- print chain.residues # [B.GLY1, B.GLY4, B.GLY3]
- print chain.in_sequence # prints false
+ print(chain.residues) # [B.GLY1, B.GLY4, B.GLY3]
+ print(chain.in_sequence) # prints false
.. attribute:: atoms
@@ -1653,7 +1653,7 @@ The View Classes
.. code-block:: python
- print ''.join([r.one_letter_code for r in chain.residues])
+ print(''.join([r.one_letter_code for r in chain.residues]))
:type: str
diff --git a/modules/mol/base/pymod/__init__.py b/modules/mol/base/pymod/__init__.py
index 512e4daf082ef7e17f8c019dc92021ff799b6ccc..7e8bf1eb6c31c6d4490224bb60ab0ab2ab07b7da 100644
--- a/modules/mol/base/pymod/__init__.py
+++ b/modules/mol/base/pymod/__init__.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
@@ -16,7 +16,7 @@
# along with this library; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
#------------------------------------------------------------------------------
-from _ost_mol import *
+from ._ost_mol import *
import ost.geom as _geom
from ost.mol import alg
diff --git a/modules/mol/base/pymod/export_atom.cc b/modules/mol/base/pymod/export_atom.cc
index d623fffba7a42096608a5e7910c22aa3c116671e..343833440b33c39bce7eb6161fd7ea610ffdd2e1 100644
--- a/modules/mol/base/pymod/export_atom.cc
+++ b/modules/mol/base/pymod/export_atom.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/pymod/export_atom_view.cc b/modules/mol/base/pymod/export_atom_view.cc
index 7f38fc56242d788d73c2dcc21b3f0cfaba5a5653..5af079a4477e6b9d5ac828460326b7b69bd473e9 100644
--- a/modules/mol/base/pymod/export_atom_view.cc
+++ b/modules/mol/base/pymod/export_atom_view.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/pymod/export_bond.cc b/modules/mol/base/pymod/export_bond.cc
index c95268df47468b0ad1c717032091c7b35600d989..5dc6e6503fdc9ce9038e595fd3a78384c1e37d56 100644
--- a/modules/mol/base/pymod/export_bond.cc
+++ b/modules/mol/base/pymod/export_bond.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/pymod/export_bounding_box.cc b/modules/mol/base/pymod/export_bounding_box.cc
index 58a464e1a39f057f7f63d985c84216062ae8e99d..84ff717b686b95cceb87bc71a0ac0bc512013337 100644
--- a/modules/mol/base/pymod/export_bounding_box.cc
+++ b/modules/mol/base/pymod/export_bounding_box.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/pymod/export_chain.cc b/modules/mol/base/pymod/export_chain.cc
index 557e62297ee80a1d09c206784d5eac1361f08784..de8e693029106d8f09fce71a6b85ca115e793a3e 100644
--- a/modules/mol/base/pymod/export_chain.cc
+++ b/modules/mol/base/pymod/export_chain.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/pymod/export_chain_view.cc b/modules/mol/base/pymod/export_chain_view.cc
index 70ee5d1d1a216c56ad6757ffa681094141d85b41..4ca48fe52dd099de69ca149ba8e7296cab88e48f 100644
--- a/modules/mol/base/pymod/export_chain_view.cc
+++ b/modules/mol/base/pymod/export_chain_view.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/pymod/export_coord_frame.cc b/modules/mol/base/pymod/export_coord_frame.cc
index 566f0a43c0c3562830401f339ea62865631d757f..82aa5e45ef755a9f56ade43826892109b260a54a 100644
--- a/modules/mol/base/pymod/export_coord_frame.cc
+++ b/modules/mol/base/pymod/export_coord_frame.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/pymod/export_coord_group.cc b/modules/mol/base/pymod/export_coord_group.cc
index 46a435ad4aaee3391d063a519d7e8cc705c84926..de040484a963dbb1cd3f6f20736daefdc43ecdf0 100644
--- a/modules/mol/base/pymod/export_coord_group.cc
+++ b/modules/mol/base/pymod/export_coord_group.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/pymod/export_editors.cc b/modules/mol/base/pymod/export_editors.cc
index 4bb64bd8ac3eb646176b7bfc6e781a5049253139..3c5ab790008016ce376da1f353ea9a5fbd4b71c9 100644
--- a/modules/mol/base/pymod/export_editors.cc
+++ b/modules/mol/base/pymod/export_editors.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
@@ -29,7 +29,15 @@ using namespace boost::python;
using namespace ost;
using namespace ost::mol;
+/* Including NumPy headers produces compiler warnings. The ones about "Using
+ deprecated NumPy API..." we can not get rid of. The highest NumPy version we
+ support is 1.6 while the non-deprecated API starts with version 1.7.
+ Also see the comment in modules/gfx/pymod/export_primlist.cc for further
+ information.
+*/
#if OST_NUMPY_SUPPORT_ENABLED
+#include <numpy/numpyconfig.h>
+#define NPY_NO_DEPRECATED_API NPY_1_6_API_VERSION
#include <numpy/arrayobject.h>
#endif
@@ -227,6 +235,9 @@ void set_t_pos(XCSEditor& e, object o1, object o2)
void export_Editors()
{
#if OST_NUMPY_SUPPORT_ENABLED
+ // The following define enforces no return value when calling import_array
+ #undef NUMPY_IMPORT_ARRAY_RETVAL
+ #define NUMPY_IMPORT_ARRAY_RETVAL
import_array();
#endif
diff --git a/modules/mol/base/pymod/export_entity.cc b/modules/mol/base/pymod/export_entity.cc
index 538921e2b7f1c7d8fc4c752584c8b665f0d0050c..c0b54781a2d85a1bcefa2a7695a21c66734c970d 100644
--- a/modules/mol/base/pymod/export_entity.cc
+++ b/modules/mol/base/pymod/export_entity.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
@@ -35,7 +35,15 @@ using namespace ost::mol;
#include <ost/export_helper/generic_property_def.hh>
+/* Including NumPy headers produces compiler warnings. The ones about "Using
+ deprecated NumPy API..." we can not get rid of. The highest NumPy version we
+ support is 1.6 while the non-deprecated API starts with version 1.7.
+ Also see the comment in modules/gfx/pymod/export_primlist.cc for further
+ information.
+*/
#if OST_NUMPY_SUPPORT_ENABLED
+#include <numpy/numpyconfig.h>
+#define NPY_NO_DEPRECATED_API NPY_1_6_API_VERSION
#include <numpy/arrayobject.h>
#endif
@@ -130,6 +138,9 @@ bool depr_is_transformation_identity(const EntityHandle& eh)
void export_Entity()
{
#if OST_NUMPY_SUPPORT_ENABLED
+ // The following define enforces no return value when calling import_array
+ #undef NUMPY_IMPORT_ARRAY_RETVAL
+ #define NUMPY_IMPORT_ARRAY_RETVAL
import_array();
#endif
diff --git a/modules/mol/base/pymod/export_entity_view.cc b/modules/mol/base/pymod/export_entity_view.cc
index fb969ce46c695932f3c73e3632aff535add1dcce..0db065a075f16a29fe887c5a0d728379477d8ff2 100644
--- a/modules/mol/base/pymod/export_entity_view.cc
+++ b/modules/mol/base/pymod/export_entity_view.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/pymod/export_property_id.cc b/modules/mol/base/pymod/export_property_id.cc
index 274742c6f7aab1a80c4476d294c43899d87de61a..a9b8c0824f39078d303c64e3d54622f17043ab49 100644
--- a/modules/mol/base/pymod/export_property_id.cc
+++ b/modules/mol/base/pymod/export_property_id.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/pymod/export_query.cc b/modules/mol/base/pymod/export_query.cc
index 8f1fc94605e6beed10d61b0f65f94733fcd05f78..f4c87ab884beb18bec10a46a01c3b44370e891e3 100644
--- a/modules/mol/base/pymod/export_query.cc
+++ b/modules/mol/base/pymod/export_query.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/pymod/export_query_view_wrapper.cc b/modules/mol/base/pymod/export_query_view_wrapper.cc
index f16c0c3cdc6c03d26d2105fcdd6fb164356df092..3d92274dac518a4e153a9feae14f4a90dcbcba89 100644
--- a/modules/mol/base/pymod/export_query_view_wrapper.cc
+++ b/modules/mol/base/pymod/export_query_view_wrapper.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/pymod/export_residue.cc b/modules/mol/base/pymod/export_residue.cc
index fad1a74bd18ee5713c4e58b55fb57ad70ad27511..02f2c845795b020056c670d57512abad08609f3c 100644
--- a/modules/mol/base/pymod/export_residue.cc
+++ b/modules/mol/base/pymod/export_residue.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/pymod/export_residue_view.cc b/modules/mol/base/pymod/export_residue_view.cc
index 79d167996ed18eb6d53d0ae57e66df3f8c2c695a..a3a7f16eaa232216a97b1091fd9048ff3a7e87c0 100644
--- a/modules/mol/base/pymod/export_residue_view.cc
+++ b/modules/mol/base/pymod/export_residue_view.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/pymod/export_surface.cc b/modules/mol/base/pymod/export_surface.cc
index c6defa5de52452cf30b8c1402fd444582459fb82..d826f3e2a698720526adf21a57ef7a27819aab49 100644
--- a/modules/mol/base/pymod/export_surface.cc
+++ b/modules/mol/base/pymod/export_surface.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/pymod/export_torsion.cc b/modules/mol/base/pymod/export_torsion.cc
index fbf9e2b726880b9e56a430e3def0aa50f0c1fd7b..dcf27a5ffc2c79ee3c07ec85d11275319cf4f69f 100644
--- a/modules/mol/base/pymod/export_torsion.cc
+++ b/modules/mol/base/pymod/export_torsion.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/pymod/export_visitor.cc b/modules/mol/base/pymod/export_visitor.cc
index 3a6d1e3285153e2bc71ff09f562d4e2e18b3645e..2ad23ea9efb9cdd17e6a35a18c270d8382027724 100644
--- a/modules/mol/base/pymod/export_visitor.cc
+++ b/modules/mol/base/pymod/export_visitor.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/pymod/wrap_mol.cc b/modules/mol/base/pymod/wrap_mol.cc
index 0c1281ad8f9b490790e32902e0f8822e559be33b..dacc3918328747bed180a6c51eb8ba0530a9d331 100644
--- a/modules/mol/base/pymod/wrap_mol.cc
+++ b/modules/mol/base/pymod/wrap_mol.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/atom_base.cc b/modules/mol/base/src/atom_base.cc
index a24ca3abb276770cebf67b00524e1ad4c401b970..b1547fb518b730f72cfc9d29cd2ab78b833c42aa 100644
--- a/modules/mol/base/src/atom_base.cc
+++ b/modules/mol/base/src/atom_base.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/atom_base.hh b/modules/mol/base/src/atom_base.hh
index c3ec3777d53e836b43d16b9ddd7dfe83f2886226..b69c8ceb006736354cc88e644adbc65bfd37f347 100644
--- a/modules/mol/base/src/atom_base.hh
+++ b/modules/mol/base/src/atom_base.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/atom_handle.cc b/modules/mol/base/src/atom_handle.cc
index cb2a219c2aad43a4ce9f3c2a9f546245e4852925..25eba43f8feea064693e91fe31c1e65b50593b57 100644
--- a/modules/mol/base/src/atom_handle.cc
+++ b/modules/mol/base/src/atom_handle.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/atom_handle.hh b/modules/mol/base/src/atom_handle.hh
index c0effc863e18e56b297a4db45e7a3db4091fe7a5..1dbdf09d5a3d7495fbe8eb5244ff9f986dca66e1 100644
--- a/modules/mol/base/src/atom_handle.hh
+++ b/modules/mol/base/src/atom_handle.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/atom_view.cc b/modules/mol/base/src/atom_view.cc
index ed16ac0f82f314a452cddbc8b35fd8fe5842b2ab..2bd424c8e8947f686f08c72bb50e98c3d7bd23be 100644
--- a/modules/mol/base/src/atom_view.cc
+++ b/modules/mol/base/src/atom_view.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/atom_view.hh b/modules/mol/base/src/atom_view.hh
index 5016e1587a97c2359327745e6d6408a74bcb4a62..a853669c1ea0dec9569732c486d6ca2b3b92ff3a 100644
--- a/modules/mol/base/src/atom_view.hh
+++ b/modules/mol/base/src/atom_view.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/bond_handle.cc b/modules/mol/base/src/bond_handle.cc
index 9a68a860dc5db33eea4a28fdc807407acb889ec1..9dd04ca1220d35e779026f4654c5a5854b5ebc50 100644
--- a/modules/mol/base/src/bond_handle.cc
+++ b/modules/mol/base/src/bond_handle.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/bond_handle.hh b/modules/mol/base/src/bond_handle.hh
index ea4425adde1f946c44b44232b66d9165f0756664..76acfff537e1a6cbf09eea762cfd69fd78209dc2 100644
--- a/modules/mol/base/src/bond_handle.hh
+++ b/modules/mol/base/src/bond_handle.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/bond_table.hh b/modules/mol/base/src/bond_table.hh
index 0ddd6d0fecdffaa30313510abf8640bcb66cba9f..b7c1f65923ea47c87989ac440d0a2af28a3a7ab9 100644
--- a/modules/mol/base/src/bond_table.hh
+++ b/modules/mol/base/src/bond_table.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/bounding_box.cc b/modules/mol/base/src/bounding_box.cc
index 85c40ed1acbb0832893da76f57af96815a3829cc..98eb33a23fc47fa72ed9982c7ef9487b6b6ebe77 100644
--- a/modules/mol/base/src/bounding_box.cc
+++ b/modules/mol/base/src/bounding_box.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/bounding_box.hh b/modules/mol/base/src/bounding_box.hh
index 069ff39b99f7b16c076eb8beb007fe65041c4522..755b54b227d089fc9219edb55f11d9d1382de60c 100644
--- a/modules/mol/base/src/bounding_box.hh
+++ b/modules/mol/base/src/bounding_box.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/builder.hh b/modules/mol/base/src/builder.hh
index d46ed485bbe0c8ebf3d2ccf54e62347034b66915..a4b72c6bca78e03d863d4cb72db1e6f81e39f05f 100644
--- a/modules/mol/base/src/builder.hh
+++ b/modules/mol/base/src/builder.hh
@@ -2,7 +2,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/chain_base.cc b/modules/mol/base/src/chain_base.cc
index bbf0cfdad68397971844ba49fb5e2ba4b378d953..4114a1462be137b7ea2e84cac6618df2309849e3 100644
--- a/modules/mol/base/src/chain_base.cc
+++ b/modules/mol/base/src/chain_base.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/chain_base.hh b/modules/mol/base/src/chain_base.hh
index 984c948fd94b934656f4920baf3e1da739efd89a..5463ef0a8627eac578b12e801618da69bc74c898 100644
--- a/modules/mol/base/src/chain_base.hh
+++ b/modules/mol/base/src/chain_base.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/chain_handle.cc b/modules/mol/base/src/chain_handle.cc
index b15f431e0b9d9ff2c3ea3503a950bd1aeefbb7e3..90a2138705b112909dd41e6b62ae6e6fd32dda85 100644
--- a/modules/mol/base/src/chain_handle.cc
+++ b/modules/mol/base/src/chain_handle.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/chain_handle.hh b/modules/mol/base/src/chain_handle.hh
index 5ab00787c6c169eb2c2acb11fffc20f140728568..9e79f2b7542a2612efc13faee52b3a40c85c93b9 100644
--- a/modules/mol/base/src/chain_handle.hh
+++ b/modules/mol/base/src/chain_handle.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/chain_type.cc b/modules/mol/base/src/chain_type.cc
index 0c292fb8d4ca8892ec7f1a2a036535c5e5a78deb..2e553cff8d33428180afffb6edcccb947a762a55 100644
--- a/modules/mol/base/src/chain_type.cc
+++ b/modules/mol/base/src/chain_type.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/chain_type.hh b/modules/mol/base/src/chain_type.hh
index a195a404281885151c56a3418fba7978a644454e..3338db7fe16a87641b86f0bef3bc00f1b0f701aa 100644
--- a/modules/mol/base/src/chain_type.hh
+++ b/modules/mol/base/src/chain_type.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/chain_view.cc b/modules/mol/base/src/chain_view.cc
index 8f8d2c0e191b6f09bfb3751c323ab41eac6f37c4..96c038460795b24ae2f91a92fb6d2cdc2a49c6c6 100644
--- a/modules/mol/base/src/chain_view.cc
+++ b/modules/mol/base/src/chain_view.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/chain_view.hh b/modules/mol/base/src/chain_view.hh
index 3f9ea30bab6d8db628a2152bc8a8a08fccfd4691..c107261d3c7d4475969ccb4c0a98e8dffb3ec268 100644
--- a/modules/mol/base/src/chain_view.hh
+++ b/modules/mol/base/src/chain_view.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/chem_class.hh b/modules/mol/base/src/chem_class.hh
index 97f80f23e393d04c86cd377966b6bc7bb46e41a5..efd838679a63a145164805143c3b84bc3ef1bf0f 100644
--- a/modules/mol/base/src/chem_class.hh
+++ b/modules/mol/base/src/chem_class.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/chem_type.hh b/modules/mol/base/src/chem_type.hh
index ff3a6b059241ebd76a9e9b77512fd87bc38147fc..afd4788a0dae1c26ea0596c09fa4e9a3a5fb17a0 100644
--- a/modules/mol/base/src/chem_type.hh
+++ b/modules/mol/base/src/chem_type.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2010 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/coord_frame.cc b/modules/mol/base/src/coord_frame.cc
index 49c294fcee0fc4ac784e79cd02935d4d4f66e2c6..8fb7a39cfcecaab0c161c76ec2dbd671077c97c3 100644
--- a/modules/mol/base/src/coord_frame.cc
+++ b/modules/mol/base/src/coord_frame.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/coord_frame.hh b/modules/mol/base/src/coord_frame.hh
index 33d24d1d402999d3c0e24bc4afa0a587d047e377..7317bb5a425686b589291315a3973683d007362e 100644
--- a/modules/mol/base/src/coord_frame.hh
+++ b/modules/mol/base/src/coord_frame.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/coord_group.cc b/modules/mol/base/src/coord_group.cc
index 53f31d9aedc7191dd361047ffaef5f4c7bec1c98..196efa167e2b326c51bcde20d89e937d32e5d0ef 100644
--- a/modules/mol/base/src/coord_group.cc
+++ b/modules/mol/base/src/coord_group.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/coord_group.hh b/modules/mol/base/src/coord_group.hh
index edce072cb3b9b1cef2d7651b3cc3ffb8416533db..20e77064fbe55a308321c9ecd02db89ab19eb294 100644
--- a/modules/mol/base/src/coord_group.hh
+++ b/modules/mol/base/src/coord_group.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/coord_source.cc b/modules/mol/base/src/coord_source.cc
index f3c0e13c9c83cc273feb7ff596b4d3e684091120..e83bc8c2a8de04a8b5a7e5ea0ce85cf68450cef1 100644
--- a/modules/mol/base/src/coord_source.cc
+++ b/modules/mol/base/src/coord_source.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/coord_source.hh b/modules/mol/base/src/coord_source.hh
index b58e3e98cf64290ffd4e36b9f2934b128cc8811f..21bed68ddb66ca00e9c6c1ef08c6e4e128049ad3 100644
--- a/modules/mol/base/src/coord_source.hh
+++ b/modules/mol/base/src/coord_source.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/editor_base.cc b/modules/mol/base/src/editor_base.cc
index fcc5bd3309e845491a498f35b25be5a4dbf9903d..0f36572b7630f0044870ddfb55fed1a645c9329d 100644
--- a/modules/mol/base/src/editor_base.cc
+++ b/modules/mol/base/src/editor_base.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/editor_base.hh b/modules/mol/base/src/editor_base.hh
index 22ca4a5616ca66a7d46e72f99a891c9f4fdd1092..5a08d2309749392612561df755154fc4966bb98a 100644
--- a/modules/mol/base/src/editor_base.hh
+++ b/modules/mol/base/src/editor_base.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/editor_type_fw.hh b/modules/mol/base/src/editor_type_fw.hh
index f1effeb787a40274722fd6d3d6d4d537b7d803a2..683b659fb7056f3744c99a37d16b81a0b7567101 100644
--- a/modules/mol/base/src/editor_type_fw.hh
+++ b/modules/mol/base/src/editor_type_fw.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/entity_base.cc b/modules/mol/base/src/entity_base.cc
index 838b9afc4065b022cf9c29210812962b1a63050e..847bc9305174c32eaf07519090a43c3a8978bea6 100644
--- a/modules/mol/base/src/entity_base.cc
+++ b/modules/mol/base/src/entity_base.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/entity_base.hh b/modules/mol/base/src/entity_base.hh
index b00ac720e9847e18419786a929d5e869735b0724..26136abd34e59ab27d23d9b3e0b3d1b1d3a2c957 100644
--- a/modules/mol/base/src/entity_base.hh
+++ b/modules/mol/base/src/entity_base.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/entity_handle.cc b/modules/mol/base/src/entity_handle.cc
index a463aa851e755d3ca3dc248793b927b9a21f15eb..b17d23f0b12edf44e6d3e3581f50bd7c0a171b36 100644
--- a/modules/mol/base/src/entity_handle.cc
+++ b/modules/mol/base/src/entity_handle.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/entity_handle.hh b/modules/mol/base/src/entity_handle.hh
index cb0ab5f0f2f6d694daac83694df3dc3af10d83a1..18383529adc27e7472876d44d104d0381d0d8af3 100644
--- a/modules/mol/base/src/entity_handle.hh
+++ b/modules/mol/base/src/entity_handle.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/entity_observer.cc b/modules/mol/base/src/entity_observer.cc
index ddbe254a2c426d6e317f2b528ac6f8722498e8cc..ee5f15eb515027edf547e2859d65b2769d15d285 100644
--- a/modules/mol/base/src/entity_observer.cc
+++ b/modules/mol/base/src/entity_observer.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/entity_observer.hh b/modules/mol/base/src/entity_observer.hh
index 25370fe25a176cea3ec49ddb0cf40dcaa77892e2..7e35c794d284e2db2988ff79d7c8450ac5c31929 100644
--- a/modules/mol/base/src/entity_observer.hh
+++ b/modules/mol/base/src/entity_observer.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/entity_observer_fw.hh b/modules/mol/base/src/entity_observer_fw.hh
index 043c8388aaae4170bc28d3df4ed42575d0314094..bab2bd72dbdc2eee1cb457dc049bc4ab168b1624 100644
--- a/modules/mol/base/src/entity_observer_fw.hh
+++ b/modules/mol/base/src/entity_observer_fw.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/entity_property_mapper.cc b/modules/mol/base/src/entity_property_mapper.cc
index fdece1e739af9d02c6a6943bcb01ced7066c744d..dfff462127fe5b5294cce6369f8b7c9ff78dec3a 100644
--- a/modules/mol/base/src/entity_property_mapper.cc
+++ b/modules/mol/base/src/entity_property_mapper.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/entity_property_mapper.hh b/modules/mol/base/src/entity_property_mapper.hh
index eaa947a5ecc5e39fc6fcc53de2acd2f8338d3f04..b80804665da1830f82fd088c44938a1494d57ab7 100644
--- a/modules/mol/base/src/entity_property_mapper.hh
+++ b/modules/mol/base/src/entity_property_mapper.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/entity_view.cc b/modules/mol/base/src/entity_view.cc
index c5b9c2ca5c4488c8cbd4f7184faa982d4375554d..26cfa75e3f44a780814e2a9a44b5c8a3b5499569 100644
--- a/modules/mol/base/src/entity_view.cc
+++ b/modules/mol/base/src/entity_view.cc
@@ -2,7 +2,7 @@
//
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/entity_view.hh b/modules/mol/base/src/entity_view.hh
index e88845d8bb8309a2eefaf66cc028fa1c9315de83..5e0243b0c3a819e2d6e8d58e2b69e45332586f3a 100644
--- a/modules/mol/base/src/entity_view.hh
+++ b/modules/mol/base/src/entity_view.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/entity_visitor.cc b/modules/mol/base/src/entity_visitor.cc
index 0a9f1a28e24d9b4778fc327b67ac4b596086e8cb..8852ec2c9311d71c274ecab805b3b35fe885c5a1 100644
--- a/modules/mol/base/src/entity_visitor.cc
+++ b/modules/mol/base/src/entity_visitor.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/entity_visitor.hh b/modules/mol/base/src/entity_visitor.hh
index 2cd6b3a82b939bf91bd0d356116a08d63049b8d7..53b3b810f8c635ca7d977217bc0bd7e47513ba02 100644
--- a/modules/mol/base/src/entity_visitor.hh
+++ b/modules/mol/base/src/entity_visitor.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/entity_visitor_fw.hh b/modules/mol/base/src/entity_visitor_fw.hh
index c4ea3aebde2be337243be7a29a9477df673464cf..d2c614bb0682330fce4823cbe2b452e7215e59af 100644
--- a/modules/mol/base/src/entity_visitor_fw.hh
+++ b/modules/mol/base/src/entity_visitor_fw.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/handle_type_fw.hh b/modules/mol/base/src/handle_type_fw.hh
index cfeb00e5da11b7c427bdc430d9c7e37ee67456b0..a5f5d6e0bda11b8e9c69455c6df830b9c7fcb8fa 100644
--- a/modules/mol/base/src/handle_type_fw.hh
+++ b/modules/mol/base/src/handle_type_fw.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/ics_editor.cc b/modules/mol/base/src/ics_editor.cc
index 910c7fd85365f747e12eed613147bde49b2a4fdb..f16dbdcf70d853f7aa2c87c18961b67b238719df 100644
--- a/modules/mol/base/src/ics_editor.cc
+++ b/modules/mol/base/src/ics_editor.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/ics_editor.hh b/modules/mol/base/src/ics_editor.hh
index eb51807432d2a9aa3f2ddeb08b48c5a8ea88d073..8bb9231f06f4a62d1dc0cae314f664f4639d1a2d 100644
--- a/modules/mol/base/src/ics_editor.hh
+++ b/modules/mol/base/src/ics_editor.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/impl/atom_group.hh b/modules/mol/base/src/impl/atom_group.hh
index 50a7c6338972313b36f41bed8072f60d42cdf21a..72625a0d145a499ea92a5347909efd354a327d76 100644
--- a/modules/mol/base/src/impl/atom_group.hh
+++ b/modules/mol/base/src/impl/atom_group.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/impl/atom_impl.cc b/modules/mol/base/src/impl/atom_impl.cc
index f0852b73845a7ae3181109154203f40a3435d64c..73d0d5e6a90c6fddcd763b62eb333fc33343f1bf 100644
--- a/modules/mol/base/src/impl/atom_impl.cc
+++ b/modules/mol/base/src/impl/atom_impl.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/impl/atom_impl.hh b/modules/mol/base/src/impl/atom_impl.hh
index b342c526ae56bc5acdfbef3942255c7ff0a9f69c..c229a2d33450be0d00aded37d909ccfe87d49419 100644
--- a/modules/mol/base/src/impl/atom_impl.hh
+++ b/modules/mol/base/src/impl/atom_impl.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/impl/atom_impl_fw.hh b/modules/mol/base/src/impl/atom_impl_fw.hh
index ab2be2112edc9503a3882be2b2cdd59d7ba84237..33cd7df9c317da218b1c8a27db43a16929989903 100644
--- a/modules/mol/base/src/impl/atom_impl_fw.hh
+++ b/modules/mol/base/src/impl/atom_impl_fw.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/impl/atom_prop.cc b/modules/mol/base/src/impl/atom_prop.cc
index ebf27f7d6d0948c30cbc52cadaca501c9089be08..a9f77496438fa42758d9a8c07d6e27d6bcc00cde 100644
--- a/modules/mol/base/src/impl/atom_prop.cc
+++ b/modules/mol/base/src/impl/atom_prop.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/impl/atom_prop.hh b/modules/mol/base/src/impl/atom_prop.hh
index b592f18e09aee1ce8008b433b8e8f21a8ff08e49..8debefa0ca704fc11d9714cc8a83bc2b3bdf1b36 100644
--- a/modules/mol/base/src/impl/atom_prop.hh
+++ b/modules/mol/base/src/impl/atom_prop.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/impl/chain_impl.cc b/modules/mol/base/src/impl/chain_impl.cc
index 48b41bac3cea4a874d3124f8aa7b9d72e21c145d..d07bc6436a2a69c06eda8c2e2178093cac54a73c 100644
--- a/modules/mol/base/src/impl/chain_impl.cc
+++ b/modules/mol/base/src/impl/chain_impl.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/impl/chain_impl.hh b/modules/mol/base/src/impl/chain_impl.hh
index b6a4a34a682fc5c5d80d3a0fbfc0a257ef1218b8..feb03df4e2ca827c930a92b4192141cf691b8d8e 100644
--- a/modules/mol/base/src/impl/chain_impl.hh
+++ b/modules/mol/base/src/impl/chain_impl.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/impl/chain_impl_fw.hh b/modules/mol/base/src/impl/chain_impl_fw.hh
index 124a24ba3af4f23a98f8d49bfc10744cefa578fa..0ed6d4697c1f2ee32f9fb53cac8283cfa6d70d62 100644
--- a/modules/mol/base/src/impl/chain_impl_fw.hh
+++ b/modules/mol/base/src/impl/chain_impl_fw.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/impl/connector_impl.cc b/modules/mol/base/src/impl/connector_impl.cc
index 3a5a61532b5e6f61c58b960c3b0ba0b3f41789c9..0c72434456c69926de7dc950fe4d6fd766171fc9 100644
--- a/modules/mol/base/src/impl/connector_impl.cc
+++ b/modules/mol/base/src/impl/connector_impl.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/impl/connector_impl.hh b/modules/mol/base/src/impl/connector_impl.hh
index acb50b57a3113585a38113bd412a1b62af7245af..ec7b52885fb3a7740a067f57e4f7bed2496fbe5f 100644
--- a/modules/mol/base/src/impl/connector_impl.hh
+++ b/modules/mol/base/src/impl/connector_impl.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/impl/connector_impl_fw.hh b/modules/mol/base/src/impl/connector_impl_fw.hh
index aa5bbf6907353358d739678fb17fd191ec3089a7..cb9aa522e668e51090be24b2ffdaea28c6e1c332 100644
--- a/modules/mol/base/src/impl/connector_impl_fw.hh
+++ b/modules/mol/base/src/impl/connector_impl_fw.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/impl/dataset_impl.hh b/modules/mol/base/src/impl/dataset_impl.hh
