From 6e60b71df07234c329fcf448ec67e26e5d84d525 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Wed, 13 Nov 2019 19:12:20 +0100
Subject: [PATCH 001/142] Initial Python 3 port commit
This commit doesn't make OpenStructure work with Python 3. The goal of this
commit was to perform an automated port of the Python code and make it compile.
The performed steps:
- Edited CMakeLists.txt to search for Python with 3.6 as min version 3.6 is the
Python version shipped by default with Ubuntu 18.04 LTS
- Add version 3.6 to cmake_support/FindPython.cmake
- Adapt setup_boost macro in cmake_support/OST.cmake to prefer versioned
libraries and not first check for boost_python.so. In the example of
Ubuntu 18.04, libboost_python.so is specific for Python 2 but
libboost_python3.so is the one we want.
- apply the following command: 2to3-2.7 -n -w <OST_DIR>
- adapt base/pymod/wrap_base.cc, gui/pymod/wrap_gui.cc and
gui/pymod/export_message_widget.cc as PyString functionalities do not exist
anymore in the Python 3 interpreter (replaced by PyUnicode)
- adapt gui/src/python_shell/python_interpreter_worker.hh to resolve issue
discussed in https://stackoverflow.com/questions/23068700/embedding-python3-in-qt-5
Long story short: Qt does a typedef for "slots" which causes trouble with
other headers that are pulled in from the Python interpreter
---
CMakeLists.txt | 2 +-
cmake_support/FindPython.cmake | 2 +-
cmake_support/OST.cmake | 8 +-
deployment/macos/deps.py | 46 +--
deployment/macos/pack.py | 36 +--
doc/conf/conf.py | 8 +-
doc/make.py | 4 +-
doc/to_sphinx.py | 12 +-
docker/test_docker.py | 2 +-
examples/demos/charmm_trj_blur.py | 2 +-
examples/demos/correlate.py | 2 +-
examples/demos/gfx_mapslab.py | 4 +-
examples/demos/load_and_display.py | 2 +-
examples/demos/the_hammer.py | 2 +-
modules/base/pymod/table.py | 36 +--
modules/base/pymod/testutils.py | 8 +-
modules/base/pymod/wrap_base.cc | 12 +-
modules/base/pymod/xmlrunner.py | 4 +-
modules/base/tests/test_table.py | 292 +++++++++---------
modules/bindings/pymod/align_3dcomb.py | 8 +-
modules/bindings/pymod/blast.py | 6 +-
modules/bindings/pymod/cadscore.py | 6 +-
modules/bindings/pymod/dssp.py | 8 +-
modules/bindings/pymod/hbplus.py | 4 +-
modules/bindings/pymod/hhblits.py | 24 +-
modules/bindings/pymod/ialign.py | 2 +-
modules/bindings/pymod/kclust.py | 2 +-
modules/bindings/pymod/lga.py | 4 +-
modules/bindings/pymod/msms.py | 6 +-
modules/bindings/pymod/naccess.py | 6 +-
modules/bindings/tests/test_blast.py | 2 +-
modules/bindings/tests/test_clustalw.py | 2 +-
modules/bindings/tests/test_hhblits.py | 4 +-
modules/bindings/tests/test_kclust.py | 2 +-
modules/bindings/tests/test_msms.py | 4 +-
modules/bindings/tests/test_naccess.py | 4 +-
modules/conop/pymod/cleanup.py | 2 +-
modules/conop/tests/test_cleanup.py | 2 +-
modules/conop/tests/test_compound.py | 2 +-
modules/geom/tests/test_geom.py | 2 +-
modules/gfx/pymod/__init__.py | 4 +-
modules/gfx/tests/test_gfx.py | 2 +-
modules/gfx/tests/test_gost_import.py | 2 +-
modules/gui/pymod/__init__.py | 4 +-
modules/gui/pymod/dng/init.py | 22 +-
modules/gui/pymod/dng/menu.py | 4 +-
modules/gui/pymod/export_message_widget.cc | 6 +-
modules/gui/pymod/helpwidget.py | 2 +-
.../gui/pymod/scene/color_options_widget.py | 8 +-
.../gui/pymod/scene/combo_options_widget.py | 2 +-
modules/gui/pymod/scene/cpk_widget.py | 2 +-
modules/gui/pymod/scene/custom_widget.py | 2 +-
.../gui/pymod/scene/gradient_editor_widget.py | 4 +-
.../gui/pymod/scene/gradient_info_handler.py | 2 +-
.../gui/pymod/scene/gradient_list_model.py | 8 +-
.../gui/pymod/scene/gradient_preset_widget.py | 4 +-
modules/gui/pymod/scene/hsc_widget.py | 2 +-
modules/gui/pymod/scene/inspector_widget.py | 10 +-
modules/gui/pymod/scene/line_trace_widget.py | 2 +-
modules/gui/pymod/scene/map_level_widget.py | 2 +-
modules/gui/pymod/scene/preset.py | 2 +-
.../pymod/scene/preset_editor_list_model.py | 2 +-
.../gui/pymod/scene/preset_editor_widget.py | 20 +-
.../gui/pymod/scene/preset_info_handler.py | 2 +-
modules/gui/pymod/scene/preset_list_model.py | 8 +-
modules/gui/pymod/scene/preset_widget.py | 8 +-
modules/gui/pymod/scene/remote.py | 6 +-
modules/gui/pymod/scene/render_mode_widget.py | 4 +-
.../gui/pymod/scene/render_options_widget.py | 22 +-
modules/gui/pymod/scene/simple_widget.py | 2 +-
modules/gui/pymod/scene/sline_widget.py | 2 +-
.../gui/pymod/scene/toolbar_options_widget.py | 2 +-
modules/gui/pymod/scene/trace_widget.py | 2 +-
modules/gui/pymod/scene/tube_widget.py | 2 +-
.../gui/pymod/scene/uniform_color_widget.py | 2 +-
modules/gui/pymod/scene/wireframe_widget.py | 2 +-
modules/gui/pymod/table.py | 2 +-
modules/gui/pymod/trajectory_viewer.py | 8 +-
modules/gui/pymod/wrap_gui.cc | 13 +-
.../python_shell/python_interpreter_worker.hh | 4 +
modules/io/pymod/__init__.py | 2 +-
modules/io/pymod/remote.py | 6 +-
modules/io/tests/test_io_mmcif.py | 172 +++++------
modules/io/tests/test_io_pdb.py | 4 +-
modules/mol/alg/pymod/hbond.py | 34 +-
modules/mol/alg/pymod/helix_kinks.py | 18 +-
modules/mol/alg/pymod/qsscoring.py | 80 ++---
modules/mol/alg/pymod/structure_analysis.py | 24 +-
modules/mol/alg/pymod/superpose.py | 10 +-
modules/mol/alg/pymod/trajectory_analysis.py | 2 +-
modules/mol/alg/pymod/views.py | 8 +-
modules/mol/alg/tests/test_accessibility.py | 4 +-
.../alg/tests/test_convenient_superpose.py | 4 +-
modules/mol/alg/tests/test_nonstandard.py | 2 +-
modules/mol/alg/tests/test_pdbize.py | 14 +-
modules/mol/alg/tests/test_qsscoring.py | 16 +-
modules/mol/alg/tests/test_sec_struct.py | 2 +-
modules/mol/base/tests/test_numpy.py | 2 +-
modules/mol/mm/pymod/__init__.py | 2 +-
modules/mol/mm/pymod/antechamber.py | 4 +-
modules/seq/alg/pymod/__init__.py | 2 +-
modules/seq/alg/tests/test_aligntoseqres.py | 2 +-
modules/seq/alg/tests/test_renumber.py | 2 +-
scripts/bump-version.py | 6 +-
scripts/code_coverage.py | 10 +-
105 files changed, 622 insertions(+), 605 deletions(-)
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 7b76c4eea..3908e11f6 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -177,7 +177,7 @@ 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 ${PYTHON_VERSION})
list(GET _python_version_list 0 PYTHON_VERSION_MAJOR)
diff --git a/cmake_support/FindPython.cmake b/cmake_support/FindPython.cmake
index 673a80219..3a2e690de 100644
--- a/cmake_support/FindPython.cmake
+++ b/cmake_support/FindPython.cmake
@@ -17,7 +17,7 @@
# Author: Marco Biasini
#-------------------------------------------------------------------------------
-set(PYTHON_VERSIONS 2.7 2.6 2.5 2.4 2.3 2.2 )
+set(PYTHON_VERSIONS 3.6 2.7 2.6 2.5 2.4 2.3 2.2 )
set(PYTHON_MIN_VERSION 2.2.1)
#-------------------------------------------------------------------------------
diff --git a/cmake_support/OST.cmake b/cmake_support/OST.cmake
index 31c304804..46c511d58 100644
--- a/cmake_support/OST.cmake
+++ b/cmake_support/OST.cmake
@@ -917,10 +917,10 @@ macro(setup_boost)
# python${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: " ${_python_lib_name})
@@ -1004,4 +1004,4 @@ macro(ost_action ACTION TARGET)
set(_ACTION_NAMES "${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/macos/deps.py b/deployment/macos/deps.py
index 91ef55c9a..63fb51cf7 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 beb7d7d74..16b516577 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/doc/conf/conf.py b/doc/conf/conf.py
index 7a7fa741f..8da3b5569 100644
--- a/doc/conf/conf.py
+++ b/doc/conf/conf.py
@@ -48,8 +48,8 @@ source_suffix = '.rst'
master_doc = 'index'
# General information about the project.
-project = u'OpenStructure'
-copyright = u'2019, OpenStructure authors'
+project = 'OpenStructure'
+copyright = '2019, OpenStructure authors'
# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
@@ -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 57da9479e..1b9f43a1d 100644
--- a/doc/make.py
+++ b/doc/make.py
@@ -48,7 +48,7 @@ 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):
@@ -99,7 +99,7 @@ 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
+ print(cmd)
_CheckCall(cmd, shell=True)
if opts.doctest:
diff --git a/doc/to_sphinx.py b/doc/to_sphinx.py
index 09809d235..eab09effc 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/test_docker.py b/docker/test_docker.py
index e191217e6..38fae4a60 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/examples/demos/charmm_trj_blur.py b/examples/demos/charmm_trj_blur.py
index f65d0dbcc..b6f848ffb 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 55bb4d068..1b65722d6 100644
--- a/examples/demos/correlate.py
+++ b/examples/demos/correlate.py
@@ -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
diff --git a/examples/demos/gfx_mapslab.py b/examples/demos/gfx_mapslab.py
index 8cc8ca334..d7ca61c30 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 6ce59673c..b4e140520 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 1c308b2d7..114e2baa2 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/pymod/table.py b/modules/base/pymod/table.py
index 994f01000..4a4a55934 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
@@ -947,13 +947,13 @@ Statistics for column %(col)s
stream=open(stream_or_filename, 'rb')
else:
stream=stream_or_filename
- return cPickle.load(stream)
+ return pickle.load(stream)
@staticmethod
def _GuessFormat(filename):
try:
filename = filename.name
- except AttributeError, e:
+ except AttributeError as e:
pass
if filename.endswith('.csv'):
return 'csv'
@@ -1085,7 +1085,7 @@ 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,
@@ -1561,7 +1561,7 @@ 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]
@@ -2197,7 +2197,7 @@ Statistics for column %(col)s
def _SavePickle(self, stream):
if not hasattr(stream, 'write'):
stream=open(stream, 'wb')
- cPickle.dump(self, stream, cPickle.HIGHEST_PROTOCOL)
+ pickle.dump(self, stream, pickle.HIGHEST_PROTOCOL)
def _SaveHTML(self, stream_or_filename):
def _escape(s):
@@ -2459,7 +2459,7 @@ Statistics for column %(col)s
a = self.GetNumpyMatrix(*args)
if len(kwargs)!=0:
- if kwargs.has_key('weights'):
+ if 'weights' in kwargs:
w = self.GetNumpyMatrix(kwargs['weights'])
b = np.multiply(b,w)
a = np.multiply(a,w)
@@ -3048,7 +3048,7 @@ 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 +3133,7 @@ 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 +3146,7 @@ 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
diff --git a/modules/base/pymod/testutils.py b/modules/base/pymod/testutils.py
index 5dd8762e2..4b701fe08 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 b0cfa8465..2b43f842e 100644
--- a/modules/base/pymod/wrap_base.cc
+++ b/modules/base/pymod/wrap_base.cc
@@ -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 e2bcae76d..0ea333262 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/tests/test_table.py b/modules/base/tests/test_table.py
index 347183262..ec2e5fcf0 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')
@@ -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()
@@ -920,15 +920,15 @@ 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')
@@ -1042,44 +1042,44 @@ 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 +1088,9 @@ 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 +1100,9 @@ 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 +1112,9 @@ 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 +1146,9 @@ 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 +1156,14 @@ 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 +1180,15 @@ 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 +1275,7 @@ 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 +1297,7 @@ 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 +1319,7 @@ 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 +1361,14 @@ 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 +1380,11 @@ 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 +1396,12 @@ 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 +1411,18 @@ 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 +1433,7 @@ 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 +1447,18 @@ 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):
@@ -1467,9 +1467,9 @@ 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):
if not HAS_NUMPY:
@@ -1519,24 +1519,24 @@ 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 +1580,12 @@ 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 +1641,30 @@ 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 +1804,8 @@ 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/bindings/pymod/align_3dcomb.py b/modules/bindings/pymod/align_3dcomb.py
index ca709fc15..f6a4b49ef 100644
--- a/modules/bindings/pymod/align_3dcomb.py
+++ b/modules/bindings/pymod/align_3dcomb.py
@@ -44,7 +44,7 @@ def _SetupFiles(structure_list):
#write out temporary pdb files
if not all([ev.IsValid() for ev in structure_list]):
- raise RuntimeError, "Invalid EntityView 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
@@ -71,7 +71,7 @@ def _Run3DCOMB(command,tpd):
outfile.close()
#check for successful completion of 3DCOMB
if returncode!=0:
- print "WARNING: 3DCOMB error\n"
+ print("WARNING: 3DCOMB error\n")
raise subprocess.CalledProcessError
return returncode
@@ -87,7 +87,7 @@ def _ParseOutput(tpd):
if l.startswith('>'):
fl=ost.FloatList()
for i in range(3):
- l=f.next()
+ l=next(f)
sl=l.split(',')
fl.extend([float(el) for el in sl[0].split()+[sl[1]]])
fl.extend([0,0,0,1])
@@ -115,7 +115,7 @@ def AlignStructures(structure_list,apply_transform=False,name_list=None,comb_exe
returncode=_Run3DCOMB(command,tpd)
try:ali,Tl,results=_ParseOutput(tpd)
except:
- print 'could not parse output'
+ print('could not parse output')
raise RuntimeError
if apply_transform:
for T,ev in zip(Tl,structure_list):
diff --git a/modules/bindings/pymod/blast.py b/modules/bindings/pymod/blast.py
index e63007f40..788d46025 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=[]
diff --git a/modules/bindings/pymod/cadscore.py b/modules/bindings/pymod/cadscore.py
index 3b0fd0a0c..6d5bb0b9a 100644
--- a/modules/bindings/pymod/cadscore.py
+++ b/modules/bindings/pymod/cadscore.py
@@ -246,16 +246,16 @@ 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
+ print(r)
return True
for r in reference.residues:
if r.GetNumber().GetInsCode() != "\0":
- print r
+ 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/dssp.py b/modules/bindings/pymod/dssp.py
index 7fe206d0a..a43696c4e 100644
--- a/modules/bindings/pymod/dssp.py
+++ b/modules/bindings/pymod/dssp.py
@@ -116,9 +116,9 @@ 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 +203,8 @@ 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/hbplus.py b/modules/bindings/pymod/hbplus.py
index 5a97df2c9..39b903359 100644
--- a/modules/bindings/pymod/hbplus.py
+++ b/modules/bindings/pymod/hbplus.py
@@ -108,5 +108,5 @@ 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 617784798..94c1a6435 100644
--- a/modules/bindings/pymod/hhblits.py
+++ b/modules/bindings/pymod/hhblits.py
@@ -161,34 +161,34 @@ 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
@@ -196,7 +196,7 @@ def ParseHHblitsOutput(output):
assert lines.next().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 +221,7 @@ 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!'):
@@ -241,7 +241,7 @@ def ParseHHblitsOutput(output):
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
@@ -758,7 +758,7 @@ 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 d5c9f570d..2c6090102 100644
--- a/modules/bindings/pymod/ialign.py
+++ b/modules/bindings/pymod/ialign.py
@@ -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))
diff --git a/modules/bindings/pymod/kclust.py b/modules/bindings/pymod/kclust.py
index 5ecdf11d0..edcbc4797 100644
--- a/modules/bindings/pymod/kclust.py
+++ b/modules/bindings/pymod/kclust.py
@@ -84,7 +84,7 @@ 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 0f5410fe3..7ab23e854 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)
diff --git a/modules/bindings/pymod/msms.py b/modules/bindings/pymod/msms.py
index 534cd3d8e..21ccf5125 100644
--- a/modules/bindings/pymod/msms.py
+++ b/modules/bindings/pymod/msms.py
@@ -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)]
@@ -154,7 +154,7 @@ 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)
raise MsmsProcessError(proc.returncode, command)
return stdout_value
diff --git a/modules/bindings/pymod/naccess.py b/modules/bindings/pymod/naccess.py
index 0d5566ea2..dc65ab4ef 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):
diff --git a/modules/bindings/tests/test_blast.py b/modules/bindings/tests/test_blast.py
index 18311abd9..fbadfccb1 100644
--- a/modules/bindings/tests/test_blast.py
+++ b/modules/bindings/tests/test_blast.py
@@ -102,7 +102,7 @@ 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_clustalw.py b/modules/bindings/tests/test_clustalw.py
index 8f295088e..222effed8 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_hhblits.py b/modules/bindings/tests/test_hhblits.py
index 2ba099ced..22a4faf20 100644
--- a/modules/bindings/tests/test_hhblits.py
+++ b/modules/bindings/tests/test_hhblits.py
@@ -399,8 +399,8 @@ 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_kclust.py b/modules/bindings/tests/test_kclust.py
index fe7251613..707288d07 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_msms.py b/modules/bindings/tests/test_msms.py
index 9041f94fa..d0cc2c42e 100755
--- a/modules/bindings/tests/test_msms.py
+++ b/modules/bindings/tests/test_msms.py
@@ -37,10 +37,10 @@ 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 c2b33b063..95949301d 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/conop/pymod/cleanup.py b/modules/conop/pymod/cleanup.py
index 1a51673d7..6866a913a 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/tests/test_cleanup.py b/modules/conop/tests/test_cleanup.py
index b0579127a..54d33a8bc 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 bd54b7dfa..01c59a233 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/geom/tests/test_geom.py b/modules/geom/tests/test_geom.py
index 46063eb4f..f84daaa84 100644
--- a/modules/geom/tests/test_geom.py
+++ b/modules/geom/tests/test_geom.py
@@ -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/gfx/pymod/__init__.py b/modules/gfx/pymod/__init__.py
index d1b59f1a7..a0525f126 100644
--- a/modules/gfx/pymod/__init__.py
+++ b/modules/gfx/pymod/__init__.py
@@ -17,7 +17,7 @@
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
#------------------------------------------------------------------------------
from _ost_gfx import *
-from py_gfx_obj import PyGfxObj
+from .py_gfx_obj import PyGfxObj
WHITE=RGB(1.0,1.0,1.0)
BLACK=RGB(0.0,0.0,0.0)
@@ -282,7 +282,7 @@ 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/tests/test_gfx.py b/modules/gfx/tests/test_gfx.py
index fcd0f8510..3889c8e2f 100644
--- a/modules/gfx/tests/test_gfx.py
+++ b/modules/gfx/tests/test_gfx.py
@@ -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_gost_import.py b/modules/gfx/tests/test_gost_import.py
index deebd2d31..357a0678d 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/gui/pymod/__init__.py b/modules/gui/pymod/__init__.py
index da6b1599a..4343829dc 100644
--- a/modules/gui/pymod/__init__.py
+++ b/modules/gui/pymod/__init__.py
@@ -24,9 +24,9 @@ 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/dng/init.py b/modules/gui/pymod/dng/init.py
index 070cace7b..ed274b5d7 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)
@@ -190,15 +190,15 @@ _ostrc=os.path.join(home, '.ostrc')
if os.path.exists(_ostrc):
try:
exec(open(_ostrc))
- except Exception, e:
- print e
+ 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 425cf6ca7..487eec75c 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/export_message_widget.cc b/modules/gui/pymod/export_message_widget.cc
index 1893c7e87..69dd6bb38 100644
--- a/modules/gui/pymod/export_message_widget.cc
+++ b/modules/gui/pymod/export_message_widget.cc
@@ -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/helpwidget.py b/modules/gui/pymod/helpwidget.py
index 9ac28e205..aee9b19ac 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/scene/color_options_widget.py b/modules/gui/pymod/scene/color_options_widget.py
index c99eb41e2..da2deb806 100644
--- a/modules/gui/pymod/scene/color_options_widget.py
+++ b/modules/gui/pymod/scene/color_options_widget.py
@@ -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/combo_options_widget.py b/modules/gui/pymod/scene/combo_options_widget.py
index 28bacce3f..b15a8a490 100644
--- a/modules/gui/pymod/scene/combo_options_widget.py
+++ b/modules/gui/pymod/scene/combo_options_widget.py
@@ -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 c40819abe..3ce8d05a2 100644
--- a/modules/gui/pymod/scene/cpk_widget.py
+++ b/modules/gui/pymod/scene/cpk_widget.py
@@ -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 e94eabd2d..2319e066c 100644
--- a/modules/gui/pymod/scene/custom_widget.py
+++ b/modules/gui/pymod/scene/custom_widget.py
@@ -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/gradient_editor_widget.py b/modules/gui/pymod/scene/gradient_editor_widget.py
index 370bd51cd..17ea07f0d 100644
--- a/modules/gui/pymod/scene/gradient_editor_widget.py
+++ b/modules/gui/pymod/scene/gradient_editor_widget.py
@@ -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 747b05860..5c7414504 100644
--- a/modules/gui/pymod/scene/gradient_info_handler.py
+++ b/modules/gui/pymod/scene/gradient_info_handler.py
@@ -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 43f3f95db..5195e7f9f 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 998714bef..e1717c98f 100644
--- a/modules/gui/pymod/scene/gradient_preset_widget.py
+++ b/modules/gui/pymod/scene/gradient_preset_widget.py
@@ -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 442639a71..8ea2d4ede 100644
--- a/modules/gui/pymod/scene/hsc_widget.py
+++ b/modules/gui/pymod/scene/hsc_widget.py
@@ -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/inspector_widget.py b/modules/gui/pymod/scene/inspector_widget.py
index 503d3acdc..d3d78d034 100644
--- a/modules/gui/pymod/scene/inspector_widget.py
+++ b/modules/gui/pymod/scene/inspector_widget.py
@@ -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 569f6dfcc..b9c6d7695 100644
--- a/modules/gui/pymod/scene/line_trace_widget.py
+++ b/modules/gui/pymod/scene/line_trace_widget.py