index 15b3b6e51560168486f8ddfad62ef6709ee0208e..cbf411af9521cf45dd0076efd22688d54c8b797b 100644
--- a/modules/mol/base/src/impl/dataset_impl.hh
+++ b/modules/mol/base/src/impl/dataset_impl.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/impl/dataset_impl_fw.hh b/modules/mol/base/src/impl/dataset_impl_fw.hh
index 74e659a6bca0765130b4275c5ec38844a5f6bb47..7b96659cf496c61086e307daa6e9a61c05268dfd 100644
--- a/modules/mol/base/src/impl/dataset_impl_fw.hh
+++ b/modules/mol/base/src/impl/dataset_impl_fw.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/impl/dihedral.cc b/modules/mol/base/src/impl/dihedral.cc
index cac771039b96ae38e478edb7c9a596e337bd869c..ee26230be4e4df8793885f133855051c48e980a9 100644
--- a/modules/mol/base/src/impl/dihedral.cc
+++ b/modules/mol/base/src/impl/dihedral.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/impl/dihedral.hh b/modules/mol/base/src/impl/dihedral.hh
index a722c93e60ff4b8d015d5f5bb97bc7d1b3a9709c..4699a96da2668a6a222319b89b304e3b869d89ea 100644
--- a/modules/mol/base/src/impl/dihedral.hh
+++ b/modules/mol/base/src/impl/dihedral.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/impl/entity_impl.cc b/modules/mol/base/src/impl/entity_impl.cc
index 90ef2ad75d3411d5ba105f97d5756ebce1031910..db0731f27583d9bc499183e56c65464188a4037d 100644
--- a/modules/mol/base/src/impl/entity_impl.cc
+++ b/modules/mol/base/src/impl/entity_impl.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/impl/entity_impl.hh b/modules/mol/base/src/impl/entity_impl.hh
index 7a1e3a30309371f1a921fa6ba598f618335b9e62..56a2b6ffbcfaf05d4ffe7da2cf3655ad2035f1af 100644
--- a/modules/mol/base/src/impl/entity_impl.hh
+++ b/modules/mol/base/src/impl/entity_impl.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/impl/entity_impl_fw.hh b/modules/mol/base/src/impl/entity_impl_fw.hh
index 5fedf14842332462e7e86454bbe22cfce9199b79..f0ef0caad2f2c717eb98e4db5f2ac78f1186d173 100644
--- a/modules/mol/base/src/impl/entity_impl_fw.hh
+++ b/modules/mol/base/src/impl/entity_impl_fw.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/impl/fragment_impl.cc b/modules/mol/base/src/impl/fragment_impl.cc
index 63459aee4febb84b0bcbdeef0d7b52842dce2bbc..1f0248755248c1afbae8f9b9b281837080de1306 100644
--- a/modules/mol/base/src/impl/fragment_impl.cc
+++ b/modules/mol/base/src/impl/fragment_impl.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/impl/fragment_impl.hh b/modules/mol/base/src/impl/fragment_impl.hh
index 71df89405ebf03792a0723c86a86ea7b29240fcd..84c7b1e411934fc7c74be9a3f3077a0763754678 100644
--- a/modules/mol/base/src/impl/fragment_impl.hh
+++ b/modules/mol/base/src/impl/fragment_impl.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/impl/fragment_impl_fw.hh b/modules/mol/base/src/impl/fragment_impl_fw.hh
index 8d8b0f4a08f86737b8dab53a5ad8d6dce4240195..592e74a57dad5ce796d26b6338b2250c7650f415 100644
--- a/modules/mol/base/src/impl/fragment_impl_fw.hh
+++ b/modules/mol/base/src/impl/fragment_impl_fw.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/impl/pointer_iterator.hh b/modules/mol/base/src/impl/pointer_iterator.hh
index 9e170f26d940452d15dc14e3de9cec347ba02b06..b8c679df84ae1c11d5a1d38375fe8f385bbde2ba 100644
--- a/modules/mol/base/src/impl/pointer_iterator.hh
+++ b/modules/mol/base/src/impl/pointer_iterator.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/impl/query_ast.cc b/modules/mol/base/src/impl/query_ast.cc
index 26e99bed2bfaca2a1d026f758cdd7a11b9c8d32f..63882ff4419d6fba2783f18f9fc912dea97a6e6e 100644
--- a/modules/mol/base/src/impl/query_ast.cc
+++ b/modules/mol/base/src/impl/query_ast.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/impl/query_ast.hh b/modules/mol/base/src/impl/query_ast.hh
index 6105213939f0f64fc63ce07c82e21b7004a862ff..7cf5fae608f73b606e3cb74393504d0e1cba30b9 100644
--- a/modules/mol/base/src/impl/query_ast.hh
+++ b/modules/mol/base/src/impl/query_ast.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/impl/query_ast_fw.hh b/modules/mol/base/src/impl/query_ast_fw.hh
index 3d0f106b51b54c7d5e9b1d45ac7cca56df317cf7..52c4553e4a8d12685c75b180423171776053aa16 100644
--- a/modules/mol/base/src/impl/query_ast_fw.hh
+++ b/modules/mol/base/src/impl/query_ast_fw.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/impl/query_impl.cc b/modules/mol/base/src/impl/query_impl.cc
index 733999f26ef6b2a3eeee7255c89db667c5825d08..a7c2cfb95c495362e1e04b104499fb109ef90263 100644
--- a/modules/mol/base/src/impl/query_impl.cc
+++ b/modules/mol/base/src/impl/query_impl.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/impl/query_impl.hh b/modules/mol/base/src/impl/query_impl.hh
index 4b81bc3dbf36924462a7e4961f0831a604e95f98..a70322975b2f52ff1ffb25685286c63a3000f1e9 100644
--- a/modules/mol/base/src/impl/query_impl.hh
+++ b/modules/mol/base/src/impl/query_impl.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/impl/query_impl_fw.hh b/modules/mol/base/src/impl/query_impl_fw.hh
index f29b7f136580f867c6035e384d1f9b331000e00f..d681ec3abc019a5c62249c8a734e5b096e09bc8d 100644
--- a/modules/mol/base/src/impl/query_impl_fw.hh
+++ b/modules/mol/base/src/impl/query_impl_fw.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/impl/residue_impl.cc b/modules/mol/base/src/impl/residue_impl.cc
index 3cf6591964f0a254d593853e7772c6639b4ed25a..c4ddfbe36e3dcfa59451f54758aa95b0c186dffd 100644
--- a/modules/mol/base/src/impl/residue_impl.cc
+++ b/modules/mol/base/src/impl/residue_impl.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/impl/residue_impl.hh b/modules/mol/base/src/impl/residue_impl.hh
index 91b6843e78ab8de6ab7034302aea3708595487a0..fea1b0a6f7d6c98e90adb7e2869e7d0aa46ed90b 100644
--- a/modules/mol/base/src/impl/residue_impl.hh
+++ b/modules/mol/base/src/impl/residue_impl.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/impl/residue_impl_fw.hh b/modules/mol/base/src/impl/residue_impl_fw.hh
index de5d67f88d4336cdc21fb12a5cb8e0d0d76b2063..4184a9cc23815c793bd96984d842105c3463de70 100644
--- a/modules/mol/base/src/impl/residue_impl_fw.hh
+++ b/modules/mol/base/src/impl/residue_impl_fw.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/impl/surface_impl.cc b/modules/mol/base/src/impl/surface_impl.cc
index 3a1d796b261c41cad70613018516b913307ebe99..e2719f368cc4d2c800f8184315aa09326042dc5e 100644
--- a/modules/mol/base/src/impl/surface_impl.cc
+++ b/modules/mol/base/src/impl/surface_impl.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/impl/surface_impl.hh b/modules/mol/base/src/impl/surface_impl.hh
index d8daf7f8f04776737b48a2dbecb2c50c0e84b0f4..b20010988f851a3cf718debeecac708bdbfb18bf 100644
--- a/modules/mol/base/src/impl/surface_impl.hh
+++ b/modules/mol/base/src/impl/surface_impl.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/impl/surface_impl_fw.hh b/modules/mol/base/src/impl/surface_impl_fw.hh
index a5ff121d2e0a7e9410ab74165de65848b362ab5b..ab7ba4274ba3cca95ec8ca3fffeb64005bf61856 100644
--- a/modules/mol/base/src/impl/surface_impl_fw.hh
+++ b/modules/mol/base/src/impl/surface_impl_fw.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/impl/torsion_impl.cc b/modules/mol/base/src/impl/torsion_impl.cc
index 9f9ffcdd9b74fa46969ed70f934b1c0a434e4602..553209a6b88ac61171dff012b0a7605402b610fe 100644
--- a/modules/mol/base/src/impl/torsion_impl.cc
+++ b/modules/mol/base/src/impl/torsion_impl.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/impl/torsion_impl.hh b/modules/mol/base/src/impl/torsion_impl.hh
index e6d441e5dba2cf1b2315bba243927e9404de889a..11d6e91735914710985a8138a5775daf5ffcf49c 100644
--- a/modules/mol/base/src/impl/torsion_impl.hh
+++ b/modules/mol/base/src/impl/torsion_impl.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/impl/torsion_impl_fw.hh b/modules/mol/base/src/impl/torsion_impl_fw.hh
index 88892cdae4498da063769c9ee0471382ebee27d4..9e4a54498255f4cb16b0557e3a55f998e58ee989 100644
--- a/modules/mol/base/src/impl/torsion_impl_fw.hh
+++ b/modules/mol/base/src/impl/torsion_impl_fw.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/in_mem_coord_source.hh b/modules/mol/base/src/in_mem_coord_source.hh
index 6b6d15f6a22c804fdbe901358817f59093f83f47..a240650e71cad7e856447e4ca62f5ce1c7cb46b8 100644
--- a/modules/mol/base/src/in_mem_coord_source.hh
+++ b/modules/mol/base/src/in_mem_coord_source.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/module_config.hh b/modules/mol/base/src/module_config.hh
index 995db6ddb9aa4c85da369c397967aa780b599386..a5aa7b2109c4397224dbdf145f6a99fb7bd98045 100644
--- a/modules/mol/base/src/module_config.hh
+++ b/modules/mol/base/src/module_config.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/mol.hh b/modules/mol/base/src/mol.hh
index 5e7b7a3337e331e48ad899b13ab2c03b901d8ca6..19fdf0d4d19a9608f8c83c690fa98e63cd1054b9 100644
--- a/modules/mol/base/src/mol.hh
+++ b/modules/mol/base/src/mol.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/not_connected_error.cc b/modules/mol/base/src/not_connected_error.cc
index 43e31f73130c02219f21ff8c9ee2290157996048..f6be45e5f1ebb796d5b4526c188a89755e5305d8 100644
--- a/modules/mol/base/src/not_connected_error.cc
+++ b/modules/mol/base/src/not_connected_error.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/not_connected_error.hh b/modules/mol/base/src/not_connected_error.hh
index ac736c74e4eff141c20a3345fd05ac9e0c31e948..ab8e5829fbe66d46d5b8ac2e5d8cb55bc5149414 100644
--- a/modules/mol/base/src/not_connected_error.hh
+++ b/modules/mol/base/src/not_connected_error.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/property_id.cc b/modules/mol/base/src/property_id.cc
index 2f80a94cf0b6f3c80dff7c6974461581d906b999..467227294144e5cdfcb9afe3f0d79f4927324f86 100644
--- a/modules/mol/base/src/property_id.cc
+++ b/modules/mol/base/src/property_id.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/property_id.hh b/modules/mol/base/src/property_id.hh
index 981b747cfe500b8b7f41c8b294036527a29522d3..7fec20853d02b62dd19adb6259ba583297255c7f 100644
--- a/modules/mol/base/src/property_id.hh
+++ b/modules/mol/base/src/property_id.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/query.cc b/modules/mol/base/src/query.cc
index 4359cc26b800e9dc9e4b53f21dc86b15ecee8234..a1672b3621007d920fd69ddb8f8dd61af021b622 100644
--- a/modules/mol/base/src/query.cc
+++ b/modules/mol/base/src/query.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/query.hh b/modules/mol/base/src/query.hh
index 4ab52ac98dfafc0cface61822bcfb143c224bbcc..0519c296b1838b1a84b72baf6fb81aca39bddd73 100644
--- a/modules/mol/base/src/query.hh
+++ b/modules/mol/base/src/query.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/query_error.cc b/modules/mol/base/src/query_error.cc
index 34bb3b83c919e7b3fcea9fd54019b908de88b27e..9f7ad521d72b43ba4fa9ee2921b29bf22889513c 100644
--- a/modules/mol/base/src/query_error.cc
+++ b/modules/mol/base/src/query_error.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/query_error.hh b/modules/mol/base/src/query_error.hh
index 84d0164997afe8a3e4d9365ef8c75b8cef064d8b..c8a092cc9c073cf5f217db4294b51cc32bf46f45 100644
--- a/modules/mol/base/src/query_error.hh
+++ b/modules/mol/base/src/query_error.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/query_state.cc b/modules/mol/base/src/query_state.cc
index 639306c903372a4b1b49b25d4dc79d7aee5c769f..2b18845d3342153ff3d8a06e0f0b741c0908aa78 100644
--- a/modules/mol/base/src/query_state.cc
+++ b/modules/mol/base/src/query_state.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/query_state.hh b/modules/mol/base/src/query_state.hh
index f2d8edfdd39762be70100a58751473c32cb4ccfb..c1957baf99fcd3b299f69df56b1ea7768076c671 100644
--- a/modules/mol/base/src/query_state.hh
+++ b/modules/mol/base/src/query_state.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/query_view_wrapper.cc b/modules/mol/base/src/query_view_wrapper.cc
index 068a1013b1e3fbbdd2806c6b43e95ca65e15d7ea..2aca92a79b374ce98df301b2b703c9192e8c241d 100644
--- a/modules/mol/base/src/query_view_wrapper.cc
+++ b/modules/mol/base/src/query_view_wrapper.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/query_view_wrapper.hh b/modules/mol/base/src/query_view_wrapper.hh
index 7b24184313340e1ca4e1906c4e6acf3f97cd9560..8996574a0736c456636f2aba37542bae38cc1be4 100644
--- a/modules/mol/base/src/query_view_wrapper.hh
+++ b/modules/mol/base/src/query_view_wrapper.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/residue_base.cc b/modules/mol/base/src/residue_base.cc
index 07950307d012a33735f6630a5d171d8e8ad8c7ce..b788d7c2ed305e946dadaefd78cdc9c3ca87c4e0 100644
--- a/modules/mol/base/src/residue_base.cc
+++ b/modules/mol/base/src/residue_base.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/residue_base.hh b/modules/mol/base/src/residue_base.hh
index 30e174b24f80da16914b740e946f54c28f38e6ca..0011a962a4162b3a2382b46dcde52d492beb2d71 100644
--- a/modules/mol/base/src/residue_base.hh
+++ b/modules/mol/base/src/residue_base.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/residue_handle.cc b/modules/mol/base/src/residue_handle.cc
index 117979652e2697d34a3a4d3495948ceb07caa596..a355f7fcfa519cfe2186e236a70750b92e954bb4 100644
--- a/modules/mol/base/src/residue_handle.cc
+++ b/modules/mol/base/src/residue_handle.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/residue_handle.hh b/modules/mol/base/src/residue_handle.hh
index 6462036c8231edb5744ebb6ddeacabe3cf541b41..1772cfc4179ea95e80de5f7c84407a3fd6be3f51 100644
--- a/modules/mol/base/src/residue_handle.hh
+++ b/modules/mol/base/src/residue_handle.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/residue_prop.hh b/modules/mol/base/src/residue_prop.hh
index ff1c5c11b3ec30947954ba023c2ae71b761c82d3..0efb534ac80b3e36d9c8639133537871b48f0e74 100644
--- a/modules/mol/base/src/residue_prop.hh
+++ b/modules/mol/base/src/residue_prop.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/residue_view.cc b/modules/mol/base/src/residue_view.cc
index 15caa6bd5e0acfc00c691d5042ea0fb77aafa5a7..ee463fe1a62b4e58f465afbedb20a650faf27a9b 100644
--- a/modules/mol/base/src/residue_view.cc
+++ b/modules/mol/base/src/residue_view.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/residue_view.hh b/modules/mol/base/src/residue_view.hh
index 289096413eccb5392fd895c2c99b3a0fc7e87435..518de3f1ab5a2ba72722e99377458acbe34d7e17 100644
--- a/modules/mol/base/src/residue_view.hh
+++ b/modules/mol/base/src/residue_view.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/sec_structure.hh b/modules/mol/base/src/sec_structure.hh
index f76b0e5f9c4508d76ed52f2efd41bc2f7c5a3aec..52ff4a501b81406cd3cb1ecf4a1f6e15cdfc64bc 100644
--- a/modules/mol/base/src/sec_structure.hh
+++ b/modules/mol/base/src/sec_structure.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/skel_link.cc b/modules/mol/base/src/skel_link.cc
index 6e2c72f8d61fed7484d15fcfbe2ed08b38b9cb32..a6ba51de3a5554fa60b00a47085a3fd5e3639a54 100644
--- a/modules/mol/base/src/skel_link.cc
+++ b/modules/mol/base/src/skel_link.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/skel_link.hh b/modules/mol/base/src/skel_link.hh
index bf1f12de5a5ef2a771048e576ca2a0a752ba1149..1fec95006be01ec76b123a5f1737b96cd7906989 100644
--- a/modules/mol/base/src/skel_link.hh
+++ b/modules/mol/base/src/skel_link.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/skel_link_fw.hh b/modules/mol/base/src/skel_link_fw.hh
index eb7a09d3ddc4abc09f0be0393b43cd6b1c7755f6..e379dcafbdfdd4dc9e2a004cae902318b4a3d010 100644
--- a/modules/mol/base/src/skel_link_fw.hh
+++ b/modules/mol/base/src/skel_link_fw.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/spatial_organizer.hh b/modules/mol/base/src/spatial_organizer.hh
index 0e9dce74005141d9103453a806a475704d0ba2b2..413bc6af478e5c50c438e2ff4ac59f223376138d 100644
--- a/modules/mol/base/src/spatial_organizer.hh
+++ b/modules/mol/base/src/spatial_organizer.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/surface.hh b/modules/mol/base/src/surface.hh
index 336acdbe74c6bc1174fe44cab2c29002ddcb6e42..d5ccc42a316d2417d9efcfe171cf4c3de153ba25 100644
--- a/modules/mol/base/src/surface.hh
+++ b/modules/mol/base/src/surface.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/surface_builder.cc b/modules/mol/base/src/surface_builder.cc
index 69cf67e4d6cf8e09bfaa92d02121ffdd2d67bdc1..9636269e85bf5628ab96a62e01b32ef6372a55e1 100644
--- a/modules/mol/base/src/surface_builder.cc
+++ b/modules/mol/base/src/surface_builder.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/surface_builder.hh b/modules/mol/base/src/surface_builder.hh
index d7199d1b26887ad7ee3c59d5c00a6a6f2fb49973..f15ec326c4d7b58195ae7fd9693ab155bfb6d3b5 100644
--- a/modules/mol/base/src/surface_builder.hh
+++ b/modules/mol/base/src/surface_builder.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/surface_handle.cc b/modules/mol/base/src/surface_handle.cc
index 6fb69167f942eb3ae29f74f896d32cbbf7c3b78d..a0ce21c186a83ca001562b86694c011bcb8ee9a3 100644
--- a/modules/mol/base/src/surface_handle.cc
+++ b/modules/mol/base/src/surface_handle.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/surface_handle.hh b/modules/mol/base/src/surface_handle.hh
index a11b3a91e9768535716c30e25f5026e8fdc04c44..9a329cdc7e843bc9f3112a51c1530db88eb911b4 100644
--- a/modules/mol/base/src/surface_handle.hh
+++ b/modules/mol/base/src/surface_handle.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/surface_prop.hh b/modules/mol/base/src/surface_prop.hh
index 5031b52363f2f0577846b753797c7f722f4a8ece..d33c277e8da2cbd6e25d471e269304202a19a3a5 100644
--- a/modules/mol/base/src/surface_prop.hh
+++ b/modules/mol/base/src/surface_prop.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/torsion_handle.cc b/modules/mol/base/src/torsion_handle.cc
index 2830bc8211ef30477693f3610b76b46fdf79d27e..ad991fbd1b9493087dd6a3b4d1e132449b2a2464 100644
--- a/modules/mol/base/src/torsion_handle.cc
+++ b/modules/mol/base/src/torsion_handle.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/torsion_handle.hh b/modules/mol/base/src/torsion_handle.hh
index 06f7e7bf0eb7283318617f8fd0a4f222718f87ad..34fadd0331bb00221b5f47cc8d59a14d925ffba8 100644
--- a/modules/mol/base/src/torsion_handle.hh
+++ b/modules/mol/base/src/torsion_handle.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/transfer_connectivity.cc b/modules/mol/base/src/transfer_connectivity.cc
index 38b1d6f151043611eac09762f9fcf4ec2f00272c..b7536f4871d261f5aa5560217d60a1af1bb0e07a 100644
--- a/modules/mol/base/src/transfer_connectivity.cc
+++ b/modules/mol/base/src/transfer_connectivity.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/transfer_connectivity.hh b/modules/mol/base/src/transfer_connectivity.hh
index e46691cd25d920ff1268f52d730ef70f2662d464..8268c4041b3aef9d39fcf8c8406d39f38fb97a8d 100644
--- a/modules/mol/base/src/transfer_connectivity.hh
+++ b/modules/mol/base/src/transfer_connectivity.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/view_op.cc b/modules/mol/base/src/view_op.cc
index 83e02b41cda6977df0e43cd87e9b4893e313b7a1..4b37c4c32e950d82583b8cd0bb5cc601ae64060f 100644
--- a/modules/mol/base/src/view_op.cc
+++ b/modules/mol/base/src/view_op.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/view_op.hh b/modules/mol/base/src/view_op.hh
index dea7c29ab58f11f2f70c9c864554c69884592c89..4c719b0d4eca0cb8b0e0df5df0644bbae7b0f7ad 100644
--- a/modules/mol/base/src/view_op.hh
+++ b/modules/mol/base/src/view_op.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/view_type_fw.hh b/modules/mol/base/src/view_type_fw.hh
index cab4b81d0e7c91c51f7a90102db441ec0c8a6d72..2355453095816365f712b547bd04a55c0abad625 100644
--- a/modules/mol/base/src/view_type_fw.hh
+++ b/modules/mol/base/src/view_type_fw.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/xcs_editor.cc b/modules/mol/base/src/xcs_editor.cc
index 4b793d33e4cba2e03526dd3a307a61d0edfdb7ab..860fbbd6f5f8b0900d30d5181985f2110045336f 100644
--- a/modules/mol/base/src/xcs_editor.cc
+++ b/modules/mol/base/src/xcs_editor.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/src/xcs_editor.hh b/modules/mol/base/src/xcs_editor.hh
index fc992d8c9d86e53bc834a73147ddf2f70d1b748d..68044862387e78ea557a8b2141b96431f3d2e8f3 100644
--- a/modules/mol/base/src/xcs_editor.hh
+++ b/modules/mol/base/src/xcs_editor.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/tests/dummy_ent.hh b/modules/mol/base/tests/dummy_ent.hh
index 1bfe911ab3836260375c74ffe836dbddd20469f8..774252ca1fb80d8166e2a28e7db0b770aaeb37cb 100644
--- a/modules/mol/base/tests/dummy_ent.hh
+++ b/modules/mol/base/tests/dummy_ent.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/tests/test_atom_groups.cc b/modules/mol/base/tests/test_atom_groups.cc
index 71898da71126d8d9324c01975d2e1deb89421a7a..d65fd864e9739f520e3356b77c6eb4db1ddc7e01 100644
--- a/modules/mol/base/tests/test_atom_groups.cc
+++ b/modules/mol/base/tests/test_atom_groups.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/tests/test_builder.cc b/modules/mol/base/tests/test_builder.cc
index 30e8bdcdd8137a8f95e5f2123de5b7fd2c87fb2f..d3b5ce90386a02858cac6d7c727645cdee9ec657 100644
--- a/modules/mol/base/tests/test_builder.cc
+++ b/modules/mol/base/tests/test_builder.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/tests/test_chain.cc b/modules/mol/base/tests/test_chain.cc
index c1442dd457995e06ed4ca6cb77e7b2fe023b85e7..3fca04ca0c3505922531bc44ed1b60e00fc6f505 100644
--- a/modules/mol/base/tests/test_chain.cc
+++ b/modules/mol/base/tests/test_chain.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/tests/test_conn.cc b/modules/mol/base/tests/test_conn.cc
index 14068218212c762993970b7cdc18d672113f3377..4a7527de490fb4c6f91d6040a6c0b713ae4c2deb 100644
--- a/modules/mol/base/tests/test_conn.cc
+++ b/modules/mol/base/tests/test_conn.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/tests/test_coord_group.cc b/modules/mol/base/tests/test_coord_group.cc
index 39be2c38ce1563be161fa34cc1f0559767a4d09c..ec0136f4267dd4e7b186013a9f8c2aa1b53c797d 100644
--- a/modules/mol/base/tests/test_coord_group.cc
+++ b/modules/mol/base/tests/test_coord_group.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/tests/test_delete.cc b/modules/mol/base/tests/test_delete.cc
index 4f7b8dbb204670d1601372411801cabd586c29e8..dfb90a80c892e11b63ac023f28f1cf8a94046e27 100644
--- a/modules/mol/base/tests/test_delete.cc
+++ b/modules/mol/base/tests/test_delete.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/tests/test_entity.cc b/modules/mol/base/tests/test_entity.cc
index 7d8ea348573d6037a699ab2f44dde05dbf6e5b58..c092858390c5d0ea773547c78956595cfcfbecd1 100644
--- a/modules/mol/base/tests/test_entity.cc
+++ b/modules/mol/base/tests/test_entity.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/tests/test_ics.cc b/modules/mol/base/tests/test_ics.cc
index 73358b98dca23c8256522458475c186efe8d2557..3a78a1f34fcdcd3bf363825d80ca662245f66517 100644
--- a/modules/mol/base/tests/test_ics.cc
+++ b/modules/mol/base/tests/test_ics.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/tests/test_iterators.cc b/modules/mol/base/tests/test_iterators.cc
index cfd61c5099faf4dca8ea02c754d1b0c68e4065d2..23e904e85f5f26c70cce98f1f72c67f8bbd822f5 100644
--- a/modules/mol/base/tests/test_iterators.cc
+++ b/modules/mol/base/tests/test_iterators.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/tests/test_numpy.py b/modules/mol/base/tests/test_numpy.py
index 27061a234cc96d72ceaeec28ffad6ab18ca44d0a..fb69b9afe1a5fd8bf0a3e9d02b3a4006c7fd6a12 100644
--- a/modules/mol/base/tests/test_numpy.py
+++ b/modules/mol/base/tests/test_numpy.py
@@ -11,7 +11,7 @@ if ost.WITH_NUMPY:
has_numpy=True
try:
import numpy
- except ImportError, e:
+ except ImportError as e:
has_numpy=False
else:
has_numpy=False
diff --git a/modules/mol/base/tests/test_query.cc b/modules/mol/base/tests/test_query.cc
index 185b0f16812ef4bc9470d593876243bf6ecc5f05..0d8b318cbd800c5aa0ec2613edc3ad9f6a89d369 100644
--- a/modules/mol/base/tests/test_query.cc
+++ b/modules/mol/base/tests/test_query.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/tests/test_residue.cc b/modules/mol/base/tests/test_residue.cc
index a06c6a6cf82630a304d1522ae7485b9cd9eae360..17ef6ee59fd3d648794e9aba33be9d73554866f7 100644
--- a/modules/mol/base/tests/test_residue.cc
+++ b/modules/mol/base/tests/test_residue.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/tests/test_surface.cc b/modules/mol/base/tests/test_surface.cc
index ecc8d40b1c56c9c0f2f31b84a1f19a25af0a5fee..8df3e10b1d5f8884cd9ef94de712b0721ba49f1e 100644
--- a/modules/mol/base/tests/test_surface.cc
+++ b/modules/mol/base/tests/test_surface.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/tests/test_transfer_connectivity.cc b/modules/mol/base/tests/test_transfer_connectivity.cc
index 1bb37feed3c729dc2a8ab9f65b350f55770d2324..36ad6dc2cd5c1a0060b594ef28fa4119dfdb904a 100644
--- a/modules/mol/base/tests/test_transfer_connectivity.cc
+++ b/modules/mol/base/tests/test_transfer_connectivity.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/tests/test_view.cc b/modules/mol/base/tests/test_view.cc
index 2aee173d32a45769f696fa448bf486ba812e7edd..703de4518ac1d0c4754efd1ce65b88d2b89f0a0a 100644
--- a/modules/mol/base/tests/test_view.cc
+++ b/modules/mol/base/tests/test_view.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/tests/test_view_op.cc b/modules/mol/base/tests/test_view_op.cc
index f61f5d5bc6502a37279fd1e2e2f4f622d6db64bb..45a762f5ea097ca9698f673bf92acf63bbcceb64 100644
--- a/modules/mol/base/tests/test_view_op.cc
+++ b/modules/mol/base/tests/test_view_op.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/base/tests/tests.cc b/modules/mol/base/tests/tests.cc
index 117985fd0151606c9216e483616d93d180396b01..5742604063df658ff4fb01fd61fe4dd39585ce41 100644
--- a/modules/mol/base/tests/tests.cc
+++ b/modules/mol/base/tests/tests.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/mm/pymod/__init__.py b/modules/mol/mm/pymod/__init__.py
index a4a7c650e1fe7c9bbb0643bdce4a8d4be6e8e6bd..0310464f70c358d90436a2fd3799dcf2bc7d9b0c 100644
--- a/modules/mol/mm/pymod/__init__.py
+++ b/modules/mol/mm/pymod/__init__.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2016 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
@@ -18,8 +18,8 @@
#------------------------------------------------------------------------------
import os.path
-from _ost_mol_mm import *
-import antechamber
+from ._ost_mol_mm import *
+from . import antechamber
import ost
def LoadAMBERForcefield():
diff --git a/modules/mol/mm/pymod/antechamber.py b/modules/mol/mm/pymod/antechamber.py
index 6fc48ce3f38effb6e1a92683e1ec0e31d318c326..258aa974d6915434e8a344327556d80441ba9660 100644
--- a/modules/mol/mm/pymod/antechamber.py
+++ b/modules/mol/mm/pymod/antechamber.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2016 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
@@ -21,7 +21,7 @@
# field parameters. Allows the execution of Antechamber and the parsing of files
# generated by it.
-import _ost_mol_mm as mm
+from ost.mol import mm
import ost
from ost import settings, mol, geom
import os, subprocess, math
@@ -226,7 +226,7 @@ def _ParseAmberForceField(filename):
if not keyword in keywords: continue
# loop until empty line found
ff_dict[keyword] = []
- line = in_file.next()
+ line = next(in_file)
while len(line.strip()) > 0:
# check for warnings
if 'ATTN' in line:
@@ -286,7 +286,7 @@ def _ParseAmberForceField(filename):
epsilon = float(s[1])
ff_dict[keyword].append([atype, Rvdw, epsilon])
# next...
- line = in_file.next()
+ line = next(in_file)
return ff_dict
###############################################################################
diff --git a/modules/mol/mm/pymod/export_block_modifiers.cc b/modules/mol/mm/pymod/export_block_modifiers.cc
index 08287f08f7b7ae33080e6e9d9948ec4b060b90e3..0a42e7b2b79904fb0980cb40726094ccaa71c7d8 100644
--- a/modules/mol/mm/pymod/export_block_modifiers.cc
+++ b/modules/mol/mm/pymod/export_block_modifiers.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/mm/pymod/export_buildingblock.cc b/modules/mol/mm/pymod/export_buildingblock.cc
index 514b7919b86cc9462921ba8f5cc5073251660786..295c3f189d42de5978dda68b81329b4394955478 100644
--- a/modules/mol/mm/pymod/export_buildingblock.cc
+++ b/modules/mol/mm/pymod/export_buildingblock.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/mm/pymod/export_ff_reader.cc b/modules/mol/mm/pymod/export_ff_reader.cc
index b8a4fa6a894f9635a50d37c4b7c550941ecdd631..8337e7eea2d9a88851cdd39df6bde9f67a14cb72 100644
--- a/modules/mol/mm/pymod/export_ff_reader.cc
+++ b/modules/mol/mm/pymod/export_ff_reader.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/mm/pymod/export_forcefield.cc b/modules/mol/mm/pymod/export_forcefield.cc
index 82c74c6d7bb8ce615b8d7e9b55dcf67eae37d44c..8c8b5f90cf80f7e3ee28b6cfafbdf57b57b1f00c 100644
--- a/modules/mol/mm/pymod/export_forcefield.cc
+++ b/modules/mol/mm/pymod/export_forcefield.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/mm/pymod/export_index.cc b/modules/mol/mm/pymod/export_index.cc
index 240f22f4b10c698d11377e49ae76888894aec78a..09f66a1ee775f40ca27df0d7a3d256cd9a0351e7 100644
--- a/modules/mol/mm/pymod/export_index.cc
+++ b/modules/mol/mm/pymod/export_index.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/mm/pymod/export_interaction.cc b/modules/mol/mm/pymod/export_interaction.cc
index 57dc7a911b8fe67996fdc7355024265c8e370595..aa2e7114a003dfd887ed3ba975df513aecc2167e 100644
--- a/modules/mol/mm/pymod/export_interaction.cc
+++ b/modules/mol/mm/pymod/export_interaction.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/mm/pymod/export_modeller.cc b/modules/mol/mm/pymod/export_modeller.cc
index c0f71609d11a1bc5f2b1a40cb98c9cababee0d00..5c91b97033c87e1c895e5bfd6a88bf6e02a06090 100644
--- a/modules/mol/mm/pymod/export_modeller.cc
+++ b/modules/mol/mm/pymod/export_modeller.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/mm/pymod/export_observers.cc b/modules/mol/mm/pymod/export_observers.cc
index 47a0236125a4033bc8529d10c5107d62c290c1e0..3ef812c9cbf44b5553436f090af3c07617e70084 100644
--- a/modules/mol/mm/pymod/export_observers.cc
+++ b/modules/mol/mm/pymod/export_observers.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/mm/pymod/export_openmm.cc b/modules/mol/mm/pymod/export_openmm.cc
index 38a09d305b51edd0df5278644832633f2100498e..7d9c6573ff12e61aca8cee312284b7d74898a60e 100644
--- a/modules/mol/mm/pymod/export_openmm.cc
+++ b/modules/mol/mm/pymod/export_openmm.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/mm/pymod/export_settings.cc b/modules/mol/mm/pymod/export_settings.cc
index 7e38401d68d3888b89e0cd9d021e07077b9b7c9b..88c6fc4bc834222e734fac515e77c84f79b73832 100644
--- a/modules/mol/mm/pymod/export_settings.cc
+++ b/modules/mol/mm/pymod/export_settings.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/mm/pymod/export_simulation.cc b/modules/mol/mm/pymod/export_simulation.cc
index b4611a680b9e83b085854eb593c238328ec3461e..2845dc27159e908270c064e2f90e43a644bf8bf0 100644
--- a/modules/mol/mm/pymod/export_simulation.cc
+++ b/modules/mol/mm/pymod/export_simulation.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/mm/pymod/export_topology.cc b/modules/mol/mm/pymod/export_topology.cc
index 1e90e1b969fab9d27d0c709c9ddf5fa9f17e74e4..c4749abe2d77d52ec946f4aba5c4ec31b3aa6259 100644
--- a/modules/mol/mm/pymod/export_topology.cc
+++ b/modules/mol/mm/pymod/export_topology.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
@@ -388,7 +388,6 @@ void export_Topology()
.def("AddExclusion",&ost::mol::mm::Topology::AddExclusion,(arg("idx_one"),arg("idx_two")))
.def("AddPositionConstraint",&ost::mol::mm::Topology::AddPositionConstraint,(arg("idx")))
.def("ResetPositionConstraints",&ost::mol::mm::Topology::ResetPositionConstraints)
- .def("SetDensity",&ost::mol::mm::Topology::SetDensity,(arg("density"),arg("resolution"),arg("scaling")=1.0))
.def("ResetExclusions",&ost::mol::mm::Topology::ResetExclusions)
.def("AddHarmonicPositionRestraint",&ost::mol::mm::Topology::AddHarmonicPositionRestraint,(arg("idx"),arg("ref_position"),arg("k"),arg("x_scale")=1.0,arg("y_scale")=1.0,arg("z_scale")=1.0))
.def("AddHarmonicDistanceRestraint",&ost::mol::mm::Topology::AddHarmonicDistanceRestraint,(arg("idx_one"),arg("idx_two"),arg("length"),arg("force_constant")))
@@ -439,9 +438,6 @@ void export_Topology()
.def("GetHarmonicDistanceRestraintParameters",&WrapGetHarmonicDistanceRestraintParam,(arg("interaction_idx")))
.def("GetFGMDHBondDonorParameters",&WrapGetFGMDHBondDonorParam,(arg("interaction_idx")))
.def("GetFGMDHBondAcceptorParameters",&WrapGetFGMDHBondAcceptorParam,(arg("interaction_idx")))
- .def("GetDensity",&ost::mol::mm::Topology::GetDensity)
- .def("GetDensityResolution",&ost::mol::mm::Topology::GetDensityResolution)
- .def("GetDensityScaling",&ost::mol::mm::Topology::GetDensityResolution)
//setter functions for interaction parameters
.def("SetHarmonicBondParameters",&ost::mol::mm::Topology::SetHarmonicBondParameters,(arg("interaction_idx"),arg("bond_length"),arg("force_constant")))
diff --git a/modules/mol/mm/pymod/wrap_mol_mm.cc b/modules/mol/mm/pymod/wrap_mol_mm.cc
index 32e36e04b3bff7e01e4d50dda9a6c1a2f98a6173..c7648fa8b0ce89361215f9f7ebea6b3a5ddcf6de 100644
--- a/modules/mol/mm/pymod/wrap_mol_mm.cc
+++ b/modules/mol/mm/pymod/wrap_mol_mm.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/mm/src/CMakeLists.txt b/modules/mol/mm/src/CMakeLists.txt
index 3ebe98ba087cfc8cd22e891ccb0ee078c769f545..46f4d4cd576f47533c6661397f7428ae414a4820 100644
--- a/modules/mol/mm/src/CMakeLists.txt
+++ b/modules/mol/mm/src/CMakeLists.txt
@@ -16,11 +16,6 @@ set(OST_MOL_MM_HEADERS
index.hh
topology.hh
steep.hh
- openmm_plugins/density_plugin/openmmapi/density_force.hh
- openmm_plugins/density_plugin/openmmapi/density_kernels.hh
- openmm_plugins/density_plugin/openmmapi/density_force_impl.hh
- openmm_plugins/density_plugin/platforms/reference/reference_density_kernels.hh
- openmm_plugins/density_plugin/platforms/reference/reference_density_kernel_factory.hh
)
set(OST_MOL_MM_SOURCES
@@ -38,8 +33,6 @@ set(OST_MOL_MM_SOURCES
topology_creator.cc
topology.cc
steep.cc
- openmm_plugins/density_plugin/openmmapi/density_force.cc
- openmm_plugins/density_plugin/openmmapi/density_force_impl.cc
)
# create settings.hh as configurational header, needed to set the plugins path
@@ -69,37 +62,3 @@ copy_if_different("${CMAKE_CURRENT_SOURCE_DIR}" "${STAGE_DIR}/share/openstructur
"ost_mol_mm")
install(FILES "CHARMM27.dat" DESTINATION "share/openstructure/forcefields/")
-#The plugins that get loaded by OpenMM have to be built seperately
-
-##########################
-#build the density plugin#
-##########################
-
-#define the sources (headers are already handled above)
-SET(DENSITY_PLUGIN_REFERENCE_SOURCES
- openmm_plugins/density_plugin/platforms/reference/reference_density_kernel_factory.cc
- openmm_plugins/density_plugin/platforms/reference/reference_density_kernels.cc
-)
-
-# Set the library name
-SET(OPENMM_DENSITY_REFERENCE_LIBRARY_NAME density_plugin_reference)
-SET(SHARED_TARGET_DENSITY_PLUGIN ${OPENMM_DENSITY_REFERENCE_LIBRARY_NAME})
-
-ADD_LIBRARY(${SHARED_TARGET_DENSITY_PLUGIN} SHARED ${DENSITY_PLUGIN_REFERENCE_SOURCES})
-ADD_DEPENDENCIES(${SHARED_TARGET_DENSITY_PLUGIN} ost_mol_mm ost_img ost_mol_mm)
-
-SET_TARGET_PROPERTIES(${SHARED_TARGET_DENSITY_PLUGIN} PROPERTIES
- LIBRARY_OUTPUT_DIRECTORY ${STAGE_DIR}/share/openstructure/openmm_plugins/
- ARCHIVE_OUTPUT_DIRECTORY ${STAGE_DIR}/share/openstructure/openmm_plugins/
- RUNTIME_OUTPUT_DIRECTORY ${STAGE_DIR}/share/openstructure/openmm_plugins/)
-
-foreach(_DEPENDENCY ${_MOL_MM_DEPS})
- TARGET_LINK_LIBRARIES(${SHARED_TARGET_DENSITY_PLUGIN} ${_DEPENDENCY})
-endforeach()
-#also link against OpenMM and the mm module
-TARGET_LINK_LIBRARIES(${SHARED_TARGET_DENSITY_PLUGIN} ${OPEN_MM_LIBRARIES})
-TARGET_LINK_LIBRARIES(${SHARED_TARGET_DENSITY_PLUGIN} ost_mol_mm)
-
-file(MAKE_DIRECTORY ${STAGE_DIR}/share/openstructure/openmm_plugins/)
-INSTALL(TARGETS ${SHARED_TARGET_DENSITY_PLUGIN} LIBRARY
- DESTINATION "share/openstructure/openmm_plugins/")
diff --git a/modules/mol/mm/src/block_modifiers.hh b/modules/mol/mm/src/block_modifiers.hh
index 4212e496bb65d5133816f019025369441ecc6ade..de201bfb7a1ff31a01cf530f77d8ed68245939b7 100644
--- a/modules/mol/mm/src/block_modifiers.hh
+++ b/modules/mol/mm/src/block_modifiers.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/mm/src/buildingblock.cc b/modules/mol/mm/src/buildingblock.cc
index 2077880c7eb0e58c3096ec0f545197a43d966f3c..1e05f944cff97ff7e343b407b3dae23b9e8d8c72 100644
--- a/modules/mol/mm/src/buildingblock.cc
+++ b/modules/mol/mm/src/buildingblock.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/mm/src/buildingblock.hh b/modules/mol/mm/src/buildingblock.hh
index aa28327d4b03f278665b3fe9d4ff9307d9298e40..37edf7ab43e96714e42fe5d557bb5956863d8925 100644
--- a/modules/mol/mm/src/buildingblock.hh
+++ b/modules/mol/mm/src/buildingblock.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/mm/src/ff_reader.cc b/modules/mol/mm/src/ff_reader.cc
index c7cb9244dabb4e970fed1293fde44b55bafedac4..f4ea82960d39a99141a44dae4aec86bd3390cb67 100644
--- a/modules/mol/mm/src/ff_reader.cc
+++ b/modules/mol/mm/src/ff_reader.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/mm/src/ff_reader.hh b/modules/mol/mm/src/ff_reader.hh
index 957e4457922c6a017c4a6983accc733a412f786f..649cbfb9ae754935a8a15c724d50ac71d1987663 100644
--- a/modules/mol/mm/src/ff_reader.hh
+++ b/modules/mol/mm/src/ff_reader.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/mm/src/forcefield.cc b/modules/mol/mm/src/forcefield.cc
index c323277a79aa833616b4aa65b2566495fdeb9939..ab9291c610aeb4f77b1990d98138973d9b9efc5e 100644
--- a/modules/mol/mm/src/forcefield.cc
+++ b/modules/mol/mm/src/forcefield.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/mm/src/forcefield.hh b/modules/mol/mm/src/forcefield.hh
index 6435226e00b7303b574b80c67775ba1488d203f5..b99ffc0b330ab175fa38b148fde97c7e186a6443 100644
--- a/modules/mol/mm/src/forcefield.hh
+++ b/modules/mol/mm/src/forcefield.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/mm/src/gromacs_block_modifiers.cc b/modules/mol/mm/src/gromacs_block_modifiers.cc
index 08e4bfefede0bd61530240da9b1a5d7762a07ac2..9818c87b301cebb77f5d935990540c05482e377f 100644
--- a/modules/mol/mm/src/gromacs_block_modifiers.cc
+++ b/modules/mol/mm/src/gromacs_block_modifiers.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/mm/src/gromacs_block_modifiers.hh b/modules/mol/mm/src/gromacs_block_modifiers.hh
index 8ee115a3bfbc929cac62fbfc7a00942efbac0ec6..4f0b8ee65d06e5c6392a5f46e0985e5b6ab7171a 100644
--- a/modules/mol/mm/src/gromacs_block_modifiers.hh
+++ b/modules/mol/mm/src/gromacs_block_modifiers.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/mm/src/heuristic_block_modifiers.cc b/modules/mol/mm/src/heuristic_block_modifiers.cc
index 09734d1dcf716d0f690f74dd7387f4fb3a20eab2..a34c75d123274bfca5fd2cc37ea5c9846079d616 100644
--- a/modules/mol/mm/src/heuristic_block_modifiers.cc
+++ b/modules/mol/mm/src/heuristic_block_modifiers.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/mm/src/heuristic_block_modifiers.hh b/modules/mol/mm/src/heuristic_block_modifiers.hh
index facf818e52cf0290761cc1fd076c0f7fb62e617d..375eb1e74e21cd6716dea4540e93aff145dd81c6 100644
--- a/modules/mol/mm/src/heuristic_block_modifiers.hh
+++ b/modules/mol/mm/src/heuristic_block_modifiers.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/mm/src/index.hh b/modules/mol/mm/src/index.hh
index 93e9d2311b48c39fc950f23f16aa68c7426172ba..d5829fdb09e8bcbd8d08844ec4b69e2ff7e6c441 100644
--- a/modules/mol/mm/src/index.hh
+++ b/modules/mol/mm/src/index.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/mm/src/interaction.cc b/modules/mol/mm/src/interaction.cc
index 72f6ba8f01b54f5c33b2dd364bc204611f5b818a..4675dc7b3724b3d3425186b8c2e771e5c27b9a37 100644
--- a/modules/mol/mm/src/interaction.cc
+++ b/modules/mol/mm/src/interaction.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/mm/src/interaction.hh b/modules/mol/mm/src/interaction.hh
index 12762e244b1c608a795ef47421960a73fee37763..4a8863718cefd35f127eb52ac219683c3413d305 100644
--- a/modules/mol/mm/src/interaction.hh
+++ b/modules/mol/mm/src/interaction.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/mm/src/modeller.cc b/modules/mol/mm/src/modeller.cc
index 1a9da309452b9c0926fd3e1d27dff00dc6120f89..ac1ec34b123e9684e09f58c7edcce576ca7e686f 100644
--- a/modules/mol/mm/src/modeller.cc
+++ b/modules/mol/mm/src/modeller.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/mm/src/modeller.hh b/modules/mol/mm/src/modeller.hh
index 2ec09e194825a93ddbd36e988477b812c3dc0d45..8c97de8970c9dda52c5934a2c6735369277f3efc 100644
--- a/modules/mol/mm/src/modeller.hh
+++ b/modules/mol/mm/src/modeller.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/mm/src/observer.cc b/modules/mol/mm/src/observer.cc
index 0364715c42d4a3d551b99cb19bbe5b1ae891bbe3..90a862083f9199b7bbc4f7041d75e4a935a96f82 100644
--- a/modules/mol/mm/src/observer.cc
+++ b/modules/mol/mm/src/observer.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/mm/src/observer.hh b/modules/mol/mm/src/observer.hh
index e9103cea3a05de0410473e5dd7d10ae75e406106..cdc2a391c81733381acdff9b3572d28f315e84ab 100644
--- a/modules/mol/mm/src/observer.hh
+++ b/modules/mol/mm/src/observer.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/mm/src/openmm_plugins/density_plugin/openmmapi/density_force.cc b/modules/mol/mm/src/openmm_plugins/density_plugin/openmmapi/density_force.cc
deleted file mode 100644
index 8ff809d9a768edb8efd64acbde96fe2e51bcae31..0000000000000000000000000000000000000000
--- a/modules/mol/mm/src/openmm_plugins/density_plugin/openmmapi/density_force.cc
+++ /dev/null
@@ -1,97 +0,0 @@
-/* -------------------------------------------------------------------------- *
- * OpenMM *
- * -------------------------------------------------------------------------- *
- * This is part of the OpenMM molecular simulation toolkit originating from *
- * Simbios, the NIH National Center for Physics-Based Simulation of *
- * Biological Structures at Stanford, funded under the NIH Roadmap for *
- * Medical Research, grant U54 GM072970. See https://simtk.org. *
- * *
- * Portions copyright (c) 2014 Stanford University and the Authors. *
- * Authors: Peter Eastman *
- * Contributors: *
- * *
- * Permission is hereby granted, free of charge, to any person obtaining a *
- * copy of this software and associated documentation files (the "Software"), *
- * to deal in the Software without restriction, including without limitation *
- * the rights to use, copy, modify, merge, publish, distribute, sublicense, *
- * and/or sell copies of the Software, and to permit persons to whom the *
- * Software is furnished to do so, subject to the following conditions: *
- * *
- * The above copyright notice and this permission notice shall be included in *
- * all copies or substantial portions of the Software. *
- * *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
- * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
- * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
- * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
- * USE OR OTHER DEALINGS IN THE SOFTWARE. *
- * -------------------------------------------------------------------------- */
-
-#include <ost/mol/mm/density_force.hh>
-#include <ost/mol/mm/density_force_impl.hh>
-#include <openmm/OpenMMException.h>
-#include <openmm/internal/AssertionUtilities.h>
-#include <string.h>
-
-namespace ost{ namespace mol{ namespace mm{
-
-OpenMM::ForceImpl* DensityForce::createImpl() const {
- return new DensityForceImpl(*this);
-}
-
-void DensityForce::updateParametersInContext(OpenMM::Context& context) {
- dynamic_cast<DensityForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
-}
-
-void DensityForce::addParticle(Real mass){
- masses_.push_back(mass);
- in_body_.push_back(false);
-}
-
-Real DensityForce::getParticleMass(int idx) const{
- if(idx >= this->getNumParticles() || idx < 0){
- throw OpenMM::OpenMMException("Invalid index provided!");
- }
- return masses_[idx];
-}
-
-bool DensityForce::isInBody(int idx) const{
- if(idx >= this->getNumParticles() || idx < 0){
- throw OpenMM::OpenMMException("Invalid index provided!");
- }
- return in_body_[idx];
-}
-
-void DensityForce::defineBody(const std::vector<int>& indices){
- //first check, whether any of the indices is invalid or already part of a body
- int num_particles = this->getNumParticles();
- for(std::vector<int>::const_iterator i = indices.begin();
- i != indices.end(); ++i){
- if(*i >= num_particles || *i < 0){
- throw OpenMM::OpenMMException("Invalid index provided!");
- }
- if(in_body_[*i]){
- throw OpenMM::OpenMMException("Particle can be part of only one body!");
- }
- }
-
- //let's change the state of the according particles
- for(std::vector<int>::const_iterator i = indices.begin();
- i != indices.end(); ++i){
- in_body_[*i] = true;
- }
-
- //and finally define the body
- bodies_.push_back(indices);
-}
-
-const std::vector<int>& DensityForce::getBody(int idx) const{
- if(idx >= this->getNumBodies() || idx < 0){
- throw OpenMM::OpenMMException("Invalid index provided!");
- }
- return bodies_[idx];
-}
-
-}}} //ns
diff --git a/modules/mol/mm/src/openmm_plugins/density_plugin/openmmapi/density_force.hh b/modules/mol/mm/src/openmm_plugins/density_plugin/openmmapi/density_force.hh
deleted file mode 100644
index f932ff797b978cd54ebe8be72c03935f587f73af..0000000000000000000000000000000000000000
--- a/modules/mol/mm/src/openmm_plugins/density_plugin/openmmapi/density_force.hh
+++ /dev/null
@@ -1,94 +0,0 @@
-#ifndef OPENMM_DENSITYFORCE_H_
-#define OPENMM_DENSITYFORCE_H_
-
-/* -------------------------------------------------------------------------- *
- * OpenMM *
- * -------------------------------------------------------------------------- *
- * This is part of the OpenMM molecular simulation toolkit originating from *
- * Simbios, the NIH National Center for Physics-Based Simulation of *
- * Biological Structures at Stanford, funded under the NIH Roadmap for *
- * Medical Research, grant U54 GM072970. See https://simtk.org. *
- * *
- * Portions copyright (c) 2014 Stanford University and the Authors. *
- * Authors: Peter Eastman *
- * Contributors: *
- * *
- * Permission is hereby granted, free of charge, to any person obtaining a *
- * copy of this software and associated documentation files (the "Software"), *
- * to deal in the Software without restriction, including without limitation *
- * the rights to use, copy, modify, merge, publish, distribute, sublicense, *
- * and/or sell copies of the Software, and to permit persons to whom the *
- * Software is furnished to do so, subject to the following conditions: *
- * *
- * The above copyright notice and this permission notice shall be included in *
- * all copies or substantial portions of the Software. *
- * *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
- * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
- * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
- * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
- * USE OR OTHER DEALINGS IN THE SOFTWARE. *
- * -------------------------------------------------------------------------- */
-
-#include <openmm/Context.h>
-#include <openmm/Force.h>
-#include <ost/img/image.hh>
-
-namespace ost { namespace mol{ namespace mm{
-
-
-class DensityForce : public OpenMM::Force {
-public:
- /**
- * Create an DensityForce. The density force only makes sense for simulation boxes
- * with orthogonal base vectors.