@@ -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 b5c0905de..e9a890be8 100644
--- a/modules/gui/pymod/scene/map_level_widget.py
+++ b/modules/gui/pymod/scene/map_level_widget.py
@@ -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 279765d7c..f06a477df 100644
--- a/modules/gui/pymod/scene/preset.py
+++ b/modules/gui/pymod/scene/preset.py
@@ -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 35fac9836..a87800695 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 c5a314efb..5c3ce6aa6 100644
--- a/modules/gui/pymod/scene/preset_editor_widget.py
+++ b/modules/gui/pymod/scene/preset_editor_widget.py
@@ -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 25237b3bd..de1331668 100644
--- a/modules/gui/pymod/scene/preset_info_handler.py
+++ b/modules/gui/pymod/scene/preset_info_handler.py
@@ -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 dbe1926ad..6bdf05db7 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 aec2f2d29..878e5268c 100644
--- a/modules/gui/pymod/scene/preset_widget.py
+++ b/modules/gui/pymod/scene/preset_widget.py
@@ -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 3f4459914..dea7de08d 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 31b33ddd7..520f6be65 100644
--- a/modules/gui/pymod/scene/render_mode_widget.py
+++ b/modules/gui/pymod/scene/render_mode_widget.py
@@ -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_options_widget.py b/modules/gui/pymod/scene/render_options_widget.py
index 90cc213e8..069b87dda 100644
--- a/modules/gui/pymod/scene/render_options_widget.py
+++ b/modules/gui/pymod/scene/render_options_widget.py
@@ -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/simple_widget.py b/modules/gui/pymod/scene/simple_widget.py
index 53e172afd..198426dd1 100644
--- a/modules/gui/pymod/scene/simple_widget.py
+++ b/modules/gui/pymod/scene/simple_widget.py
@@ -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 c42f2f98f..890506bed 100644
--- a/modules/gui/pymod/scene/sline_widget.py
+++ b/modules/gui/pymod/scene/sline_widget.py
@@ -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 55e45b046..638ee2228 100644
--- a/modules/gui/pymod/scene/toolbar_options_widget.py
+++ b/modules/gui/pymod/scene/toolbar_options_widget.py
@@ -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 8705d18d8..b68663e70 100644
--- a/modules/gui/pymod/scene/trace_widget.py
+++ b/modules/gui/pymod/scene/trace_widget.py
@@ -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 682fd0b05..2d7538f4d 100644
--- a/modules/gui/pymod/scene/tube_widget.py
+++ b/modules/gui/pymod/scene/tube_widget.py
@@ -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 2459cbc4c..fb97cb853 100644
--- a/modules/gui/pymod/scene/uniform_color_widget.py
+++ b/modules/gui/pymod/scene/uniform_color_widget.py
@@ -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/wireframe_widget.py b/modules/gui/pymod/scene/wireframe_widget.py
index 458a8f09b..76f2662f3 100644
--- a/modules/gui/pymod/scene/wireframe_widget.py
+++ b/modules/gui/pymod/scene/wireframe_widget.py
@@ -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/table.py b/modules/gui/pymod/table.py
index d45b5d74e..cc6537a9b 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 133091fce..32960ffa1 100644
--- a/modules/gui/pymod/trajectory_viewer.py
+++ b/modules/gui/pymod/trajectory_viewer.py
@@ -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 b24863ca8..64952c829 100644
--- a/modules/gui/pymod/wrap_gui.cc
+++ b/modules/gui/pymod/wrap_gui.cc
@@ -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/python_shell/python_interpreter_worker.hh b/modules/gui/src/python_shell/python_interpreter_worker.hh
index 557604900..66639a2cd 100644
--- a/modules/gui/src/python_shell/python_interpreter_worker.hh
+++ b/modules/gui/src/python_shell/python_interpreter_worker.hh
@@ -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/io/pymod/__init__.py b/modules/io/pymod/__init__.py
index 2a8232118..eee7af12d 100644
--- a/modules/io/pymod/__init__.py
+++ b/modules/io/pymod/__init__.py
@@ -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
#------------------------------------------------------------------------------
-import os, tempfile, ftplib, httplib
+import os, tempfile, ftplib, http.client
from _ost_io import *
from ost import mol, geom, conop, seq
diff --git a/modules/io/pymod/remote.py b/modules/io/pymod/remote.py
index 1f593060f..c0d8990e0 100644
--- a/modules/io/pymod/remote.py
+++ b/modules/io/pymod/remote.py
@@ -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
@@ -49,12 +49,12 @@ 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)' \
diff --git a/modules/io/tests/test_io_mmcif.py b/modules/io/tests/test_io_mmcif.py
index e0672fc39..8a3773b0a 100644
--- a/modules/io/tests/test_io_mmcif.py
+++ b/modules/io/tests/test_io_mmcif.py
@@ -10,51 +10,51 @@ 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 +64,31 @@ 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 +96,11 @@ 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 +110,40 @@ 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 +151,11 @@ 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 +165,22 @@ 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 +188,10 @@ 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 +209,26 @@ 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 +236,18 @@ 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')
if __name__== '__main__':
from ost import testutils
diff --git a/modules/io/tests/test_io_pdb.py b/modules/io/tests/test_io_pdb.py
index f3f3acbdf..3ba3539dc 100644
--- a/modules/io/tests/test_io_pdb.py
+++ b/modules/io/tests/test_io_pdb.py
@@ -7,9 +7,9 @@ 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()
diff --git a/modules/mol/alg/pymod/hbond.py b/modules/mol/alg/pymod/hbond.py
index 33545bd2f..0807fe833 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 3bfb86047..7d9de7da0 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 3ed23ae9e..ba9c2af9d 100644
--- a/modules/mol/alg/pymod/qsscoring.py
+++ b/modules/mol/alg/pymod/qsscoring.py
@@ -1098,7 +1098,7 @@ 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)
@@ -1259,7 +1259,7 @@ 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
@@ -1633,8 +1633,8 @@ 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)
@@ -1646,24 +1646,24 @@ 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'
@@ -1714,7 +1714,7 @@ 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
@@ -1770,9 +1770,9 @@ 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...')
@@ -1878,7 +1878,7 @@ 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
@@ -1906,7 +1906,7 @@ 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
@@ -1928,8 +1928,8 @@ 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))
@@ -2035,16 +2035,16 @@ 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):
@@ -2066,8 +2066,8 @@ 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:
@@ -2104,14 +2104,14 @@ 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]
@@ -2215,7 +2215,7 @@ 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)
@@ -2247,7 +2247,7 @@ 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)
@@ -2266,12 +2266,12 @@ 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):
@@ -2306,14 +2306,14 @@ 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:
@@ -2324,7 +2324,7 @@ 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)
@@ -2341,7 +2341,7 @@ 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
@@ -2387,7 +2387,7 @@ 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)
@@ -2436,10 +2436,10 @@ 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
@@ -2461,7 +2461,7 @@ 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:
@@ -2480,7 +2480,7 @@ 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):
@@ -2496,7 +2496,7 @@ 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)
@@ -2566,7 +2566,7 @@ 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 75ae223e1..2103b14a7 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 546d71c46..515a49703 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 2d71b5a4d..9ff4b341e 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 f4a203077..888953824 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/tests/test_accessibility.py b/modules/mol/alg/tests/test_accessibility.py
index c3d857fd5..8a951529f 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_convenient_superpose.py b/modules/mol/alg/tests/test_convenient_superpose.py
index 30f062429..8e01b4937 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 c81c92479..cbe8257a7 100644
--- a/modules/mol/alg/tests/test_nonstandard.py
+++ b/modules/mol/alg/tests/test_nonstandard.py
@@ -121,4 +121,4 @@ 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_pdbize.py b/modules/mol/alg/tests/test_pdbize.py
index abf2bc892..0048f9b36 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 c241eea49..770c95f6e 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
@@ -605,7 +605,7 @@ 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)
@@ -646,12 +646,12 @@ class TestQSscore(unittest.TestCase):
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 +678,10 @@ 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 207f8600c..c6b6a928e 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/base/tests/test_numpy.py b/modules/mol/base/tests/test_numpy.py
index 27061a234..fb69b9afe 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/mm/pymod/__init__.py b/modules/mol/mm/pymod/__init__.py
index a4a7c650e..f10fd7e6b 100644
--- a/modules/mol/mm/pymod/__init__.py
+++ b/modules/mol/mm/pymod/__init__.py
@@ -19,7 +19,7 @@
import os.path
from _ost_mol_mm import *
-import antechamber
+from . import antechamber
import ost
def LoadAMBERForcefield():
diff --git a/modules/mol/mm/pymod/antechamber.py b/modules/mol/mm/pymod/antechamber.py
index 6fc48ce3f..979dd4d99 100644
--- a/modules/mol/mm/pymod/antechamber.py
+++ b/modules/mol/mm/pymod/antechamber.py
@@ -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/seq/alg/pymod/__init__.py b/modules/seq/alg/pymod/__init__.py
index 44fa50acf..8d9b9c806 100644
--- a/modules/seq/alg/pymod/__init__.py
+++ b/modules/seq/alg/pymod/__init__.py
@@ -188,7 +188,7 @@ 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/tests/test_aligntoseqres.py b/modules/seq/alg/tests/test_aligntoseqres.py
index 2aa1bb4fe..5664ff837 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_renumber.py b/modules/seq/alg/tests/test_renumber.py
index 0309f5a1b..f587d588f 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/scripts/bump-version.py b/scripts/bump-version.py
index 053b08bfd..ddf414cd6 100755
--- a/scripts/bump-version.py
+++ b/scripts/bump-version.py
@@ -2,9 +2,9 @@
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
diff --git a/scripts/code_coverage.py b/scripts/code_coverage.py
index 6df65830e..1cb87bc3a 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)
--
GitLab
From 70c2e161a854c73a13387865a030d575a6cb5034 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Fri, 15 Nov 2019 09:05:05 +0100
Subject: [PATCH 002/142] Apply 2to3 to file not ending with .py
Executed command: 2to3-2.7 -n -w scripts/ost_startup.py.in
---
scripts/ost_startup.py.in | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/scripts/ost_startup.py.in b/scripts/ost_startup.py.in
index d3cac43d8..ed156415b 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''')
@@ -74,8 +74,8 @@ _ostrc=os.path.join(home, '.ostrc')
if os.path.exists(_ostrc):
try:
exec(open(_ostrc))
- except Exception, e:
- print e
+ 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).read(), script, 'exec'))
finally:
sys.argv=sys_argv_backup
--
GitLab
From b4a37afc3a246458eab01e21931fc5149a4ec748 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Fri, 15 Nov 2019 09:13:26 +0100
Subject: [PATCH 003/142] Fixed implicit relative import for Python modules in
shared object files
That's the Python modules we generate with boost.python. 2to3 misses them
---
modules/base/pymod/__init__.py.in | 4 ++--
modules/bindings/pymod/__init__.py | 2 +-
modules/conop/pymod/__init__.py | 2 +-
modules/db/pymod/__init__.py | 2 +-
modules/geom/pymod/__init__.py | 2 +-
modules/gfx/pymod/__init__.py | 2 +-
modules/gfx/pymod/py_gfx_obj.py | 2 +-
modules/gui/pymod/__init__.py | 2 +-
modules/img/alg/pymod/__init__.py | 2 +-
modules/img/base/pymod/__init__.py | 2 +-
modules/info/pymod/__init__.py | 2 +-
modules/io/pymod/__init__.py | 2 +-
modules/mol/alg/pymod/__init__.py | 2 +-
modules/mol/base/pymod/__init__.py | 2 +-
modules/mol/mm/pymod/__init__.py | 2 +-
modules/seq/alg/pymod/__init__.py | 2 +-
modules/seq/base/pymod/__init__.py | 2 +-
17 files changed, 18 insertions(+), 18 deletions(-)
diff --git a/modules/base/pymod/__init__.py.in b/modules/base/pymod/__init__.py.in
index 89316b831..2676aa771 100644
--- a/modules/base/pymod/__init__.py.in
+++ b/modules/base/pymod/__init__.py.in
@@ -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/bindings/pymod/__init__.py b/modules/bindings/pymod/__init__.py
index 4510f10ef..c61b4e974 100644
--- a/modules/bindings/pymod/__init__.py
+++ b/modules/bindings/pymod/__init__.py
@@ -8,4 +8,4 @@ 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/conop/pymod/__init__.py b/modules/conop/pymod/__init__.py
index 3b7856fe1..b70493ec9 100644
--- a/modules/conop/pymod/__init__.py
+++ b/modules/conop/pymod/__init__.py
@@ -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/db/pymod/__init__.py b/modules/db/pymod/__init__.py
index d443def87..38881c6df 100644
--- a/modules/db/pymod/__init__.py
+++ b/modules/db/pymod/__init__.py
@@ -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/geom/pymod/__init__.py b/modules/geom/pymod/__init__.py
index bd4691781..88ad89786 100644
--- a/modules/geom/pymod/__init__.py
+++ b/modules/geom/pymod/__init__.py
@@ -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/gfx/pymod/__init__.py b/modules/gfx/pymod/__init__.py
index a0525f126..60ad84ec6 100644
--- a/modules/gfx/pymod/__init__.py
+++ b/modules/gfx/pymod/__init__.py
@@ -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_gfx import *
+from ._ost_gfx import *
from .py_gfx_obj import PyGfxObj
WHITE=RGB(1.0,1.0,1.0)
diff --git a/modules/gfx/pymod/py_gfx_obj.py b/modules/gfx/pymod/py_gfx_obj.py
index ac91e9073..557e645ec 100644
--- a/modules/gfx/pymod/py_gfx_obj.py
+++ b/modules/gfx/pymod/py_gfx_obj.py
@@ -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/gui/pymod/__init__.py b/modules/gui/pymod/__init__.py
index 4343829dc..68b4a7300 100644
--- a/modules/gui/pymod/__init__.py
+++ b/modules/gui/pymod/__init__.py
@@ -17,7 +17,7 @@
# 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
diff --git a/modules/img/alg/pymod/__init__.py b/modules/img/alg/pymod/__init__.py
index d67a86754..805731f76 100644
--- a/modules/img/alg/pymod/__init__.py
+++ b/modules/img/alg/pymod/__init__.py
@@ -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/base/pymod/__init__.py b/modules/img/base/pymod/__init__.py
index 82a290219..398809616 100644
--- a/modules/img/base/pymod/__init__.py
+++ b/modules/img/base/pymod/__init__.py
@@ -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/info/pymod/__init__.py b/modules/info/pymod/__init__.py
index 4243e15ac..5d78be195 100644
--- a/modules/info/pymod/__init__.py
+++ b/modules/info/pymod/__init__.py
@@ -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/io/pymod/__init__.py b/modules/io/pymod/__init__.py
index eee7af12d..85e1a325e 100644
--- a/modules/io/pymod/__init__.py
+++ b/modules/io/pymod/__init__.py
@@ -18,7 +18,7 @@
#------------------------------------------------------------------------------
import os, tempfile, ftplib, http.client
-from _ost_io import *
+from ._ost_io import *
from ost import mol, geom, conop, seq
profiles=None
diff --git a/modules/mol/alg/pymod/__init__.py b/modules/mol/alg/pymod/__init__.py
index 73d5bd802..16127a166 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/base/pymod/__init__.py b/modules/mol/base/pymod/__init__.py
index 512e4daf0..e6dd8d59a 100644
--- a/modules/mol/base/pymod/__init__.py
+++ b/modules/mol/base/pymod/__init__.py
@@ -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/mm/pymod/__init__.py b/modules/mol/mm/pymod/__init__.py
index f10fd7e6b..ac671a2b6 100644
--- a/modules/mol/mm/pymod/__init__.py
+++ b/modules/mol/mm/pymod/__init__.py
@@ -18,7 +18,7 @@
#------------------------------------------------------------------------------
import os.path
-from _ost_mol_mm import *
+from ._ost_mol_mm import *
from . import antechamber
import ost
diff --git a/modules/seq/alg/pymod/__init__.py b/modules/seq/alg/pymod/__init__.py
index 8d9b9c806..9ce2fff11 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):
diff --git a/modules/seq/base/pymod/__init__.py b/modules/seq/base/pymod/__init__.py
index 1594a2553..2e45c5a10 100644
--- a/modules/seq/base/pymod/__init__.py
+++ b/modules/seq/base/pymod/__init__.py
@@ -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
--
GitLab
From 0bb56aafaf610625f97def33980561846197fbc7 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Fri, 15 Nov 2019 09:47:45 +0100
Subject: [PATCH 004/142] fix unicode escape characters
---
modules/base/tests/test_table.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/modules/base/tests/test_table.py b/modules/base/tests/test_table.py
index ec2e5fcf0..1d6c91d11 100644
--- a/modules/base/tests/test_table.py
+++ b/modules/base/tests/test_table.py
@@ -931,7 +931,7 @@ class TestTable(unittest.TestCase):
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()
--
GitLab
From 8f07b677cf8e72162024f7494b698e56e8dbea65 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Fri, 15 Nov 2019 09:52:11 +0100
Subject: [PATCH 005/142] Writing csv file does not require 'b' (binary) flag
---
modules/base/pymod/table.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/modules/base/pymod/table.py b/modules/base/pymod/table.py
index 4a4a55934..70b8b3371 100644
--- a/modules/base/pymod/table.py
+++ b/modules/base/pymod/table.py
@@ -2274,7 +2274,7 @@ Statistics for column %(col)s
def _SaveCSV(self, stream, sep):
if not hasattr(stream, 'write'):
- stream=open(stream, 'wb')
+ stream=open(stream, 'w')
writer=csv.writer(stream, delimiter=sep)
writer.writerow(['%s' % n for n in self.col_names])
--
GitLab
From 5b0a9768918868d8385816166e50c6fe0aa44666 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Fri, 15 Nov 2019 09:55:20 +0100
Subject: [PATCH 006/142] Check for None
Python 2 allows for boolean comparisons with None, Python 3 does not.
---
modules/base/pymod/table.py | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/modules/base/pymod/table.py b/modules/base/pymod/table.py
index 70b8b3371..c442061fb 100644
--- a/modules/base/pymod/table.py
+++ b/modules/base/pymod/table.py
@@ -1468,7 +1468,8 @@ 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
--
GitLab
From 2841fd315eae0ce80ec35cafa0ce37d358854ddb Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Fri, 15 Nov 2019 09:57:07 +0100
Subject: [PATCH 007/142] fix another implicit relative import
---
modules/base/pymod/table.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/modules/base/pymod/table.py b/modules/base/pymod/table.py
index c442061fb..6a8a9abe3 100644
--- a/modules/base/pymod/table.py
+++ b/modules/base/pymod/table.py
@@ -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!")
--
GitLab
From a61db892d09332495fc673c4340bcc502fd9ddb1 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Fri, 15 Nov 2019 10:00:41 +0100
Subject: [PATCH 008/142] Custom comparison function in sorting algorithms must
be provided as "key".
A simple function returing True or False is also not sufficient anymore.
functools.cmp_to_key comes to the rescue.
---
modules/base/pymod/table.py | 16 ++++++++++++++--
1 file changed, 14 insertions(+), 2 deletions(-)
diff --git a/modules/base/pymod/table.py b/modules/base/pymod/table.py
index 6a8a9abe3..dc59194e0 100644
--- a/modules/base/pymod/table.py
+++ b/modules/base/pymod/table.py
@@ -1043,8 +1043,20 @@ 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):
"""
--
GitLab
From 2aff00662dda83b9f745ef9fb24a8d40d759d4ca Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Fri, 15 Nov 2019 10:06:17 +0100
Subject: [PATCH 009/142] Fix issue with changed rounding behaviour in Python
3.
Python 3 rounds towards the nearest even number if its in the middle
of two integers as opposed to Python 2 that simply rounds to the higher
integer number. By doing that we avoid biases towards higher numbers.
---
modules/base/pymod/table.py | 6 ++++--
1 file changed, 4 insertions(+), 2 deletions(-)
diff --git a/modules/base/pymod/table.py b/modules/base/pymod/table.py
index dc59194e0..bb7714f03 100644
--- a/modules/base/pymod/table.py
+++ b/modules/base/pymod/table.py
@@ -2002,7 +2002,7 @@ 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''
@@ -2033,7 +2033,9 @@ 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
--
GitLab
From 70d8dc82da3b5de412356cb148c0d35b8d062ae7 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Fri, 15 Nov 2019 10:15:11 +0100
Subject: [PATCH 010/142] enforce integer division
in Python 2: 1/2=0 in Python 3: 1/2 = 0.5
---
modules/base/pymod/stutil.py | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/modules/base/pymod/stutil.py b/modules/base/pymod/stutil.py
index 506675f12..705b56f8d 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):
"""
--
GitLab
From c2407570abb56683dc2fa460456b2bfb682cf5ae Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Fri, 15 Nov 2019 10:21:59 +0100
Subject: [PATCH 011/142] we're not reading a binary file here
---
modules/base/tests/test_table.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/modules/base/tests/test_table.py b/modules/base/tests/test_table.py
index 1d6c91d11..640e7c366 100644
--- a/modules/base/tests/test_table.py
+++ b/modules/base/tests/test_table.py
@@ -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')
--
GitLab
From f8b3f610d40442807256ac934e7e2e6698253f3b Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Fri, 15 Nov 2019 10:41:00 +0100
Subject: [PATCH 012/142] Add __next__ function in iterators we export with
boost.python
Previously we only had next, which is Python 2 compatible. Now
we have both.