- */
-
- //since the density is scaled in Angstrom, the resolution is also in Angstrom
- DensityForce(const ost::img::ImageHandle& d, Real r, Real s): density_(d),
- resolution_(r),
- scaling_(s) { }
-
- void addParticle(Real mass);
-
- int getNumParticles() const { return masses_.size(); }
-
- int getNumBodies() const { return bodies_.size(); }
-
- Real getParticleMass(int idx) const;
-
- bool isInBody(int idx) const;
-
- void defineBody(const std::vector<int>& indices);
-
- const std::vector<int>& getBody(int idx) const;
-
- void setScaling(Real scaling) { scaling_ = scaling; }
-
- Real getScaling() const { return scaling_; }
-
- ost::img::ImageHandle getDensity() const { return density_; }
-
- Real getResolution() const { return resolution_; }
-
- void updateParametersInContext(OpenMM::Context& context);
-
- bool usesPeriodicBoundaryConditions() const { return false; }
-
-protected:
- OpenMM::ForceImpl* createImpl() const;
-private:
-
- ost::img::ImageHandle density_;
- std::vector<Real> masses_;
- std::vector<bool> in_body_;
- std::vector<std::vector<int> > bodies_;
- Real resolution_;
- Real scaling_;
-};
-
-}}} // ns
-
-#endif /*OPENMM_DENSITYFORCE_H_*/
diff --git a/modules/mol/mm/src/openmm_plugins/density_plugin/openmmapi/density_force_impl.cc b/modules/mol/mm/src/openmm_plugins/density_plugin/openmmapi/density_force_impl.cc
deleted file mode 100644
index 1d2b859a0eb006fe13c389a9818d2958bc69a801..0000000000000000000000000000000000000000
--- a/modules/mol/mm/src/openmm_plugins/density_plugin/openmmapi/density_force_impl.cc
+++ /dev/null
@@ -1,71 +0,0 @@
-/* -------------------------------------------------------------------------- *
- * OpenMM *
- * -------------------------------------------------------------------------- *
- * This is part of the OpenMM molecular simulation toolkit originating from *
- * Simbios, the NIH National Center for Physics-Based Simulation of *
- * Biological Structures at Stanford, funded under the NIH Roadmap for *
- * Medical Research, grant U54 GM072970. See https://simtk.org. *
- * *
- * Portions copyright (c) 2014 Stanford University and the Authors. *
- * Authors: Peter Eastman *
- * Contributors: *
- * *
- * Permission is hereby granted, free of charge, to any person obtaining a *
- * copy of this software and associated documentation files (the "Software"), *
- * to deal in the Software without restriction, including without limitation *
- * the rights to use, copy, modify, merge, publish, distribute, sublicense, *
- * and/or sell copies of the Software, and to permit persons to whom the *
- * Software is furnished to do so, subject to the following conditions: *
- * *
- * The above copyright notice and this permission notice shall be included in *
- * all copies or substantial portions of the Software. *
- * *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
- * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
- * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
- * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
- * USE OR OTHER DEALINGS IN THE SOFTWARE. *
- * -------------------------------------------------------------------------- */
-
-#include <ost/mol/mm/density_force_impl.hh>
-#include <ost/mol/mm/density_kernels.hh>
-#include <openmm/OpenMMException.h>
-#include <openmm/internal/ContextImpl.h>
-#include <cmath>
-#include <map>
-#include <set>
-#include <sstream>
-
-namespace ost{ namespace mol{ namespace mm{
-
-DensityForceImpl::DensityForceImpl(const DensityForce& owner) : owner(owner) {
-}
-
-DensityForceImpl::~DensityForceImpl() {
-}
-
-void DensityForceImpl::initialize(OpenMM::ContextImpl& context) {
- kernel = context.getPlatform().createKernel(CalcDensityForceKernel::Name(), context);
- kernel.getAs<CalcDensityForceKernel>().initialize(context.getSystem(), owner);
-}
-
-double DensityForceImpl::calcForcesAndEnergy(OpenMM::ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
- if ((groups&(1<<owner.getForceGroup())) != 0)
- return kernel.getAs<CalcDensityForceKernel>().execute(context, includeForces, includeEnergy);
- return 0.0;
-}
-
-std::vector<std::string> DensityForceImpl::getKernelNames() {
- std::vector<std::string> names;
- names.push_back(CalcDensityForceKernel::Name());
- return names;
-}
-
-void DensityForceImpl::updateParametersInContext(OpenMM::ContextImpl& context) {
- kernel.getAs<CalcDensityForceKernel>().copyParametersToContext(context, owner);
-}
-
-}}} //ns
-
diff --git a/modules/mol/mm/src/openmm_plugins/density_plugin/openmmapi/density_force_impl.hh b/modules/mol/mm/src/openmm_plugins/density_plugin/openmmapi/density_force_impl.hh
deleted file mode 100644
index 850b2c5c23a33b48773bcc29b5001f1ad904353b..0000000000000000000000000000000000000000
--- a/modules/mol/mm/src/openmm_plugins/density_plugin/openmmapi/density_force_impl.hh
+++ /dev/null
@@ -1,74 +0,0 @@
-#ifndef OPENMM_DENSITYFORCEIMPL_H_
-#define OPENMM_DENSITYFORCEIMPL_H_
-
-/* -------------------------------------------------------------------------- *
- * OpenMM *
- * -------------------------------------------------------------------------- *
- * This is part of the OpenMM molecular simulation toolkit originating from *
- * Simbios, the NIH National Center for Physics-Based Simulation of *
- * Biological Structures at Stanford, funded under the NIH Roadmap for *
- * Medical Research, grant U54 GM072970. See https://simtk.org. *
- * *
- * Portions copyright (c) 2014 Stanford University and the Authors. *
- * Authors: Peter Eastman *
- * Contributors: *
- * *
- * Permission is hereby granted, free of charge, to any person obtaining a *
- * copy of this software and associated documentation files (the "Software"), *
- * to deal in the Software without restriction, including without limitation *
- * the rights to use, copy, modify, merge, publish, distribute, sublicense, *
- * and/or sell copies of the Software, and to permit persons to whom the *
- * Software is furnished to do so, subject to the following conditions: *
- * *
- * The above copyright notice and this permission notice shall be included in *
- * all copies or substantial portions of the Software. *
- * *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
- * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
- * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
- * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
- * USE OR OTHER DEALINGS IN THE SOFTWARE. *
- * -------------------------------------------------------------------------- */
-
-#include <ost/mol/mm/density_force.hh>
-#include <openmm/internal/ForceImpl.h>
-#include <openmm/Kernel.h>
-#include <utility>
-#include <set>
-#include <string>
-
-namespace ost{ namespace mol{ namespace mm{
-
-/**
- * This is the internal implementation of DensityForce.
- */
-
-class DensityForceImpl : public OpenMM::ForceImpl {
-public:
- DensityForceImpl(const DensityForce& owner);
- ~DensityForceImpl();
- void initialize(OpenMM::ContextImpl& context);
- const DensityForce& getOwner() const {
- return owner;
- }
- void updateContextState(OpenMM::ContextImpl& context) {
- // This force field doesn't update the state directly.
- }
- double calcForcesAndEnergy(OpenMM::ContextImpl& context, bool includeForces, bool includeEnergy, int groups);
- std::map<std::string, double> getDefaultParameters() {
- return std::map<std::string, double>(); // This force field doesn't define any parameters.
- }
- std::vector<std::string> getKernelNames();
-
- void updateParametersInContext(OpenMM::ContextImpl& context);
-private:
- const DensityForce& owner;
- OpenMM::Kernel kernel;
-};
-
-}}} //ns
-
-#endif /*OPENMM_DENSITYFORCEIMPL_H_*/
-
diff --git a/modules/mol/mm/src/openmm_plugins/density_plugin/openmmapi/density_kernels.hh b/modules/mol/mm/src/openmm_plugins/density_plugin/openmmapi/density_kernels.hh
deleted file mode 100644
index 78e16cfa795519c82252b7edce168329ea404e97..0000000000000000000000000000000000000000
--- a/modules/mol/mm/src/openmm_plugins/density_plugin/openmmapi/density_kernels.hh
+++ /dev/null
@@ -1,80 +0,0 @@
-#ifndef DENSITY_KERNELS_H_
-#define DENSITY_KERNELS_H_
-
-/* -------------------------------------------------------------------------- *
- * OpenMM *
- * -------------------------------------------------------------------------- *
- * This is part of the OpenMM molecular simulation toolkit originating from *
- * Simbios, the NIH National Center for Physics-Based Simulation of *
- * Biological Structures at Stanford, funded under the NIH Roadmap for *
- * Medical Research, grant U54 GM072970. See https://simtk.org. *
- * *
- * Portions copyright (c) 2014 Stanford University and the Authors. *
- * Authors: Peter Eastman *
- * Contributors: *
- * *
- * Permission is hereby granted, free of charge, to any person obtaining a *
- * copy of this software and associated documentation files (the "Software"), *
- * to deal in the Software without restriction, including without limitation *
- * the rights to use, copy, modify, merge, publish, distribute, sublicense, *
- * and/or sell copies of the Software, and to permit persons to whom the *
- * Software is furnished to do so, subject to the following conditions: *
- * *
- * The above copyright notice and this permission notice shall be included in *
- * all copies or substantial portions of the Software. *
- * *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
- * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
- * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
- * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
- * USE OR OTHER DEALINGS IN THE SOFTWARE. *
- * -------------------------------------------------------------------------- */
-
-#include <ost/mol/mm/density_force.hh>
-#include <openmm/KernelImpl.h>
-#include <openmm/Platform.h>
-#include <openmm/System.h>
-#include <string>
-
-namespace ost{ namespace mol{ namespace mm{
-
-/**
- * This kernel is invoked by DensityForce to calculate the forces acting on the system and the energy of the system.
- */
-class CalcDensityForceKernel : public OpenMM::KernelImpl {
-public:
- static std::string Name() {
- return "CalcDensityForce";
- }
- CalcDensityForceKernel(std::string name, const OpenMM::Platform& platform) : OpenMM::KernelImpl(name, platform) {
- }
- /**
- * Initialize the kernel.
- *
- * @param system the System this kernel will be applied to
- * @param force the DensityForce this kernel will be used for
- */
- virtual void initialize(const OpenMM::System& system, const DensityForce& force) = 0;
- /**
- * Execute the kernel to calculate the forces and/or energy.
- *
- * @param context the context in which to execute this kernel
- * @param includeForces true if forces should be calculated
- * @param includeEnergy true if the energy should be calculated
- * @return the potential energy due to the force
- */
- virtual double execute(OpenMM::ContextImpl& context, bool includeForces, bool includeEnergy) = 0;
- /**
- * Copy changed parameters over to a context.
- *
- * @param context the context to copy parameters to
- * @param force the DensityForce to copy the parameters from
- */
- virtual void copyParametersToContext(OpenMM::ContextImpl& context, const DensityForce& force) = 0;
-};
-
-}}} //ns
-
-#endif /*DENSITY_KERNELS_H_*/
diff --git a/modules/mol/mm/src/openmm_plugins/density_plugin/platforms/reference/reference_density_kernel_factory.cc b/modules/mol/mm/src/openmm_plugins/density_plugin/platforms/reference/reference_density_kernel_factory.cc
deleted file mode 100644
index 8df88868d90895b7b48b89e436799fd3bde97956..0000000000000000000000000000000000000000
--- a/modules/mol/mm/src/openmm_plugins/density_plugin/platforms/reference/reference_density_kernel_factory.cc
+++ /dev/null
@@ -1,62 +0,0 @@
-/* -------------------------------------------------------------------------- *
- * OpenMMExample *
- * -------------------------------------------------------------------------- *
- * This is part of the OpenMM molecular simulation toolkit originating from *
- * Simbios, the NIH National Center for Physics-Based Simulation of *
- * Biological Structures at Stanford, funded under the NIH Roadmap for *
- * Medical Research, grant U54 GM072970. See https://simtk.org. *
- * *
- * Portions copyright (c) 2014 Stanford University and the Authors. *
- * Authors: Peter Eastman *
- * Contributors: *
- * *
- * Permission is hereby granted, free of charge, to any person obtaining a *
- * copy of this software and associated documentation files (the "Software"), *
- * to deal in the Software without restriction, including without limitation *
- * the rights to use, copy, modify, merge, publish, distribute, sublicense, *
- * and/or sell copies of the Software, and to permit persons to whom the *
- * Software is furnished to do so, subject to the following conditions: *
- * *
- * The above copyright notice and this permission notice shall be included in *
- * all copies or substantial portions of the Software. *
- * *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
- * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
- * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
- * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
- * USE OR OTHER DEALINGS IN THE SOFTWARE. *
- * -------------------------------------------------------------------------- */
-
-#include <ost/mol/mm/reference_density_kernel_factory.hh>
-#include <ost/mol/mm/reference_density_kernels.hh>
-#include <openmm/reference/ReferencePlatform.h>
-#include <openmm/internal/ContextImpl.h>
-#include <openmm/OpenMMException.h>
-
-using namespace ost::mol::mm;
-
-extern "C" void registerPlatforms() {
-}
-
-extern "C" void registerKernelFactories() {
- for (int i = 0; i < OpenMM::Platform::getNumPlatforms(); i++) {
- OpenMM::Platform& platform = OpenMM::Platform::getPlatform(i);
- if (dynamic_cast<OpenMM::ReferencePlatform*>(&platform) != NULL) {
- ReferenceDensityKernelFactory* factory = new ReferenceDensityKernelFactory();
- platform.registerKernelFactory(CalcDensityForceKernel::Name(), factory);
- }
- }
-}
-
-extern "C" void registerDensityReferenceKernelFactories() {
- registerKernelFactories();
-}
-
-OpenMM::KernelImpl* ReferenceDensityKernelFactory::createKernelImpl(std::string name, const OpenMM::Platform& platform, OpenMM::ContextImpl& context) const {
- OpenMM::ReferencePlatform::PlatformData& data = *static_cast<OpenMM::ReferencePlatform::PlatformData*>(context.getPlatformData());
- if (name == CalcDensityForceKernel::Name())
- return new ReferenceCalcDensityForceKernel(name, platform);
- throw OpenMM::OpenMMException((std::string("Tried to create kernel with illegal kernel name '")+name+"'").c_str());
-}
diff --git a/modules/mol/mm/src/openmm_plugins/density_plugin/platforms/reference/reference_density_kernel_factory.hh b/modules/mol/mm/src/openmm_plugins/density_plugin/platforms/reference/reference_density_kernel_factory.hh
deleted file mode 100644
index 14dfdf44c23060f65f12c3939815b8bd27664608..0000000000000000000000000000000000000000
--- a/modules/mol/mm/src/openmm_plugins/density_plugin/platforms/reference/reference_density_kernel_factory.hh
+++ /dev/null
@@ -1,53 +0,0 @@
-#ifndef OPENMM_REFERENCEDensityKERNELFACTORY_H_
-#define OPENMM_REFERENCEDensityKERNELFACTORY_H_
-
-/* -------------------------------------------------------------------------- *
- * OpenMM *
- * -------------------------------------------------------------------------- *
- * This is part of the OpenMM molecular simulation toolkit originating from *
- * Simbios, the NIH National Center for Physics-Based Simulation of *
- * Biological Structures at Stanford, funded under the NIH Roadmap for *
- * Medical Research, grant U54 GM072970. See https://simtk.org. *
- * *
- * Portions copyright (c) 2014 Stanford University and the Authors. *
- * Authors: Peter Eastman *
- * Contributors: *
- * *
- * Permission is hereby granted, free of charge, to any person obtaining a *
- * copy of this software and associated documentation files (the "Software"), *
- * to deal in the Software without restriction, including without limitation *
- * the rights to use, copy, modify, merge, publish, distribute, sublicense, *
- * and/or sell copies of the Software, and to permit persons to whom the *
- * Software is furnished to do so, subject to the following conditions: *
- * *
- * The above copyright notice and this permission notice shall be included in *
- * all copies or substantial portions of the Software. *
- * *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
- * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
- * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
- * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
- * USE OR OTHER DEALINGS IN THE SOFTWARE. *
- * -------------------------------------------------------------------------- */
-
-#include <openmm/KernelFactory.h>
-
-/**
- * This KernelFactory creates kernels for the reference implementation of the Density plugin.
- */
-
-namespace ost{ namespace mol{ namespace mm{
-
-class ReferenceDensityKernelFactory : public OpenMM::KernelFactory {
-public:
- OpenMM::KernelImpl* createKernelImpl(std::string name,
- const OpenMM::Platform& platform,
- OpenMM::ContextImpl& context) const;
-};
-
-
-}}} //ns
-
-#endif /*OPENMM_REFERENCEDENSITYKERNELFACTORY_H_*/
diff --git a/modules/mol/mm/src/openmm_plugins/density_plugin/platforms/reference/reference_density_kernels.cc b/modules/mol/mm/src/openmm_plugins/density_plugin/platforms/reference/reference_density_kernels.cc
deleted file mode 100644
index 77edcd5524b5a5eb3df997727f36a25104a0876a..0000000000000000000000000000000000000000
--- a/modules/mol/mm/src/openmm_plugins/density_plugin/platforms/reference/reference_density_kernels.cc
+++ /dev/null
@@ -1,342 +0,0 @@
-/* -------------------------------------------------------------------------- *
- * OpenMM *
- * -------------------------------------------------------------------------- *
- * This is part of the OpenMM molecular simulation toolkit originating from *
- * Simbios, the NIH National Center for Physics-Based Simulation of *
- * Biological Structures at Stanford, funded under the NIH Roadmap for *
- * Medical Research, grant U54 GM072970. See https://simtk.org. *
- * *
- * Portions copyright (c) 2014 Stanford University and the Authors. *
- * Authors: Peter Eastman *
- * Contributors: *
- * *
- * Permission is hereby granted, free of charge, to any person obtaining a *
- * copy of this software and associated documentation files (the "Software"), *
- * to deal in the Software without restriction, including without limitation *
- * the rights to use, copy, modify, merge, publish, distribute, sublicense, *
- * and/or sell copies of the Software, and to permit persons to whom the *
- * Software is furnished to do so, subject to the following conditions: *
- * *
- * The above copyright notice and this permission notice shall be included in *
- * all copies or substantial portions of the Software. *
- * *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
- * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
- * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
- * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
- * USE OR OTHER DEALINGS IN THE SOFTWARE. *
- * -------------------------------------------------------------------------- */
-
-#include <ost/mol/mm/reference_density_kernels.hh>
-#include <ost/mol/mm/density_force.hh>
-#include <openmm/OpenMMException.h>
-#include <openmm/internal/ContextImpl.h>
-#include <openmm/reference/RealVec.h>
-#include <openmm/reference/ReferencePlatform.h>
-
-using namespace OpenMM;
-using namespace std;
-
-namespace{
-
-static vector<RealVec>& extractPositions(ContextImpl& context) {
- ReferencePlatform::PlatformData* data =
- reinterpret_cast<ReferencePlatform::PlatformData*>(context.getPlatformData());
- return *((vector<RealVec>*) data->positions);
-}
-
-static vector<RealVec>& extractForces(ContextImpl& context) {
- ReferencePlatform::PlatformData* data =
- reinterpret_cast<ReferencePlatform::PlatformData*>(context.getPlatformData());
- return *((vector<RealVec>*) data->forces);
-}
-
-} //anon ns
-
-
-namespace ost{ namespace mol { namespace mm{
-
-ReferenceCalcDensityForceKernel::~ReferenceCalcDensityForceKernel(){
- if(data_ != NULL) delete [] data_;
-}
-
-void ReferenceCalcDensityForceKernel::initialize(const System& system, const DensityForce& force) {
-
- if(system.getNumParticles() != force.getNumParticles()){
- std::string err = "DensityForce must contain same number of";
- err += " particles as system!";
- throw OpenMM::OpenMMException(err);
- }
-
- if(data_ != NULL) delete [] data_;
-
- ost::img::ImageHandle density = force.getDensity();
-
- x_sampling_ = density.GetSpatialSampling()[0] * 0.1;
- y_sampling_ = density.GetSpatialSampling()[1] * 0.1;
- z_sampling_ = density.GetSpatialSampling()[2] * 0.1;
- one_over_x_sampling_ = Real(1.0) / x_sampling_;
- one_over_y_sampling_ = Real(1.0) / y_sampling_;
- one_over_z_sampling_ = Real(1.0) / z_sampling_;
- half_x_sampling_ = Real(0.5) * x_sampling_;
- half_y_sampling_ = Real(0.5) * y_sampling_;
- half_z_sampling_ = Real(0.5) * z_sampling_;
- x_origin_ = density.GetAbsoluteOrigin()[0] * 0.1;
- y_origin_ = density.GetAbsoluteOrigin()[1] * 0.1;
- z_origin_ = density.GetAbsoluteOrigin()[2] * 0.1;
- x_extent_ = density.GetSize()[0];
- y_extent_ = density.GetSize()[1];
- z_extent_ = density.GetSize()[2];
-
- data_ = new Real[x_extent_ * y_extent_ * z_extent_];
- int current_idx = 0;
- for(int i = 0; i < x_extent_; ++i){
- for(int j = 0; j < y_extent_; ++j){
- for(int k = 0; k < z_extent_; ++k){
- data_[current_idx] = density.GetReal(ost::img::Point(i,j,k));
- ++current_idx;
- }
- }
- }
-
- idx_helper_one_ = y_extent_ * z_extent_;
- idx_helper_two_ = z_extent_;
-
- //sigma for gaussian like representations of the atoms
- resolution_ = force.getResolution() * 0.1;
- s_ = resolution_ * 0.425;
- one_s_ = Real(1.0) / s_;
- square_one_s_ = Real(1.0) / (s_ * s_);
- one_sqrt_2_pi_s_ = Real(1.0) / std::sqrt(Real(2.0) * Real(M_PI) * s_);
- padding_dist_ = s_ * Real(3.0);
- scaling_ = 10000 * force.getScaling();
-
- //let's get body and particle info...
-
- num_particles_ = system.getNumParticles();
- num_bodies_ = force.getNumBodies();
-
- particle_masses_.resize(num_particles_);
-
- for(int i = 0; i < num_particles_; ++i){
- particle_masses_[i] = force.getParticleMass(i);
- }
-
- bodies_.clear();
- //let's set every particle not belonging to a body to its own body
- for(int i = 0; i < num_particles_; ++i){
- if(force.isInBody(i)) continue;
- std::vector<int> body(1,i);
- bodies_.push_back(body);
- }
-
- //let's fill the defined bodies!
- for(int i = 0; i < num_bodies_; ++i){
- const std::vector<int>& current_body = force.getBody(i);
- bodies_.push_back(current_body);
- }
-
- //let's update the num_bodies_ !!!
- num_bodies_ = bodies_.size();
-}
-
-double ReferenceCalcDensityForceKernel::execute(ContextImpl& context,
- bool includeForces,
- bool includeEnergy) {
-
-
-
- vector<RealVec>& pos = extractPositions(context);
- vector<RealVec>& force = extractForces(context);
-
- //distance of a density position towards a particle
- Real x_d;
- Real y_d;
- Real z_d;
-
- //derivative of a full body
- Real body_dx;
- Real body_dy;
- Real body_dz;
-
- //return value for the full energy, will be updated when iterating over
- //all bodies
- Real overall_energy = 0.0;
-
- //some helper variables
- Real dd;
- Real e_term;
- Real density;
- Real p_density;
- std::vector<Real> p_dx;
- std::vector<Real> p_dy;
- std::vector<Real> p_dz;
- std::vector<Real> p_m;
- Real denominator;
- Real nominator;
- Real a, b;
- Real temp_one, temp_two;
- Real prefac;
- Real min_x_pos, max_x_pos;
- Real min_y_pos, max_y_pos;
- Real min_z_pos, max_z_pos;
- Real body_x_origin, body_y_origin, body_z_origin;
- int body_x_extent, body_y_extent, body_z_extent;
- int num_voxels;
-
- for(int body_idx = 0; body_idx < num_bodies_; ++body_idx){
-
- int body_size = bodies_[body_idx].size();
-
- //set derivatives for every particle in each direction to zero
- //and extract the required masses
- p_dx.assign(body_size,0.0);
- p_dy.assign(body_size,0.0);
- p_dz.assign(body_size,0.0);
- p_m.resize(body_size);
-
- for(int p_idx = 0; p_idx < body_size; ++p_idx){
- p_m[p_idx] = particle_masses_[bodies_[body_idx][p_idx]];
- }
-
- min_x_pos = std::numeric_limits<Real>::max();
- max_x_pos = -std::numeric_limits<Real>::max();
- min_y_pos = std::numeric_limits<Real>::max();
- max_y_pos = -std::numeric_limits<Real>::max();
- min_z_pos = std::numeric_limits<Real>::max();
- max_z_pos = -std::numeric_limits<Real>::max();
-
- //let's find out how big this thing is...
- for(int p_idx = 0; p_idx < body_size; ++p_idx){
- RealVec& p = pos[bodies_[body_idx][p_idx]];
- min_x_pos = (p[0] < min_x_pos) ? p[0]: min_x_pos;
- max_x_pos = (p[0] > max_x_pos) ? p[0]: max_x_pos;
- min_y_pos = (p[1] < min_y_pos) ? p[1]: min_y_pos;
- max_y_pos = (p[1] > max_y_pos) ? p[1]: max_y_pos;
- min_z_pos = (p[2] < min_z_pos) ? p[2]: min_z_pos;
- max_z_pos = (p[2] > max_z_pos) ? p[2]: max_z_pos;
- }
-
- //we add some padding
- min_x_pos -= padding_dist_;
- max_x_pos += padding_dist_;
- min_y_pos -= padding_dist_;
- max_y_pos += padding_dist_;
- min_z_pos -= padding_dist_;
- max_z_pos += padding_dist_;
-
- body_x_extent = std::max(3,
- static_cast<int>(std::ceil((max_x_pos - min_x_pos)*one_over_x_sampling_)));
- body_y_extent = std::max(3,
- static_cast<int>(std::ceil((max_y_pos - min_y_pos)*one_over_y_sampling_)));
- body_z_extent = std::max(3,
- static_cast<int>(std::ceil((max_z_pos - min_z_pos)*one_over_z_sampling_)));
- num_voxels = body_x_extent * body_y_extent * body_z_extent;
-
- Real overlap = min_x_pos + body_x_extent * x_sampling_ - max_x_pos;
- body_x_origin = min_x_pos - 0.5 * overlap;
- overlap = min_y_pos + body_y_extent * y_sampling_ - max_y_pos;
- body_y_origin = min_y_pos - 0.5 * overlap;
- overlap = min_z_pos + body_z_extent * z_sampling_ - max_z_pos;
- body_z_origin = min_z_pos - 0.5 * overlap;
-
-
- density_values_.resize(num_voxels);
- body_values_.assign(num_voxels,0.0);
-
- //let's fill the density values
- int current_idx = 0;
- for(int i = 0; i < body_x_extent; ++i){
- for(int j = 0; j < body_y_extent; ++j){
- for(int k = 0; k < body_z_extent; ++k){
- density_values_[current_idx] =
- this->GetIntpolValue(body_x_origin + i * x_sampling_ + half_x_sampling_,
- body_y_origin + j * y_sampling_ + half_y_sampling_,
- body_z_origin + k * z_sampling_ + half_z_sampling_);
- ++current_idx;
- }
- }
- }
-
- for(int p_idx = 0; p_idx < body_size; ++p_idx){
-
- //the actual position of the particle
- RealVec& p = pos[bodies_[body_idx][p_idx]];
- current_idx = 0;
-
- for(int i = 0; i < body_x_extent; ++i){
-
- x_d = p[0] - (body_x_origin + i * x_sampling_ + half_x_sampling_);
-
- for(int j = 0; j < body_y_extent; ++j){
-
- y_d = p[1] - (body_y_origin + j * y_sampling_ + half_y_sampling_);
-
- for(int k = 0; k < body_z_extent; ++k){
-
- z_d = p[2] - (body_z_origin + k * z_sampling_ + half_z_sampling_);
-
- dd = x_d * x_d + y_d * y_d + z_d * z_d;
-
- e_term = std::exp(Real(-0.5) * dd * square_one_s_);
- density = density_values_[current_idx];
- p_dx[p_idx] += (density * (x_d * one_s_) * e_term);
- p_dy[p_idx] += (density * (y_d * one_s_) * e_term);
- p_dz[p_idx] += (density * (z_d * one_s_) * e_term);
- p_density = p_m[p_idx] * one_sqrt_2_pi_s_ * e_term;
- body_values_[current_idx] += p_density;
- ++current_idx;
-
- }
- }
- }
- }
-
- nominator = 0.0;
- denominator = 0.0;
- temp_one = 0.0;
- temp_two = 0.0;
-
- for(int i = 0; i < num_voxels; ++i){
- a = density_values_[i];
- b = body_values_[i];
- nominator += (a * b);
- temp_one += (a * a);
- temp_two += (b * b);
- }
-
- if(temp_one == 0.0 || temp_two == 0.0) continue;
-
- denominator = std::sqrt(temp_one * temp_two);
- prefac = scaling_ / denominator * one_sqrt_2_pi_s_;
-
- body_dx = 0.0;
- body_dy = 0.0;
- body_dz = 0.0;
-
- for(int p_idx = 0; p_idx < body_size; ++p_idx){
- body_dx -= prefac * p_m[p_idx] * p_dx[p_idx];
- body_dy -= prefac * p_m[p_idx] * p_dy[p_idx];
- body_dz -= prefac * p_m[p_idx] * p_dz[p_idx];
- }
-
- //finally update the forces accordingly
- for(int p_idx = 0; p_idx < body_size; ++p_idx){
- force[bodies_[body_idx][p_idx]][0] += body_dx;
- force[bodies_[body_idx][p_idx]][1] += body_dy;
- force[bodies_[body_idx][p_idx]][2] += body_dz;
- }
-
- overall_energy -= (scaling_ * nominator/denominator);
- }
-
- return overall_energy;
-}
-
-void ReferenceCalcDensityForceKernel::copyParametersToContext(ContextImpl& context, const DensityForce& force) {
- //ToDo
-}
-
-}}} //ns
diff --git a/modules/mol/mm/src/openmm_plugins/density_plugin/platforms/reference/reference_density_kernels.hh b/modules/mol/mm/src/openmm_plugins/density_plugin/platforms/reference/reference_density_kernels.hh
deleted file mode 100644
index 7a06088ee572d7d91e606601d2fe9eb0b41725a2..0000000000000000000000000000000000000000
--- a/modules/mol/mm/src/openmm_plugins/density_plugin/platforms/reference/reference_density_kernels.hh
+++ /dev/null
@@ -1,164 +0,0 @@
-#ifndef REFERENCE_DENSITY_KERNELS_H_
-#define REFERENCE_DENSITY_KERNELS_H_
-
-/* -------------------------------------------------------------------------- *
- * OpenMM *
- * -------------------------------------------------------------------------- *
- * This is part of the OpenMM molecular simulation toolkit originating from *
- * Simbios, the NIH National Center for Physics-Based Simulation of *
- * Biological Structures at Stanford, funded under the NIH Roadmap for *
- * Medical Research, grant U54 GM072970. See https://simtk.org. *
- * *
- * Portions copyright (c) 2014 Stanford University and the Authors. *
- * Authors: Peter Eastman *
- * Contributors: *
- * *
- * Permission is hereby granted, free of charge, to any person obtaining a *
- * copy of this software and associated documentation files (the "Software"), *
- * to deal in the Software without restriction, including without limitation *
- * the rights to use, copy, modify, merge, publish, distribute, sublicense, *
- * and/or sell copies of the Software, and to permit persons to whom the *
- * Software is furnished to do so, subject to the following conditions: *
- * *
- * The above copyright notice and this permission notice shall be included in *
- * all copies or substantial portions of the Software. *
- * *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
- * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
- * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
- * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
- * USE OR OTHER DEALINGS IN THE SOFTWARE. *
- * -------------------------------------------------------------------------- */
-
-#include <ost/mol/mm/density_kernels.hh>
-#include <openmm/Platform.h>
-#include <vector>
-#include <set>
-#include <limits>
-
-namespace ost{ namespace mol{ namespace mm{
-
-/**
- * This kernel is invoked by DensityForce to calculate the forces acting on the system and the energy of the system.
- */
-class ReferenceCalcDensityForceKernel : public CalcDensityForceKernel {
-public:
- ReferenceCalcDensityForceKernel(std::string name, const OpenMM::Platform& platform) : CalcDensityForceKernel(name, platform), data_(NULL) {
- }
-
- ~ReferenceCalcDensityForceKernel();
-
- /**
- * Initialize the kernel.
- *
- * @param system the System this kernel will be applied to
- * @param force the DensityForce this kernel will be used for
- */
- void initialize(const OpenMM::System& system, const DensityForce& force);
- /**
- * Execute the kernel to calculate the forces and/or energy.
- *
- * @param context the context in which to execute this kernel
- * @param includeForces true if forces should be calculated
- * @param includeEnergy true if the energy should be calculated
- * @return the potential energy due to the force
- */
- double execute(OpenMM::ContextImpl& context, bool includeForces, bool includeEnergy);
- /**
- * Copy changed parameters over to a context.
- *
- * @param context the context to copy parameters to
- * @param force the DensityForce to copy the parameters from
- */
- void copyParametersToContext(OpenMM::ContextImpl& context, const DensityForce& force);
-private:
-
- inline Real GetValue(int a, int b, int c){
- return data_[a * idx_helper_one_ + b * idx_helper_two_ + c];
- }
-
- inline Real GetIntpolValue(Real x, Real y, Real z){
-
- //distances to origin
- Real dx = x - x_origin_;
- Real dy = y - y_origin_;
- Real dz = z - z_origin_;
-
- int x_bin = std::floor(dx * one_over_x_sampling_);
- int y_bin = std::floor(dy * one_over_y_sampling_);
- int z_bin = std::floor(dz * one_over_z_sampling_);
-
- if(x_bin < 0 || x_bin >= (x_extent_-1) ||
- y_bin < 0 || y_bin >= (y_extent_-1) ||
- z_bin < 0 || z_bin >= (z_extent_-1)) return 0.0;
-
- //distances in fraction of bin towards base bin
- dx = (dx - x_bin * x_sampling_) * one_over_x_sampling_;
- dy = (dy - y_bin * y_sampling_) * one_over_y_sampling_;
- dz = (dz - z_bin * z_sampling_) * one_over_z_sampling_;
-
- intpol_values_[0] = this->GetValue(x_bin,y_bin,z_bin);
- intpol_values_[1] = this->GetValue(x_bin+1,y_bin,z_bin);
- intpol_values_[2] = this->GetValue(x_bin,y_bin+1,z_bin);
- intpol_values_[3] = this->GetValue(x_bin+1,y_bin+1,z_bin);
- intpol_values_[4] = this->GetValue(x_bin,y_bin,z_bin+1);
- intpol_values_[5] = this->GetValue(x_bin+1,y_bin,z_bin+1);
- intpol_values_[6] = this->GetValue(x_bin,y_bin+1,z_bin+1);
- intpol_values_[7] = this->GetValue(x_bin+1,y_bin+1,z_bin+1);
-
- //do first bilinear interpolation
- Real f11 = (1.0 - dx) * intpol_values_[0] + dx * intpol_values_[1];
- Real f12 = (1.0 - dx) * intpol_values_[2] + dx * intpol_values_[3];
- Real f21 = (1.0 - dx) * intpol_values_[4] + dx * intpol_values_[5];
- Real f22 = (1.0 - dx) * intpol_values_[6] + dx * intpol_values_[7];
-
- Real f1 = (1.0 - dy) * f11 + dy * f12;
- Real f2 = (1.0 - dy) * f21 + dy * f22;
-
- return (1.0 - dz) * f1 + dz * f2;
- }
-
- //this stuff is required to store and extract the internal density values
- Real* data_;
- Real intpol_values_[8];
- int idx_helper_one_;
- int idx_helper_two_;
- Real x_sampling_;
- Real y_sampling_;
- Real z_sampling_;
- Real one_over_x_sampling_;
- Real one_over_y_sampling_;
- Real one_over_z_sampling_;
- Real half_x_sampling_;
- Real half_y_sampling_;
- Real half_z_sampling_;
- Real x_origin_;
- Real y_origin_;
- Real z_origin_;
- int x_extent_;
- int y_extent_;
- int z_extent_;
-
- //this is stuff used in the actual force calculation
- Real resolution_;
- Real s_;
- Real one_s_;
- Real square_one_s_;
- Real one_sqrt_2_pi_s_;
- Real padding_dist_;
- Real scaling_;
- std::vector<Real> density_values_;
- std::vector<Real> body_values_;
-
- //this is stuff containing information of the simulated system
- int num_bodies_;
- int num_particles_;
- std::vector<float> particle_masses_;
- std::vector<std::vector<int> > bodies_;
-};
-
-}}} // ns
-
-#endif /*REFERENCE_DENSITY_KERNELS_H_*/
diff --git a/modules/mol/mm/src/settings.hh.in b/modules/mol/mm/src/settings.hh.in
index d94e516424b97402367720221b2c1c3eaf7b3b55..d379447ff64f451ecb35a6032c02dff332619111 100644
--- a/modules/mol/mm/src/settings.hh.in
+++ b/modules/mol/mm/src/settings.hh.in
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/mm/src/simulation.cc b/modules/mol/mm/src/simulation.cc
index dea985213bf993a1a49f0ec06c17f7b34d4e36fe..5e7f179a02de3ed0069e483d68662b1f73cc0c52 100644
--- a/modules/mol/mm/src/simulation.cc
+++ b/modules/mol/mm/src/simulation.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/mm/src/simulation.hh b/modules/mol/mm/src/simulation.hh
index 7cbf06d1aededa101f55658b14f50f42d73dd6ca..c10487ae7bb66b7d31045876f2c58fa0e4607b72 100644
--- a/modules/mol/mm/src/simulation.hh
+++ b/modules/mol/mm/src/simulation.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/mm/src/state_extractor.cc b/modules/mol/mm/src/state_extractor.cc
index 478174f7f37cb9ac591094c5a0d0fab70807e34e..ae5e5a83fff61517b2556023806e6b2cea412ab6 100644
--- a/modules/mol/mm/src/state_extractor.cc
+++ b/modules/mol/mm/src/state_extractor.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/mm/src/state_extractor.hh b/modules/mol/mm/src/state_extractor.hh
index 38ecece645c0e343ce5812d3379ecbafa53a9290..3cb830344382a467b8c6e794049ab49633637c4f 100644
--- a/modules/mol/mm/src/state_extractor.hh
+++ b/modules/mol/mm/src/state_extractor.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/mm/src/steep.cc b/modules/mol/mm/src/steep.cc
index 94d987d2c7ee8d568f51cb3a469a614ab0bfae72..d32a23a2febf16b9910f9b84fa2708fb9b497b1b 100644
--- a/modules/mol/mm/src/steep.cc
+++ b/modules/mol/mm/src/steep.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/mm/src/steep.hh b/modules/mol/mm/src/steep.hh
index 1d58267104a74be5ddece2b2c8c03bafd285c254..1c1c7cd004495c683c022f5d0b3d8c9967e7325c 100644
--- a/modules/mol/mm/src/steep.hh
+++ b/modules/mol/mm/src/steep.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/mm/src/system_creator.cc b/modules/mol/mm/src/system_creator.cc
index aa365ee2926740ee5d99c853da708ebcfe254722..5f102933099791961ba98ed73e285586e0724a1d 100644
--- a/modules/mol/mm/src/system_creator.cc
+++ b/modules/mol/mm/src/system_creator.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
@@ -18,7 +18,6 @@
//------------------------------------------------------------------------------
#include <ost/mol/mm/system_creator.hh>
-#include <ost/mol/mm/density_force.hh>
#include <OpenMM.h>
namespace ost{ namespace mol{ namespace mm{
@@ -443,26 +442,6 @@ SystemPtr SystemCreator::Create(const TopologyPtr top,
sys->addForce(&barostat);
}
- //add density if valid
- ost::img::ImageHandle density = top->GetDensity();
- if(density.IsValid()){
- Real r = top->GetDensityResolution();
- Real s = top->GetDensityScaling();
- DensityForce* density_force_ptr = new DensityForce(density,r,s);
- for(std::vector<Real>::iterator i = masses.begin();
- i != masses.end(); ++i){
- density_force_ptr->addParticle(*i);
- }
- const std::vector<std::vector<int> >& density_bodies = top->GetDensityBodies();
- for(std::vector<std::vector<int> >::const_iterator i = density_bodies.begin();
- i != density_bodies.end(); ++i){
- density_force_ptr->defineBody(*i);
- }
- sys->addForce(density_force_ptr);
- }
-
-
-
return sys;
}
}}} //ns
diff --git a/modules/mol/mm/src/system_creator.hh b/modules/mol/mm/src/system_creator.hh
index 274c9453b3c56e8bb928749f36fdb6e767f53949..b0dc6d7480ac4889168436b6fff141e905a66ce2 100644
--- a/modules/mol/mm/src/system_creator.hh
+++ b/modules/mol/mm/src/system_creator.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/mm/src/topology.cc b/modules/mol/mm/src/topology.cc
index 58a72827d7d5f81dd3b8013a88223fafc352eb9c..836bf4a9f6457625ca9024464d275d659b9d07a7 100644
--- a/modules/mol/mm/src/topology.cc
+++ b/modules/mol/mm/src/topology.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
@@ -255,41 +255,6 @@ void Topology::AddPositionConstraint(uint index){
position_constraints_.push_back(index);
}
-void Topology::SetDensity(const ost::img::ImageHandle& d, Real r, Real s){
- density_ = d;
- density_resolution_ = r;
- density_scaling_ = s;
- in_density_body_.assign(num_particles_,false);
- density_bodies_.clear();
-}
-
-void Topology::DefineDensityBody(const std::vector<int>& indices){
-
- if(!density_.IsValid()){
- throw ost::Error("Must set valid density before you can define density bodies");
- }
-
- //first check, whether any of the indices is invalid or already part of a body
- for(std::vector<int>::const_iterator i = indices.begin();
- i != indices.end(); ++i){
- if(*i >= static_cast<int>(num_particles_) || *i < 0){
- throw ost::Error("Invalid index provided!");
- }
- if(in_density_body_[*i]){
- throw ost::Error("Particle can be part of only one body!");
- }
- }
-
- //let's change the state of the according particles
- for(std::vector<int>::const_iterator i = indices.begin();
- i != indices.end(); ++i){
- in_density_body_[*i] = true;
- }
-
- //and finally define the body
- density_bodies_.push_back(indices);
-}
-
uint Topology::AddHarmonicPositionRestraint(uint ind, const geom::Vec3& ref_position, Real k,
Real x_scale, Real y_scale, Real z_scale){
if(ind >= num_particles_){
diff --git a/modules/mol/mm/src/topology.hh b/modules/mol/mm/src/topology.hh
index 486accf1eb55c6ba1fe0db5fea040a445d6bb182..e7c8e70ecee8e3195b06241121cdb803feacaa18 100644
--- a/modules/mol/mm/src/topology.hh
+++ b/modules/mol/mm/src/topology.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
@@ -128,12 +128,6 @@ public:
void AddPositionConstraint(uint index);
- void SetDensity(const ost::img::ImageHandle& d, Real r, Real s = 1.0);
-
- void DefineDensityBody(const std::vector<int>& indices);
-
- int GetNumDensityBodies() const { return density_bodies_.size(); }
-
void ResetPositionConstraints() { position_constraints_.clear(); }
void ResetExclusions() { exclusions_.clear(); }
@@ -219,12 +213,6 @@ public:
void GetFGMDHBondAcceptorParameters(uint index, uint& index_one, uint& index_two) const;
- ost::img::ImageHandle GetDensity() { return density_; }
-
- Real GetDensityResolution() { return density_resolution_; }
-
- Real GetDensityScaling() { return density_scaling_; }
-
void SetHarmonicBondParameters(uint index, const Real bond_length, const Real force_constant);
void SetHarmonicAngleParameters(uint index, const Real angle, const Real force_constant);
@@ -285,8 +273,6 @@ public:
const std::vector<Index<2> >& GetFGMDHBondAcceptors() const { return fgmd_hbond_acceptors_; }
- const std::vector<std::vector<int> >& GetDensityBodies() const { return density_bodies_; }
-
std::vector<Real> GetSigmas() const { return sigmas_; }
@@ -811,13 +797,6 @@ private:
std::set<Index<2> > added_lj_pairs_;
std::set<Index<2> > added_distance_constraints_;
std::set<Index<2> > added_exclusions_;
-
- //density map
- ost::img::ImageHandle density_;
- Real density_resolution_;
- Real density_scaling_;
- std::vector<std::vector<int> > density_bodies_;
- std::vector<bool> in_density_body_;
};
diff --git a/modules/mol/mm/src/topology_creator.cc b/modules/mol/mm/src/topology_creator.cc
index 453bf132f39c5797884199ddd46217b3ce7b3d43..c80ec9da466d22ada1bbfc4f55b05f78a22ce8d7 100644
--- a/modules/mol/mm/src/topology_creator.cc
+++ b/modules/mol/mm/src/topology_creator.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/mm/src/topology_creator.hh b/modules/mol/mm/src/topology_creator.hh
index 026abdc5cd4ba660c1f63848bf49b39157f0f2d7..04be4684a4566081176163def2c1c45668e3a8ff 100644
--- a/modules/mol/mm/src/topology_creator.hh
+++ b/modules/mol/mm/src/topology_creator.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/mm/tests/test_block.cc b/modules/mol/mm/tests/test_block.cc
index 93826f8256a738256f22fe8192f0728f5bbbd983..b0f0613a61ff0576a62d6d8f0ac451905c35f509 100644
--- a/modules/mol/mm/tests/test_block.cc
+++ b/modules/mol/mm/tests/test_block.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/mm/tests/test_block_modifiers.cc b/modules/mol/mm/tests/test_block_modifiers.cc
index 46b9c03c645cd7824187148ea871c593d36bfc7f..493e1842baf23edaeceaa93c6e3a794909535e99 100644
--- a/modules/mol/mm/tests/test_block_modifiers.cc
+++ b/modules/mol/mm/tests/test_block_modifiers.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/mm/tests/test_forcefield.cc b/modules/mol/mm/tests/test_forcefield.cc
index 45b658a1df29b4f81bffb788323ce2c17a5ccd9c..89bc16b03be9c349138770d465f833ce27f8cd76 100644
--- a/modules/mol/mm/tests/test_forcefield.cc
+++ b/modules/mol/mm/tests/test_forcefield.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/mm/tests/test_interaction.cc b/modules/mol/mm/tests/test_interaction.cc
index 5c198079039c4bece741c5c45026c3703866d77c..6223cfe7dbfbb5e3d26f416fb3a55309bc0aa0e0 100644
--- a/modules/mol/mm/tests/test_interaction.cc
+++ b/modules/mol/mm/tests/test_interaction.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/mm/tests/test_simulation.cc b/modules/mol/mm/tests/test_simulation.cc
index 4836f2f2a76f878ec4502d3bc6cebd3a2ffef103..ba9c282d6ebc45240a8a57e1d4952e0de713505e 100644
--- a/modules/mol/mm/tests/test_simulation.cc
+++ b/modules/mol/mm/tests/test_simulation.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/mm/tests/test_topology.cc b/modules/mol/mm/tests/test_topology.cc
index e74b79a4b194febe06c24519ed5d61bc77c562a8..e7d56a66befccb23115449e7747ddfb665977fc0 100644
--- a/modules/mol/mm/tests/test_topology.cc
+++ b/modules/mol/mm/tests/test_topology.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/mol/mm/tests/tests.cc b/modules/mol/mm/tests/tests.cc
index 973da7b137ef0990ea16d0b634201b24bf44a4ab..95e3ae428b1f67db1e1f318f9398b76e11a04c0e 100644
--- a/modules/mol/mm/tests/tests.cc
+++ b/modules/mol/mm/tests/tests.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/alg/doc/seqalg.rst b/modules/seq/alg/doc/seqalg.rst
index 265892530eb97227216348523af3a1830c656c7e..5e5b5a7c864906d37c202768746d4c38f41b6c32 100644
--- a/modules/seq/alg/doc/seqalg.rst
+++ b/modules/seq/alg/doc/seqalg.rst
@@ -60,14 +60,14 @@ Algorithms for Alignments
aln_a = seq.CreateAlignment()
aln_a.AddSequence(seq_a1)
aln_a.AddSequence(seq_a2)
- print aln_a
+ print(aln_a)
# >>> A1 acdefghikl-mn
# >>> A2 atd-fghikllmn
aln_b = seq.CreateAlignment()
aln_b.AddSequence(seq_b1)
aln_b.AddSequence(seq_b2)
- print aln_b
+ print(aln_b)
# >>> B1 acdefg-hiklmn
# >>> B2 acd---qhirlmn
@@ -76,7 +76,7 @@ Algorithms for Alignments
aln_list.append(aln_b)
merged_aln = ost.seq.alg.MergePairwiseAlignments(aln_list, ref_seq)
- print merged_aln
+ print(merged_aln)
# >>> ref acdefg-hikl-mn
# >>> A2 atd-fg-hikllmn
# >>> B2 acd---qhirl-mn
@@ -121,7 +121,7 @@ Algorithms for Alignments
seq_a = seq.CreateSequence('A', 'acdefghiklmn')
seq_b = seq.CreateSequence('B', 'acdhiklmn')
alns = seq.alg.LocalAlign(seq_a, seq_b, seq.alg.BLOSUM62)
- print alns[0].ToString(80)
+ print(alns[0].ToString(80))
# >>> A acdefghiklmn
# >>> B acd---hiklmn
@@ -150,7 +150,7 @@ Algorithms for Alignments
seq_a = seq.CreateSequence('A', 'acdefghiklmn')
seq_b = seq.CreateSequence('B', 'acdhiklmn')
alns = seq.alg.GlobalAlign(seq_a, seq_b, seq.alg.BLOSUM62)
- print alns[0].ToString(80)
+ print(alns[0].ToString(80))
# >>> A acdefghiklmn
# >>> B acd---hiklmn
@@ -193,11 +193,11 @@ Algorithms for Alignments
seq_a = seq.CreateSequence('A', 'abcdefghijklmnok')
seq_b = seq.CreateSequence('B', 'cdehijk')
alns = seq.alg.GlobalAlign(seq_a, seq_b, seq.alg.BLOSUM62)
- print alns[0].ToString(80)
+ print(alns[0].ToString(80))
# >>> A abcdefghijklmnok
# >>> B --cde--hi-----jk
alns = seq.alg.SemiGlobalAlign(seq_a, seq_b, seq.alg.BLOSUM62)
- print alns[0].ToString(80)
+ print(alns[0].ToString(80))
# >>> A abcdefghijklmnok
# >>> B --cde--hijk-----
@@ -370,7 +370,7 @@ differences between the structures.