---
modules/img/base/pymod/export_extent.cc | 1 +
modules/seq/base/pymod/export_sequence.cc | 4 ++++
2 files changed, 5 insertions(+)
diff --git a/modules/img/base/pymod/export_extent.cc b/modules/img/base/pymod/export_extent.cc
index 421fa2f89..57e3c6f1b 100644
--- a/modules/img/base/pymod/export_extent.cc
+++ b/modules/img/base/pymod/export_extent.cc
@@ -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/seq/base/pymod/export_sequence.cc b/modules/seq/base/pymod/export_sequence.cc
index e8331c7fc..e881187c5 100644
--- a/modules/seq/base/pymod/export_sequence.cc
+++ b/modules/seq/base/pymod/export_sequence.cc
@@ -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)
--
GitLab
From 4d2eadbf096b9dfaaaa1953e3d9db20b45ff1e46 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Fri, 15 Nov 2019 10:50:45 +0100
Subject: [PATCH 013/142] fix import
---
modules/mol/mm/pymod/antechamber.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/modules/mol/mm/pymod/antechamber.py b/modules/mol/mm/pymod/antechamber.py
index 979dd4d99..0092f406c 100644
--- a/modules/mol/mm/pymod/antechamber.py
+++ b/modules/mol/mm/pymod/antechamber.py
@@ -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
--
GitLab
From 00ebde86d16f384a92cb498eb535fbd06d063ca6 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Fri, 15 Nov 2019 11:05:15 +0100
Subject: [PATCH 014/142] Fix ost startup scripts execfile has been replaced by
exec in Python 3
---
scripts/ost.in | 4 ++--
scripts/ost_startup.py.in | 2 +-
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/scripts/ost.in b/scripts/ost.in
index a20bef97b..6da63bda4 100755
--- a/scripts/ost.in
+++ b/scripts/ost.in
@@ -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_startup.py.in b/scripts/ost_startup.py.in
index ed156415b..6a5addab2 100644
--- a/scripts/ost_startup.py.in
+++ b/scripts/ost_startup.py.in
@@ -73,7 +73,7 @@ home = os.getenv('HOME') or os.getenv('USERPROFILE')
_ostrc=os.path.join(home, '.ostrc')
if os.path.exists(_ostrc):
try:
- exec(open(_ostrc))
+ exec(compile(open(_ostrc).read(), _ostrc, 'exec'))
except Exception as e:
print(e)
PushVerbosityLevel(options.vlevel)
--
GitLab
From e33da01ae8155f3a5488d1620f0393fed79364e9 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Fri, 15 Nov 2019 11:21:36 +0100
Subject: [PATCH 015/142] port code that we directly feed into the Python
interpreter from C++
---
modules/gui/src/gosty.cc | 14 +++++++++-----
modules/gui/src/python_shell/python_interpreter.cc | 2 +-
2 files changed, 10 insertions(+), 6 deletions(-)
diff --git a/modules/gui/src/gosty.cc b/modules/gui/src/gosty.cc
index b5275bb3e..350b1f520 100644
--- a/modules/gui/src/gosty.cc
+++ b/modules/gui/src/gosty.cc
@@ -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/python_shell/python_interpreter.cc b/modules/gui/src/python_shell/python_interpreter.cc
index 29178f2c0..08b0c3471 100644
--- a/modules/gui/src/python_shell/python_interpreter.cc
+++ b/modules/gui/src/python_shell/python_interpreter.cc
@@ -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");
--
GitLab
From c933f04e246d03811247273f9e645978160d0bcd Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Fri, 15 Nov 2019 11:34:30 +0100
Subject: [PATCH 016/142] need to explicitely call read in new urllib
---
modules/io/pymod/remote.py | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
diff --git a/modules/io/pymod/remote.py b/modules/io/pymod/remote.py
index c0d8990e0..d23770774 100644
--- a/modules/io/pymod/remote.py
+++ b/modules/io/pymod/remote.py
@@ -60,8 +60,7 @@ class RemoteRepository:
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
--
GitLab
From 0f693890b3903c9e341e3a0a5525524f2d3bff4e Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Fri, 15 Nov 2019 11:40:06 +0100
Subject: [PATCH 017/142] Fix exec that runs ostrc
---
modules/gui/pymod/dng/init.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/modules/gui/pymod/dng/init.py b/modules/gui/pymod/dng/init.py
index ed274b5d7..c555d9166 100644
--- a/modules/gui/pymod/dng/init.py
+++ b/modules/gui/pymod/dng/init.py
@@ -189,7 +189,7 @@ home = os.getenv('HOME') or os.getenv('USERPROFILE')
_ostrc=os.path.join(home, '.ostrc')
if os.path.exists(_ostrc):
try:
- exec(open(_ostrc))
+ exec(compile(open(_ostrc).read(), _ostrc, 'exec'))
except Exception as e:
print(e)
else:
--
GitLab
From 8d00ad2ecd5eeb7ea9e486f76828d237f82234b0 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Fri, 15 Nov 2019 14:04:25 +0100
Subject: [PATCH 018/142] Apply 2to3 to file not ending with .py
Executed command: 2to3-2.7 -n -w actions/ost-compare-structures
---
actions/ost-compare-structures | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/actions/ost-compare-structures b/actions/ost-compare-structures
index 8ae9ff19e..41f1080ce 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 reverted_chains.items()]
ost.LogInfo("Reverted chains: %s" % ", ".join(rev_out))
--
GitLab
From 8d1a0447c7abaea3716d551a8e383543dbc75f30 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Wed, 20 Nov 2019 11:35:35 +0100
Subject: [PATCH 019/142] set universal_newlines flag in Popen
This enables string encoding in passed streams => stdout and stderr
---
modules/bindings/pymod/blast.py | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/modules/bindings/pymod/blast.py b/modules/bindings/pymod/blast.py
index 788d46025..7ecff0896 100644
--- a/modules/bindings/pymod/blast.py
+++ b/modules/bindings/pymod/blast.py
@@ -192,7 +192,7 @@ def BlastVersion(blast_location=None):
pattern=re.compile(r'\s*Package: blast (\d+\.\d+\.\d+),\s+')
blast_pipe=subprocess.Popen(args, stdout=subprocess.PIPE,
- stderr=subprocess.PIPE)
+ stderr=subprocess.PIPE, universal_newlines=True)
lines=blast_pipe.stdout.readlines()
for line in lines:
@@ -264,7 +264,8 @@ def Blast(query, database, gap_open=11, gap_ext=1, matrix='BLOSUM62',
ost.LogInfo('running BLAST (%s)' % ' '.join(args))
blast_pipe=subprocess.Popen(args, stderr=subprocess.PIPE,
- stdout=subprocess.PIPE, stdin=subprocess.PIPE)
+ stdout=subprocess.PIPE, stdin=subprocess.PIPE,
+ universal_newlines=True)
if isinstance(query, str):
stdout, stderr=blast_pipe.communicate(query)
else:
--
GitLab
From 4bb2241510854402af6668909ba059216409c3d8 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Wed, 20 Nov 2019 11:38:25 +0100
Subject: [PATCH 020/142] set universal_newlines flag in Popen
This enables string encoding in passed streams => stdout and stderr
---
modules/bindings/pymod/msms.py | 6 ++++--
1 file changed, 4 insertions(+), 2 deletions(-)
diff --git a/modules/bindings/pymod/msms.py b/modules/bindings/pymod/msms.py
index 21ccf5125..b7d338e50 100644
--- a/modules/bindings/pymod/msms.py
+++ b/modules/bindings/pymod/msms.py
@@ -43,7 +43,8 @@ def GetVersion(msms_exe=None, msms_env=None):
"""
msms_executable = _GetExecutable(msms_exe, msms_env)
command = "%s" % (msms_executable)
- proc = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE)
+ proc = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE,
+ universal_newlines=True)
stdout_value, stderr_value = proc.communicate()
version = ""
@@ -149,7 +150,8 @@ def _RunMSMS(command):
:returns: stdout of MSMS
:raises: :class:`CalledProcessError` for non-zero return value
"""
- proc = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE)
+ proc = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE,
+ universal_newlines=True)
stdout_value, stderr_value = proc.communicate()
#check for successful completion of msms
--
GitLab
From ff2ca6411a1a40c041a3ef50ed6d1c3fed244baf Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Wed, 20 Nov 2019 11:39:13 +0100
Subject: [PATCH 021/142] increase test coverage of msms binding
---
modules/bindings/tests/test_msms.py | 32 ++++++++++++++++++-----------
1 file changed, 20 insertions(+), 12 deletions(-)
diff --git a/modules/bindings/tests/test_msms.py b/modules/bindings/tests/test_msms.py
index d0cc2c42e..e4320a878 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.assertEqual(self.ases, msms_ases[0])
+ self.assertEqual(self.asas, msms_asas[0])
+ def testCalculateSurfaceVolume(self):
+ volume=msms.CalculateSurfaceVolume(self.protein, \
+ msms_env='MSMSSERVER',
+ density=3,
+ radius=1.4)
+ self.assertEqual(self.volume, volume)
if __name__ == "__main__":
# test if msms package is available on system, otherwise ignore tests
--
GitLab
From 1467412458273c9f81f0ba91a5a22d6f6d65c08d Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Wed, 20 Nov 2019 11:55:38 +0100
Subject: [PATCH 022/142] set universal_newlines flag in Popen
This enables string encoding in passed streams => stdout and stderr
---
modules/bindings/pymod/naccess.py | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/modules/bindings/pymod/naccess.py b/modules/bindings/pymod/naccess.py
index dc65ab4ef..d2592c6b2 100644
--- a/modules/bindings/pymod/naccess.py
+++ b/modules/bindings/pymod/naccess.py
@@ -192,7 +192,7 @@ def _RunACCALL(command, temp_dir, query):
"""
proc = subprocess.Popen(command, stdout=subprocess.PIPE,
stderr=subprocess.PIPE, stdin=subprocess.PIPE,
- cwd=temp_dir)
+ cwd=temp_dir, universal_newlines=True)
stdout_value, stderr_value = proc.communicate(query)
# check for successful completion of naccess
@@ -215,7 +215,7 @@ def _RunNACCESS(command, temp_dir):
:exception: CalledProcessError for non-zero return value
"""
proc = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE,
- cwd=temp_dir)
+ cwd=temp_dir, universal_newlines=True)
stdout_value, stderr_value = proc.communicate()
# check for successful completion of naccess
--
GitLab
From b70d56269a5688da3ba65bbc8e6ea1f03986f044 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Wed, 20 Nov 2019 14:17:58 +0100
Subject: [PATCH 023/142] set universal_newlines flag in Popen
This enables string encoding in passed streams => stdout and stderr
---
modules/bindings/pymod/cadscore.py | 14 ++++++++------
1 file changed, 8 insertions(+), 6 deletions(-)
diff --git a/modules/bindings/pymod/cadscore.py b/modules/bindings/pymod/cadscore.py
index 6d5bb0b9a..90fa77e4a 100644
--- a/modules/bindings/pymod/cadscore.py
+++ b/modules/bindings/pymod/cadscore.py
@@ -185,16 +185,19 @@ def _RunCAD(tmp_dir, mode, cad_bin_path, old_regime):
os.path.join(tmp_dir,
"cadtemp"))
- ps1=subprocess.Popen(command1, shell=True, stdout=subprocess.PIPE)
+ ps1=subprocess.Popen(command1, shell=True, stdout=subprocess.PIPE,
+ universal_newlines=True)
ps1.wait()
- ps2=subprocess.Popen(command2, shell=True, stdout=subprocess.PIPE)
+ ps2=subprocess.Popen(command2, shell=True, stdout=subprocess.PIPE,
+ universal_newlines=True)
ps2.wait()
lines=ps2.stdout.readlines()
try:
globalAA=_ParseCADGlobal(lines)
except:
raise RuntimeError("CAD calculation failed")
- ps3=subprocess.Popen(command3, shell=True, stdout=subprocess.PIPE)
+ ps3=subprocess.Popen(command3, shell=True, stdout=subprocess.PIPE,
+ universal_newlines=True)
ps3.wait()
lines=ps3.stdout.readlines()
try:
@@ -225,7 +228,8 @@ def _RunCAD(tmp_dir, mode, cad_bin_path, old_regime):
if old_regime:
cmd.append("--old-regime")
cmd = ' '.join(cmd)
- ps = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE)
+ ps = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE,
+ universal_newlines=True)
ps.wait()
try:
globalAA = _ParseVoronotaGlobal(ps.stdout.readlines())
@@ -246,11 +250,9 @@ 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
--
GitLab
From 6d4fec60460de7999dd0f380cafb50a704d3f11d Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Wed, 20 Nov 2019 14:18:22 +0100
Subject: [PATCH 024/142] add basic unit test for cadscore binding
---
modules/bindings/tests/CMakeLists.txt | 1 +
modules/bindings/tests/test_cadscore.py | 74 +++++++++++++++++++++++++
2 files changed, 75 insertions(+)
create mode 100644 modules/bindings/tests/test_cadscore.py
diff --git a/modules/bindings/tests/CMakeLists.txt b/modules/bindings/tests/CMakeLists.txt
index dd257c1cb..b5a44d108 100644
--- a/modules/bindings/tests/CMakeLists.txt
+++ b/modules/bindings/tests/CMakeLists.txt
@@ -5,6 +5,7 @@ set(OST_BINDINGS_UNIT_TESTS
test_blast.py
test_kclust.py
test_naccess.py
+ test_cadscore.py
)
ost_unittest(MODULE bindings
diff --git a/modules/bindings/tests/test_cadscore.py b/modules/bindings/tests/test_cadscore.py
new file mode 100644
index 000000000..be3bab50d
--- /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()
--
GitLab
From cfd8447f019c4a28299bf5bdc5a1a007d4e0bc38 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Wed, 20 Nov 2019 15:37:41 +0100
Subject: [PATCH 025/142] set universal_newlines flag in Popen
This enables string encoding in passed streams => stdout and stderr
---
modules/bindings/pymod/tmtools.py | 9 ++++++---
1 file changed, 6 insertions(+), 3 deletions(-)
diff --git a/modules/bindings/pymod/tmtools.py b/modules/bindings/pymod/tmtools.py
index 0d158d77f..7b26d50a8 100644
--- a/modules/bindings/pymod/tmtools.py
+++ b/modules/bindings/pymod/tmtools.py
@@ -80,7 +80,8 @@ def _RunTmAlign(tmalign, tmp_dir):
else:
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=subprocess.Popen(command, shell=True, stdout=subprocess.PIPE,
+ universal_newlines=True)
ps.wait()
lines=ps.stdout.readlines()
if (len(lines))<22:
@@ -128,7 +129,8 @@ def _RunMmAlign(mmalign, tmp_dir):
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=subprocess.Popen(command, shell=True, stdout=subprocess.PIPE,
+ universal_newlines=True)
ps.wait()
lines=ps.stdout.readlines()
if (len(lines))<22:
@@ -205,7 +207,8 @@ def _RunTmScore(tmscore, tmp_dir):
tmscore_path=settings.Locate('tmscore', explicit_file_name=tmscore)
command="\"%s\" \"%s\" \"%s\"" % (tmscore_path, model1_filename,
model2_filename)
- ps=subprocess.Popen(command, shell=True, stdout=subprocess.PIPE)
+ ps=subprocess.Popen(command, shell=True, stdout=subprocess.PIPE,
+ universal_newlines=True)
ps.wait()
lines=ps.stdout.readlines()
if (len(lines))<22:
--
GitLab
From 7be99f6bcbb0c69b09cb50faaa3e2ee17b568648 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Wed, 20 Nov 2019 15:38:30 +0100
Subject: [PATCH 026/142] basic unit tests for TMAlign and TMScore
---
modules/bindings/tests/CMakeLists.txt | 1 +
modules/bindings/tests/test_tmtools.py | 59 ++++++++++++++++++++++++++
2 files changed, 60 insertions(+)
create mode 100644 modules/bindings/tests/test_tmtools.py
diff --git a/modules/bindings/tests/CMakeLists.txt b/modules/bindings/tests/CMakeLists.txt
index b5a44d108..089f1ae9b 100644
--- a/modules/bindings/tests/CMakeLists.txt
+++ b/modules/bindings/tests/CMakeLists.txt
@@ -6,6 +6,7 @@ set(OST_BINDINGS_UNIT_TESTS
test_kclust.py
test_naccess.py
test_cadscore.py
+ test_tmtools.py
)
ost_unittest(MODULE bindings
diff --git a/modules/bindings/tests/test_tmtools.py b/modules/bindings/tests/test_tmtools.py
new file mode 100644
index 000000000..148e6263c
--- /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()
--
GitLab
From 33e8b86a6ec1d167266b5df956d4a15f0660ddea Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Wed, 20 Nov 2019 17:00:32 +0100
Subject: [PATCH 027/142] set universal_newlines flag in Popen
This enables string encoding in passed streams => stdout and stderr
---
modules/bindings/pymod/ialign.py | 5 ++++-
1 file changed, 4 insertions(+), 1 deletion(-)
diff --git a/modules/bindings/pymod/ialign.py b/modules/bindings/pymod/ialign.py
index 2c6090102..176a5dbe4 100644
--- a/modules/bindings/pymod/ialign.py
+++ b/modules/bindings/pymod/ialign.py
@@ -140,9 +140,12 @@ 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=subprocess.Popen(command, shell=True, stdout=subprocess.PIPE,
+ universal_newlines=True)
ps.wait()
lines=ps.stdout.readlines()
+
if (len(lines))<22:
_CleanupFiles(tmp_dir)
#for l in lines:
--
GitLab
From 8e46c4e1a041b1b8c7e01185123a7d8357fc94f3 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Wed, 20 Nov 2019 17:00:51 +0100
Subject: [PATCH 028/142] set universal_newlines flag in Popen
This enables string encoding in passed streams => stdout and stderr
---
modules/bindings/pymod/hbplus.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/modules/bindings/pymod/hbplus.py b/modules/bindings/pymod/hbplus.py
index 39b903359..3ca6361a4 100644
--- a/modules/bindings/pymod/hbplus.py
+++ b/modules/bindings/pymod/hbplus.py
@@ -63,7 +63,7 @@ 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)
+ stdin=subprocess.PIPE, universal_newlines=True)
file_name=os.path.join(temp_d, 'ent.pdb')
io.SaveEntity(ent, file_name)
hb_proc.stdin.write('%s\n' % temp_d)
--
GitLab
From 2cb47edc13807225098fa448493ef17907fe9c64 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Wed, 20 Nov 2019 17:01:49 +0100
Subject: [PATCH 029/142] basic unit tests for ialign
---
modules/bindings/tests/CMakeLists.txt | 1 +
modules/bindings/tests/test_ialign.py | 37 +++++++++++++++++++++++++++
2 files changed, 38 insertions(+)
create mode 100644 modules/bindings/tests/test_ialign.py
diff --git a/modules/bindings/tests/CMakeLists.txt b/modules/bindings/tests/CMakeLists.txt
index 089f1ae9b..3d3efc3ab 100644
--- a/modules/bindings/tests/CMakeLists.txt
+++ b/modules/bindings/tests/CMakeLists.txt
@@ -7,6 +7,7 @@ set(OST_BINDINGS_UNIT_TESTS
test_naccess.py
test_cadscore.py
test_tmtools.py
+ test_ialign.py
)
ost_unittest(MODULE bindings
diff --git a/modules/bindings/tests/test_ialign.py b/modules/bindings/tests/test_ialign.py
new file mode 100644
index 000000000..33b6f610d
--- /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()
--
GitLab
From 85ef16b06e6805f0c762a5d49fc98e4737bfe34b Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Wed, 20 Nov 2019 17:31:00 +0100
Subject: [PATCH 030/142] remove MMalign support as current binding is broken
with latest MMalign exec
---
modules/bindings/pymod/tmtools.py | 55 -------------------------------
1 file changed, 55 deletions(-)
diff --git a/modules/bindings/pymod/tmtools.py b/modules/bindings/pymod/tmtools.py
index 7b26d50a8..b91dd6676 100644
--- a/modules/bindings/pymod/tmtools.py
+++ b/modules/bindings/pymod/tmtools.py
@@ -92,51 +92,6 @@ 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,
- universal_newlines=True)
- ps.wait()
- lines=ps.stdout.readlines()
- if (len(lines))<22:
- _CleanupFiles(tmp_dir)
- raise RuntimeError("mmalign superposition failed")
- return _ParseMmAlign(lines)
class TMScoreResult:
"""
@@ -241,16 +196,6 @@ 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,
--
GitLab
From c9a07fd61adff60d78bdbcf29c38363b19bf7ffa Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Thu, 21 Nov 2019 11:19:06 +0100
Subject: [PATCH 031/142] remove 3dcomb binding as it is broken with latest
code
checked with: https://github.com/realbigws/DeepAlign
commit: cff7c39c89c6706858532b55567083823a0f2657
---
modules/bindings/pymod/CMakeLists.txt | 1 -
modules/bindings/pymod/__init__.py | 1 -
modules/bindings/pymod/align_3dcomb.py | 129 -------------------------
3 files changed, 131 deletions(-)
delete mode 100644 modules/bindings/pymod/align_3dcomb.py
diff --git a/modules/bindings/pymod/CMakeLists.txt b/modules/bindings/pymod/CMakeLists.txt
index 468151bc5..17bd42b19 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 c61b4e974..5e8e38a42 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 *
diff --git a/modules/bindings/pymod/align_3dcomb.py b/modules/bindings/pymod/align_3dcomb.py
deleted file mode 100644
index f6a4b49ef..000000000
--- 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=next(f)
- 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
-
-
-
-
--
GitLab
From c40bc7993cbaa88e92d2594ab2481c6f1dfa56ca Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Sat, 23 Nov 2019 18:03:14 +0100
Subject: [PATCH 032/142] IOException does not have message attribute in Python
3
---
modules/bindings/tests/test_hhblits.py | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/modules/bindings/tests/test_hhblits.py b/modules/bindings/tests/test_hhblits.py
index 22a4faf20..eaff9a3f7 100644
--- a/modules/bindings/tests/test_hhblits.py
+++ b/modules/bindings/tests/test_hhblits.py
@@ -182,7 +182,7 @@ 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):
@@ -287,7 +287,7 @@ class TestHHblitsBindings(unittest.TestCase):
# get info from an HHM file
with self.assertRaises(IOError) as ioe:
hhblits.ParseHHM(open('testfiles/testali.a3m'))
- self.assertEqual(ioe.exception.message,
+ self.assertEqual(ioe.exception.args[0],
'Profile file "testfiles/testali.a3m" is missing '+
'the "Consensus" section')
--
GitLab
From 38a4f735d752b8a6961bce9b3276f3af28834811 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Sat, 23 Nov 2019 18:05:45 +0100
Subject: [PATCH 033/142] port of hhblits binding to Python 3
---
modules/bindings/pymod/hhblits.py | 23 +++++++++++++----------
1 file changed, 13 insertions(+), 10 deletions(-)
diff --git a/modules/bindings/pymod/hhblits.py b/modules/bindings/pymod/hhblits.py
index 94c1a6435..9749507c5 100644
--- a/modules/bindings/pymod/hhblits.py
+++ b/modules/bindings/pymod/hhblits.py
@@ -193,7 +193,8 @@ def ParseHHblitsOutput(output):
return header
def _ParseTableOfContents(lines):
- assert lines.next().startswith(' No Hit')
+ line = next(lines)
+ assert line.startswith(' No Hit')
hits = []
while True:
line = next(lines)
@@ -236,7 +237,8 @@ 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
@@ -566,7 +568,8 @@ class HHblits:
(self.hhblits_bin, self.filename, a3m_file, full_nrdb,
opt_cmd)
job = subprocess.Popen(hhblits_cmd, shell=True, cwd=self.working_dir,
- stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+ stdout=subprocess.PIPE, stderr=subprocess.PIPE,
+ universal_newlines=True)
sout, _ = job.communicate()
lines = sout.splitlines()
for line in lines:
@@ -586,7 +589,7 @@ class HHblits:
os.environ['PATH'])})
job = subprocess.Popen(addss_cmd, shell=True, cwd=self.working_dir,
env=env, stdout=subprocess.PIPE,
- stderr=subprocess.PIPE)
+ stderr=subprocess.PIPE, universal_newlines=True)
sout, serr = job.communicate()
lines = sout.splitlines()
for line in lines:
@@ -623,7 +626,7 @@ class HHblits:
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):
+ shell=True, universal_newlines=True):
raise IOError('could not convert a3m to hhm file')
return hhm_file
@@ -665,10 +668,9 @@ 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)
@@ -734,7 +736,8 @@ class HHblits:
ost.LogInfo('searching %s' % database)
ost.LogVerbose(search_cmd)
job = subprocess.Popen(search_cmd, shell=True, cwd=self.working_dir,
- stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+ stdout=subprocess.PIPE, stderr=subprocess.PIPE,
+ universal_newlines=True)
sout, serr = job.communicate()
if job.returncode != 0:
lines = sout.splitlines()
--
GitLab
From cbe33a36e9bfa3201b1c944b1ad9e0016942a331 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Mon, 25 Nov 2019 14:41:11 +0100
Subject: [PATCH 034/142] assume that the intention was to check for a non
empty list
python 2: [1,2,3,4,5,6] >= whatever_int => True
python 3: [1,2,3,4,5,6] >= whatever_int => TypeError
---
modules/mol/alg/tests/test_qsscoring.py | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/modules/mol/alg/tests/test_qsscoring.py b/modules/mol/alg/tests/test_qsscoring.py
index 770c95f6e..b8c31e22e 100644
--- a/modules/mol/alg/tests/test_qsscoring.py
+++ b/modules/mol/alg/tests/test_qsscoring.py
@@ -634,12 +634,12 @@ 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),
--
GitLab
From 66cc18beb20d22344692209c4c242743ebd3ccf4 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Tue, 26 Nov 2019 08:57:40 +0100
Subject: [PATCH 035/142] Python 3 disallows overwriting class properties
In Python 2, this assignment had the effect that the whole property
(and it's lazy evaluation functionality) was completely overwritten
and the private _chain_mapping was useless afterwards. Python 3 raises
an AttributeError instead ("can't set attribute").