dist_to_mean = seq.alg.CreateDist2Mean(d_map)
# report min. and max. variances
- print "MIN-MAX:", var_map.Min(), "-", var_map.Max()
+ print("MIN-MAX:", var_map.Min(), "-", var_map.Max())
# get data and json-strings for further processing
var_map_data = var_map.GetData()
var_map_json = var_map.GetJsonString()
diff --git a/modules/seq/alg/pymod/__init__.py b/modules/seq/alg/pymod/__init__.py
index 27582d340c88a966e9d737b11b6af863c3f42e24..2e9c5fcffca4375afb80a13cea941658f62c508a 100644
--- a/modules/seq/alg/pymod/__init__.py
+++ b/modules/seq/alg/pymod/__init__.py
@@ -1,4 +1,4 @@
-from _ost_seq_alg import *
+from ._ost_seq_alg import *
from ost.seq.alg.mat import *
def ValidateSEQRESAlignment(aln, chain=None):
@@ -190,7 +190,7 @@ def PredictContacts(ali):
import math
from ost import seq
if not type(ali)==type(seq.AlignmentHandle()):
- print "Parameter should be an AlignmentHandle"
+ print("Parameter should be an AlignmentHandle")
return
mi=CalculateMutualInformation(ali)
CoEvoSc=CalculateContactSubstitutionScore(ali)
diff --git a/modules/seq/alg/pymod/wrap_seq_alg.cc b/modules/seq/alg/pymod/wrap_seq_alg.cc
index 30909790c3c9b61944523e4f966d42d1ffb0a40d..9df107976a60ce166bfebdb1fc5dc1943be9d6ba 100644
--- a/modules/seq/alg/pymod/wrap_seq_alg.cc
+++ b/modules/seq/alg/pymod/wrap_seq_alg.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2016 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/alg/src/alignment_opts.hh b/modules/seq/alg/src/alignment_opts.hh
index 38aaa11547b9e61a92f839256ef784c1373efdb8..84687af405a404959dbaf3ad60c2964ab0700dfb 100644
--- a/modules/seq/alg/src/alignment_opts.hh
+++ b/modules/seq/alg/src/alignment_opts.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/alg/src/clip_alignment.cc b/modules/seq/alg/src/clip_alignment.cc
index 02ff9c14b572ff46f0386ae57ce9adb3f81a2d9a..18b31c1a863737deae17d719fe5d39a863686b82 100644
--- a/modules/seq/alg/src/clip_alignment.cc
+++ b/modules/seq/alg/src/clip_alignment.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2016 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/alg/src/clip_alignment.hh b/modules/seq/alg/src/clip_alignment.hh
index 7af6abf5bd04bd2f33f9721b9e1edf9b0e81e272..d5f568476698a234d007a52ba1611d227ab12972 100644
--- a/modules/seq/alg/src/clip_alignment.hh
+++ b/modules/seq/alg/src/clip_alignment.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2016 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/alg/src/conservation.cc b/modules/seq/alg/src/conservation.cc
index e80077efd254deead27d156cd556d0da2f90721f..30253a37bf9e59ee038bb78f48f2dfa409d8adbd 100644
--- a/modules/seq/alg/src/conservation.cc
+++ b/modules/seq/alg/src/conservation.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/alg/src/conservation.hh b/modules/seq/alg/src/conservation.hh
index 651b5bdd150348ef812bf839e37e458e2fc2eb86..b9d7a267374a4dee9b39371e334b00674e4bbb72 100644
--- a/modules/seq/alg/src/conservation.hh
+++ b/modules/seq/alg/src/conservation.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/alg/src/contact_prediction_score.cc b/modules/seq/alg/src/contact_prediction_score.cc
index c01653c2f08179e85aaec0fa039dd5933e32937d..892aecd5c44a0ea2f7c3e4f7f6c8b6455da3f5cc 100644
--- a/modules/seq/alg/src/contact_prediction_score.cc
+++ b/modules/seq/alg/src/contact_prediction_score.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/alg/src/contact_prediction_score.hh b/modules/seq/alg/src/contact_prediction_score.hh
index c88001e1dd250a1c04c67f8d6f4aebb6308b74ce..a22eecaa7890ebb12aca20b058b736f290e10f9d 100644
--- a/modules/seq/alg/src/contact_prediction_score.hh
+++ b/modules/seq/alg/src/contact_prediction_score.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/alg/src/contact_weight_matrix.cc b/modules/seq/alg/src/contact_weight_matrix.cc
index fd1701827a126575ff11d63ce2460969147dd20f..fa1c9a1b85ac940d892a1993b42b36abce682db4 100644
--- a/modules/seq/alg/src/contact_weight_matrix.cc
+++ b/modules/seq/alg/src/contact_weight_matrix.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/alg/src/contact_weight_matrix.hh b/modules/seq/alg/src/contact_weight_matrix.hh
index 7039690b7aee677c698bc6c9325fe9e6c22a6e03..19822d9d7bf48627c718b2b689137090c9c3772d 100644
--- a/modules/seq/alg/src/contact_weight_matrix.hh
+++ b/modules/seq/alg/src/contact_weight_matrix.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/alg/src/data/BLOSUM100 b/modules/seq/alg/src/data/BLOSUM100
new file mode 100644
index 0000000000000000000000000000000000000000..46e9e851608adcec2ccd8906f5c10b8555714959
--- /dev/null
+++ b/modules/seq/alg/src/data/BLOSUM100
@@ -0,0 +1,31 @@
+# Matrix made by matblas from blosum100_3.iij
+# * column uses minimum score
+# BLOSUM Clustered Scoring Matrix in 1/3 Bit Units
+# Blocks Database = /data/blocks_5.0/blocks.dat
+# Cluster Percentage: >= 100
+# Entropy = 1.4516, Expected = -1.0948
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 8 -3 -4 -5 -2 -2 -3 -1 -4 -4 -4 -2 -3 -5 -2 1 -1 -6 -5 -2 -4 -2 -2 -10
+R -3 10 -2 -5 -8 0 -2 -6 -1 -7 -6 3 -4 -6 -5 -3 -3 -7 -5 -6 -4 -1 -3 -10
+N -4 -2 11 1 -5 -1 -2 -2 0 -7 -7 -1 -5 -7 -5 0 -1 -8 -5 -7 5 -2 -3 -10
+D -5 -5 1 10 -8 -2 2 -4 -3 -8 -8 -3 -8 -8 -5 -2 -4 -10 -7 -8 6 0 -4 -10
+C -2 -8 -5 -8 14 -7 -9 -7 -8 -3 -5 -8 -4 -4 -8 -3 -3 -7 -6 -3 -7 -8 -5 -10
+Q -2 0 -1 -2 -7 11 2 -5 1 -6 -5 2 -2 -6 -4 -2 -3 -5 -4 -5 -2 5 -2 -10
+E -3 -2 -2 2 -9 2 10 -6 -2 -7 -7 0 -5 -8 -4 -2 -3 -8 -7 -5 0 7 -3 -10
+G -1 -6 -2 -4 -7 -5 -6 9 -6 -9 -8 -5 -7 -8 -6 -2 -5 -7 -8 -8 -3 -5 -4 -10
+H -4 -1 0 -3 -8 1 -2 -6 13 -7 -6 -3 -5 -4 -5 -3 -4 -5 1 -7 -2 -1 -4 -10
+I -4 -7 -7 -8 -3 -6 -7 -9 -7 8 2 -6 1 -2 -7 -5 -3 -6 -4 4 -8 -7 -3 -10
+L -4 -6 -7 -8 -5 -5 -7 -8 -6 2 8 -6 3 0 -7 -6 -4 -5 -4 0 -8 -6 -3 -10
+K -2 3 -1 -3 -8 2 0 -5 -3 -6 -6 10 -4 -6 -3 -2 -3 -8 -5 -5 -2 0 -3 -10
+M -3 -4 -5 -8 -4 -2 -5 -7 -5 1 3 -4 12 -1 -5 -4 -2 -4 -5 0 -7 -4 -3 -10
+F -5 -6 -7 -8 -4 -6 -8 -8 -4 -2 0 -6 -1 11 -7 -5 -5 0 4 -3 -7 -7 -4 -10
+P -2 -5 -5 -5 -8 -4 -4 -6 -5 -7 -7 -3 -5 -7 12 -3 -4 -8 -7 -6 -5 -4 -4 -10
+S 1 -3 0 -2 -3 -2 -2 -2 -3 -5 -6 -2 -4 -5 -3 9 2 -7 -5 -4 -1 -2 -2 -10
+T -1 -3 -1 -4 -3 -3 -3 -5 -4 -3 -4 -3 -2 -5 -4 2 9 -7 -5 -1 -2 -3 -2 -10
+W -6 -7 -8 -10 -7 -5 -8 -7 -5 -6 -5 -8 -4 0 -8 -7 -7 17 2 -5 -9 -7 -6 -10
+Y -5 -5 -5 -7 -6 -4 -7 -8 1 -4 -4 -5 -5 4 -7 -5 -5 2 12 -5 -6 -6 -4 -10
+V -2 -6 -7 -8 -3 -5 -5 -8 -7 4 0 -5 0 -3 -6 -4 -1 -5 -5 8 -7 -5 -3 -10
+B -4 -4 5 6 -7 -2 0 -3 -2 -8 -8 -2 -7 -7 -5 -1 -2 -9 -6 -7 6 0 -4 -10
+Z -2 -1 -2 0 -8 5 7 -5 -1 -7 -6 0 -4 -7 -4 -2 -3 -7 -6 -5 0 6 -2 -10
+X -2 -3 -3 -4 -5 -2 -3 -4 -4 -3 -3 -3 -3 -4 -4 -2 -2 -6 -4 -3 -4 -2 -3 -10
+* -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 1
diff --git a/modules/seq/alg/src/data/BLOSUM45 b/modules/seq/alg/src/data/BLOSUM45
new file mode 100644
index 0000000000000000000000000000000000000000..18c3323896f4f802558e6eda688f467a582a3d5e
--- /dev/null
+++ b/modules/seq/alg/src/data/BLOSUM45
@@ -0,0 +1,31 @@
+# Matrix made by matblas from blosum45.iij
+# * column uses minimum score
+# BLOSUM Clustered Scoring Matrix in 1/3 Bit Units
+# Blocks Database = /data/blocks_5.0/blocks.dat
+# Cluster Percentage: >= 45
+# Entropy = 0.3795, Expected = -0.2789
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 5 -2 -1 -2 -1 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -2 -2 0 -1 -1 0 -5
+R -2 7 0 -1 -3 1 0 -2 0 -3 -2 3 -1 -2 -2 -1 -1 -2 -1 -2 -1 0 -1 -5
+N -1 0 6 2 -2 0 0 0 1 -2 -3 0 -2 -2 -2 1 0 -4 -2 -3 4 0 -1 -5
+D -2 -1 2 7 -3 0 2 -1 0 -4 -3 0 -3 -4 -1 0 -1 -4 -2 -3 5 1 -1 -5
+C -1 -3 -2 -3 12 -3 -3 -3 -3 -3 -2 -3 -2 -2 -4 -1 -1 -5 -3 -1 -2 -3 -2 -5
+Q -1 1 0 0 -3 6 2 -2 1 -2 -2 1 0 -4 -1 0 -1 -2 -1 -3 0 4 -1 -5
+E -1 0 0 2 -3 2 6 -2 0 -3 -2 1 -2 -3 0 0 -1 -3 -2 -3 1 4 -1 -5
+G 0 -2 0 -1 -3 -2 -2 7 -2 -4 -3 -2 -2 -3 -2 0 -2 -2 -3 -3 -1 -2 -1 -5
+H -2 0 1 0 -3 1 0 -2 10 -3 -2 -1 0 -2 -2 -1 -2 -3 2 -3 0 0 -1 -5
+I -1 -3 -2 -4 -3 -2 -3 -4 -3 5 2 -3 2 0 -2 -2 -1 -2 0 3 -3 -3 -1 -5
+L -1 -2 -3 -3 -2 -2 -2 -3 -2 2 5 -3 2 1 -3 -3 -1 -2 0 1 -3 -2 -1 -5
+K -1 3 0 0 -3 1 1 -2 -1 -3 -3 5 -1 -3 -1 -1 -1 -2 -1 -2 0 1 -1 -5
+M -1 -1 -2 -3 -2 0 -2 -2 0 2 2 -1 6 0 -2 -2 -1 -2 0 1 -2 -1 -1 -5
+F -2 -2 -2 -4 -2 -4 -3 -3 -2 0 1 -3 0 8 -3 -2 -1 1 3 0 -3 -3 -1 -5
+P -1 -2 -2 -1 -4 -1 0 -2 -2 -2 -3 -1 -2 -3 9 -1 -1 -3 -3 -3 -2 -1 -1 -5
+S 1 -1 1 0 -1 0 0 0 -1 -2 -3 -1 -2 -2 -1 4 2 -4 -2 -1 0 0 0 -5
+T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -1 -1 2 5 -3 -1 0 0 -1 0 -5
+W -2 -2 -4 -4 -5 -2 -3 -2 -3 -2 -2 -2 -2 1 -3 -4 -3 15 3 -3 -4 -2 -2 -5
+Y -2 -1 -2 -2 -3 -1 -2 -3 2 0 0 -1 0 3 -3 -2 -1 3 8 -1 -2 -2 -1 -5
+V 0 -2 -3 -3 -1 -3 -3 -3 -3 3 1 -2 1 0 -3 -1 0 -3 -1 5 -3 -3 -1 -5
+B -1 -1 4 5 -2 0 1 -1 0 -3 -3 0 -2 -3 -2 0 0 -4 -2 -3 4 2 -1 -5
+Z -1 0 0 1 -3 4 4 -2 0 -3 -2 1 -1 -3 -1 0 -1 -2 -2 -3 2 4 -1 -5
+X 0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 0 0 -2 -1 -1 -1 -1 -1 -5
+* -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1
diff --git a/modules/seq/alg/src/data/BLOSUM62 b/modules/seq/alg/src/data/BLOSUM62
new file mode 100644
index 0000000000000000000000000000000000000000..205f139aa2f8c879f6426708fe316be8bf55f771
--- /dev/null
+++ b/modules/seq/alg/src/data/BLOSUM62
@@ -0,0 +1,31 @@
+# Matrix made by matblas from blosum62.iij
+# * column uses minimum score
+# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units
+# Blocks Database = /data/blocks_5.0/blocks.dat
+# Cluster Percentage: >= 62
+# Entropy = 0.6979, Expected = -0.5209
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 4 -1 -2 -2 0 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -3 -2 0 -2 -1 0 -4
+R -1 5 0 -2 -3 1 0 -2 0 -3 -2 2 -1 -3 -2 -1 -1 -3 -2 -3 -1 0 -1 -4
+N -2 0 6 1 -3 0 0 0 1 -3 -3 0 -2 -3 -2 1 0 -4 -2 -3 3 0 -1 -4
+D -2 -2 1 6 -3 0 2 -1 -1 -3 -4 -1 -3 -3 -1 0 -1 -4 -3 -3 4 1 -1 -4
+C 0 -3 -3 -3 9 -3 -4 -3 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1 -3 -3 -2 -4
+Q -1 1 0 0 -3 5 2 -2 0 -3 -2 1 0 -3 -1 0 -1 -2 -1 -2 0 3 -1 -4
+E -1 0 0 2 -4 2 5 -2 0 -3 -3 1 -2 -3 -1 0 -1 -3 -2 -2 1 4 -1 -4
+G 0 -2 0 -1 -3 -2 -2 6 -2 -4 -4 -2 -3 -3 -2 0 -2 -2 -3 -3 -1 -2 -1 -4
+H -2 0 1 -1 -3 0 0 -2 8 -3 -3 -1 -2 -1 -2 -1 -2 -2 2 -3 0 0 -1 -4
+I -1 -3 -3 -3 -1 -3 -3 -4 -3 4 2 -3 1 0 -3 -2 -1 -3 -1 3 -3 -3 -1 -4
+L -1 -2 -3 -4 -1 -2 -3 -4 -3 2 4 -2 2 0 -3 -2 -1 -2 -1 1 -4 -3 -1 -4
+K -1 2 0 -1 -3 1 1 -2 -1 -3 -2 5 -1 -3 -1 0 -1 -3 -2 -2 0 1 -1 -4
+M -1 -1 -2 -3 -1 0 -2 -3 -2 1 2 -1 5 0 -2 -1 -1 -1 -1 1 -3 -1 -1 -4
+F -2 -3 -3 -3 -2 -3 -3 -3 -1 0 0 -3 0 6 -4 -2 -2 1 3 -1 -3 -3 -1 -4
+P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4 7 -1 -1 -4 -3 -2 -2 -1 -2 -4
+S 1 -1 1 0 -1 0 0 0 -1 -2 -2 0 -1 -2 -1 4 1 -3 -2 -2 0 0 0 -4
+T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 1 5 -2 -2 0 -1 -1 0 -4
+W -3 -3 -4 -4 -2 -2 -3 -2 -2 -3 -2 -3 -1 1 -4 -3 -2 11 2 -3 -4 -3 -2 -4
+Y -2 -2 -2 -3 -2 -1 -2 -3 2 -1 -1 -2 -1 3 -3 -2 -2 2 7 -1 -3 -2 -1 -4
+V 0 -3 -3 -3 -1 -2 -2 -3 -3 3 1 -2 1 -1 -2 -2 0 -3 -1 4 -3 -2 -1 -4
+B -2 -1 3 4 -3 0 1 -1 0 -3 -4 0 -3 -3 -2 0 -1 -4 -3 -3 4 1 -1 -4
+Z -1 0 0 1 -3 3 4 -2 0 -3 -3 1 -1 -3 -1 0 -1 -3 -2 -2 1 4 -1 -4
+X 0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2 0 0 -2 -1 -1 -1 -1 -1 -4
+* -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 1
diff --git a/modules/seq/alg/src/data/BLOSUM80 b/modules/seq/alg/src/data/BLOSUM80
new file mode 100644
index 0000000000000000000000000000000000000000..78172a3592b5322c5e9429e2e4661dc5c374d9eb
--- /dev/null
+++ b/modules/seq/alg/src/data/BLOSUM80
@@ -0,0 +1,31 @@
+# Matrix made by matblas from blosum80_3.iij
+# * column uses minimum score
+# BLOSUM Clustered Scoring Matrix in 1/3 Bit Units
+# Blocks Database = /data/blocks_5.0/blocks.dat
+# Cluster Percentage: >= 80
+# Entropy = 0.9868, Expected = -0.7442
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 7 -3 -3 -3 -1 -2 -2 0 -3 -3 -3 -1 -2 -4 -1 2 0 -5 -4 -1 -3 -2 -1 -8
+R -3 9 -1 -3 -6 1 -1 -4 0 -5 -4 3 -3 -5 -3 -2 -2 -5 -4 -4 -2 0 -2 -8
+N -3 -1 9 2 -5 0 -1 -1 1 -6 -6 0 -4 -6 -4 1 0 -7 -4 -5 5 -1 -2 -8
+D -3 -3 2 10 -7 -1 2 -3 -2 -7 -7 -2 -6 -6 -3 -1 -2 -8 -6 -6 6 1 -3 -8
+C -1 -6 -5 -7 13 -5 -7 -6 -7 -2 -3 -6 -3 -4 -6 -2 -2 -5 -5 -2 -6 -7 -4 -8
+Q -2 1 0 -1 -5 9 3 -4 1 -5 -4 2 -1 -5 -3 -1 -1 -4 -3 -4 -1 5 -2 -8
+E -2 -1 -1 2 -7 3 8 -4 0 -6 -6 1 -4 -6 -2 -1 -2 -6 -5 -4 1 6 -2 -8
+G 0 -4 -1 -3 -6 -4 -4 9 -4 -7 -7 -3 -5 -6 -5 -1 -3 -6 -6 -6 -2 -4 -3 -8
+H -3 0 1 -2 -7 1 0 -4 12 -6 -5 -1 -4 -2 -4 -2 -3 -4 3 -5 -1 0 -2 -8
+I -3 -5 -6 -7 -2 -5 -6 -7 -6 7 2 -5 2 -1 -5 -4 -2 -5 -3 4 -6 -6 -2 -8
+L -3 -4 -6 -7 -3 -4 -6 -7 -5 2 6 -4 3 0 -5 -4 -3 -4 -2 1 -7 -5 -2 -8
+K -1 3 0 -2 -6 2 1 -3 -1 -5 -4 8 -3 -5 -2 -1 -1 -6 -4 -4 -1 1 -2 -8
+M -2 -3 -4 -6 -3 -1 -4 -5 -4 2 3 -3 9 0 -4 -3 -1 -3 -3 1 -5 -3 -2 -8
+F -4 -5 -6 -6 -4 -5 -6 -6 -2 -1 0 -5 0 10 -6 -4 -4 0 4 -2 -6 -6 -3 -8
+P -1 -3 -4 -3 -6 -3 -2 -5 -4 -5 -5 -2 -4 -6 12 -2 -3 -7 -6 -4 -4 -2 -3 -8
+S 2 -2 1 -1 -2 -1 -1 -1 -2 -4 -4 -1 -3 -4 -2 7 2 -6 -3 -3 0 -1 -1 -8
+T 0 -2 0 -2 -2 -1 -2 -3 -3 -2 -3 -1 -1 -4 -3 2 8 -5 -3 0 -1 -2 -1 -8
+W -5 -5 -7 -8 -5 -4 -6 -6 -4 -5 -4 -6 -3 0 -7 -6 -5 16 3 -5 -8 -5 -5 -8
+Y -4 -4 -4 -6 -5 -3 -5 -6 3 -3 -2 -4 -3 4 -6 -3 -3 3 11 -3 -5 -4 -3 -8
+V -1 -4 -5 -6 -2 -4 -4 -6 -5 4 1 -4 1 -2 -4 -3 0 -5 -3 7 -6 -4 -2 -8
+B -3 -2 5 6 -6 -1 1 -2 -1 -6 -7 -1 -5 -6 -4 0 -1 -8 -5 -6 6 0 -3 -8
+Z -2 0 -1 1 -7 5 6 -4 0 -6 -5 1 -3 -6 -2 -1 -2 -5 -4 -4 0 6 -1 -8
+X -1 -2 -2 -3 -4 -2 -2 -3 -2 -2 -2 -2 -2 -3 -3 -1 -1 -5 -3 -2 -3 -1 -2 -8
+* -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1
diff --git a/modules/seq/alg/src/data/generate_blosum_data.py b/modules/seq/alg/src/data/generate_blosum_data.py
new file mode 100644
index 0000000000000000000000000000000000000000..cb0dc1f607826ee223dd63b9b02d914dc9c317ff
--- /dev/null
+++ b/modules/seq/alg/src/data/generate_blosum_data.py
@@ -0,0 +1,47 @@
+# code generation for subst_weight_matrix.cc
+# loads BLOSUM substitution matrices from files provided by NCBI at:
+# ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/
+
+def Generate(filename, matrix_name):
+
+ with open(filename) as f:
+ data = f.readlines()
+
+ scores = dict()
+ olcs = None
+ for line in data:
+ if line.startswith('#'):
+ continue
+ if olcs is None:
+ if " A " in line and " R " in line and " N " in line:
+ # very high likelihood that this line contains the olcs
+ olcs = line.strip().split()
+ continue
+ split_line = line.strip().split()
+ if split_line[0] in olcs:
+ olc = split_line[0]
+ for score_idx, score in enumerate(split_line[1:]):
+ scores[(olc, olcs[score_idx])] = score
+
+ ost_olcs = "ABCDEFGHIKLMNPQRSTVWXYZ"
+ print("short %s[23][23]={"%(matrix_name))
+ for a in ost_olcs:
+ score_string = ""
+ for b in ost_olcs:
+ score = scores[(a,b)]
+ if len(score_string) == 0:
+ entry = [' ', ' ']
+ else:
+ entry = [',', ' ', ' ', ' ']
+ for i in range(len(score)):
+ entry[-1-i] = score[-1-i]
+ score_string += ''.join(entry)
+ print(" {%s},"%(score_string))
+ print("};")
+ print()
+
+Generate("BLOSUM45", "RAW_BLOSUM45_DATA")
+Generate("BLOSUM62", "RAW_BLOSUM62_DATA")
+Generate("BLOSUM80", "RAW_BLOSUM80_DATA")
+Generate("BLOSUM100", "RAW_BLOSUM100_DATA")
+
diff --git a/modules/seq/alg/src/distance_map.cc b/modules/seq/alg/src/distance_map.cc
index 57a1729135147b1707c47221e67d3768a304064e..0dbcb04007fbbcb6e11060ef4d0e34ad289cebb5 100644
--- a/modules/seq/alg/src/distance_map.cc
+++ b/modules/seq/alg/src/distance_map.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2016 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/alg/src/distance_map.hh b/modules/seq/alg/src/distance_map.hh
index faf1f553ccfee616d58d40a760234a5dc8f8dd63..bfb85b54aa430ebdbf344db7302a2abcd557c7cb 100644
--- a/modules/seq/alg/src/distance_map.hh
+++ b/modules/seq/alg/src/distance_map.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2016 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/alg/src/entropy.cc b/modules/seq/alg/src/entropy.cc
index ed4f091d64678dc763b561f208873dd6795e4e85..ed608776fa2b88e47e6bdcf87c5bc48838465b3f 100644
--- a/modules/seq/alg/src/entropy.cc
+++ b/modules/seq/alg/src/entropy.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/alg/src/entropy.hh b/modules/seq/alg/src/entropy.hh
index 85ec4ac0d6a9ab60cda514d64e4e277f6d6f80a9..b336ed00a0bc055d4fed9279168ec676308d001b 100644
--- a/modules/seq/alg/src/entropy.hh
+++ b/modules/seq/alg/src/entropy.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/alg/src/global_align.cc b/modules/seq/alg/src/global_align.cc
index ad8275c9c8688128aaede9b0cc5a15b19d92652b..2c5de2629536e165ee481db86588f2ca4d38c74a 100644
--- a/modules/seq/alg/src/global_align.cc
+++ b/modules/seq/alg/src/global_align.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/alg/src/global_align.hh b/modules/seq/alg/src/global_align.hh
index a920832d7e97f66a6a60d211fa5911106262ac54..b664cd625c6b131988da4e0207721fae6ccc5a60 100644
--- a/modules/seq/alg/src/global_align.hh
+++ b/modules/seq/alg/src/global_align.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/alg/src/impl/align_impl.hh b/modules/seq/alg/src/impl/align_impl.hh
index 33c1afe760f8a70f5b6cdadff69bb26e9e2353f9..c31b76bb94d1949854446a8f34571106e52ec6c7 100644
--- a/modules/seq/alg/src/impl/align_impl.hh
+++ b/modules/seq/alg/src/impl/align_impl.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/alg/src/ins_del.cc b/modules/seq/alg/src/ins_del.cc
index 50e915990ab7562df1c2a0ed02dd4e9997aaadd8..6996e56977608d2f57e0b8a1dd652ea6d8db3576 100644
--- a/modules/seq/alg/src/ins_del.cc
+++ b/modules/seq/alg/src/ins_del.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/alg/src/ins_del.hh b/modules/seq/alg/src/ins_del.hh
index eb4bfe396aaa9a463c5fa424208b2a3275b49d07..572cb5b88de4b8025d7c5eb8a453cbd047035ec8 100644
--- a/modules/seq/alg/src/ins_del.hh
+++ b/modules/seq/alg/src/ins_del.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/alg/src/local_align.cc b/modules/seq/alg/src/local_align.cc
index bea994306b9b69e98d7eb41f121c6ea5160f8e48..fdcdd662e4018749689dc791fcfe555fe211b1dc 100644
--- a/modules/seq/alg/src/local_align.cc
+++ b/modules/seq/alg/src/local_align.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/alg/src/local_align.hh b/modules/seq/alg/src/local_align.hh
index 14b8f9af5f797f41f46296d2623ebb1d52a1b8f6..49ebdaf110bb5ae566f151160d4d928775cefdad 100644
--- a/modules/seq/alg/src/local_align.hh
+++ b/modules/seq/alg/src/local_align.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/alg/src/merge_pairwise_alignments.cc b/modules/seq/alg/src/merge_pairwise_alignments.cc
index aa90c13598f3446d56deee80419dcbb74c1c94cb..a3e4ebfcc5af39d44b4742c6be4d1e3cbfbff58b 100644
--- a/modules/seq/alg/src/merge_pairwise_alignments.cc
+++ b/modules/seq/alg/src/merge_pairwise_alignments.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/alg/src/merge_pairwise_alignments.hh b/modules/seq/alg/src/merge_pairwise_alignments.hh
index 04bc8832d4e6f40dc10084439a3d5bb38eb6a7f6..eb75c7c7b8fa0cdc07903ed6fe30ca7b855e751a 100644
--- a/modules/seq/alg/src/merge_pairwise_alignments.hh
+++ b/modules/seq/alg/src/merge_pairwise_alignments.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/alg/src/module_config.hh b/modules/seq/alg/src/module_config.hh
index b111b7eced6902222901fbeff019361d1ca813d3..3a9da2e0c565eca6bc4a52ba07efabc6a118eb11 100644
--- a/modules/seq/alg/src/module_config.hh
+++ b/modules/seq/alg/src/module_config.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/alg/src/pair_subst_weight_matrix.cc b/modules/seq/alg/src/pair_subst_weight_matrix.cc
index 2d1f0705b67d4ae5401f8e4846736da0213fdcf9..050408ff4ca41860987d05ef4f043c9d51d2f1e5 100644
--- a/modules/seq/alg/src/pair_subst_weight_matrix.cc
+++ b/modules/seq/alg/src/pair_subst_weight_matrix.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/alg/src/pair_subst_weight_matrix.hh b/modules/seq/alg/src/pair_subst_weight_matrix.hh
index 6c0a247aec90a4034d078791763029669e790012..5989850601d7a0102877d04a154871fa90aadd25 100644
--- a/modules/seq/alg/src/pair_subst_weight_matrix.hh
+++ b/modules/seq/alg/src/pair_subst_weight_matrix.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/alg/src/semiglobal_align.cc b/modules/seq/alg/src/semiglobal_align.cc
index 4b89fd15cd1f21d0d56013138adb9c34d9fa06e6..07bd59dc74e4e2c4d2bf387f63e9fd770812189d 100644
--- a/modules/seq/alg/src/semiglobal_align.cc
+++ b/modules/seq/alg/src/semiglobal_align.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/alg/src/semiglobal_align.hh b/modules/seq/alg/src/semiglobal_align.hh
index 6d1ca5002476b05ac10b013ee63dea0020e3cf4b..39439fec50e8dd0d7288dfa92f1da65845adc144 100644
--- a/modules/seq/alg/src/semiglobal_align.hh
+++ b/modules/seq/alg/src/semiglobal_align.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/alg/src/sequence_identity.cc b/modules/seq/alg/src/sequence_identity.cc
index ed88a5048a7358f2d9afe53fefb56f0af6a2ddcf..080dc3810398e467c2cbe021006337b60e69bd29 100644
--- a/modules/seq/alg/src/sequence_identity.cc
+++ b/modules/seq/alg/src/sequence_identity.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/alg/src/sequence_identity.hh b/modules/seq/alg/src/sequence_identity.hh
index 93d233213ef178bf65762103b45867950be65f9c..a1f81b6fd1c24b70835823bff74e1710891bd297 100644
--- a/modules/seq/alg/src/sequence_identity.hh
+++ b/modules/seq/alg/src/sequence_identity.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/alg/src/sequence_similarity.cc b/modules/seq/alg/src/sequence_similarity.cc
index 67f2e063710830f508375a3dff3fe4245f7664b7..4d20e7134f723e39a006db1b39a179b91d120a4d 100644
--- a/modules/seq/alg/src/sequence_similarity.cc
+++ b/modules/seq/alg/src/sequence_similarity.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/alg/src/sequence_similarity.hh b/modules/seq/alg/src/sequence_similarity.hh
index daaa09a7b54e819679b51113edc42c353e6ffe9a..222567b18825af75aafca348c7f3d2722f2cc13d 100644
--- a/modules/seq/alg/src/sequence_similarity.hh
+++ b/modules/seq/alg/src/sequence_similarity.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/alg/src/subst_weight_matrix.cc b/modules/seq/alg/src/subst_weight_matrix.cc
index 315b00f10f9069ecaf08c8fde8afd684eb3dfea7..f382e4f8edeb423938d6b3b4a0f9c6dcef629efe 100644
--- a/modules/seq/alg/src/subst_weight_matrix.cc
+++ b/modules/seq/alg/src/subst_weight_matrix.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
@@ -23,6 +23,9 @@
namespace{
+// The data for the following matrices can be reproduced by running generate_blosum_data.py
+// in OST_SOURCE/modules/seq/alg/src/data
+
short RAW_BLOSUM45_DATA[23][23]={
{ 5, -1, -1, -2, -1, -2, 0, -2, -1, -1, -1, -1, -1, -1, -1, -2, 1, 0, 0, -2, 0, -2, -1},
{-1, 4, -2, 5, 1, -3, -1, 0, -3, 0, -3, -2, 4, -2, 0, -1, 0, 0, -3, -4, -1, -2, 2},
@@ -48,7 +51,7 @@ short RAW_BLOSUM45_DATA[23][23]={
{-2, -2, -3, -2, -2, 3, -3, 2, 0, -1, 0, 0, -2, -3, -1, -1, -2, -1, -1, 3, -1, 8, -2},
{-1, 2, -3, 1, 4, -3, -2, 0, -3, 1, -2, -1, 0, -1, 4, 0, 0, -1, -3, -2, -1, -2, 4},
};
-
+
short RAW_BLOSUM62_DATA[23][23]={
{ 4, -2, 0, -2, -1, -2, 0, -2, -1, -1, -1, -1, -2, -1, -1, -1, 1, 0, 0, -3, 0, -2, -1},
{-2, 4, -3, 4, 1, -3, -1, 0, -3, 0, -4, -3, 3, -2, 0, -1, 0, -1, -3, -4, -1, -3, 1},
@@ -121,7 +124,7 @@ short RAW_BLOSUM100_DATA[23][23]={
{ 1, -1, -3, -2, -2, -5, -2, -3, -5, -2, -6, -4, 0, -3, -2, -3, 9, 2, -4, -7, -2, -5, -2},
{-1, -2, -3, -4, -3, -5, -5, -4, -3, -3, -4, -2, -1, -4, -3, -3, 2, 9, -1, -7, -2, -5, -3},
{-2, -7, -3, -8, -5, -3, -8, -7, 4, -5, 0, 0, -7, -6, -5, -6, -4, -1, 8, -5, -3, -5, -5},
- {-6, -9, -7, 10, -8, 0, -7, -5, -6, -8, -5, -4, -8, -8, -5, -7, -7, -7, -5, 17, -6, 2, -7},
+ {-6, -9, -7,-10, -8, 0, -7, -5, -6, -8, -5, -4, -8, -8, -5, -7, -7, -7, -5, 17, -6, 2, -7},
{-2, -4, -5, -4, -3, -4, -4, -4, -3, -3, -3, -3, -3, -4, -2, -3, -2, -2, -3, -6, -3, -4, -2},
{-5, -6, -6, -7, -7, 4, -8, 1, -4, -5, -4, -5, -5, -7, -4, -5, -5, -5, -5, 2, -4, 12, -6},
{-2, 0, -8, 0, 7, -7, -5, -1, -7, 0, -6, -4, -2, -4, 5, -1, -2, -3, -5, -7, -2, -6, 6},
diff --git a/modules/seq/alg/src/subst_weight_matrix.hh b/modules/seq/alg/src/subst_weight_matrix.hh
index c3bb6d6057607b87969b1f7179614173f014b5da..25f74dc1a19bb422e4b9c82ff18605b71d4eb29c 100644
--- a/modules/seq/alg/src/subst_weight_matrix.hh
+++ b/modules/seq/alg/src/subst_weight_matrix.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/alg/src/variance_map.cc b/modules/seq/alg/src/variance_map.cc
index c3c214f836f124096bd4ddc2a08ffafe4a575b35..c50527ac3a2b9169d11ab62c6b73135c5461fd6e 100644
--- a/modules/seq/alg/src/variance_map.cc
+++ b/modules/seq/alg/src/variance_map.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2016 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/alg/src/variance_map.hh b/modules/seq/alg/src/variance_map.hh
index 0c7e02824241a7cee6becbc580cc408b6bf41747..6bf4780f9f7e1e35763343b1579e7189fbb36394 100644
--- a/modules/seq/alg/src/variance_map.hh
+++ b/modules/seq/alg/src/variance_map.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2016 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/alg/tests/CMakeLists.txt b/modules/seq/alg/tests/CMakeLists.txt
index 81b69d15f81565dbee47ddfa00ef38e3f2219b97..9348d402b69025862766b5f94ac0a85866b3bc90 100644
--- a/modules/seq/alg/tests/CMakeLists.txt
+++ b/modules/seq/alg/tests/CMakeLists.txt
@@ -8,6 +8,7 @@ set(OST_SEQ_ALG_UNIT_TESTS
test_global_align.py
test_semiglobal_align.py
test_weight_matrix.py
+ test_alignment_from_chain_view.py
)
if (COMPOUND_LIB)
diff --git a/modules/seq/alg/tests/test_alignment_from_chain_view.py b/modules/seq/alg/tests/test_alignment_from_chain_view.py
new file mode 100644
index 0000000000000000000000000000000000000000..0e6b183265822431a4c95a8129f403b231b69456
--- /dev/null
+++ b/modules/seq/alg/tests/test_alignment_from_chain_view.py
@@ -0,0 +1,36 @@
+import unittest
+import os
+import ost
+from ost import seq, io, mol
+
+class TestAlignmentFromChainView(unittest.TestCase):
+
+ def testAlignment(self):
+
+ prot = io.LoadPDB(os.path.join("testfiles", "dummy.pdb"))
+ view_resnums = [2,3,4,7,8]
+ query = "rnum=" + ','.join([str(item) for item in view_resnums])
+ prot_view = prot.Select(query)
+
+ exp_handle_seq = ''.join([r.one_letter_code for r in prot.residues])
+
+ exp_view_seq = ['-'] * len(prot.residues)
+ for rnum in view_resnums:
+ exp_view_seq[rnum-1] = prot.residues[rnum-1].one_letter_code
+ exp_view_seq = ''.join(exp_view_seq)
+
+ aln = seq.alg.AlignmentFromChainView(prot_view.chains[0],
+ handle_seq_name='custom_handle_name',
+ view_seq_name='custom_view_name')
+
+ handle_seq = aln.GetSequence(0)
+ view_seq = aln.GetSequence(1)
+
+ self.assertEqual(handle_seq.GetName(), 'custom_handle_name')
+ self.assertEqual(view_seq.GetName(), 'custom_view_name')
+ self.assertEqual(exp_handle_seq, handle_seq.GetString())
+ self.assertEqual(exp_view_seq, view_seq.GetString())
+
+if __name__ == "__main__":
+ from ost import testutils
+ testutils.RunTests()
diff --git a/modules/seq/alg/tests/test_aligntoseqres.py b/modules/seq/alg/tests/test_aligntoseqres.py
index 2aa1bb4fed038ef28671f0feee2c46e878e1a207..5664ff8378a30667bf543d2463b2a6c29a51b385 100644
--- a/modules/seq/alg/tests/test_aligntoseqres.py
+++ b/modules/seq/alg/tests/test_aligntoseqres.py
@@ -71,4 +71,4 @@ if __name__ == "__main__":
if testutils.SetDefaultCompoundLib():
testutils.RunTests()
else:
- print 'No compound library available. Ignoring test_aligntoseqres.py tests.'
+ print('No compound library available. Ignoring test_aligntoseqres.py tests.')
diff --git a/modules/seq/alg/tests/test_distance_analysis.cc b/modules/seq/alg/tests/test_distance_analysis.cc
index 928c00ead3741f43be5f763823f15b1e235a0273..9be0d6fe0065a55dde64dd980e7ee4214bed49c0 100644
--- a/modules/seq/alg/tests/test_distance_analysis.cc
+++ b/modules/seq/alg/tests/test_distance_analysis.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2016 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/alg/tests/test_merge_pairwise_alignments.cc b/modules/seq/alg/tests/test_merge_pairwise_alignments.cc
index bcdca910fd34a4a01a35a41397b8b6c2ae09a9e5..649735af8b76b1594d07bfedc8fab0beb893cf17 100644
--- a/modules/seq/alg/tests/test_merge_pairwise_alignments.cc
+++ b/modules/seq/alg/tests/test_merge_pairwise_alignments.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/alg/tests/test_renumber.py b/modules/seq/alg/tests/test_renumber.py
index 0309f5a1b9166f1a2e4a2febd947832c06487218..f587d588fec5b0104a9c7760894cf6a749d7758a 100644
--- a/modules/seq/alg/tests/test_renumber.py
+++ b/modules/seq/alg/tests/test_renumber.py
@@ -167,6 +167,6 @@ if __name__ == "__main__":
# test renumbering
# test if clustalw package is available on system, otherwise ignore tests
if not clustalw_path:
- print "Could not find clustalw executable: ignoring some renumber unit tests"
+ print("Could not find clustalw executable: ignoring some renumber unit tests")
from ost import testutils
testutils.RunTests()
diff --git a/modules/seq/alg/tests/test_sequence_identity.cc b/modules/seq/alg/tests/test_sequence_identity.cc
index 87bd3f33e2d4bb8b210a62a7a99c06bc8562ab48..0f0d44be839b028bce4e3381799a9a8ec6b83a49 100644
--- a/modules/seq/alg/tests/test_sequence_identity.cc
+++ b/modules/seq/alg/tests/test_sequence_identity.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/alg/tests/tests.cc b/modules/seq/alg/tests/tests.cc
index 5a9ec9d000e545ebf3036f5c08a5e01b1f73ef89..ffa56935cb49f66b0217e93aeca497d3f269279a 100644
--- a/modules/seq/alg/tests/tests.cc
+++ b/modules/seq/alg/tests/tests.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/base/doc/seq.rst b/modules/seq/base/doc/seq.rst
index 8e7e91f57722c1d28ab3a37a444a4a4c4c7a7d9a..510241c8b95dddf82466800e33bc2c67c6e1cc59 100644
--- a/modules/seq/base/doc/seq.rst
+++ b/modules/seq/base/doc/seq.rst
@@ -56,7 +56,7 @@ input methods, sequences can also be loaded from a string:
seq_string = '''>sequence
abcdefghiklmnop'''
s = io.SequenceFromString(seq_string, 'fasta')
- print s.name, s # will print "sequence abcdefghiklmnop"
+ print(s.name, s) # will print "sequence abcdefghiklmnop"
Note that, in that case specifying the format is mandatory.
@@ -92,8 +92,8 @@ The SequenceHandle
.. code-block:: python
s=seq.CreateSequence("A", "abc---def")
- print s.GetPos(1) # prints 1
- print s.GetPos(3) # prints 6
+ print(s.GetPos(1)) # prints 1
+ print(s.GetPos(3)) # prints 6
The reverse mapping, that is from position in the sequence to residue index
can be achieved with :meth:`GetResidueIndex`.
@@ -108,12 +108,12 @@ The SequenceHandle
.. code-block:: python
s=seq.CreateSequence("A", "abc--def")
- print s.GetResidueIndex(1) # prints 1
- print s.GetResidueIndex(6) # prints 4
+ print(s.GetResidueIndex(1)) # prints 1
+ print(s.GetResidueIndex(6)) # prints 4
# the following line raises an exception of type
# Error with the message "requested position contains
# a gap"
- print s.GetResidueIndex(3)
+ print(s.GetResidueIndex(3))
.. method:: GetResidue(pos)
@@ -319,11 +319,11 @@ an alignment:
aln=io.LoadAlignment('aln.fasta')
# iterate over the columns
for col in aln:
- print col
+ print(col)
# iterate over the sequences
for s in aln.sequences:
- print s
+ print(s)
.. function:: CreateAlignment()
@@ -376,7 +376,7 @@ an alignment:
aln.AddSequence(seq.CreateSequence("A", "abcdefghik"))
aln.AddSequence(seq.CreateSequence("B", "1234567890"))
# The following command will print the output given below
- print aln.ToString(7)
+ print(aln.ToString(7))
# A abcde
# B 12345
#
@@ -431,7 +431,7 @@ an alignment:
aln.AddSequence(seq.CreateSequence("B", "1234567890"))
aln.Cut(4, 7)
- print aln.ToString(80)
+ print(aln.ToString(80))
# will print
# A abcdhik
# B 1234890
diff --git a/modules/seq/base/pymod/__init__.py b/modules/seq/base/pymod/__init__.py
index 1594a25530766d92b4817954e7e129f8cfaafe6d..726f3f5afdf111399120efa54c634e40abc6def7 100644
--- a/modules/seq/base/pymod/__init__.py
+++ b/modules/seq/base/pymod/__init__.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
@@ -16,7 +16,7 @@
# along with this library; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
#------------------------------------------------------------------------------
-from _ost_seq import *
+from ._ost_seq import *
from ost.seq import alg
_CreateAlignment=CreateAlignment
diff --git a/modules/seq/base/pymod/const_seq_list_export_def.hh b/modules/seq/base/pymod/const_seq_list_export_def.hh
index cd1f52853b4ad241301d4c55b7e08752027a18cd..e6320c15f3d5eaf8737e3c5be8cec6f7381ff714 100644
--- a/modules/seq/base/pymod/const_seq_list_export_def.hh
+++ b/modules/seq/base/pymod/const_seq_list_export_def.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/base/pymod/export_profile_handle.cc b/modules/seq/base/pymod/export_profile_handle.cc
index 101446d4584f3c26ffd9e57f9241e51a60953e64..2458a43551b2f6db77348fdf3b91bd26bd11263b 100644
--- a/modules/seq/base/pymod/export_profile_handle.cc
+++ b/modules/seq/base/pymod/export_profile_handle.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/base/pymod/export_sequence.cc b/modules/seq/base/pymod/export_sequence.cc
index e8331c7fc198eca9ab1cd4befcf136811543b4ae..2b23ef15a11fed7b24075db37845cd3174c70dc7 100644
--- a/modules/seq/base/pymod/export_sequence.cc
+++ b/modules/seq/base/pymod/export_sequence.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
@@ -328,15 +328,19 @@ void export_sequence()
;*/
class_<RegionRangeIter>("RegionRangeIter", no_init)
.def("next", &RegionRangeIter::next)
+ .def("__next__", &RegionRangeIter::next)
;
class_<RevRegionRangeIter>("RevRegionRangeIter", no_init)
.def("next", &RevRegionRangeIter::next)
+ .def("__next__", &RevRegionRangeIter::next)
;
class_<ConstSeqListIter>("ConstSeqListIter", no_init)
.def("next", &ConstSeqListIter::next)
+ .def("__next__", &ConstSeqListIter::next)
;
class_<SeqListIter>("SeqListIter", no_init)
.def("next", &SeqListIter::next)
+ .def("__next__", &SeqListIter::next)
;
class_<AlignmentHandle>("AlignmentHandle", init<>())
.def("GetCount", &AlignmentHandle::GetCount)
diff --git a/modules/seq/base/pymod/wrap_seq.cc b/modules/seq/base/pymod/wrap_seq.cc
index 1dbc2ba17e65435db1480db4c8330d04718d1300..e2b107792f0b8151c455f03520beacebb2eee3c3 100644
--- a/modules/seq/base/pymod/wrap_seq.cc
+++ b/modules/seq/base/pymod/wrap_seq.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/base/src/aligned_column.cc b/modules/seq/base/src/aligned_column.cc
index 5960a04ee0f73d9ab59e22af11ea67ab34c03fd5..2e9c5a0ef5e2e6fcee4831916c9fafe71c4a9236 100644
--- a/modules/seq/base/src/aligned_column.cc
+++ b/modules/seq/base/src/aligned_column.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/base/src/aligned_column.hh b/modules/seq/base/src/aligned_column.hh
index 5b197d733d71a4ce37624f49eb408bdafdb9700f..554a145236fae880595644c5ab78a2062263b0c4 100644
--- a/modules/seq/base/src/aligned_column.hh
+++ b/modules/seq/base/src/aligned_column.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/base/src/aligned_column_iterator.hh b/modules/seq/base/src/aligned_column_iterator.hh
index 95bef716e3d866a2d258b6ea95ad18cbdb3603cf..72fba01a8a56b7ba2d52e36ee876abc3ce9fef9a 100644
--- a/modules/seq/base/src/aligned_column_iterator.hh
+++ b/modules/seq/base/src/aligned_column_iterator.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/base/src/aligned_region.cc b/modules/seq/base/src/aligned_region.cc
index 50b358c643fe357780973bd8241efb9ad48598f5..0abbecf0328db1adb4f38f0c1512af22764b66ae 100644
--- a/modules/seq/base/src/aligned_region.cc
+++ b/modules/seq/base/src/aligned_region.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/base/src/aligned_region.hh b/modules/seq/base/src/aligned_region.hh
index 2c197d35c2f635be39fb89f392456f311bc7d39a..280ac151d48dc92120490b844d3768c92b16019b 100644
--- a/modules/seq/base/src/aligned_region.hh
+++ b/modules/seq/base/src/aligned_region.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/base/src/alignment_handle.cc b/modules/seq/base/src/alignment_handle.cc
index 8b8f2fc282bd50c14f1c2cce31130e59fac29e68..06cb9d5bf15397ec98421fbd86c2e7bd008ca3ba 100644
--- a/modules/seq/base/src/alignment_handle.cc
+++ b/modules/seq/base/src/alignment_handle.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/base/src/alignment_handle.hh b/modules/seq/base/src/alignment_handle.hh
index 6ac044cfdbd8ecf8dc3d33c16fbd3ce4b8c7ff27..bd268a0d3cbc21cbb63df39b05c309b9126875e2 100644
--- a/modules/seq/base/src/alignment_handle.hh
+++ b/modules/seq/base/src/alignment_handle.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/base/src/impl/sequence_impl.cc b/modules/seq/base/src/impl/sequence_impl.cc
index 9864fe8e5f375c3434b7050e5eca5d3ebd99da2d..d95cb9d72279f75188df024837f8c0be60ffb456 100644
--- a/modules/seq/base/src/impl/sequence_impl.cc
+++ b/modules/seq/base/src/impl/sequence_impl.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/base/src/impl/sequence_impl.hh b/modules/seq/base/src/impl/sequence_impl.hh
index ccb64b7754e9e20e2cd6683f612dbe533f86423e..1e851c4171d8fc93fdef230a1d3311836c838ff1 100644
--- a/modules/seq/base/src/impl/sequence_impl.hh
+++ b/modules/seq/base/src/impl/sequence_impl.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/base/src/impl/sequence_impl_fw.hh b/modules/seq/base/src/impl/sequence_impl_fw.hh
index 233afacba701f60c88fc77d50f82b102cb8470dd..38d185c01486a249d873520fd1339344877a95ab 100644
--- a/modules/seq/base/src/impl/sequence_impl_fw.hh
+++ b/modules/seq/base/src/impl/sequence_impl_fw.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/base/src/impl/sequence_list_impl.cc b/modules/seq/base/src/impl/sequence_list_impl.cc
index 6580aac92bf8032f3b40de53a28a3df23670565f..8349210d374991bc491baf29b44631a7808e2b3c 100644
--- a/modules/seq/base/src/impl/sequence_list_impl.cc
+++ b/modules/seq/base/src/impl/sequence_list_impl.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/base/src/impl/sequence_list_impl.hh b/modules/seq/base/src/impl/sequence_list_impl.hh
index cb69e41ead9bfbc91975b3ce5062bde00b836eef..3910ed9e7a41bfbd295f31a652d225728cd1dca4 100644
--- a/modules/seq/base/src/impl/sequence_list_impl.hh
+++ b/modules/seq/base/src/impl/sequence_list_impl.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/base/src/impl/sequence_list_impl_fw.hh b/modules/seq/base/src/impl/sequence_list_impl_fw.hh
index 095d21b30e5e40bea20f775dda253ecb6a0eb35d..dba2686bcf004fba3c663fcec6c1de35362f766b 100644
--- a/modules/seq/base/src/impl/sequence_list_impl_fw.hh
+++ b/modules/seq/base/src/impl/sequence_list_impl_fw.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/base/src/impl/sequence_list_iterator.hh b/modules/seq/base/src/impl/sequence_list_iterator.hh
index 9af6bbaabc5c3b0aab31e17fb0dfac28ffbd7ace..c798e92ab20fa8425fde0e643d717be95f7ad674 100644
--- a/modules/seq/base/src/impl/sequence_list_iterator.hh
+++ b/modules/seq/base/src/impl/sequence_list_iterator.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/base/src/invalid_sequence.hh b/modules/seq/base/src/invalid_sequence.hh
index da74ebd9cf04092ab411e14586082d31326a66f3..b7162169fc2433f1a82960161cc5a90c740ae0f2 100644
--- a/modules/seq/base/src/invalid_sequence.hh
+++ b/modules/seq/base/src/invalid_sequence.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/base/src/module_config.hh b/modules/seq/base/src/module_config.hh
index e01b2e96f6f062c9443cce257e3c1daa00d06370..e977356b6b67ecbbd43cf8b45342e4474d726e3f 100644
--- a/modules/seq/base/src/module_config.hh
+++ b/modules/seq/base/src/module_config.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/base/src/profile_handle.cc b/modules/seq/base/src/profile_handle.cc
index c6aee7a587e45d95ee063e93472de52aafdd3a60..7fc3785754d9905a2cf79880f87274a2da35c134 100644
--- a/modules/seq/base/src/profile_handle.cc
+++ b/modules/seq/base/src/profile_handle.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/base/src/profile_handle.hh b/modules/seq/base/src/profile_handle.hh
index 4a06461b86940a96eb3b76945324984bdeb9e03b..dcbe4d3326315213bafe63b0021ef17a755d3808 100644
--- a/modules/seq/base/src/profile_handle.hh
+++ b/modules/seq/base/src/profile_handle.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/base/src/sequence_handle.cc b/modules/seq/base/src/sequence_handle.cc
index f57a624e7634410910b4b479debcd5db6b25a4cd..22ba482c2f79d54ef0abba0054bec4b31f3536fc 100644
--- a/modules/seq/base/src/sequence_handle.cc
+++ b/modules/seq/base/src/sequence_handle.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/base/src/sequence_handle.hh b/modules/seq/base/src/sequence_handle.hh
index cf9aa732d1d2a85c154e0dd774790a724ac0e2b2..4e91befaf4da051176deb515b38b0cccaee3413e 100644
--- a/modules/seq/base/src/sequence_handle.hh
+++ b/modules/seq/base/src/sequence_handle.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/base/src/sequence_list.cc b/modules/seq/base/src/sequence_list.cc
index 1242720cd4320b9d7f98d93acdde19ddf2223c56..01fef4a2031f1f7bd2dfe1f10a7061ed098f1375 100644
--- a/modules/seq/base/src/sequence_list.cc
+++ b/modules/seq/base/src/sequence_list.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/base/src/sequence_list.hh b/modules/seq/base/src/sequence_list.hh
index 2e6895c6e62b19b52e31aad3cebc1d9de8904cec..89d302f4b287a916feb85f053a920c3bfcfbf7e6 100644
--- a/modules/seq/base/src/sequence_list.hh
+++ b/modules/seq/base/src/sequence_list.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/base/src/sequence_op.cc b/modules/seq/base/src/sequence_op.cc
index 17e36da506a6a2e7db955e902153c11854dbff72..b6a5dfda5c886bf63af15de16eea13cab607b72d 100644
--- a/modules/seq/base/src/sequence_op.cc
+++ b/modules/seq/base/src/sequence_op.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/base/src/sequence_op.hh b/modules/seq/base/src/sequence_op.hh
index d3f9fc6a1e8903b1e332368f4b85698b87c1211c..5f24281d9adfb47991ef4ebf07c9570a218eff8d 100644
--- a/modules/seq/base/src/sequence_op.hh
+++ b/modules/seq/base/src/sequence_op.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/base/src/views_from_sequences.cc b/modules/seq/base/src/views_from_sequences.cc
index 1ef113248d45309502f59db3f6dded1d5243cc96..65afd7e58e40b762688191a61c76bbc6d441ad4b 100644
--- a/modules/seq/base/src/views_from_sequences.cc
+++ b/modules/seq/base/src/views_from_sequences.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/base/src/views_from_sequences.hh b/modules/seq/base/src/views_from_sequences.hh
index 363319d4af7e349650007f2d4c857c0bebe056a2..14e328da5647781b880a013cb490d6bb53bf8b48 100644
--- a/modules/seq/base/src/views_from_sequences.hh
+++ b/modules/seq/base/src/views_from_sequences.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/base/tests/test_aligned_column.cc b/modules/seq/base/tests/test_aligned_column.cc
index 73e75310ca7d71f111a19e4eb8b35adc3107563b..678933eba63b5ad9025a1521ec17ea1f88432b48 100644
--- a/modules/seq/base/tests/test_aligned_column.cc
+++ b/modules/seq/base/tests/test_aligned_column.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/base/tests/test_aligned_region.cc b/modules/seq/base/tests/test_aligned_region.cc
index 27ddc299b5b9939a94cab31b9a292d07b213983c..ab027782777b34dbf821319e9fbce857e012c2ea 100644
--- a/modules/seq/base/tests/test_aligned_region.cc
+++ b/modules/seq/base/tests/test_aligned_region.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/base/tests/test_alignment.cc b/modules/seq/base/tests/test_alignment.cc
index 05a405b37378fec6af5a7a932bf0752a2eace60a..1018310ebdacbe91f9b9d82f9e03a94caeb8f5de 100644
--- a/modules/seq/base/tests/test_alignment.cc
+++ b/modules/seq/base/tests/test_alignment.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/base/tests/test_profile.cc b/modules/seq/base/tests/test_profile.cc
index 252add767447ae29a6f97585bf5227de787fa749..44338d0aa2deb680f41055fc9738249d86b32faa 100644
--- a/modules/seq/base/tests/test_profile.cc
+++ b/modules/seq/base/tests/test_profile.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2015 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/base/tests/test_sequence.cc b/modules/seq/base/tests/test_sequence.cc
index b18855bdd95c38e5d87fe5cfb37fd60e29914a47..f731b8db6445db085f06ff8d0f357cf0fba2ba3e 100644
--- a/modules/seq/base/tests/test_sequence.cc
+++ b/modules/seq/base/tests/test_sequence.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/modules/seq/base/tests/tests.cc b/modules/seq/base/tests/tests.cc
index 4d3b8b161269ae40f50241b4d1643f03117d9ddd..aac4b1128d54905222d98605fce6a2878b49068e 100644
--- a/modules/seq/base/tests/tests.cc
+++ b/modules/seq/base/tests/tests.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library 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
diff --git a/scripts/bump-version.py b/scripts/bump-version.py
index 053b08bfd7863accecff7e3302d7b43a5f78e651..25873539b389ad80b481086c7f23e50751e637ce 100755
--- a/scripts/bump-version.py
+++ b/scripts/bump-version.py
@@ -1,10 +1,9 @@
-#!/usr/bin/env python
import sys
if len(sys.argv) < 2:
- print "USAGE: python scripts/bump-version.py OST_VERSION"
- print "-> OST_VERSION is MAJOR.MINOR.PATCH (e.g. 1.9.1)"
- print "-> assumption is that a git tag OST_VERSION will exist"
+ print("USAGE: python scripts/bump-version.py OST_VERSION")
+ print("-> OST_VERSION is MAJOR.MINOR.PATCH (e.g. 1.9.1)")
+ print("-> assumption is that a git tag OST_VERSION will exist")
sys.exit(1)
# split up version number
@@ -38,8 +37,11 @@ for i, line in enumerate(lines):
open("docker/Dockerfile", "w").writelines(lines)
# fix Singularity recipe
-lines = open("singularity/Singularity").readlines()
+vfile = "singularity/Singularity"
+lines = open(vfile).readlines()
for i, line in enumerate(lines):
- if line.startswith("export OPENSTRUCTURE_VERSION="):
- lines[i] = 'export OPENSTRUCTURE_VERSION="%s"\n' % version_string
-open("singularity/Singularity", "w").writelines(lines)
+ if line.startswith("From: registry.scicore.unibas.ch/schwede/openstructure:"):
+ lines[i] = 'From: registry.scicore.unibas.ch/schwede/openstructure:'+\
+ '%s' % version_string
+ break
+open(vfile, "w").writelines(lines)
diff --git a/scripts/code_coverage.py b/scripts/code_coverage.py
index 6df65830ef09f91c88df5ff64d117ef58c4a2c05..1cb87bc3ab51ae3bf7133b94ceac760b35623ea5 100644
--- a/scripts/code_coverage.py
+++ b/scripts/code_coverage.py
@@ -42,7 +42,7 @@ def ParseOptions():
def CheckLCOV():
if not Which('lcov'):
- print 'please install lcov to run this script'
+ print('please install lcov to run this script')
sys.exit(-1)
CheckLCOV()
@@ -50,9 +50,9 @@ CheckLCOV()
opts=ParseOptions()
def Print(message):
- print '~~~~~~'
- print '| * |', message
- print '~~~~~~'
+ print('~~~~~~')
+ print('| * |', message)
+ print('~~~~~~')
def RemoveFiles(directory, extension):
glob_pattern='*.%s' % extension
@@ -113,7 +113,7 @@ def RunTests(modules):
if os.path.exists(test_dir):
test_binary=os.path.join(os.path.join(test_dir, 'tests'))
if os.path.exists(test_binary) and os.access(test_binary, os.X_OK):
- print 'running tests for module', module
+ print('running tests for module', module)
Cleanup(modules)
cmd='cd "%s"; ./tests' % test_dir
os.system(cmd)
diff --git a/scripts/dng.bat.in b/scripts/dng.bat.in
index 202d75f67c4d4b7d373eb23dd028d5be361adb52..d012f7b7458e36de0a23964d5584748413c35747 100644
--- a/scripts/dng.bat.in
+++ b/scripts/dng.bat.in
@@ -2,7 +2,7 @@
REM ------------------------------------------------------------------------------
REM This file is part of the OpenStructure project <www.openstructure.org>
REM
-REM Copyright (C) 2008-2011 by the OpenStructure authors
+REM Copyright (C) 2008-2020 by the OpenStructure authors
REM
REM This library is free software; you can redistribute it and/or modify it under
REM the terms of the GNU Lesser General Public License as published by the Free
@@ -30,4 +30,4 @@ REM set PATH=%BIN_DIR%;%DNG_ROOT%\@LIBDIR@\@BUILD_TYPE@;%DNG_ROOT%\@LIBDIR@;%DNG
REM "%BIN_DIR%\@BUILD_TYPE@\gosty.exe" "%DNG_ROOT%\@LIBDIR@\openstructure\dng_startup" ost %*
set PATH=%BIN_DIR%;%DNG_ROOT%\@LIBDIR@\;%PATH%
-"%DNG_ROOT%\libexec\openstructure\gosty.exe" "%DNG_ROOT%\@LIBDIR@\python2.7\site-packages\ost\dng_startup" ost %*
+"%DNG_ROOT%\libexec\openstructure\gosty.exe" "%DNG_ROOT%\@LIBDIR@\python3.6\site-packages\ost\dng_startup" ost %*
diff --git a/scripts/dng.in b/scripts/dng.in
index c04f6b3073fafe9ae03d20e649673dcbc1fd77df..93e7d862e853343728468587dd96b5f4466771aa 100755
--- a/scripts/dng.in
+++ b/scripts/dng.in
@@ -2,7 +2,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
diff --git a/scripts/ost-nightly-build.sh b/scripts/ost-nightly-build.sh
index b8c45866164bd10df5abc477f3b9e121afda18fd..6f6cbddfe935c30af3beb5c1bfb13ead342c31bf 100644
--- a/scripts/ost-nightly-build.sh
+++ b/scripts/ost-nightly-build.sh
@@ -113,9 +113,9 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'}
sources = ['$TARBALL_NAME']
-builddependencies = [('CMake', '2.8.12')]
+builddependencies = [('CMake', '3.10.2')]
-pythonversion = "2.7.5"
+pythonversion = "3.6.6"
pythonshortversion = ".".join(pythonversion.split(".")[:-1])
dependencies = [
@@ -149,7 +149,7 @@ sanity_check_paths = {
'dirs': ["include/ost"],
}
-# add \$INSTALLDIR/lib64/python2.7/site-packages to PYTHONPATH
+# add \$INSTALLDIR/lib64/python3.6/site-packages to PYTHONPATH
modextrapaths = {
'PYTHONPATH': 'lib64/python%s/site-packages' % (pythonshortversion)
}
diff --git a/scripts/ost.bat.in b/scripts/ost.bat.in
index 006fffe522ce9ef072e3283ee87361e309e8a11e..77056f5c434716c9fe379895d1d64a546e41a284 100644
--- a/scripts/ost.bat.in
+++ b/scripts/ost.bat.in
@@ -2,7 +2,7 @@
REM ------------------------------------------------------------------------------
REM This file is part of the OpenStructure project <www.openstructure.org>
REM
-REM Copyright (C) 2008-2011 by the OpenStructure authors
+REM Copyright (C) 2008-2020 by the OpenStructure authors
REM
REM This library is free software; you can redistribute it and/or modify it under
REM the terms of the GNU Lesser General Public License as published by the Free
diff --git a/scripts/ost.in b/scripts/ost.in
index a20bef97b4fea5f3b1d98690aadea2c2d83f5677..ee1f600a6c5ece646530c20ed434b7f7d2a4392f 100755
--- a/scripts/ost.in
+++ b/scripts/ost.in
@@ -2,7 +2,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
@@ -47,7 +47,7 @@ if test -e "${OST_SCRIPT}" ; then
fi
done
IFS="#"
- $pyexec -c "execfile('$DNG_ROOT/@LIBDIR@/python@PYTHON_VERSION@/site-packages/ost/ost_startup.py')" "${OST_SCRIPT}" $opts
+ $pyexec -c "exec(open('$DNG_ROOT/@LIBDIR@/python@PYTHON_VERSION@/site-packages/ost/ost_startup.py').read())" "${OST_SCRIPT}" $opts
RC=$?