---
modules/mol/alg/tests/test_qsscoring.py | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/modules/mol/alg/tests/test_qsscoring.py b/modules/mol/alg/tests/test_qsscoring.py
index b8c31e22e..ad2620a2f 100644
--- a/modules/mol/alg/tests/test_qsscoring.py
+++ b/modules/mol/alg/tests/test_qsscoring.py
@@ -163,7 +163,8 @@ class TestQSscore(unittest.TestCase):
# enforce different chain mapping
enforced_cm = {'C': 'C', 'E': 'A', 'D': 'D', 'F': 'B'}
qs_scorer_2 = QSscorer(qs_scorer.qs_ent_1, qs_scorer.qs_ent_2)
- qs_scorer_2.chain_mapping = enforced_cm
+ # directly overwrite variable intended to be private. Have mercy with me.
+ qs_scorer_2._chain_mapping = enforced_cm
self.assertAlmostEqual(qs_scorer_2.global_score, 0.356, 2)
self.assertAlmostEqual(qs_scorer_2.best_score, 0.419, 2)
self.assertEqual(qs_scorer_2.chain_mapping, enforced_cm)
--
GitLab
From c52b5d1c10616275aa6a647201702c70baae66fe Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Tue, 26 Nov 2019 15:03:16 +0100
Subject: [PATCH 036/142] find include directory / library for python with
'm'-suffix
This can happen if python has been compiled with a specialized
malloc.
---
cmake_support/FindPython.cmake | 12 ++++++++----
1 file changed, 8 insertions(+), 4 deletions(-)
diff --git a/cmake_support/FindPython.cmake b/cmake_support/FindPython.cmake
index 3a2e690de..808f0ef32 100644
--- a/cmake_support/FindPython.cmake
+++ b/cmake_support/FindPython.cmake
@@ -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()
--
GitLab
From 5f9ab1dcf76a37f984792801053b97b4d76bd9d1 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Tue, 26 Nov 2019 15:07:05 +0100
Subject: [PATCH 037/142] Fix cmake findnumpy
- Fix python code that is injected into python interpreter
- Proper error handling => fatal_error to stop cmake run if numpy not found
---
cmake_support/FindNumpy.cmake | 17 ++++++++---------
1 file changed, 8 insertions(+), 9 deletions(-)
diff --git a/cmake_support/FindNumpy.cmake b/cmake_support/FindNumpy.cmake
index 6348b9c91..e5bd94454 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)
--
GitLab
From e69b79e872d112c9bebf78c816c515ecd0d80964 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Tue, 26 Nov 2019 15:10:19 +0100
Subject: [PATCH 038/142] Fix import_array() call when exporting numpy
functionality
import_array() must be called when the numpy C-API is called.
This is a macro that in our case defined a return value that makes
the compiler complain. The added #define statement enforces no return value
---
modules/gfx/pymod/export_primlist.cc | 2 ++
modules/mol/base/pymod/export_editors.cc | 2 ++
modules/mol/base/pymod/export_entity.cc | 2 ++
3 files changed, 6 insertions(+)
diff --git a/modules/gfx/pymod/export_primlist.cc b/modules/gfx/pymod/export_primlist.cc
index d11d74656..ba586fe62 100644
--- a/modules/gfx/pymod/export_primlist.cc
+++ b/modules/gfx/pymod/export_primlist.cc
@@ -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/mol/base/pymod/export_editors.cc b/modules/mol/base/pymod/export_editors.cc
index 4bb64bd8a..50aa16842 100644
--- a/modules/mol/base/pymod/export_editors.cc
+++ b/modules/mol/base/pymod/export_editors.cc
@@ -227,6 +227,8 @@ 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
+ #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 538921e2b..35b918b16 100644
--- a/modules/mol/base/pymod/export_entity.cc
+++ b/modules/mol/base/pymod/export_entity.cc
@@ -130,6 +130,8 @@ 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
+ #define NUMPY_IMPORT_ARRAY_RETVAL
import_array();
#endif
--
GitLab
From 1a4cdf97551f3791bf3f35476a49dd4e35e440c4 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Wed, 27 Nov 2019 09:31:09 +0100
Subject: [PATCH 039/142] relax testing of found symmetries
Due to different sorting behaviour in Python 2 and 3, the found symmetry
groups might differ while still being conceptually correct. Instead of
expecting exact results, the unit test now only checks for the number
of found groups and their size. Size is checked on the first element,
equal size of those elements is checked elsewhere.
---
modules/mol/alg/tests/test_qsscoring.py | 104 +++++++++++-------------
1 file changed, 48 insertions(+), 56 deletions(-)
diff --git a/modules/mol/alg/tests/test_qsscoring.py b/modules/mol/alg/tests/test_qsscoring.py
index ad2620a2f..29aaa6210 100644
--- a/modules/mol/alg/tests/test_qsscoring.py
+++ b/modules/mol/alg/tests/test_qsscoring.py
@@ -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
@@ -191,8 +195,10 @@ 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):
@@ -208,11 +214,10 @@ 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'})
@@ -303,8 +308,10 @@ 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):
@@ -320,8 +327,10 @@ 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)
@@ -425,11 +434,10 @@ 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'})
@@ -448,14 +456,10 @@ 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',
@@ -474,12 +478,10 @@ 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):
@@ -496,14 +498,10 @@ 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',
@@ -523,12 +521,10 @@ 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',
@@ -548,14 +544,10 @@ 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(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': 'J', 'C': 'L', 'B': 'K', 'E': 'P', 'D': 'R',
'G': 'O', 'F': 'Q', 'I': 'T', 'H': 'X', 'K': 'S',
--
GitLab
From b288d57d7844ddb00dbe49f76f82b71411a5ace5 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Wed, 27 Nov 2019 09:37:54 +0100
Subject: [PATCH 040/142] Implement setters for QSscorer properties
Requirement of Python 3 to fulfill our promise of being able to set
various things. This also removes an ugly hack of setting a variable
intended to be private in the unit test.
---
modules/mol/alg/pymod/qsscoring.py | 28 +++++++++++++++++++++++++
modules/mol/alg/tests/test_qsscoring.py | 3 +--
2 files changed, 29 insertions(+), 2 deletions(-)
diff --git a/modules/mol/alg/pymod/qsscoring.py b/modules/mol/alg/pymod/qsscoring.py
index ba9c2af9d..8f9286b49 100644
--- a/modules/mol/alg/pymod/qsscoring.py
+++ b/modules/mol/alg/pymod/qsscoring.py
@@ -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.
diff --git a/modules/mol/alg/tests/test_qsscoring.py b/modules/mol/alg/tests/test_qsscoring.py
index 29aaa6210..0e57f2a3e 100644
--- a/modules/mol/alg/tests/test_qsscoring.py
+++ b/modules/mol/alg/tests/test_qsscoring.py
@@ -167,8 +167,7 @@ class TestQSscore(unittest.TestCase):
# enforce different chain mapping
enforced_cm = {'C': 'C', 'E': 'A', 'D': 'D', 'F': 'B'}
qs_scorer_2 = QSscorer(qs_scorer.qs_ent_1, qs_scorer.qs_ent_2)
- # directly overwrite variable intended to be private. Have mercy with me.
- qs_scorer_2._chain_mapping = enforced_cm
+ qs_scorer_2.chain_mapping = enforced_cm
self.assertAlmostEqual(qs_scorer_2.global_score, 0.356, 2)
self.assertAlmostEqual(qs_scorer_2.best_score, 0.419, 2)
self.assertEqual(qs_scorer_2.chain_mapping, enforced_cm)
--
GitLab
From 690c219d1742e60f37836bd5b0bea41eefbee9a3 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Wed, 27 Nov 2019 17:26:50 +0100
Subject: [PATCH 041/142] use encode/decode at required locations instead of
using universal_newlines=True in Popen
Don't ask, just feels better that way
---
modules/bindings/pymod/blast.py | 16 ++++++++--------
modules/bindings/pymod/cadscore.py | 24 ++++++++++--------------
modules/bindings/pymod/clustalw.py | 2 +-
modules/bindings/pymod/dssp.py | 5 ++---
modules/bindings/pymod/hbplus.py | 2 +-
modules/bindings/pymod/hhblits.py | 18 ++++++++----------
modules/bindings/pymod/ialign.py | 7 +++----
modules/bindings/pymod/msms.py | 12 +++++-------
modules/bindings/pymod/naccess.py | 21 +++++++++++----------
modules/bindings/pymod/tmtools.py | 14 ++++++--------
10 files changed, 55 insertions(+), 66 deletions(-)
diff --git a/modules/bindings/pymod/blast.py b/modules/bindings/pymod/blast.py
index 7ecff0896..80409f492 100644
--- a/modules/bindings/pymod/blast.py
+++ b/modules/bindings/pymod/blast.py
@@ -192,8 +192,9 @@ def BlastVersion(blast_location=None):
pattern=re.compile(r'\s*Package: blast (\d+\.\d+\.\d+),\s+')
blast_pipe=subprocess.Popen(args, stdout=subprocess.PIPE,
- stderr=subprocess.PIPE, universal_newlines=True)
- lines=blast_pipe.stdout.readlines()
+ stderr=subprocess.PIPE)
+ stdout, _ = blast_pipe.communicate()
+ lines=stdout.decode().splitlines()
for line in lines:
m=pattern.match(line)
@@ -264,20 +265,19 @@ def Blast(query, database, gap_open=11, gap_ext=1, matrix='BLOSUM62',
ost.LogInfo('running BLAST (%s)' % ' '.join(args))
blast_pipe=subprocess.Popen(args, stderr=subprocess.PIPE,
- stdout=subprocess.PIPE, stdin=subprocess.PIPE,
- universal_newlines=True)
+ 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
diff --git a/modules/bindings/pymod/cadscore.py b/modules/bindings/pymod/cadscore.py
index 90fa77e4a..362325c87 100644
--- a/modules/bindings/pymod/cadscore.py
+++ b/modules/bindings/pymod/cadscore.py
@@ -185,21 +185,18 @@ def _RunCAD(tmp_dir, mode, cad_bin_path, old_regime):
os.path.join(tmp_dir,
"cadtemp"))
- ps1=subprocess.Popen(command1, shell=True, stdout=subprocess.PIPE,
- universal_newlines=True)
+ ps1=subprocess.Popen(command1, shell=True, stdout=subprocess.PIPE)
ps1.wait()
- ps2=subprocess.Popen(command2, shell=True, stdout=subprocess.PIPE,
- universal_newlines=True)
- ps2.wait()
- lines=ps2.stdout.readlines()
+ ps2=subprocess.Popen(command2, shell=True, stdout=subprocess.PIPE)
+ 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,
- universal_newlines=True)
- ps3.wait()
- lines=ps3.stdout.readlines()
+ ps3=subprocess.Popen(command3, shell=True, stdout=subprocess.PIPE)
+ stdout,_ = ps3.communicate()
+ lines=stdout.decode().splitlines()
try:
localAA=_ParseCADLocal(lines)
except:
@@ -228,11 +225,10 @@ def _RunCAD(tmp_dir, mode, cad_bin_path, old_regime):
if old_regime:
cmd.append("--old-regime")
cmd = ' '.join(cmd)
- ps = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE,
- universal_newlines=True)
- ps.wait()
+ ps = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE)
+ stdout, _ = ps.communicate()
try:
- globalAA = _ParseVoronotaGlobal(ps.stdout.readlines())
+ globalAA = _ParseVoronotaGlobal(stdout.decode().splitlines())
except:
raise RuntimeError("CAD calculation failed")
try:
diff --git a/modules/bindings/pymod/clustalw.py b/modules/bindings/pymod/clustalw.py
index 29af869f4..7ed4e8259 100644
--- a/modules/bindings/pymod/clustalw.py
+++ b/modules/bindings/pymod/clustalw.py
@@ -130,7 +130,7 @@ def ClustalW(seq1, seq2=None, clustalw=None, keep_files=False, nopgap=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()
+ ps.wait()
aln=io.LoadAlignment(out)
diff --git a/modules/bindings/pymod/dssp.py b/modules/bindings/pymod/dssp.py
index a43696c4e..b03468789 100644
--- a/modules/bindings/pymod/dssp.py
+++ b/modules/bindings/pymod/dssp.py
@@ -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()
+ ps=subprocess.Popen([dssp_abs_path, path, temp_dssp_path])
+ ps.wait()
return temp_dssp_path
diff --git a/modules/bindings/pymod/hbplus.py b/modules/bindings/pymod/hbplus.py
index 3ca6361a4..39b903359 100644
--- a/modules/bindings/pymod/hbplus.py
+++ b/modules/bindings/pymod/hbplus.py
@@ -63,7 +63,7 @@ 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, universal_newlines=True)
+ 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)
diff --git a/modules/bindings/pymod/hhblits.py b/modules/bindings/pymod/hhblits.py
index 9749507c5..5567dd229 100644
--- a/modules/bindings/pymod/hhblits.py
+++ b/modules/bindings/pymod/hhblits.py
@@ -568,10 +568,9 @@ class HHblits:
(self.hhblits_bin, self.filename, a3m_file, full_nrdb,
opt_cmd)
job = subprocess.Popen(hhblits_cmd, shell=True, cwd=self.working_dir,
- stdout=subprocess.PIPE, stderr=subprocess.PIPE,
- universal_newlines=True)
+ 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):
@@ -589,9 +588,9 @@ class HHblits:
os.environ['PATH'])})
job = subprocess.Popen(addss_cmd, shell=True, cwd=self.working_dir,
env=env, stdout=subprocess.PIPE,
- stderr=subprocess.PIPE, universal_newlines=True)
+ 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 '+
@@ -626,7 +625,7 @@ class HHblits:
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, universal_newlines=True):
+ shell=True):
raise IOError('could not convert a3m to hhm file')
return hhm_file
@@ -736,14 +735,13 @@ class HHblits:
ost.LogInfo('searching %s' % database)
ost.LogVerbose(search_cmd)
job = subprocess.Popen(search_cmd, shell=True, cwd=self.working_dir,
- stdout=subprocess.PIPE, stderr=subprocess.PIPE,
- universal_newlines=True)
+ 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
diff --git a/modules/bindings/pymod/ialign.py b/modules/bindings/pymod/ialign.py
index 176a5dbe4..aa7105cd6 100644
--- a/modules/bindings/pymod/ialign.py
+++ b/modules/bindings/pymod/ialign.py
@@ -141,10 +141,9 @@ def _RuniAlign(ialign, tmp_dir, options={}):
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,
- universal_newlines=True)
- ps.wait()
- lines=ps.stdout.readlines()
+ ps=subprocess.Popen(command, shell=True, stdout=subprocess.PIPE)
+ stdout,_=ps.communicate()
+ lines=stdout.decode().splitlines()
if (len(lines))<22:
_CleanupFiles(tmp_dir)
diff --git a/modules/bindings/pymod/msms.py b/modules/bindings/pymod/msms.py
index b7d338e50..38f37008a 100644
--- a/modules/bindings/pymod/msms.py
+++ b/modules/bindings/pymod/msms.py
@@ -43,12 +43,11 @@ def GetVersion(msms_exe=None, msms_env=None):
"""
msms_executable = _GetExecutable(msms_exe, msms_env)
command = "%s" % (msms_executable)
- proc = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE,
- universal_newlines=True)
+ proc = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE)
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
@@ -150,16 +149,15 @@ def _RunMSMS(command):
:returns: stdout of MSMS
:raises: :class:`CalledProcessError` for non-zero return value
"""
- proc = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE,
- universal_newlines=True)
+ proc = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE)
stdout_value, stderr_value = proc.communicate()
#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 d2592c6b2..57d1c5740 100644
--- a/modules/bindings/pymod/naccess.py
+++ b/modules/bindings/pymod/naccess.py
@@ -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, universal_newlines=True)
- 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, universal_newlines=True)
+ 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 b91dd6676..3c1ef12c8 100644
--- a/modules/bindings/pymod/tmtools.py
+++ b/modules/bindings/pymod/tmtools.py
@@ -80,10 +80,9 @@ def _RunTmAlign(tmalign, tmp_dir):
else:
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,
- universal_newlines=True)
- ps.wait()
- lines=ps.stdout.readlines()
+ ps=subprocess.Popen(command, shell=True, stdout=subprocess.PIPE)
+ stdout,_=ps.communicate()
+ lines=stdout.decode().splitlines()
if (len(lines))<22:
_CleanupFiles(tmp_dir)
raise RuntimeError("tmalign superposition failed")
@@ -162,10 +161,9 @@ def _RunTmScore(tmscore, tmp_dir):
tmscore_path=settings.Locate('tmscore', explicit_file_name=tmscore)
command="\"%s\" \"%s\" \"%s\"" % (tmscore_path, model1_filename,
model2_filename)
- ps=subprocess.Popen(command, shell=True, stdout=subprocess.PIPE,
- universal_newlines=True)
- ps.wait()
- lines=ps.stdout.readlines()
+ ps=subprocess.Popen(command, shell=True, stdout=subprocess.PIPE)
+ stdout,_=ps.communicate()
+ lines=stdout.decode().splitlines()
if (len(lines))<22:
_CleanupFiles(tmp_dir)
raise RuntimeError("tmscore superposition failed")
--
GitLab
From 8723a6ed6ce938136e27cf546d799a09575c8896 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Thu, 28 Nov 2019 13:49:54 +0100
Subject: [PATCH 042/142] silence resource warnings for non-closed files etc
This only happens when running the unit tests due to increased log levels.
These warnings could manually be triggered for normal scripts with:
python -Wd world_domination.py.
---
modules/base/pymod/table.py | 38 ++++++++++++++++++++++++--
modules/base/tests/test_table.py | 1 +
modules/bindings/pymod/blast.py | 7 +++--
modules/bindings/pymod/cadscore.py | 5 ++--
modules/bindings/pymod/clustalw.py | 4 +--
modules/bindings/pymod/kclust.py | 6 ++--
modules/bindings/tests/test_blast.py | 3 +-
modules/bindings/tests/test_hhblits.py | 32 ++++++++++++----------
8 files changed, 69 insertions(+), 27 deletions(-)
diff --git a/modules/base/pymod/table.py b/modules/base/pymod/table.py
index bb7714f03..8697d63d0 100644
--- a/modules/base/pymod/table.py
+++ b/modules/base/pymod/table.py
@@ -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')
@@ -943,11 +957,16 @@ 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 pickle.load(stream)
+ tab = pickle.load(stream)
+ if file_opened:
+ stream.close()
+ return tab
@staticmethod
def _GuessFormat(filename):
@@ -2210,9 +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')
+ file_opened=True
pickle.dump(self, stream, pickle.HIGHEST_PROTOCOL)
+ if file_opened:
+ stream.close()
def _SaveHTML(self, stream_or_filename):
def _escape(s):
@@ -2288,8 +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, 'w')
+ file_opened=True
writer=csv.writer(stream, delimiter=sep)
writer.writerow(['%s' % n for n in self.col_names])
@@ -2299,13 +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)])
@@ -2315,7 +2345,9 @@ Statistics for column %(col)s
if c==None:
row[i]='NA'
writer.writerow(row)
-
+ if file_opened:
+ stream.close()
+
def GetNumpyMatrix(self, *args):
'''
diff --git a/modules/base/tests/test_table.py b/modules/base/tests/test_table.py
index 640e7c366..5d56f67ee 100644
--- a/modules/base/tests/test_table.py
+++ b/modules/base/tests/test_table.py
@@ -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()
diff --git a/modules/bindings/pymod/blast.py b/modules/bindings/pymod/blast.py
index 80409f492..89893323a 100644
--- a/modules/bindings/pymod/blast.py
+++ b/modules/bindings/pymod/blast.py
@@ -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):
"""
diff --git a/modules/bindings/pymod/cadscore.py b/modules/bindings/pymod/cadscore.py
index 362325c87..193bfc87f 100644
--- a/modules/bindings/pymod/cadscore.py
+++ b/modules/bindings/pymod/cadscore.py
@@ -186,7 +186,7 @@ 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)
stdout,_ = ps2.communicate()
lines=stdout.decode().splitlines()
@@ -232,7 +232,8 @@ def _RunCAD(tmp_dir, mode, cad_bin_path, old_regime):
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")
diff --git a/modules/bindings/pymod/clustalw.py b/modules/bindings/pymod/clustalw.py
index 7ed4e8259..074199283 100644
--- a/modules/bindings/pymod/clustalw.py
+++ b/modules/bindings/pymod/clustalw.py
@@ -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.wait()
+ with subprocess.Popen(command, shell=True, stdout=subprocess.PIPE) as ps:
+ ps.wait()
aln=io.LoadAlignment(out)
diff --git a/modules/bindings/pymod/kclust.py b/modules/bindings/pymod/kclust.py
index edcbc4797..076141f6b 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()
diff --git a/modules/bindings/tests/test_blast.py b/modules/bindings/tests/test_blast.py
index fbadfccb1..9be501b00 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)
diff --git a/modules/bindings/tests/test_hhblits.py b/modules/bindings/tests/test_hhblits.py
index eaff9a3f7..1bc6b3652 100644
--- a/modules/bindings/tests/test_hhblits.py
+++ b/modules/bindings/tests/test_hhblits.py
@@ -129,10 +129,10 @@ 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 +147,10 @@ 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')):
@@ -244,10 +244,12 @@ 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')):
@@ -286,7 +288,8 @@ 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'))
+ 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 +320,8 @@ 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)
--
GitLab
From 25aee9dd1f487176499994c5c540da18dee63c33 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Thu, 28 Nov 2019 14:18:14 +0100
Subject: [PATCH 043/142] Relax QSscorer unit test for highly symmetric
structures
Several chain mappings are valid in this case. Only check whether we found an
automated mapping with strict (stuff must really match) chain_mapping_scheme
---
modules/mol/alg/tests/test_qsscoring.py | 18 ++++++++++++------
1 file changed, 12 insertions(+), 6 deletions(-)
diff --git a/modules/mol/alg/tests/test_qsscoring.py b/modules/mol/alg/tests/test_qsscoring.py
index 0e57f2a3e..e8f18b369 100644
--- a/modules/mol/alg/tests/test_qsscoring.py
+++ b/modules/mol/alg/tests/test_qsscoring.py
@@ -547,12 +547,18 @@ class TestQSscore(unittest.TestCase):
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': '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'})
+
+ # 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'})
###########################################################################
--
GitLab
From ba502e47b691ea5c3de9007e4a7107d5275d8553 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Thu, 28 Nov 2019 15:30:18 +0100
Subject: [PATCH 044/142] test weighted_lddt and sc_lddt of OligoLDDTScorer
---
modules/mol/alg/tests/test_qsscoring.py | 16 ++++++++++++++++
1 file changed, 16 insertions(+)
diff --git a/modules/mol/alg/tests/test_qsscoring.py b/modules/mol/alg/tests/test_qsscoring.py
index e8f18b369..b8f727120 100644
--- a/modules/mol/alg/tests/test_qsscoring.py
+++ b/modules/mol/alg/tests/test_qsscoring.py
@@ -395,9 +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,
@@ -405,11 +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')})
--
GitLab
From e024243571f571ea62fddf08ba848c5fdfeb0faa Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Fri, 29 Nov 2019 11:24:20 +0100
Subject: [PATCH 045/142] sorting by custom key has changed in Python 3
---
modules/gfx/pymod/__init__.py | 7 +++++--
1 file changed, 5 insertions(+), 2 deletions(-)
diff --git a/modules/gfx/pymod/__init__.py b/modules/gfx/pymod/__init__.py
index 60ad84ec6..8c87ec211 100644
--- a/modules/gfx/pymod/__init__.py
+++ b/modules/gfx/pymod/__init__.py
@@ -18,6 +18,7 @@
#------------------------------------------------------------------------------
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):
--
GitLab
From 87c339eee31466c800ab92bb8a438067cd4c13eb Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Fri, 29 Nov 2019 11:24:54 +0100
Subject: [PATCH 046/142] test remote loading in LoadPDB/LoadMMCIF
---
modules/io/tests/test_io_mmcif.py | 14 ++++++++++++++
modules/io/tests/test_io_pdb.py | 17 +++++++++++++++++
2 files changed, 31 insertions(+)
diff --git a/modules/io/tests/test_io_mmcif.py b/modules/io/tests/test_io_mmcif.py
index 8a3773b0a..cfa10798c 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 *
@@ -249,6 +250,19 @@ class TestMMCifInfo(unittest.TestCase):
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
testutils.RunTests()
diff --git a/modules/io/tests/test_io_pdb.py b/modules/io/tests/test_io_pdb.py
index 3ba3539dc..77a504fd8 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):
@@ -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
--
GitLab
From 7354fd38ee7a8018eea613acd44cb354a5f6ee28 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Mon, 2 Dec 2019 11:56:32 +0100
Subject: [PATCH 047/142] update dependencies in CI yml file
---
.gitlab-ci.yml | 34 +++++++++++++++++-----------------
1 file changed, 17 insertions(+), 17 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index a67298e77..48628be59 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -27,18 +27,18 @@ test:centos7.3:
- 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 HH-suite/2.0.16-foss-2018b
+ - 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 +62,16 @@ 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
-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='-Wno-unused-local-typedefs -L/scicore/soft/apps/libpng/1.6.34-GCCcore-7.3.0/lib/ -L/scicore/soft/apps/LibTIFF/4.0.9-GCCcore-7.3.0/lib/ -L/scicore/soft/apps/zlib/1.2.11-GCCcore-7.3.0/lib'
+ -DCMAKE_CXX_FLAGS='-Wno-unused-local-typedefs -L/scicore/soft/apps/libpng/1.6.34-GCCcore-7.3.0/lib/ -L/scicore/soft/apps/LibTIFF/4.0.9-GCCcore-7.3.0/lib/ -L/scicore/soft/apps/zlib/1.2.11-GCCcore-7.3.0/lib'
+ -DCMAKE_EXE_LINKER_FLAGS=" -pthread"
- make -j 2
- echo " ... done building OST."
- echo " Running unit tests for OST..."
--
GitLab
From 3feccbd5205d4e92a508767c70f9aca7120c1506 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Mon, 2 Dec 2019 17:13:23 +0100
Subject: [PATCH 048/142] reenable CI
---
.gitlab-ci.yml | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 48628be59..7bf2dd628 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -18,10 +18,8 @@ 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
@@ -33,7 +31,9 @@ test:centos7.3:
- 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
@@ -63,7 +63,7 @@ test:centos7.3:
-DSQLITE3_INCLUDE_DIR=$EBROOTSQLITE/include
-DBOOST_ROOT=$EBROOTBOOST
-DPNG_LIBRARY=$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
--
GitLab
From 8ab1af867d31eb93eb748eff7009287750417cf1 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Mon, 2 Dec 2019 18:43:57 +0100
Subject: [PATCH 049/142] parse lga output from binary stream
---
modules/bindings/pymod/lga.py | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/modules/bindings/pymod/lga.py b/modules/bindings/pymod/lga.py
index 7ab23e854..59f5d53fb 100644
--- a/modules/bindings/pymod/lga.py
+++ b/modules/bindings/pymod/lga.py
@@ -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
--
GitLab
From f4a4e273ceb082fca426e1ac3f45ea5a07235e63 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Mon, 2 Dec 2019 18:44:48 +0100
Subject: [PATCH 050/142] simple unit test for lga binding
---
modules/bindings/tests/CMakeLists.txt | 1 +
modules/bindings/tests/test_lga.py | 30 +++++++++++++++++++++++++++
2 files changed, 31 insertions(+)
create mode 100644 modules/bindings/tests/test_lga.py
diff --git a/modules/bindings/tests/CMakeLists.txt b/modules/bindings/tests/CMakeLists.txt
index 3d3efc3ab..17a60fa55 100644
--- a/modules/bindings/tests/CMakeLists.txt
+++ b/modules/bindings/tests/CMakeLists.txt
@@ -8,6 +8,7 @@ set(OST_BINDINGS_UNIT_TESTS
test_cadscore.py
test_tmtools.py
test_ialign.py
+ test_lga.py
)
ost_unittest(MODULE bindings
diff --git a/modules/bindings/tests/test_lga.py b/modules/bindings/tests/test_lga.py
new file mode 100644
index 000000000..dfdcea972
--- /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()
--
GitLab
From 166919ad5d2ee13e283d11aa8934f5d96479458b Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Tue, 3 Dec 2019 09:13:22 +0100
Subject: [PATCH 051/142] add unit test for AlignmentFromChainView in seq.alg
---
modules/seq/alg/tests/CMakeLists.txt | 1 +
.../tests/test_alignment_from_chain_view.py | 36 +++++++++++++++++++
2 files changed, 37 insertions(+)
create mode 100644 modules/seq/alg/tests/test_alignment_from_chain_view.py
diff --git a/modules/seq/alg/tests/CMakeLists.txt b/modules/seq/alg/tests/CMakeLists.txt
index 81b69d15f..9348d402b 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 000000000..0e6b18326
--- /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()
--
GitLab
From a4dbfec1e3fd2f0b59397ea5a8809497f3d8063c Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Thu, 5 Dec 2019 11:35:06 +0100
Subject: [PATCH 052/142] also look for Python 3.7 and 3.8
---
cmake_support/FindPython.cmake | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/cmake_support/FindPython.cmake b/cmake_support/FindPython.cmake
index 808f0ef32..b36e9aa44 100644
--- a/cmake_support/FindPython.cmake
+++ b/cmake_support/FindPython.cmake
@@ -17,7 +17,7 @@
# Author: Marco Biasini
#-------------------------------------------------------------------------------
-set(PYTHON_VERSIONS 3.6 2.7 2.6 2.5 2.4 2.3 2.2 )
+set(PYTHON_VERSIONS 3.8 3.7 3.6 2.7 2.6 2.5 2.4 2.3 2.2 )
set(PYTHON_MIN_VERSION 2.2.1)
#-------------------------------------------------------------------------------
--
GitLab
From 104b8d8e0bfa5aaf14707066d2d4168004de10ca Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Thu, 5 Dec 2019 11:36:59 +0100
Subject: [PATCH 053/142] port hbplus binding to Python 3
---
modules/bindings/pymod/hbplus.py | 16 ++++++++++------
1 file changed, 10 insertions(+), 6 deletions(-)
diff --git a/modules/bindings/pymod/hbplus.py b/modules/bindings/pymod/hbplus.py
index 39b903359..372809400 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):
--
GitLab
From 94d8a51c39ce09b6edbc9a6d4eaea97a4097a88d Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Thu, 5 Dec 2019 11:38:07 +0100
Subject: [PATCH 054/142] simple unit test for hbplus
---
modules/bindings/tests/CMakeLists.txt | 1 +
modules/bindings/tests/test_hbplus.py | 25 +++++++++++++++++++++++++
2 files changed, 26 insertions(+)
create mode 100644 modules/bindings/tests/test_hbplus.py
diff --git a/modules/bindings/tests/CMakeLists.txt b/modules/bindings/tests/CMakeLists.txt
index 17a60fa55..d99953fe2 100644
--- a/modules/bindings/tests/CMakeLists.txt
+++ b/modules/bindings/tests/CMakeLists.txt
@@ -9,6 +9,7 @@ set(OST_BINDINGS_UNIT_TESTS
test_tmtools.py
test_ialign.py
test_lga.py
+ test_hbplus.py
)
ost_unittest(MODULE bindings
diff --git a/modules/bindings/tests/test_hbplus.py b/modules/bindings/tests/test_hbplus.py
new file mode 100644
index 000000000..87a32d282
--- /dev/null
+++ b/modules/bindings/tests/test_hbplus.py
@@ -0,0 +1,25 @@
+import unittest
+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()
--
GitLab
From eb2b220446f4f969706b9877fdc469b9c7e6b94e Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Thu, 5 Dec 2019 11:53:49 +0100
Subject: [PATCH 055/142] add missing import
---
modules/bindings/tests/test_hbplus.py | 1 +
1 file changed, 1 insertion(+)
diff --git a/modules/bindings/tests/test_hbplus.py b/modules/bindings/tests/test_hbplus.py
index 87a32d282..ecc91fbc2 100644
--- a/modules/bindings/tests/test_hbplus.py
+++ b/modules/bindings/tests/test_hbplus.py
@@ -1,4 +1,5 @@
import unittest
+import sys
from ost import *
from ost import settings
from ost.bindings import hbplus
--
GitLab
From 81bba2f8ce50f17c2d908caa4c8624518993d417 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Thu, 5 Dec 2019 16:06:12 +0100
Subject: [PATCH 056/142] relax msms unit test
---
modules/bindings/tests/test_msms.py | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/modules/bindings/tests/test_msms.py b/modules/bindings/tests/test_msms.py
index e4320a878..fb49a2cfa 100755
--- a/modules/bindings/tests/test_msms.py
+++ b/modules/bindings/tests/test_msms.py
@@ -29,15 +29,15 @@ class TestMSMSBindings(unittest.TestCase):
msms_env='MSMSSERVER',
density=3,
radius=1.4)
- self.assertEqual(self.ases, msms_ases[0])
- self.assertEqual(self.asas, msms_asas[0])
+ 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.assertEqual(self.volume, volume)
+ self.assertAlmostEqual(self.volume, volume, 1)
if __name__ == "__main__":
# test if msms package is available on system, otherwise ignore tests
--
GitLab
From b20db1d8f612e528793dcdb663c718791a7ca84f Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Fri, 6 Dec 2019 15:50:17 +0100
Subject: [PATCH 057/142] we don't want to find Python 2.x anymore
---
cmake_support/FindPython.cmake | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/cmake_support/FindPython.cmake b/cmake_support/FindPython.cmake
index b36e9aa44..852c91d44 100644
--- a/cmake_support/FindPython.cmake
+++ b/cmake_support/FindPython.cmake
@@ -17,8 +17,8 @@
# Author: Marco Biasini
#-------------------------------------------------------------------------------
-set(PYTHON_VERSIONS 3.8 3.7 3.6 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
--
GitLab
From 6a3ee3558d7ba194022af2e1949f7a14c2f19ff7 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Fri, 6 Dec 2019 15:52:22 +0100
Subject: [PATCH 058/142] updated Dockerfile
---
docker/Dockerfile | 122 +++++++++++++---------------------------------
1 file changed, 34 insertions(+), 88 deletions(-)
diff --git a/docker/Dockerfile b/docker/Dockerfile
index a02301453..3846bddbd 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -2,67 +2,47 @@ FROM ubuntu:18.04
# ARGUMENTS
###########
-
-ARG OPENSTRUCTURE_VERSION="1.10.0"
+ARG OPENSTRUCTURE_VERSION="python3_port"
ARG SRC_FOLDER="/usr/local/src"
-ARG CPUS_FOR_MAKE=8
-ARG PYTHONPATH="/usr/local/lib64/python2.7/site-packages:${PYTHONPATH}"
+ARG CPUS_FOR_MAKE=2
ARG OPENSTRUCTURE_SHARE="/usr/local/share/ost"
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 +53,8 @@ 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} && \
@@ -83,23 +63,20 @@ 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 \
+ 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 \
@@ -109,52 +86,21 @@ 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 && \
- # 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 $OPENSTRUCTURE_SHARE
-
-# Build and install OST
-RUN cmake .. -DPYTHON_LIBRARIES=/usr/lib/x86_64-linux-gnu/libpython2.7.so \
- -DOPTIMIZE=ON \
- -DENABLE_MM=ON \
- -DCOMPILE_TMTOOLS=1 \
- -DUSE_NUMPY=1 \
- -DOPEN_MM_LIBRARY=$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 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
+ 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 && \
+ mkdir -p $OPENSTRUCTURE_SHARE && chmod a+rw -R $OPENSTRUCTURE_SHARE && mv compounds.chemlib $OPENSTRUCTURE_SHARE && \
+ cmake .. -DCOMPOUND_LIB=$OPENSTRUCTURE_SHARE/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
ENTRYPOINT ["ost"]
--
GitLab
From cb5a91a165534a1abfee319a2c0e97a7294d732a Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Sun, 8 Dec 2019 09:50:15 +0100
Subject: [PATCH 059/142] fix doc generation
- os.path.walk does not exist in Python3 anymore, use os.walk instead
(changed interface)
- sphinx-build tried really hard to use Python 2. Import sphinx from
current interpreter instead and directly call its __main__ function
---
doc/make.py | 34 +++++++++++-----------------------
1 file changed, 11 insertions(+), 23 deletions(-)
diff --git a/doc/make.py b/doc/make.py
index 1b9f43a1d..4d0ce533f 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
+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]
@@ -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")
@@ -93,25 +87,19 @@ if opts.quiet:
opt_str=' -Q '
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'])
+ print("start walking")
+ for directory, dirnames, filenames in os.walk(sub_dir):
+ _CollectRstDocs('doc/source', directory, filenames)
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)
+ sphinx.main([opt_str, '-b', 'html', '-c', 'doc/conf', 'doc/source', 'doc/build/html'])
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)
+ sphinx.main([opt_str, '-b', 'doctest', '-c', 'doc/conf', 'doc/source', 'doc/build/html'])
+
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)
+ sphinx.main([opt_str, '-b', 'json', '-c', 'doc/conf', 'doc/source', 'doc/build/html'])
+
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)
+ sphinx.main([opt_str, '-b', 'linkcheck', '-c', 'doc/conf', 'doc/source', 'doc/build/html'])
+
--
GitLab
From 802969a3a32e6c0e3cb2ea54fadf66927f7af987 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Sun, 8 Dec 2019 09:52:34 +0100
Subject: [PATCH 060/142] update version numbers in install doc
---
modules/doc/install.rst | 21 +++++++++++----------
1 file changed, 11 insertions(+), 10 deletions(-)
diff --git a/modules/doc/install.rst b/modules/doc/install.rst
index b86672515..b49b82fd2 100644
--- a/modules/doc/install.rst
+++ b/modules/doc/install.rst
@@ -7,7 +7,7 @@ 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>`_.
+`Singularity <https://sylabs.io/singularity/>`_.
The latest recipes and instructions can be found on our GitLab site
(`Docker instructions`_ and `Singularity instructions`_).
@@ -23,13 +23,14 @@ 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)
+* `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 +46,7 @@ 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:
@@ -69,7 +70,7 @@ 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::
@@ -298,7 +299,7 @@ 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
@@ -309,7 +310,7 @@ 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
--
GitLab
From 33d64b5abfd0373f5a04e7b84067ad1953bec110 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Mon, 9 Dec 2019 09:56:15 +0100
Subject: [PATCH 061/142] another sorting port for Python3
---
examples/demos/correlate.py | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/examples/demos/correlate.py b/examples/demos/correlate.py
index 1b65722d6..f7ff13f29 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')
@@ -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):
--
GitLab
From 7845f46e90e88bc50f2a19309b3dd902fb820505 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Mon, 9 Dec 2019 11:01:36 +0100
Subject: [PATCH 062/142] update widget example
So sad to remove our beloved tetris. However, it somehow broke with Python3
and I did not have the nerves to fix it. Any resurection effort is very welcome.