else
opts=""
@@ -59,7 +59,7 @@ else
fi
done
IFS="#"
- $pyexec $interactive -c "execfile('$DNG_ROOT/@LIBDIR@/python@PYTHON_VERSION@/site-packages/ost/ost_startup.py')" $opts
+ $pyexec $interactive -c "exec(open('$DNG_ROOT/@LIBDIR@/python@PYTHON_VERSION@/site-packages/ost/ost_startup.py').read())" $opts
RC=$?
fi
IFS=$OLDIFS
diff --git a/scripts/ost_config.in b/scripts/ost_config.in
index cda517095e9a64426b97e670bb3f130c44113860..c8a170a32867eca70cac323aaf723f38f9d0a49a 100644
--- a/scripts/ost_config.in
+++ b/scripts/ost_config.in
@@ -2,7 +2,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library 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
diff --git a/scripts/ost_startup.py.in b/scripts/ost_startup.py.in
index d3cac43d8daa106a882f696bf8ee02db7ccb5c39..3d22c7e7ea0bf7def822d4d0e37a92644d0c6787 100644
--- a/scripts/ost_startup.py.in
+++ b/scripts/ost_startup.py.in
@@ -31,7 +31,7 @@ class OstOptionParser(optparse.OptionParser):
def __init__(self, **kwargs):
optparse.OptionParser.__init__(self, **kwargs)
def exit(self, status_code, error_message):
- print error_message,
+ print(error_message, end=' ')
sys.exit(-1)
parser=OstOptionParser(usage=usage,conflict_handler="resolve", prog='ost''')
@@ -73,9 +73,9 @@ home = os.getenv('HOME') or os.getenv('USERPROFILE')
_ostrc=os.path.join(home, '.ostrc')
if os.path.exists(_ostrc):
try:
- exec(open(_ostrc))
- except Exception, e:
- print e
+ exec(compile(open(_ostrc).read(), _ostrc, 'exec'))
+ except Exception as e:
+ print(e)
PushVerbosityLevel(options.vlevel)
# this should probably only be added when running an interactive shell
@@ -86,7 +86,7 @@ if len(parser.rargs)>0 :
sys_argv_backup=sys.argv
sys.argv=parser.rargs
try:
- execfile(script)
+ exec(compile(open(script,'rb').read(), script, 'exec'))
finally:
sys.argv=sys_argv_backup
diff --git a/singularity/README.rst b/singularity/README.rst
index 69daf50bce89ee1c4530eea41b33cb74ff853810..3f0391c0fbae1a48df9035f3b5fae777b1f5aada 100644
--- a/singularity/README.rst
+++ b/singularity/README.rst
@@ -19,9 +19,8 @@ One can chose any name for an image. For the purose of this file we will assume
that the image name is ``ost.img``.
Here we only keep the recipe for the most recent version of OpenStructure. To
-build an image for a different version, you can either adapt the
-``OPENSTRUCTURE_VERSION`` variable in the recipe or look in the git history for
-an older recipe.
+build an image for a different version, edit the source line (``From:``) in the
+recipe or look in the git history for an older recipe.
Available apps
--------------
@@ -38,13 +37,13 @@ To see the help for each individual app run:
.. code-block:: bash
- singularity help --app <APP NAME> <PATH TO OST IMAGE>
+ singularity run-help --app <APP NAME> <PATH TO OST IMAGE>
Eg.:
.. code-block:: bash
- singularity help --app OST ost.img
+ singularity run-help --app OST ost.img
Facilitating the usage
diff --git a/singularity/Singularity b/singularity/Singularity
index 584c643d5c1b6898ae4cac18f4243f9cd4f5467c..a9b790a9c8ad776c03e56aa973240aed32fa007b 100644
--- a/singularity/Singularity
+++ b/singularity/Singularity
@@ -1,64 +1,24 @@
BootStrap: docker
-From: ubuntu:18.04
+From: registry.scicore.unibas.ch/schwede/openstructure:2.0.0
%post
##############################################################################
# POST
##############################################################################
+
# CHANGE DASH TO BASH
rm /bin/sh
ln -sf /bin/bash /bin/sh
-# DEFINE SOME ENV VARS USED DURING THE IMAGE BUILD
-##########################
-export SRC_FOLDER="/usr/local/src"
-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="1.11.0"
-export OPENSTRUCTURE_SHARE="/usr/local/share/ost"
-export MSMS_VERSION="2.6.1"
-export OPENMM_VERSION="7.1.1"
-export OPENMM_INCLUDE_PATH=/usr/local/openmm/include/
-export OPENMM_LIB_PATH=/usr/local/openmm/lib/
-export JUPYTER_CONFIG_DIR="/usr/local/etc/jupyter"
-export JUPYTER_PATH="/usr/local/share/jupyter"
-export JUPYTER_RUNTIME_DIR="$JUPYTER_PATH/runtime"
-export VIRTUALENV_DIR="/usr/local/share/ost_venv"
-
# INSTALL SYSTEM DEPS
#####################
-apt-get update -y && apt-get install -y cmake \
- g++ \
- sip-dev \
- libtiff-dev \
- libfftw3-dev \
- libeigen3-dev \
- libboost-all-dev \
- libpng-dev \
- python-all \
- python2.7 \
- python-pyqt5 \
- qt5-qmake \
- qtbase5-dev \
- wget \
- git \
- gfortran \
- python-pip \
- tar \
- libbz2-dev \
- doxygen \
- swig \
- clustalw \
- python-virtualenv \
- libsqlite3-dev \
- dssp \
- python-enum34 \
- python-ipaddress \
- locales
+apt-get update -y && apt-get install -y python3-pip
+pip3 install nglview \
+ ipython \
+ jupyter \
+ six
# SET LOCALE
############
@@ -67,105 +27,16 @@ echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen
echo "LANG=en_US.UTF-8" > /etc/locale.conf
locale-gen en_US.UTF-8
-# INSTALL SOME PYTHON PACKAGES GLOBALY
-######################################
-pip install --no-cache-dir numpy==1.10.4 \
- scipy==1.0.0 \
- pandas==0.22.0
-
-
-# SET UP VIRTUALENV
-###################
-virtualenv --system-site-packages $VIRTUALENV_DIR
-. $VIRTUALENV_DIR/bin/activate
-
-
-# INSTALL REQUIRED PYTHON PACKAGES
-##################################
-pip install jupyter==1.0.0 \
- nglview==1.1.6 \
- six==1.13.0
-
-# DOWNLOAD AND INSTALL MSMS
-##############
-cd ${SRC_FOLDER}
-if [ ! -f msms_i86_64Linux2_${MSMS_VERSION}.tar.gz ]; then
- mkdir -p msms
- cd msms
- wget http://mgltools.scripps.edu/downloads/tars/releases/MSMSRELEASE/REL${MSMS_VERSION}/msms_i86_64Linux2_${MSMS_VERSION}.tar.gz
- tar -xvzf msms_i86_64Linux2_${MSMS_VERSION}.tar.gz
- cp -v ${SRC_FOLDER}/msms/msms.x86_64Linux2.${MSMS_VERSION} /usr/local/bin/msms
- cp -v ${SRC_FOLDER}/msms/pdb_to_xyzr /usr/local/bin/pdb_to_xyzr
- cp -v ${SRC_FOLDER}/msms/pdb_to_xyzrn /usr/local/bin/pdb_to_xyzrn
-fi
-
-# COMPILE OPENMM FROM SOURCES. INSTALL TO /usr/local
-############################
-cd ${SRC_FOLDER}
-if [ ! -f openmm-${OPENMM_VERSION}.tar.gz ]; then
- wget -O openmm-${OPENMM_VERSION}.tar.gz -nc https://github.com/pandegroup/openmm/archive/${OPENMM_VERSION}.tar.gz
- mkdir ${SRC_FOLDER}/openmm-${OPENMM_VERSION}
- tar xf openmm-${OPENMM_VERSION}.tar.gz -C ${SRC_FOLDER}/openmm-${OPENMM_VERSION} --strip-components=1
- mkdir -p ${SRC_FOLDER}/openmm-${OPENMM_VERSION}/build && cd ${SRC_FOLDER}/openmm-${OPENMM_VERSION}/build
- cmake .. && make -j $CPUS_FOR_MAKE && make install
- cd ${SRC_FOLDER}/openmm-${OPENMM_VERSION}/build/python && python setup.py build && python setup.py install
-fi
-
-# INSTALL OST
-#############
-
-cd ${SRC_FOLDER}
-if [ ! -f openstructure-${OPENSTRUCTURE_VERSION}.tar.gz ]; then
- # copy ost release
- wget -O openstructure-${OPENSTRUCTURE_VERSION}.tar.gz -nc https://git.scicore.unibas.ch/schwede/openstructure/repository/${OPENSTRUCTURE_VERSION}/archive.tar.gz
- mkdir openstructure-${OPENSTRUCTURE_VERSION}
- tar xf openstructure-${OPENSTRUCTURE_VERSION}.tar.gz -C ${SRC_FOLDER}/openstructure-${OPENSTRUCTURE_VERSION} --strip-components=1
- mkdir -p ${SRC_FOLDER}/openstructure-${OPENSTRUCTURE_VERSION}/build && cd ${SRC_FOLDER}/openstructure-${OPENSTRUCTURE_VERSION}/build
-
- # cmake ost
- cmake .. -DPYTHON_LIBRARIES=/usr/lib/x86_64-linux-gnu/libpython2.7.so \
- -DOPTIMIZE=ON \
- -DENABLE_MM=ON \
- -DCOMPILE_TMTOOLS=1 \
- -DUSE_NUMPY=1 \
- -DOPEN_MM_LIBRARY=$OPENMM_LIB_PATH/libOpenMM.so \
- -DOPEN_MM_INCLUDE_DIR=$OPENMM_INCLUDE_PATH \
- -DOPEN_MM_PLUGIN_DIR=$OPENMM_LIB_PATH/plugins \
- -DENABLE_GFX=ON \
- -DENABLE_GUI=ON
-
- # Build chemdict_tool
- make -j ${CPUS_FOR_MAKE} chemdict_tool
-
- # get the compound library
- wget ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif.gz
- stage/bin/chemdict_tool create components.cif.gz compounds.chemlib pdb
- stage/bin/chemdict_tool update ../modules/conop/data/charmm.cif compounds.chemlib charmm
- mkdir -p $OPENSTRUCTURE_SHARE
- chmod a+rw -R $OPENSTRUCTURE_SHARE
- mv compounds.chemlib $OPENSTRUCTURE_SHARE
-
- # Build and install OST
- cmake .. -DPYTHON_LIBRARIES=/usr/lib/x86_64-linux-gnu/libpython2.7.so \
- -DOPTIMIZE=ON \
- -DENABLE_MM=ON \
- -DCOMPILE_TMTOOLS=1 \
- -DUSE_NUMPY=1 \
- -DOPEN_MM_LIBRARY=$OPENMM_LIB_PATH/libOpenMM.so \
- -DOPEN_MM_INCLUDE_DIR=$OPENMM_INCLUDE_PATH \
- -DOPEN_MM_PLUGIN_DIR=$OPENMM_LIB_PATH/plugins \
- -DENABLE_GFX=ON \
- -DENABLE_GUI=ON \
- -DCOMPOUND_LIB=$OPENSTRUCTURE_SHARE/compounds.chemlib
-
- # Build chemdict_tool
- make -j ${CPUS_FOR_MAKE}
- make check
- make install
-fi
-
-# SETUP JUPYTER
-###############
+# SETUP IPYTHON / JUPYTER
+#########################
+# As the Singularity mounts $HOME by default Jupyter and Ipython config files
+# are moved to separate directories. Proper environmental variables are also
+# set
+export IPYTHONDIR="/usr/local/share/ipython"
+export JUPYTER_CONFIG_DIR="/usr/local/etc/jupyter"
+export JUPYTER_PATH="/usr/local/share/jupyter"
+export JUPYTER_RUNTIME_DIR="/tmp/jupyter_runtime"
+
mkdir -p /usr/local/share/ipython
mkdir -p $JUPYTER_PATH
mkdir -p $JUPYTER_RUNTIME_DIR
@@ -177,54 +48,34 @@ chmod a+rw -R $JUPYTER_CONFIG_DIR
chmod a+rw -R $JUPYTER_RUNTIME_DIR
cat > $JUPYTER_PATH/kernels/ost-kernel/kernel.json <<EOF
{
- "display_name": "OST",
- "language": "python",
- "argv": [
- "python",
- "-m", "ipykernel",
+ "display_name": "OST",
+ "language": "python",
+ "argv": [
+ "python",
+ "-m", "ipykernel",
"-f", "{connection_file}",
- "--InteractiveShellApp.exec_PYTHONSTARTUP=False",
- "--InteractiveShellApp.exec_files=['/usr/local/lib64/python2.7/site-packages/ost/ost_startup.py']"
- ],
- "env": {
- }
+ "--InteractiveShellApp.exec_PYTHONSTARTUP=False",
+ "--InteractiveShellApp.exec_files=['/usr/local/lib64/python3.6/site-packages/ost/ost_startup.py']"
+ ],
+ "env": {
+ }
}
EOF
jupyter nbextension enable nglview --py --sys-prefix
-# GO HOME AND CLEANUP
-#####################
-apt-get purge -y cmake \
- wget \
- git \
- gfortran \
- python-pip \
- libbz2-dev \
- doxygen \
- swig
-apt-get clean
-apt-get autoremove -y
-
-cd $SRC_FOLDER && rm -rf $SRC_FOLDER/*
-
-cd /home
-
%environment
##############################################################################
# ENVIRONMENT
##############################################################################
-export OST_ROOT="/usr/local"
-export OPENSTRUCTURE_VERSION="1.11.0"
-export OPENMM_LIB_PATH=/usr/local/openmm/lib/
-export PYTHONPATH="/usr/local/lib64/python2.7/site-packages:${PYTHONPATH}"
-export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/local/lib64:${OPENMM_LIB_PATH}"
-export QT_X11_NO_MITSHM=1
+export TEMP="/tmp"
+export TEMPDIR="/tmp"
+export TMPDIR="/tmp"
+export TMP="/tmp"
export IPYTHONDIR="/usr/local/share/ipython"
export JUPYTER_CONFIG_DIR="/usr/local/etc/jupyter"
export JUPYTER_PATH="/usr/local/share/jupyter"
-export JUPYTER_RUNTIME_DIR="$JUPYTER_PATH/runtime"
-export VIRTUALENV_DIR="/usr/local/share/ost_venv"
+export JUPYTER_RUNTIME_DIR="$TMPDIR/jupyter_runtime"
%apprun ChemdictTool
##############################################################################
@@ -232,6 +83,7 @@ export VIRTUALENV_DIR="/usr/local/share/ost_venv"
##############################################################################
$OST_ROOT/bin/chemdict_tool "$@"
+
%apprun lDDT
##############################################################################
# lDDT APP
@@ -259,6 +111,7 @@ Options:
-e print version
-x ignore residue name consistency checks
+
%apprun Molck
##############################################################################
# MOLCK APP
@@ -292,6 +145,7 @@ Options:
--map-nonstd maps modified residues back to the parent amino acid, for example
MSE -> MET, SEP -> SER.
+
%apprun OST
##############################################################################
# OST APP
@@ -299,11 +153,12 @@ Options:
$OST_ROOT/bin/ost "$@"
%apphelp OST
-The OST app exposes OpenStructure binary and can be used to run interactive shell
-and scripts.
+The OST app exposes OpenStructure binary and can be used to run interactive
+shell and scripts.
Usage:
- singularity run --app OST <IMAGE> [ost options] [script to execute] [script parameters]
+ singularity run --app OST <IMAGE> [ost options] [script to execute]
+ [script parameters]
Options:
-i, --interactive start interpreter interactively (must be first
@@ -322,13 +177,14 @@ goes to CWD. Thus this sould work as expected out of the box.
# NOTEBOOK ENV
##############################################################################
export DNG_ROOT=$OST_ROOT
-export DNG_INITDIR=${DNG_ROOT}/lib64/python2.7/site-packages/ost
+export DNG_INITDIR=${DNG_ROOT}/lib64/python3.6/site-packages/ost
+
%apprun IPython
##############################################################################
# OST IPYTON APP
##############################################################################
-. $VIRTUALENV_DIR/bin/activate && ipython -i $DNG_INITDIR/ost_startup.py "$@"
+ipython3 -i $DNG_INITDIR/ost_startup.py "$@"
%apphelp IPython
OST-powered iPython shell.
@@ -341,6 +197,7 @@ Detailed help:
singularity run --app IPython <IMAGE> --help
+
%appenv Notebook
##############################################################################
# NOTEBOOK ENV
@@ -349,14 +206,15 @@ export BIN_DIR=$OST_ROOT/bin
export XDG_RUNTIME_DIR=""
. $OST_ROOT/libexec/openstructure/ost_config
+
%apprun Notebook
##############################################################################
# NOTEBOOK APP
##############################################################################
-. $VIRTUALENV_DIR/bin/activate && jupyter notebook --NotebookApp.iopub_data_rate_limit=10000000 --no-browser "$@"
+jupyter notebook --NotebookApp.iopub_data_rate_limit=10000000 --no-browser "$@"
%apphelp Notebook
-A Jupyter notebook palyground with OST and nglview.
+A Jupyter notebook playground with OST and nglview.
Usage:
@@ -380,8 +238,6 @@ For more details on how to use nglview see http://nglviewer.org/nglview/latest/.
As the Singularity mounts $HOME by default Jupyter and Ipython config files
are moved to separate directories. Proper environmental variables are also set.
-In addition, Jupyter is run in a separate virtualenv to not interact with possibly
-installed host version.
To list of all available options:
@@ -422,5 +278,3 @@ This container includes the following apps:
To see the help for each individual app run:
singularity help --app <APP NAME> <IMAGE NAME>
-
-
diff --git a/tools/molck/main.cc b/tools/molck/main.cc
index 8507a1895b2d6f13d2aeecec94a826a392ce0dd0..efed0e21fc749d05491edb4c74febe05b08f6051 100644
--- a/tools/molck/main.cc
+++ b/tools/molck/main.cc
@@ -23,28 +23,32 @@ namespace po=boost::program_options;
namespace fs=boost::filesystem;
const char* USAGE=
-"this is molck - the molecule checker\n"
-"usage: molck [options] file1.pdb [file2.pdb [...]]\n"
-"options \n"
-" --complib=path location of the compound library file. If not provided, the \n"
-" following locations are searched in this order: \n"
-" 1. Working directory, 2. OpenStructure standard library location (if the \n"
-" executable is part of a standard OpenStructure installation) \n"
-" --rm=<a>,<b> remove atoms and residues matching some criteria \n"
-" zeroocc - Remove atoms with zero occupancy \n"
-" hyd - Remove hydrogen atoms \n"
-" oxt - Remove terminal oxygens \n"
-" nonstd - Remove all residues not one of the 20 standard amino acids \n"
-" unk - Remove unknown and atoms not following the nomenclature\n"
-" --fix-ele clean up element column\n"
-" --stdout write cleaned file(s) to stdout \n"
-" --out=filename write cleaned file(s) to disk. % characters in the filename are \n"
-" replaced with the basename of the input file without extension. \n"
-" Default: %-molcked.pdb \n"
-" --color=auto|on|off \n"
-" whether output should be colored\n"
-" --map-nonstd maps modified residues back to the parent amino acid, for example\n"
-" MSE -> MET, SEP -> SER.\n";
+"This is molck - the molecule checker\n"
+"Usage: molck [options] file1.pdb [file2.pdb [...]]\n"
+"Options\n"
+" --complib=path Location of the compound library file. If not provided,\n"
+" the following locations are searched in this order:\n"
+" 1. Working directory,\n"
+" 2. OpenStructure standard library location (if the\n"
+" executable is part of a standard OpenStructure\n"
+" installation)\n"
+" --rm=<a>,<b> Remove atoms and residues matching some criteria:\n"
+" - zeroocc - Remove atoms with zero occupancy\n"
+" - hyd - Remove hydrogen atoms\n"
+" - oxt - Remove terminal oxygens\n"
+" - nonstd - Remove all residues not one of the\n"
+" 20 standard amino acids\n"
+" - unk - Remove unknown atoms not following\n"
+" the nomenclature\n"
+" Default: hyd\n"
+" --fix-ele Clean up element column\n"
+" --stdout Write cleaned file(s) to stdout\n"
+" --out=filename Write cleaned file(s) to disk. % characters in the\n"
+" filename are replaced with the basename of the input\n"
+" file without extension. Default: %-molcked.pdb\n"
+" --color=auto|on|off Whether output should be colored. Delault: auto\n"
+" --map-nonstd Maps modified residues back to the parent amino acid,\n"
+" for example: MSE -> MET, SEP -> SER.\n";
void usage()
{
@@ -56,15 +60,15 @@ EntityHandle load_x(const String& file, const IOProfile& profile)
{
try {
EntityHandle ent = CreateEntity();
- if(file.compare(file.length() - 6, 6, ".mmcif") == 0 ||
- file.compare(file.length() - 4, 4, ".cif") == 0){
- MMCifReader reader(file,ent,profile);
+ const size_t fl = file.length();
+ if ( (fl > 6 && file.compare(fl - 6, 6, ".mmcif") == 0)
+ || (fl > 4 && file.compare(fl - 4, 4, ".cif") == 0)) {
+ MMCifReader reader(file, ent, profile);
reader.Parse();
return ent;
- }
- //if its not mmcif, we assume the file to be in pdb format without even
- //looking at the filename
- else{
+ } else {
+ // if its not mmcif, we assume the file to be in pdb format without even
+ // looking at the filename
PDBReader reader(file, profile);
if (reader.HasNext()) {
reader.Import(ent);
@@ -139,8 +143,10 @@ int main(int argc, char *argv[])
usage();
}
IOProfile prof;
- prof.fault_tolerant=true;
- ost::mol::alg::MolckSettings settings;
+ prof.fault_tolerant = true;
+ // set all settings to false by default (set to true if args given)
+ ost::mol::alg::MolckSettings settings(false, false, false, false, false,
+ false, false, false);
String rm;
String color;
@@ -152,15 +158,15 @@ int main(int argc, char *argv[])
po::options_description desc("Options");
desc.add_options()
("rm", po::value<String>(&rm)->default_value("hyd"), "atoms to be removed")
- ("color", po::value<String>(&color)->default_value("auto"),
+ ("color", po::value<String>(&color)->default_value("auto"),
"whether the output should be colored.")
("files", po::value< std::vector<String> >(), "input file(s)")
("stdout", "write cleaned file(s) to stdout")
- ("out,o", po::value<String>(&output_blueprint_string)->default_value("%-molcked.pdb"),
+ ("out,o", po::value<String>(&output_blueprint_string)->default_value("%-molcked.pdb"),
"write cleaned file to output using blueprint to determine path")
("map-nonstd", "map non standard residues back to standard ones (e.g.: MSE->MET,SEP->SER,etc.)")
- ("fix-ele", "insert element")
- ("complib", po::value<String>(&custom_path)->default_value(""),"location of the compound library file")
+ ("fix-ele", "insert element")
+ ("complib", po::value<String>(&custom_path)->default_value(""),"location of the compound library file")
;
po::positional_options_description p;
p.add("files", -1);