---
examples/code_fragments/ui/board.py | 345 -------------------
examples/code_fragments/ui/widget_example.py | 15 +-
2 files changed, 8 insertions(+), 352 deletions(-)
delete mode 100644 examples/code_fragments/ui/board.py
diff --git a/examples/code_fragments/ui/board.py b/examples/code_fragments/ui/board.py
deleted file mode 100644
index 6717d7291..000000000
--- 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/widget_example.py b/examples/code_fragments/ui/widget_example.py
index ced1d02fa..ae9f73be7 100644
--- a/examples/code_fragments/ui/widget_example.py
+++ b/examples/code_fragments/ui/widget_example.py
@@ -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()
--
GitLab
From a67af630c55618104c88d277ab4bd6249af16be6 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Mon, 9 Dec 2019 16:51:31 +0100
Subject: [PATCH 063/142] export OPENSTRUCTURE_VERSION variable in docker
container
---
docker/Dockerfile | 1 +
1 file changed, 1 insertion(+)
diff --git a/docker/Dockerfile b/docker/Dockerfile
index 3846bddbd..81784dce2 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -102,6 +102,7 @@ ENV OST_ROOT="/usr/local"
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=$OPENSTRUCTURE_VERSION
ENTRYPOINT ["ost"]
CMD ["-i"]
--
GitLab
From 60dcf524bb33ba7c11eae537ab95b670bf6afc64 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Mon, 9 Dec 2019 16:52:19 +0100
Subject: [PATCH 064/142] Python 3 Singularity Container
biggest change: make it rely on ost docker-container as base image
---
singularity/Singularity | 236 ++++++++--------------------------------
1 file changed, 45 insertions(+), 191 deletions(-)
diff --git a/singularity/Singularity b/singularity/Singularity
index 429cb86a5..ea57eab41 100644
--- a/singularity/Singularity
+++ b/singularity/Singularity
@@ -1,170 +1,38 @@
BootStrap: docker
-From: ubuntu:18.04
+From: registry.scicore.unibas.ch/schwede/openstructure:python3_test
+
%post
##############################################################################
# POST
##############################################################################
+
# CHANGE DASH TO BASH
rm /bin/sh
ln -sf /bin/bash /bin/sh
-# DEFINE SOME ENV VARS USED DURING THE IMAGE BUILD
-##########################
-export SRC_FOLDER="/usr/local/src"
-export CPUS_FOR_MAKE=8
-export PYTHONPATH="/usr/local/lib64/python2.7/site-packages:${PYTHONPATH}"
-# When changing OPENSTRUCTURE_VERSION make sure to change it also in the
-# environment section of singularity recipe (this file).
-export OPENSTRUCTURE_VERSION="1.10.0"
-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
-
-# SET LOCALE
-############
-echo "LC_ALL=en_US.UTF-8" >> /etc/environment
-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
+apt-get update -y && apt-get install -y python3-pip \
+ python3-venv
# SET UP VIRTUALENV
###################
-virtualenv --system-site-packages $VIRTUALENV_DIR
+export VIRTUALENV_DIR="/usr/local/share/ost_venv"
+python3 -m venv --system-site-packages $VIRTUALENV_DIR
. $VIRTUALENV_DIR/bin/activate
+pip3 install nglview \
+ ipython \
+ jupyter
-
-# INSTALL REQUIRED PYTHON PACKAGES
-##################################
-pip install jupyter==1.0.0 \
- nglview==1.1.6
-
-# 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 ${CPUS_FOR_MAKE}
- make check
- make install
-fi
-
-# SETUP JUPYTER
-###############
+# SETUP IPYTHON / JUPYTER
+#########################
+export JUPYTER_CONFIG_DIR="/usr/local/etc/jupyter"
+export JUPYTER_PATH="/usr/local/share/jupyter"
+export JUPYTER_RUNTIME_DIR="$JUPYTER_PATH/runtime"
mkdir -p /usr/local/share/ipython
mkdir -p $JUPYTER_PATH
mkdir -p $JUPYTER_RUNTIME_DIR
@@ -176,61 +44,43 @@ 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 $SRC_FOLDER/*
-
-cd /home
-
%environment
##############################################################################
# ENVIRONMENT
##############################################################################
-export OST_ROOT="/usr/local"
-export OPENSTRUCTURE_VERSION="1.10.0"
-export OPENMM_LIB_PATH=/usr/local/openmm/lib/
-export PYTHONPATH="/usr/local/lib64/python2.7/site-packages:${PYTHONPATH}"
-export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/local/lib64:${OPENMM_LIB_PATH}"
-export QT_X11_NO_MITSHM=1
+# As the Singularity mounts $HOME by default Jupyter and Ipython config files
+# are moved to separate directories. Proper environmental variables are also
+# set
export IPYTHONDIR="/usr/local/share/ipython"
export JUPYTER_CONFIG_DIR="/usr/local/etc/jupyter"
export JUPYTER_PATH="/usr/local/share/jupyter"
-export JUPYTER_RUNTIME_DIR="$JUPYTER_PATH/runtime"
+export JUPYTER_RUNTIME_DIR="/usr/local/share/jupyter/runtime"
export VIRTUALENV_DIR="/usr/local/share/ost_venv"
+
%apprun ChemdictTool
##############################################################################
# CHEMDICT TOOL APP
##############################################################################
$OST_ROOT/bin/chemdict_tool "$@"
+
%apprun lDDT
##############################################################################
# lDDT APP
@@ -258,6 +108,7 @@ Options:
-e print version
-x ignore residue name consistency checks
+
%apprun Molck
##############################################################################
# MOLCK APP
@@ -291,6 +142,7 @@ Options:
--map-nonstd maps modified residues back to the parent amino acid, for example
MSE -> MET, SEP -> SER.
+
%apprun OST
##############################################################################
# OST APP
@@ -298,11 +150,12 @@ 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
@@ -321,13 +174,14 @@ 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 $DNG_INITDIR/ost_startup.py "$@"
+. $VIRTUALENV_DIR/bin/activate && ipython3 -i $DNG_INITDIR/ost_startup.py "$@"
%apphelp IPython
OST-powered iPython shell.
@@ -340,6 +194,7 @@ Detailed help:
singularity run --app IPython <IMAGE> --help
+
%appenv Notebook
##############################################################################
# NOTEBOOK ENV
@@ -348,6 +203,7 @@ export BIN_DIR=$OST_ROOT/bin
export XDG_RUNTIME_DIR=""
. $OST_ROOT/libexec/openstructure/ost_config
+
%apprun Notebook
##############################################################################
# NOTEBOOK APP
@@ -355,7 +211,7 @@ export XDG_RUNTIME_DIR=""
. $VIRTUALENV_DIR/bin/activate && jupyter notebook --NotebookApp.iopub_data_rate_limit=10000000 --no-browser "$@"
%apphelp Notebook
-A Jupyter notebook palyground with OST and nglview.
+A Jupyter notebook playground with OST and nglview.
Usage:
@@ -379,8 +235,8 @@ 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.
+In addition, Jupyter is run in a separate virtualenv to not interact with
+possibly installed host version.
To list of all available options:
@@ -421,5 +277,3 @@ This container includes the following apps:
To see the help for each individual app run:
singularity help --app <APP NAME> <IMAGE NAME>
-
-
--
GitLab
From a3d9620b07b15078d50eacf13afbba90465966d7 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Mon, 9 Dec 2019 16:58:50 +0100
Subject: [PATCH 065/142] Manual Python 3 port of doc example code
---
modules/base/doc/generic.rst | 10 ++++----
modules/base/doc/logging.rst | 4 ++--
modules/bindings/doc/dssp.rst | 2 +-
modules/bindings/doc/hhblits.rst | 6 ++---
modules/bindings/doc/tmtools.rst | 10 ++++----
modules/conop/doc/compoundlib.rst | 2 +-
modules/doc/external.rst | 16 ++++++-------
modules/doc/intro-01.rst | 18 +++++++-------
modules/doc/intro-02.rst | 2 +-
modules/doc/table.rst | 12 +++++-----
modules/geom/doc/mat.rst | 6 ++---
modules/geom/doc/vec.rst | 14 +++++------
modules/gui/doc/python_cpp.rst | 2 +-
modules/img/base/doc/point-size-extent.rst | 4 ++--
modules/io/doc/io.rst | 22 -----------------
modules/mol/alg/doc/lddt.rst | 2 +-
modules/mol/alg/doc/molalg.rst | 2 +-
modules/mol/base/doc/entity.rst | 28 +++++++++++-----------
modules/seq/alg/doc/seqalg.rst | 16 ++++++-------
modules/seq/base/doc/seq.rst | 20 ++++++++--------
20 files changed, 88 insertions(+), 110 deletions(-)
diff --git a/modules/base/doc/generic.rst b/modules/base/doc/generic.rst
index 919497f39..2d71160da 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 adb5a5768..e9cff1360 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/bindings/doc/dssp.rst b/modules/bindings/doc/dssp.rst
index bb9d2b57b..3a51a870c 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 9ffb1c0c6..62b3262a0 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 7a39ba987..51b786efc 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
--------------------------------------------------------------------------------
@@ -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/conop/doc/compoundlib.rst b/modules/conop/doc/compoundlib.rst
index 195614fbd..194979cfd 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/doc/external.rst b/modules/doc/external.rst
index 3d75fa80b..0d7f7d204 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/intro-01.rst b/modules/doc/intro-01.rst
index 25c092f8a..98c3427e7 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 4470a9d8c..67bfc4ddb 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 d0dd45691..4a8748e50 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 c8736733a..a05dab465 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 bc88b3f2b..c55dcbb65 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/gui/doc/python_cpp.rst b/modules/gui/doc/python_cpp.rst
index 0f4be50a6..f7f726251 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/img/base/doc/point-size-extent.rst b/modules/img/base/doc/point-size-extent.rst
index af2731adb..344f0ea28 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/io/doc/io.rst b/modules/io/doc/io.rst
index 995950ed2..10be9a055 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/mol/alg/doc/lddt.rst b/modules/mol/alg/doc/lddt.rst
index 3201243bd..711c06f9f 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 300852d95..5262c236a 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`
diff --git a/modules/mol/base/doc/entity.rst b/modules/mol/base/doc/entity.rst
index fd99d80cc..1e7b00886 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/seq/alg/doc/seqalg.rst b/modules/seq/alg/doc/seqalg.rst
index 265892530..5e5b5a7c8 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/base/doc/seq.rst b/modules/seq/base/doc/seq.rst
index 8e7e91f57..510241c8b 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
--
GitLab
From 19b45180e6d2fdd0affa74aadfc9744562e9dbbc Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Mon, 16 Dec 2019 14:08:37 +0100
Subject: [PATCH 066/142] avoid duplication of compound library
Make install automatically moves the specified into the default share
directory, so the initially build library can go with the whole build dir
---
docker/Dockerfile | 5 ++---
1 file changed, 2 insertions(+), 3 deletions(-)
diff --git a/docker/Dockerfile b/docker/Dockerfile
index 81784dce2..56d87ebcf 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -5,7 +5,6 @@ FROM ubuntu:18.04
ARG OPENSTRUCTURE_VERSION="python3_port"
ARG SRC_FOLDER="/usr/local/src"
ARG CPUS_FOR_MAKE=2
-ARG OPENSTRUCTURE_SHARE="/usr/local/share/ost"
ARG MSMS_VERSION="2.6.1"
ARG OPENMM_VERSION="7.1.1"
ARG OPENMM_INCLUDE_PATH="/usr/local/openmm/include/"
@@ -89,8 +88,7 @@ RUN cd ${SRC_FOLDER} && \
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 && \
- mkdir -p $OPENSTRUCTURE_SHARE && chmod a+rw -R $OPENSTRUCTURE_SHARE && mv compounds.chemlib $OPENSTRUCTURE_SHARE && \
- cmake .. -DCOMPOUND_LIB=$OPENSTRUCTURE_SHARE/compounds.chemlib && \
+ 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}
@@ -106,3 +104,4 @@ ENV OPENSTRUCTURE_VERSION=$OPENSTRUCTURE_VERSION
ENTRYPOINT ["ost"]
CMD ["-i"]
+
--
GitLab
From 84430c065baf40ee46b72c210fc96c9f3add565d Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Mon, 16 Dec 2019 14:09:45 +0100
Subject: [PATCH 067/142] don't use virtualenv to make container simpler
---
singularity/Singularity | 17 +++--------------
1 file changed, 3 insertions(+), 14 deletions(-)
diff --git a/singularity/Singularity b/singularity/Singularity
index ea57eab41..125f21324 100644
--- a/singularity/Singularity
+++ b/singularity/Singularity
@@ -15,15 +15,7 @@ ln -sf /bin/bash /bin/sh
# INSTALL SYSTEM DEPS
#####################
-apt-get update -y && apt-get install -y python3-pip \
- python3-venv
-
-
-# SET UP VIRTUALENV
-###################
-export VIRTUALENV_DIR="/usr/local/share/ost_venv"
-python3 -m venv --system-site-packages $VIRTUALENV_DIR
-. $VIRTUALENV_DIR/bin/activate
+apt-get update -y && apt-get install -y python3-pip
pip3 install nglview \
ipython \
jupyter
@@ -71,7 +63,6 @@ export IPYTHONDIR="/usr/local/share/ipython"
export JUPYTER_CONFIG_DIR="/usr/local/etc/jupyter"
export JUPYTER_PATH="/usr/local/share/jupyter"
export JUPYTER_RUNTIME_DIR="/usr/local/share/jupyter/runtime"
-export VIRTUALENV_DIR="/usr/local/share/ost_venv"
%apprun ChemdictTool
@@ -181,7 +172,7 @@ export DNG_INITDIR=${DNG_ROOT}/lib64/python3.6/site-packages/ost
##############################################################################
# OST IPYTON APP
##############################################################################
-. $VIRTUALENV_DIR/bin/activate && ipython3 -i $DNG_INITDIR/ost_startup.py "$@"
+ipython3 -i $DNG_INITDIR/ost_startup.py "$@"
%apphelp IPython
OST-powered iPython shell.
@@ -208,7 +199,7 @@ export XDG_RUNTIME_DIR=""
##############################################################################
# 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 playground with OST and nglview.
@@ -235,8 +226,6 @@ 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:
--
GitLab
From 16889bc63886f1e2de401ab661c57296f525a24d Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Mon, 16 Dec 2019 14:11:11 +0100
Subject: [PATCH 068/142] port compare-structures action
---
actions/ost-compare-structures | 17 ++++++++++++++---
1 file changed, 14 insertions(+), 3 deletions(-)
diff --git a/actions/ost-compare-structures b/actions/ost-compare-structures
index 41f1080ce..e884b7bad 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.items()]
+ rev_out = ["%s -> %s" % (on, nn) for on, nn in list(reverted_chains.items())]
ost.LogInfo("Reverted chains: %s" % ", ".join(rev_out))
@@ -989,9 +989,20 @@ def _Main():
with open(opts.output, "w") as outfile:
json.dump(result, outfile, indent=4, sort_keys=True)
+class _Unbuffered(object):
+ # https://stackoverflow.com/questions/45263064/how-can-i-fix-this-valueerror-cant-have-unbuffered-text-i-o-in-python-3/45263101
+ def __init__(self, stream):
+ self.stream = stream
+ def write(self, data):
+ self.stream.write(data)
+ self.stream.flush()
+ def writelines(self, datas):
+ self.stream.writelines(datas)
+ self.stream.flush()
+ def __getattr__(self, attr):
+ return getattr(self.stream, attr)
if __name__ == '__main__':
# make script 'hot'
- unbuffered = os.fdopen(sys.stdout.fileno(), 'w', 0)
- sys.stdout = unbuffered
+ sys.stdout = _Unbuffered(sys.stdout)
_Main()
--
GitLab
From 2bf97e0faf2d409a9eb7b87454195a7a4ba40c1f Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Mon, 16 Dec 2019 15:10:10 +0100
Subject: [PATCH 069/142] use buffered stdout in compare-structures
---
actions/ost-compare-structures | 16 +---------------
1 file changed, 1 insertion(+), 15 deletions(-)
diff --git a/actions/ost-compare-structures b/actions/ost-compare-structures
index e884b7bad..60a2b8c95 100644
--- a/actions/ost-compare-structures
+++ b/actions/ost-compare-structures
@@ -989,20 +989,6 @@ def _Main():
with open(opts.output, "w") as outfile:
json.dump(result, outfile, indent=4, sort_keys=True)
-class _Unbuffered(object):
- # https://stackoverflow.com/questions/45263064/how-can-i-fix-this-valueerror-cant-have-unbuffered-text-i-o-in-python-3/45263101
- def __init__(self, stream):
- self.stream = stream
- def write(self, data):
- self.stream.write(data)
- self.stream.flush()
- def writelines(self, datas):
- self.stream.writelines(datas)
- self.stream.flush()
- def __getattr__(self, attr):
- return getattr(self.stream, attr)
-
if __name__ == '__main__':
- # make script 'hot'
- sys.stdout = _Unbuffered(sys.stdout)
_Main()
+
--
GitLab
From 9f4b18ebfb96713c66e11f89bdebf61086dbe95a Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Tue, 17 Dec 2019 19:09:46 +0100
Subject: [PATCH 070/142] Temporary error to remind for careful checks in
versions etc. in first Python 3 release
---
scripts/bump-version.py | 4 ++++
1 file changed, 4 insertions(+)
diff --git a/scripts/bump-version.py b/scripts/bump-version.py
index ddf414cd6..0df1088bf 100755
--- a/scripts/bump-version.py
+++ b/scripts/bump-version.py
@@ -1,6 +1,10 @@
#!/usr/bin/env python
import sys
+raise RuntimeError("Many things have changed in the Python 3 port. " +
+ "bump-version.py might require updates. " +
+ "Only remove this error after careful checking!")
+
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)")
--
GitLab
From 0d69b33c441d0a992e3c685cafd95f36b6ef99c7 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Tue, 17 Dec 2019 19:14:56 +0100
Subject: [PATCH 071/142] add note on Python 2 support in install instructions
---
modules/doc/install.rst | 3 +++
1 file changed, 3 insertions(+)
diff --git a/modules/doc/install.rst b/modules/doc/install.rst
index bf0038767..4d8d306a4 100644
--- a/modules/doc/install.rst
+++ b/modules/doc/install.rst
@@ -57,6 +57,9 @@ 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
--------------------------------------------------------------------------------
--
GitLab
From 0a706cba4d9fd944c74e682a1547d9680fedba86 Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavier.robin@unibas.ch>
Date: Wed, 18 Dec 2019 11:16:05 +0100
Subject: [PATCH 072/142] Update call to sphinx to build documentation.
This likely requires an up-to-date sphinx (tested with current version, 2.3.0)
---
doc/make.py | 15 +++++++--------
1 file changed, 7 insertions(+), 8 deletions(-)
diff --git a/doc/make.py b/doc/make.py
index 4d0ce533f..426ee6028 100644
--- a/doc/make.py
+++ b/doc/make.py
@@ -5,7 +5,7 @@ import shutil
from ost import settings
from optparse import OptionParser
import subprocess
-import sphinx
+import sphinx.cmd.build
if len(sys.argv)==2:
root_dir=sys.argv[1]
@@ -82,24 +82,23 @@ if not opts.html and\
not opts.doctest:
opts.html=True
-opt_str=''
+extra_opts=[]
if opts.quiet:
- opt_str=' -Q '
+ extra_opts=['-Q']
for sub_dir in ('modules',):
- print("start walking")
for directory, dirnames, filenames in os.walk(sub_dir):
_CollectRstDocs('doc/source', directory, filenames)
if opts.html:
- sphinx.main([opt_str, '-b', 'html', '-c', 'doc/conf', 'doc/source', 'doc/build/html'])
+ sphinx.cmd.build.main(extra_opts + ['-b', 'html', '-c', 'doc/conf', 'doc/source', 'doc/build/html'])
if opts.doctest:
- sphinx.main([opt_str, '-b', 'doctest', '-c', 'doc/conf', 'doc/source', 'doc/build/html'])
+ sphinx.cmd.build.main(extra_opts + ['-b', 'doctest', '-c', 'doc/conf', 'doc/source', 'doc/build/html'])
if opts.build_json:
- sphinx.main([opt_str, '-b', 'json', '-c', 'doc/conf', 'doc/source', 'doc/build/html'])
+ sphinx.cmd.build.main(extra_opts + ['-b', 'json', '-c', 'doc/conf', 'doc/source', 'doc/build/html'])
if opts.linkcheck:
- sphinx.main([opt_str, '-b', 'linkcheck', '-c', 'doc/conf', 'doc/source', 'doc/build/html'])
+ sphinx.cmd.build.main(extra_opts + ['-b', 'linkcheck', '-c', 'doc/conf', 'doc/source', 'doc/build/html'])
--
GitLab
From fdc51c7448a1d4aecf5d3b8a4f465ce981463640 Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavier.robin@unibas.ch>
Date: Wed, 18 Dec 2019 11:22:07 +0100
Subject: [PATCH 073/142] Decode output of Blast to return a string with
outfmt=1.
---
modules/bindings/pymod/blast.py | 11 +++++++----
1 file changed, 7 insertions(+), 4 deletions(-)
diff --git a/modules/bindings/pymod/blast.py b/modules/bindings/pymod/blast.py
index 89893323a..2cff9231c 100644
--- a/modules/bindings/pymod/blast.py
+++ b/modules/bindings/pymod/blast.py
@@ -208,8 +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`
@@ -224,10 +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:
@@ -281,4 +284,4 @@ def Blast(query, database, gap_open=11, gap_ext=1, matrix='BLOSUM62',
if outfmt==0:
return ParseBlastOutput(stdout.decode())
else:
- return stdout
+ return stdout.decode()
--
GitLab
From ef7bfdb6c85a4ef9cd1fe886d3dd569c472a0860 Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavier.robin@unibas.ch>
Date: Thu, 19 Dec 2019 14:50:18 +0100
Subject: [PATCH 074/142] Attempt to restore compatibility with older versions
of Sphinx
---
doc/make.py | 15 ++++++++++-----
1 file changed, 10 insertions(+), 5 deletions(-)
diff --git a/doc/make.py b/doc/make.py
index 426ee6028..cc6cc1feb 100644
--- a/doc/make.py
+++ b/doc/make.py
@@ -5,7 +5,12 @@ import shutil
from ost import settings
from optparse import OptionParser
import subprocess
-import sphinx.cmd.build
+try:
+ # Import for new versions of Sphinx (tested with 2.3.0)
+ from sphinx.cmd.build import main as sphinx_main
+except ImportError:
+ # Import for older versions of Sphinx (should work with 1.6.7)
+ from sphinx import main as sphinx_main
if len(sys.argv)==2:
root_dir=sys.argv[1]
@@ -91,14 +96,14 @@ for sub_dir in ('modules',):
_CollectRstDocs('doc/source', directory, filenames)
if opts.html:
- sphinx.cmd.build.main(extra_opts + ['-b', 'html', '-c', 'doc/conf', 'doc/source', 'doc/build/html'])
+ sphinx_main(extra_opts + ['-b', 'html', '-c', 'doc/conf', 'doc/source', 'doc/build/html'])
if opts.doctest:
- sphinx.cmd.build.main(extra_opts + ['-b', 'doctest', '-c', 'doc/conf', 'doc/source', 'doc/build/html'])
+ sphinx_main(extra_opts + ['-b', 'doctest', '-c', 'doc/conf', 'doc/source', 'doc/build/html'])
if opts.build_json:
- sphinx.cmd.build.main(extra_opts + ['-b', 'json', '-c', 'doc/conf', 'doc/source', 'doc/build/html'])
+ sphinx_main(extra_opts + ['-b', 'json', '-c', 'doc/conf', 'doc/source', 'doc/build/html'])
if opts.linkcheck:
- sphinx.cmd.build.main(extra_opts + ['-b', 'linkcheck', '-c', 'doc/conf', 'doc/source', 'doc/build/html'])
+ sphinx_main(extra_opts + ['-b', 'linkcheck', '-c', 'doc/conf', 'doc/source', 'doc/build/html'])
--
GitLab
From fcb8d6f4c9ab827e549fd7de7383336216e9538e Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavier.robin@unibas.ch>
Date: Thu, 19 Dec 2019 16:25:54 +0100
Subject: [PATCH 075/142] Revert "Attempt to restore compatibility with older
versions of Sphinx"
This reverts commit ef7bfdb6c85a4ef9cd1fe886d3dd569c472a0860.
Didn't work with Sphinx 1.6.7 which needs an extra option at the start.
This needs to be fixed cleanly, or we need to upgrade the Sphinx version
requirements
---
doc/make.py | 15 +++++----------
1 file changed, 5 insertions(+), 10 deletions(-)
diff --git a/doc/make.py b/doc/make.py
index cc6cc1feb..426ee6028 100644
--- a/doc/make.py
+++ b/doc/make.py
@@ -5,12 +5,7 @@ import shutil
from ost import settings
from optparse import OptionParser
import subprocess
-try:
- # Import for new versions of Sphinx (tested with 2.3.0)
- from sphinx.cmd.build import main as sphinx_main
-except ImportError:
- # Import for older versions of Sphinx (should work with 1.6.7)
- from sphinx import main as sphinx_main
+import sphinx.cmd.build
if len(sys.argv)==2:
root_dir=sys.argv[1]
@@ -96,14 +91,14 @@ for sub_dir in ('modules',):
_CollectRstDocs('doc/source', directory, filenames)
if opts.html:
- sphinx_main(extra_opts + ['-b', 'html', '-c', 'doc/conf', 'doc/source', 'doc/build/html'])
+ sphinx.cmd.build.main(extra_opts + ['-b', 'html', '-c', 'doc/conf', 'doc/source', 'doc/build/html'])
if opts.doctest:
- sphinx_main(extra_opts + ['-b', 'doctest', '-c', 'doc/conf', 'doc/source', 'doc/build/html'])
+ sphinx.cmd.build.main(extra_opts + ['-b', 'doctest', '-c', 'doc/conf', 'doc/source', 'doc/build/html'])
if opts.build_json:
- sphinx_main(extra_opts + ['-b', 'json', '-c', 'doc/conf', 'doc/source', 'doc/build/html'])
+ sphinx.cmd.build.main(extra_opts + ['-b', 'json', '-c', 'doc/conf', 'doc/source', 'doc/build/html'])
if opts.linkcheck:
- sphinx_main(extra_opts + ['-b', 'linkcheck', '-c', 'doc/conf', 'doc/source', 'doc/build/html'])
+ sphinx.cmd.build.main(extra_opts + ['-b', 'linkcheck', '-c', 'doc/conf', 'doc/source', 'doc/build/html'])
--
GitLab
From d78faecbfabeb23467efda0d1946c116062bc761 Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavier.robin@unibas.ch>
Date: Fri, 20 Dec 2019 14:30:58 +0100
Subject: [PATCH 076/142] Use sphinx.application.Sphinx instead of a main
function.
---
doc/make.py | 43 +++++++++++++++++++++++++++++--------------
1 file changed, 29 insertions(+), 14 deletions(-)
diff --git a/doc/make.py b/doc/make.py
index 426ee6028..5d088e798 100644
--- a/doc/make.py
+++ b/doc/make.py
@@ -5,7 +5,7 @@ import shutil
from ost import settings
from optparse import OptionParser
import subprocess
-import sphinx.cmd.build
+from sphinx.application import Sphinx
if len(sys.argv)==2:
root_dir=sys.argv[1]
@@ -76,29 +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
-extra_opts=[]
+extra_args = {}
if opts.quiet:
- extra_opts=['-Q']
+ extra_args['warning'] = None
+ extra_args['status'] = None
for sub_dir in ('modules',):
for directory, dirnames, filenames in os.walk(sub_dir):
_CollectRstDocs('doc/source', directory, filenames)
-if opts.html:
- sphinx.cmd.build.main(extra_opts + ['-b', 'html', '-c', 'doc/conf', 'doc/source', 'doc/build/html'])
-
-if opts.doctest:
- sphinx.cmd.build.main(extra_opts + ['-b', 'doctest', '-c', 'doc/conf', 'doc/source', 'doc/build/html'])
-
-if opts.build_json:
- sphinx.cmd.build.main(extra_opts + ['-b', 'json', '-c', 'doc/conf', 'doc/source', 'doc/build/html'])
-
-if opts.linkcheck:
- sphinx.cmd.build.main(extra_opts + ['-b', 'linkcheck', '-c', 'doc/conf', 'doc/source', 'doc/build/html'])
+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)
--
GitLab
From ba9dc5070c31c64d749ebc27a893ec2b89f0a7ce Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Fri, 20 Dec 2019 15:02:49 +0100
Subject: [PATCH 077/142] replace deprecated import
---
modules/mol/alg/pymod/qsscoring.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/modules/mol/alg/pymod/qsscoring.py b/modules/mol/alg/pymod/qsscoring.py
index adab36d6c..f9753788c 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
--
GitLab
From 1a0f9f5b9b5d5832dbc472075fa080b5278a751e Mon Sep 17 00:00:00 2001
From: Andrew Waterhouse <andrew.waterhouse@unibas.ch>
Date: Mon, 30 Dec 2019 10:35:07 +0100
Subject: [PATCH 078/142] decode subprocess sout
---
modules/bindings/pymod/hhblits.py | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/modules/bindings/pymod/hhblits.py b/modules/bindings/pymod/hhblits.py
index 5567dd229..23d267518 100644
--- a/modules/bindings/pymod/hhblits.py
+++ b/modules/bindings/pymod/hhblits.py
@@ -667,7 +667,8 @@ class HHblits:
job = subprocess.Popen(cs_cmd, shell=True, cwd=self.working_dir,
stdout=subprocess.PIPE, stderr=subprocess.PIPE)
sout, _ = job.communicate()
- if b'Wrote abstract state sequence to' in sout:
+ lines = sout.decode()
+ if 'Wrote abstract state sequence to' in sout:
return cs_file
ost.LogWarning('Creating column state sequence file (%s) failed' % \
--
GitLab
From 11d979fc9351cd498f24ee43d5b8d3f2f611f053 Mon Sep 17 00:00:00 2001
From: Andrew Waterhouse <andrew.waterhouse@unibas.ch>
Date: Mon, 30 Dec 2019 10:37:23 +0100
Subject: [PATCH 079/142] decode subprocess sout
---
modules/bindings/pymod/hhblits.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/modules/bindings/pymod/hhblits.py b/modules/bindings/pymod/hhblits.py
index 23d267518..85dc65255 100644
--- a/modules/bindings/pymod/hhblits.py
+++ b/modules/bindings/pymod/hhblits.py
@@ -667,7 +667,7 @@ class HHblits:
job = subprocess.Popen(cs_cmd, shell=True, cwd=self.working_dir,
stdout=subprocess.PIPE, stderr=subprocess.PIPE)
sout, _ = job.communicate()
- lines = sout.decode()
+ sout = sout.decode()
if 'Wrote abstract state sequence to' in sout:
return cs_file
--
GitLab
From a00f318a8ad22ce1ccc49d51d05cb89bc5b4371a Mon Sep 17 00:00:00 2001
From: Andrew Waterhouse <andrew.waterhouse@unibas.ch>
Date: Thu, 2 Jan 2020 15:51:50 +0100
Subject: [PATCH 080/142] Read as binary in exec compile open
---
scripts/ost_startup.py.in | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/scripts/ost_startup.py.in b/scripts/ost_startup.py.in
index 6a5addab2..3d22c7e7e 100644
--- a/scripts/ost_startup.py.in
+++ b/scripts/ost_startup.py.in
@@ -86,7 +86,7 @@ if len(parser.rargs)>0 :
sys_argv_backup=sys.argv
sys.argv=parser.rargs
try:
- exec(compile(open(script).read(), script, 'exec'))
+ exec(compile(open(script,'rb').read(), script, 'exec'))
finally:
sys.argv=sys_argv_backup
--
GitLab
From d5c9ab52c90f452f4558a5f1826af3e44bac7e6e Mon Sep 17 00:00:00 2001
From: Andrew Waterhouse <andrew.waterhouse@unibas.ch>
Date: Tue, 7 Jan 2020 16:13:56 +0100
Subject: [PATCH 081/142] keep this as bytes Wrote abstract state sequence to
---
modules/bindings/pymod/hhblits.py | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
diff --git a/modules/bindings/pymod/hhblits.py b/modules/bindings/pymod/hhblits.py
index 85dc65255..5567dd229 100644
--- a/modules/bindings/pymod/hhblits.py
+++ b/modules/bindings/pymod/hhblits.py
@@ -667,8 +667,7 @@ class HHblits:
job = subprocess.Popen(cs_cmd, shell=True, cwd=self.working_dir,
stdout=subprocess.PIPE, stderr=subprocess.PIPE)
sout, _ = job.communicate()
- sout = sout.decode()
- if 'Wrote abstract state sequence to' in sout:
+ if b'Wrote abstract state sequence to' in sout:
return cs_file
ost.LogWarning('Creating column state sequence file (%s) failed' % \
--
GitLab
From 51225d1b7d8e80eb682cd375d57f1c03816fa13f Mon Sep 17 00:00:00 2001
From: Andrew Waterhouse <andrew.waterhouse@unibas.ch>
Date: Fri, 17 Jan 2020 11:44:33 +0100
Subject: [PATCH 082/142] Subprocess wait in deadlock averted
---
modules/bindings/pymod/clustalw.py | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/modules/bindings/pymod/clustalw.py b/modules/bindings/pymod/clustalw.py
index 074199283..aab374f07 100644
--- a/modules/bindings/pymod/clustalw.py
+++ b/modules/bindings/pymod/clustalw.py
@@ -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
- with subprocess.Popen(command, shell=True, stdout=subprocess.PIPE) as ps:
- ps.wait()
+ subprocess.run(command, shell=True, stdout=subprocess.DEVNULL)
+
aln=io.LoadAlignment(out)
--
GitLab
From 01eca9016b369b3e75c9941151994428936848af Mon Sep 17 00:00:00 2001
From: Andrew Waterhouse <andrew.waterhouse@unibas.ch>
Date: Fri, 17 Jan 2020 13:30:31 +0100
Subject: [PATCH 083/142] Replace all subprocess wait with run
---
modules/bindings/pymod/dssp.py | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/modules/bindings/pymod/dssp.py b/modules/bindings/pymod/dssp.py
index b03468789..36c5d1af2 100644
--- a/modules/bindings/pymod/dssp.py
+++ b/modules/bindings/pymod/dssp.py
@@ -55,8 +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])
- ps.wait()
+ subprocess.run([dssp_abs_path, path, temp_dssp_path])
+
return temp_dssp_path
--
GitLab
From dd7fe4f88be71fb7f3ae2202c00ebf68fcd4ce75 Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavier.robin@unibas.ch>
Date: Wed, 29 Jan 2020 13:48:26 +0100
Subject: [PATCH 084/142] doc: document filtering of chains by qsscoring
---
modules/doc/actions.rst | 4 ++++
1 file changed, 4 insertions(+)
diff --git a/modules/doc/actions.rst b/modules/doc/actions.rst
index 993612233..6d7391a21 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
--
GitLab
From 1f2dae67c5e9aaf4e5e29f37929c686aa0f9003d Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavier.robin@unibas.ch>
Date: Mon, 3 Feb 2020 18:03:57 +0100
Subject: [PATCH 085/142] doc: fix indexing of ost.bindings
---
modules/bindings/doc/tmtools.rst | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/modules/bindings/doc/tmtools.rst b/modules/bindings/doc/tmtools.rst
index 51b786efc..823a35eca 100644
--- a/modules/bindings/doc/tmtools.rst
+++ b/modules/bindings/doc/tmtools.rst
@@ -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
--
GitLab
From 543a4e2c93bed1670d300b98186c726dfcbfe40d Mon Sep 17 00:00:00 2001
From: Gerardo Tauriello <gerardo.tauriello@unibas.ch>
Date: Wed, 5 Feb 2020 18:24:37 +0100
Subject: [PATCH 086/142] Try to force C++11 for older compilers.
---
cmake_support/OST.cmake | 2 +-
modules/doc/install.rst | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/cmake_support/OST.cmake b/cmake_support/OST.cmake
index 46c511d58..41e8f7a78 100644
--- a/cmake_support/OST.cmake
+++ b/cmake_support/OST.cmake
@@ -897,7 +897,7 @@ 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()
diff --git a/modules/doc/install.rst b/modules/doc/install.rst
index 4d8d306a4..7d342fd6f 100644
--- a/modules/doc/install.rst
+++ b/modules/doc/install.rst
@@ -23,7 +23,7 @@ the steps which we describe in detail below. In essence, these steps are:
Installing the Dependencies
--------------------------------------------------------------------------------
-OpenStructure requires a c++11 enabled compiler (e.g. recent gcc/clang) and uses
+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.
--
GitLab
From d0796500779c63351536372ccb6d1b75fe9247f6 Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Wed, 5 Feb 2020 13:17:36 +0100
Subject: [PATCH 087/142] SCHWED-4612: Get rid of '-Wmaybe-uninitialized' from
Vec3
---
modules/geom/src/vec3.hh | 20 +++++++++++++++++++-
1 file changed, 19 insertions(+), 1 deletion(-)
diff --git a/modules/geom/src/vec3.hh b/modules/geom/src/vec3.hh
index 47137476e..6ce79ff3d 100644
--- a/modules/geom/src/vec3.hh
+++ b/modules/geom/src/vec3.hh
@@ -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
{
--
GitLab
From 5b6da8c8daff8b302441bb18d7fbaa0dbeb3647b Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Thu, 6 Feb 2020 07:20:58 +0100
Subject: [PATCH 088/142] SCHWED-4612: Remove use of deprecated function.
---
modules/io/pymod/__init__.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/modules/io/pymod/__init__.py b/modules/io/pymod/__init__.py
index 9dea7dbc5..dbc139f63 100644
--- a/modules/io/pymod/__init__.py
+++ b/modules/io/pymod/__init__.py
@@ -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
--
GitLab
From 4d1a5f685b18eb706672ac2d6b5b108c04b2b84b Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Thu, 6 Feb 2020 08:49:06 +0100
Subject: [PATCH 089/142] SCHWED-4612: Fix warning on unused (static) function.
---
modules/img/alg/src/alg_shift.hh | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/modules/img/alg/src/alg_shift.hh b/modules/img/alg/src/alg_shift.hh
index dc47beb77..7519c57b3 100644
--- a/modules/img/alg/src/alg_shift.hh
+++ b/modules/img/alg/src/alg_shift.hh
@@ -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) {
--
GitLab
From 910170cab61a5940f44437b770021e40d8ec1683 Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Thu, 6 Feb 2020 10:21:52 +0100
Subject: [PATCH 090/142] SCHWED-4612: Ignore warning about unused functions by
GCC, while the functions are used by unit tests.
---
modules/img/alg/src/fill.hh | 6 ++++++
1 file changed, 6 insertions(+)
diff --git a/modules/img/alg/src/fill.hh b/modules/img/alg/src/fill.hh
index b023d70f5..34e50e72e 100644
--- a/modules/img/alg/src/fill.hh
+++ b/modules/img/alg/src/fill.hh
@@ -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)
--
GitLab
From a1263ab76bc87bbb9e10b20d687e91a0e4671d9a Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Fri, 7 Feb 2020 08:49:15 +0100
Subject: [PATCH 091/142] SCHWED-4612: Dealing with the NumPy deprecation
compiler warning.
---
modules/mol/base/pymod/export_entity.cc | 9 +++++++++
1 file changed, 9 insertions(+)
diff --git a/modules/mol/base/pymod/export_entity.cc b/modules/mol/base/pymod/export_entity.cc
index 35b918b16..62d26b5b5 100644
--- a/modules/mol/base/pymod/export_entity.cc
+++ b/modules/mol/base/pymod/export_entity.cc
@@ -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
@@ -131,6 +139,7 @@ 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
--
GitLab
From 23342853809dbbe1b52cf53e5e7c7d701da5df93 Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Fri, 7 Feb 2020 11:38:40 +0100
Subject: [PATCH 092/142] SCHWED-4612: Update CMake call for CI.
---
.gitlab-ci.yml | 6 ++++--
1 file changed, 4 insertions(+), 2 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 7bf2dd628..362e73431 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -68,9 +68,11 @@ test:centos7.3:
-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='-Wno-unused-local-typedefs -L/scicore/soft/apps/libpng/1.6.34-GCCcore-7.3.0/lib/ -L/scicore/soft/apps/LibTIFF/4.0.9-GCCcore-7.3.0/lib/ -L/scicore/soft/apps/zlib/1.2.11-GCCcore-7.3.0/lib'
- -DCMAKE_CXX_FLAGS='-Wno-unused-local-typedefs -L/scicore/soft/apps/libpng/1.6.34-GCCcore-7.3.0/lib/ -L/scicore/soft/apps/LibTIFF/4.0.9-GCCcore-7.3.0/lib/ -L/scicore/soft/apps/zlib/1.2.11-GCCcore-7.3.0/lib'
+ -DCMAKE_C_FLAGS='-Wno-unused-local-typedefs -L/scicore/soft/apps/libpng/1.6.34-GCCcore-7.3.0/lib/ -L/scicore/soft/apps/LibTIFF/4.0.9-GCCcore-7.3.0/lib/ -L/scicore/soft/apps/zlib/1.2.11-GCCcore-7.3.0/lib/ -isystem ${EBROOTBOOST}/include -isystem ${EBROOTOPENMM}/include'
+ -DCMAKE_CXX_FLAGS='-Wno-unused-local-typedefs -L/scicore/soft/apps/libpng/1.6.34-GCCcore-7.3.0/lib/ -L/scicore/soft/apps/LibTIFF/4.0.9-GCCcore-7.3.0/lib/ -L/scicore/soft/apps/zlib/1.2.11-GCCcore-7.3.0/lib/ -isystem ${EBROOTBOOST}/include -isystem ${EBROOTOPENMM}/include'
-DCMAKE_EXE_LINKER_FLAGS=" -pthread"
- make -j 2
- echo " ... done building OST."
--
GitLab
From cb2f10d8ec779b7ec39990d5071e86e4d5b7351f Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Fri, 7 Feb 2020 13:33:02 +0100
Subject: [PATCH 093/142] remove openmm density plugin which has always been
experimental and was never thoroughly tested
---
modules/mol/mm/pymod/export_topology.cc | 4 -
modules/mol/mm/src/CMakeLists.txt | 41 ---
.../density_plugin/openmmapi/density_force.cc | 97 -----
.../density_plugin/openmmapi/density_force.hh | 94 -----
.../openmmapi/density_force_impl.cc | 71 ----
.../openmmapi/density_force_impl.hh | 74 ----
.../openmmapi/density_kernels.hh | 80 ----
.../reference_density_kernel_factory.cc | 62 ----
.../reference_density_kernel_factory.hh | 53 ---
.../reference/reference_density_kernels.cc | 342 ------------------
.../reference/reference_density_kernels.hh | 164 ---------
modules/mol/mm/src/system_creator.cc | 21 --
modules/mol/mm/src/topology.cc | 35 --
modules/mol/mm/src/topology.hh | 21 --
14 files changed, 1159 deletions(-)
delete mode 100644 modules/mol/mm/src/openmm_plugins/density_plugin/openmmapi/density_force.cc
delete mode 100644 modules/mol/mm/src/openmm_plugins/density_plugin/openmmapi/density_force.hh
delete mode 100644 modules/mol/mm/src/openmm_plugins/density_plugin/openmmapi/density_force_impl.cc
delete mode 100644 modules/mol/mm/src/openmm_plugins/density_plugin/openmmapi/density_force_impl.hh
delete mode 100644 modules/mol/mm/src/openmm_plugins/density_plugin/openmmapi/density_kernels.hh
delete mode 100644 modules/mol/mm/src/openmm_plugins/density_plugin/platforms/reference/reference_density_kernel_factory.cc
delete mode 100644 modules/mol/mm/src/openmm_plugins/density_plugin/platforms/reference/reference_density_kernel_factory.hh
delete mode 100644 modules/mol/mm/src/openmm_plugins/density_plugin/platforms/reference/reference_density_kernels.cc
delete mode 100644 modules/mol/mm/src/openmm_plugins/density_plugin/platforms/reference/reference_density_kernels.hh
diff --git a/modules/mol/mm/pymod/export_topology.cc b/modules/mol/mm/pymod/export_topology.cc
index 1e90e1b96..fa5320904 100644
--- a/modules/mol/mm/pymod/export_topology.cc
+++ b/modules/mol/mm/pymod/export_topology.cc
@@ -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/src/CMakeLists.txt b/modules/mol/mm/src/CMakeLists.txt
index 3ebe98ba0..46f4d4cd5 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/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 8ff809d9a..000000000
--- 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 f932ff797..000000000
--- 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 1d2b859a0..000000000
--- 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 850b2c5c2..000000000
--- 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 78e16cfa7..000000000
--- 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 8df88868d..000000000
--- 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 14dfdf44c..000000000
--- 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 77edcd552..000000000
--- 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 7a06088ee..000000000
--- 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/system_creator.cc b/modules/mol/mm/src/system_creator.cc
index aa365ee29..7d51c905e 100644
--- a/modules/mol/mm/src/system_creator.cc
+++ b/modules/mol/mm/src/system_creator.cc
@@ -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/topology.cc b/modules/mol/mm/src/topology.cc
index 58a72827d..d9810ce34 100644
--- a/modules/mol/mm/src/topology.cc
+++ b/modules/mol/mm/src/topology.cc
@@ -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 486accf1e..501d4e901 100644
--- a/modules/mol/mm/src/topology.hh
+++ b/modules/mol/mm/src/topology.hh
@@ -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_;
};
--
GitLab
From ff5e49cdc7205223a0fb5d32ee12b409562e0c8e Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Fri, 7 Feb 2020 13:49:19 +0100
Subject: [PATCH 094/142] slightly relax dcd io unit test
The reason is that the check just scratches floating point accuracy and
occasionally failed on some machines
---
modules/io/tests/test_io_dcd.cc | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/modules/io/tests/test_io_dcd.cc b/modules/io/tests/test_io_dcd.cc
index 270d371e8..1ae165d16 100644
--- a/modules/io/tests/test_io_dcd.cc
+++ b/modules/io/tests/test_io_dcd.cc
@@ -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);
}
}
--
GitLab
From eb2a9384a644c9731d1d90c2ea3866e942edb48c Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Mon, 10 Feb 2020 11:11:53 +0100
Subject: [PATCH 095/142] SCHWED-4612: Reduce Numpy compilation warnings
---
modules/mol/base/pymod/export_editors.cc | 9 +++++++++
1 file changed, 9 insertions(+)
diff --git a/modules/mol/base/pymod/export_editors.cc b/modules/mol/base/pymod/export_editors.cc
index 50aa16842..ebdbcf2b2 100644
--- a/modules/mol/base/pymod/export_editors.cc
+++ b/modules/mol/base/pymod/export_editors.cc
@@ -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
@@ -228,6 +236,7 @@ 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
--
GitLab
From c663c88093e00cd91fe7327f4dccad10f51058ce Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Mon, 10 Feb 2020 11:12:30 +0100
Subject: [PATCH 096/142] SCHWED-4382: Better logging for HHblits
---
modules/bindings/pymod/hhblits.py | 13 +++++++++++--
1 file changed, 11 insertions(+), 2 deletions(-)
diff --git a/modules/bindings/pymod/hhblits.py b/modules/bindings/pymod/hhblits.py
index 5567dd229..ff08319a4 100644
--- a/modules/bindings/pymod/hhblits.py
+++ b/modules/bindings/pymod/hhblits.py
@@ -624,8 +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
--
GitLab
From b6c8152d60eb25f3ed959d0384ae31afa9e2be9e Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Mon, 10 Feb 2020 16:53:48 +0100
Subject: [PATCH 097/142] SCHWED-4612: Get rid of TMalign compiler warnings
---
modules/bindings/src/tmalign/TMalign.h | 22 ++++++++++------------
modules/bindings/src/tmalign/basic_fun.h | 13 ++++++-------
2 files changed, 16 insertions(+), 19 deletions(-)
diff --git a/modules/bindings/src/tmalign/TMalign.h b/modules/bindings/src/tmalign/TMalign.h
index 79abc61af..08caeec3a 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 8274428ee..3dadccc30 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.");
--
GitLab
From 37ab35622f054f16dc8a02d5b8a5544b92fb12e3 Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Tue, 11 Feb 2020 14:40:26 +0100
Subject: [PATCH 098/142] SCHWED-4612: Get rid of some Numpy warnings, move
from np.matrix to np.array, keeping the matrix variant as deprecated method.
---
modules/base/pymod/table.py | 59 ++++++++++++++++++++++++--------
modules/base/tests/test_table.py | 26 +++++++-------
2 files changed, 57 insertions(+), 28 deletions(-)
diff --git a/modules/base/pymod/table.py b/modules/base/pymod/table.py
index 8697d63d0..4277edf94 100644
--- a/modules/base/pymod/table.py
+++ b/modules/base/pymod/table.py
@@ -2348,16 +2348,19 @@ Statistics for column %(col)s
if file_opened:
stream.close()
-
- def GetNumpyMatrix(self, *args):
+ 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*
'''
@@ -2372,16 +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):
@@ -2502,20 +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 'weights' in kwargs:
- w = self.GetNumpyMatrix(kwargs['weights'])
+ 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.")
@@ -3202,3 +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/tests/test_table.py b/modules/base/tests/test_table.py
index 5d56f67ee..52dee4de4 100644
--- a/modules/base/tests/test_table.py
+++ b/modules/base/tests/test_table.py
@@ -1472,7 +1472,7 @@ class TestTable(unittest.TestCase):
mcc = tab.ComputeMCC(score_col='prediction2', class_col='reference')
self.assertAlmostEqual(mcc, 0.882089673321)
- def testTableAsNumpyMatrix(self):
+ def testTableAsNumpyMatrixAsArray(self):
if not HAS_NUMPY:
return
@@ -1488,24 +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:
--
GitLab
From f38cb6a85fc8e48917026f7e13513b33b70ade44 Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Wed, 12 Feb 2020 10:16:26 +0100
Subject: [PATCH 099/142] SCHWED-4612: Get rid of some Numpy warnings, move
from np.matrix to np.array.
---
modules/mol/alg/pymod/qsscoring.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/modules/mol/alg/pymod/qsscoring.py b/modules/mol/alg/pymod/qsscoring.py
index f9753788c..fa838faab 100644
--- a/modules/mol/alg/pymod/qsscoring.py
+++ b/modules/mol/alg/pymod/qsscoring.py
@@ -1618,7 +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
--
GitLab
From e07e29d8b17deed41f576b777538db195d3753b9 Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Wed, 12 Feb 2020 13:17:14 +0100
Subject: [PATCH 100/142] SCHWED-4612: Update CI Yaml file.
---
.gitlab-ci.yml | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 362e73431..755fed9fc 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -71,8 +71,8 @@ test:centos7.3:
-DZLIB_INCLUDE_DIR=$EBROOTZLIB/include
-DZLIB_LIBRARY=$EBROOTZLIB/lib/libz.so
-DOPTIMIZE=1
- -DCMAKE_C_FLAGS='-Wno-unused-local-typedefs -L/scicore/soft/apps/libpng/1.6.34-GCCcore-7.3.0/lib/ -L/scicore/soft/apps/LibTIFF/4.0.9-GCCcore-7.3.0/lib/ -L/scicore/soft/apps/zlib/1.2.11-GCCcore-7.3.0/lib/ -isystem ${EBROOTBOOST}/include -isystem ${EBROOTOPENMM}/include'
- -DCMAKE_CXX_FLAGS='-Wno-unused-local-typedefs -L/scicore/soft/apps/libpng/1.6.34-GCCcore-7.3.0/lib/ -L/scicore/soft/apps/LibTIFF/4.0.9-GCCcore-7.3.0/lib/ -L/scicore/soft/apps/zlib/1.2.11-GCCcore-7.3.0/lib/ -isystem ${EBROOTBOOST}/include -isystem ${EBROOTOPENMM}/include'
+ -DCMAKE_C_FLAGS='-L/scicore/soft/apps/libpng/1.6.34-GCCcore-7.3.0/lib/ -L/scicore/soft/apps/LibTIFF/4.0.9-GCCcore-7.3.0/lib/ -L/scicore/soft/apps/zlib/1.2.11-GCCcore-7.3.0/lib/ -isystem ${EBROOTBOOST}/include -isystem ${EBROOTOPENMM}/include'
+ -DCMAKE_CXX_FLAGS='-L/scicore/soft/apps/libpng/1.6.34-GCCcore-7.3.0/lib/ -L/scicore/soft/apps/LibTIFF/4.0.9-GCCcore-7.3.0/lib/ -L/scicore/soft/apps/zlib/1.2.11-GCCcore-7.3.0/lib/ -isystem ${EBROOTBOOST}/include -isystem ${EBROOTOPENMM}/include'
-DCMAKE_EXE_LINKER_FLAGS=" -pthread"
- make -j 2
- echo " ... done building OST."
--
GitLab
From 6218e8d3b667f2ce279ce90ea1c60a5adb1e5623 Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Wed, 12 Feb 2020 15:02:16 +0100
Subject: [PATCH 101/142] SCHWED-4612: Remove a message from HHblits bindings
test.
---
modules/bindings/tests/test_hhblits.py | 18 ++++++++++++++++++
1 file changed, 18 insertions(+)
diff --git a/modules/bindings/tests/test_hhblits.py b/modules/bindings/tests/test_hhblits.py
index 1bc6b3652..7e0e3a7fc 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')
--
GitLab
From 33624e06eb581392bd3685d47e6f72d7147478bf Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Thu, 13 Feb 2020 10:42:56 +0100
Subject: [PATCH 102/142] Bump copyright to 2020
---
modules/db/pymod/export_linear_db.cc | 2 +-
modules/db/pymod/wrap_db.cc | 2 +-
modules/db/src/binary_container.cc | 2 +-
modules/db/src/binary_container.hh | 2 +-
modules/db/src/extract_data_helper.cc | 2 +-
modules/db/src/extract_data_helper.hh | 4 ++--
modules/db/src/linear_indexer.cc | 2 +-
modules/db/src/linear_indexer.hh | 2 +-
modules/db/src/paged_array.hh | 2 +-
9 files changed, 10 insertions(+), 10 deletions(-)
diff --git a/modules/db/pymod/export_linear_db.cc b/modules/db/pymod/export_linear_db.cc
index 8b9f7f942..597f4243e 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 883c6a33e..2bc2223a4 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 a82723c52..37f01e402 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 3648513d4..6477e7452 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 607499e8f..f95ff73e3 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 288ed9536..271d03b3d 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 c0a586582..d03471f08 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 3507ae12d..a6c77a1d1 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/paged_array.hh b/modules/db/src/paged_array.hh
index 5512c7a9d..776754bc7 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
--
GitLab
From 043e9ad7ac1175ec3e15c7fbff7369240c37241b Mon Sep 17 00:00:00 2001
From: Gerardo Tauriello <gerardo.tauriello@unibas.ch>
Date: Thu, 13 Feb 2020 15:25:52 +0100
Subject: [PATCH 103/142] Fix/clarify use of old legacy doxygen doc
---
doxygen/Doxyfile | 5 ++++-
1 file changed, 4 insertions(+), 1 deletion(-)
diff --git a/doxygen/Doxyfile b/doxygen/Doxyfile
index d44e235b5..1c694fd73 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 \
--
GitLab
From aea78e77172e4b3712c6da0456fabbe637b28369 Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Thu, 13 Feb 2020 15:34:02 +0100
Subject: [PATCH 104/142] Bum copyright to 2020
---
deployment/CMakeLists.txt | 2 +-
deployment/README.html.in | 2 +-
deployment/win/dng.bat | 2 +-
doc/conf/conf.py | 2 +-
examples/code_fragments/ui/mdi_example.py | 2 +-
examples/code_fragments/ui/menubar_example.py | 2 +-
examples/code_fragments/ui/widget_example.py | 2 +-
modules/base/pymod/__init__.py.in | 2 +-
modules/base/pymod/export_generic_property.cc | 2 +-
modules/base/pymod/export_logger.cc | 2 +-
modules/base/pymod/export_range.cc | 2 +-
modules/base/pymod/export_units.cc | 2 +-
modules/base/pymod/wrap_base.cc | 2 +-
modules/base/src/boost_filesystem_helper.cc | 2 +-
modules/base/src/boost_filesystem_helper.hh | 2 +-
modules/base/src/dyn_cast.hh | 2 +-
modules/base/src/export_helper/generic_property_def.hh | 2 +-
modules/base/src/export_helper/pair_to_tuple_conv.hh | 2 +-
modules/base/src/export_helper/vec_to_list_conv.hh | 2 +-
modules/base/src/generic_property.cc | 2 +-
modules/base/src/generic_property.hh | 2 +-
modules/base/src/integrity_error.hh | 2 +-
modules/base/src/invalid_handle.hh | 2 +-
modules/base/src/log.cc | 2 +-
modules/base/src/log.hh | 2 +-
modules/base/src/log_sink.cc | 2 +-
modules/base/src/log_sink.hh | 2 +-
modules/base/src/message.cc | 2 +-
modules/base/src/message.hh | 2 +-
modules/base/src/module_config.hh | 2 +-
modules/base/src/platform.cc | 2 +-
modules/base/src/platform.hh | 2 +-
modules/base/src/pod_vector.hh | 2 +-
modules/base/src/profile.cc | 2 +-
modules/base/src/profile.hh | 2 +-
modules/base/src/ptr_observer.hh | 2 +-
modules/base/src/range.hh | 2 +-
modules/base/src/string_ref.cc | 2 +-
modules/base/src/string_ref.hh | 2 +-
modules/base/src/test_utils/compare_files.cc | 2 +-
modules/base/src/test_utils/compare_files.hh | 2 +-
modules/base/src/units.cc | 2 +-
modules/base/src/units.hh | 2 +-
modules/base/tests/test_generic_property.cc | 2 +-
modules/base/tests/test_pod_vector.cc | 2 +-
modules/base/tests/test_string_ref.cc | 2 +-
modules/base/tests/tests.cc | 2 +-
modules/bindings/pymod/cadscore.py | 2 +-
modules/bindings/pymod/dssp.py | 2 +-
modules/bindings/pymod/export_tmalign.cc | 2 +-
modules/bindings/pymod/ialign.py | 2 +-
modules/bindings/pymod/tmtools.py | 2 +-
modules/bindings/pymod/wrap_bindings.cc | 2 +-
modules/bindings/src/wrap_tmalign.cc | 2 +-
modules/bindings/src/wrap_tmalign.hh | 2 +-
modules/config/base.hh | 2 +-
modules/config/config.hh.in | 2 +-
modules/config/dllexport.hh | 2 +-
modules/config/version.hh.in | 2 +-
modules/conop/pymod/__init__.py | 2 +-
modules/conop/pymod/export_amino_acids.cc | 2 +-
modules/conop/pymod/export_compound.cc | 2 +-
modules/conop/pymod/export_conop.cc | 2 +-
modules/conop/pymod/export_diag.cc | 2 +-
modules/conop/pymod/export_heuristic.cc | 2 +-
modules/conop/pymod/export_processor.cc | 2 +-
modules/conop/pymod/export_ring_finder.cc | 2 +-
modules/conop/pymod/export_rule_based.cc | 2 +-
modules/conop/pymod/wrap_conop.cc | 2 +-
modules/conop/src/amino_acids.cc | 2 +-
modules/conop/src/amino_acids.hh | 2 +-
modules/conop/src/chemdict_tool.cc | 2 +-
modules/conop/src/compound.cc | 2 +-
modules/conop/src/compound.hh | 2 +-
modules/conop/src/compound_lib.cc | 2 +-
modules/conop/src/compound_lib.hh | 2 +-
modules/conop/src/conop.cc | 2 +-
modules/conop/src/conop.hh | 2 +-
modules/conop/src/diag.cc | 2 +-
modules/conop/src/diag.hh | 2 +-
modules/conop/src/heuristic.cc | 2 +-
modules/conop/src/heuristic.hh | 2 +-
modules/conop/src/module_config.hh | 2 +-
modules/conop/src/processor.cc | 2 +-
modules/conop/src/processor.hh | 2 +-
modules/conop/src/ring_finder.cc | 2 +-
modules/conop/src/ring_finder.hh | 2 +-
modules/conop/src/rule_based.cc | 2 +-
modules/conop/src/rule_based.hh | 2 +-
modules/conop/tests/test_amino_acids.cc | 2 +-
modules/conop/tests/test_heuristic_builder.cc | 2 +-
modules/conop/tests/test_heuristic_conop.cc | 2 +-
modules/conop/tests/test_rule_based_conop.cc | 2 +-
modules/conop/tests/tests.cc | 2 +-
modules/db/pymod/__init__.py | 2 +-
modules/db/src/module_config.hh | 2 +-
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modules/mol/base/src/query_state.hh | 2 +-
modules/mol/base/src/query_view_wrapper.cc | 2 +-
modules/mol/base/src/query_view_wrapper.hh | 2 +-
modules/mol/base/src/residue_base.cc | 2 +-
modules/mol/base/src/residue_base.hh | 2 +-
modules/mol/base/src/residue_handle.cc | 2 +-
modules/mol/base/src/residue_handle.hh | 2 +-
modules/mol/base/src/residue_prop.hh | 2 +-
modules/mol/base/src/residue_view.cc | 2 +-
modules/mol/base/src/residue_view.hh | 2 +-
modules/mol/base/src/sec_structure.hh | 2 +-
modules/mol/base/src/skel_link.cc | 2 +-
modules/mol/base/src/skel_link.hh | 2 +-
modules/mol/base/src/skel_link_fw.hh | 2 +-
modules/mol/base/src/spatial_organizer.hh | 2 +-
modules/mol/base/src/surface.hh | 2 +-
modules/mol/base/src/surface_builder.cc | 2 +-
modules/mol/base/src/surface_builder.hh | 2 +-
modules/mol/base/src/surface_handle.cc | 2 +-
modules/mol/base/src/surface_handle.hh | 2 +-
modules/mol/base/src/surface_prop.hh | 2 +-
modules/mol/base/src/torsion_handle.cc | 2 +-
modules/mol/base/src/torsion_handle.hh | 2 +-
modules/mol/base/src/transfer_connectivity.cc | 2 +-
modules/mol/base/src/transfer_connectivity.hh | 2 +-
modules/mol/base/src/view_op.cc | 2 +-
modules/mol/base/src/view_op.hh | 2 +-
modules/mol/base/src/view_type_fw.hh | 2 +-
modules/mol/base/src/xcs_editor.cc | 2 +-
modules/mol/base/src/xcs_editor.hh | 2 +-
modules/mol/base/tests/dummy_ent.hh | 2 +-
modules/mol/base/tests/test_atom_groups.cc | 2 +-
modules/mol/base/tests/test_builder.cc | 2 +-
modules/mol/base/tests/test_chain.cc | 2 +-
modules/mol/base/tests/test_conn.cc | 2 +-
modules/mol/base/tests/test_coord_group.cc | 2 +-
modules/mol/base/tests/test_delete.cc | 2 +-
modules/mol/base/tests/test_entity.cc | 2 +-
modules/mol/base/tests/test_ics.cc | 2 +-
modules/mol/base/tests/test_iterators.cc | 2 +-
modules/mol/base/tests/test_query.cc | 2 +-
modules/mol/base/tests/test_residue.cc | 2 +-
modules/mol/base/tests/test_surface.cc | 2 +-
modules/mol/base/tests/test_transfer_connectivity.cc | 2 +-
modules/mol/base/tests/test_view.cc | 2 +-
modules/mol/base/tests/test_view_op.cc | 2 +-
modules/mol/base/tests/tests.cc | 2 +-
modules/mol/mm/pymod/__init__.py | 2 +-
modules/mol/mm/pymod/antechamber.py | 2 +-
modules/mol/mm/pymod/export_block_modifiers.cc | 2 +-
modules/mol/mm/pymod/export_buildingblock.cc | 2 +-
modules/mol/mm/pymod/export_ff_reader.cc | 2 +-
modules/mol/mm/pymod/export_forcefield.cc | 2 +-
modules/mol/mm/pymod/export_index.cc | 2 +-
modules/mol/mm/pymod/export_interaction.cc | 2 +-
modules/mol/mm/pymod/export_modeller.cc | 2 +-
modules/mol/mm/pymod/export_observers.cc | 2 +-
modules/mol/mm/pymod/export_openmm.cc | 2 +-
modules/mol/mm/pymod/export_settings.cc | 2 +-
modules/mol/mm/pymod/export_simulation.cc | 2 +-
modules/mol/mm/pymod/export_topology.cc | 2 +-
modules/mol/mm/pymod/wrap_mol_mm.cc | 2 +-
modules/mol/mm/src/block_modifiers.hh | 2 +-
modules/mol/mm/src/buildingblock.cc | 2 +-
modules/mol/mm/src/buildingblock.hh | 2 +-
modules/mol/mm/src/ff_reader.cc | 2 +-
modules/mol/mm/src/ff_reader.hh | 2 +-
modules/mol/mm/src/forcefield.cc | 2 +-
modules/mol/mm/src/forcefield.hh | 2 +-
modules/mol/mm/src/gromacs_block_modifiers.cc | 2 +-
modules/mol/mm/src/gromacs_block_modifiers.hh | 2 +-
modules/mol/mm/src/heuristic_block_modifiers.cc | 2 +-
modules/mol/mm/src/heuristic_block_modifiers.hh | 2 +-
modules/mol/mm/src/index.hh | 2 +-
modules/mol/mm/src/interaction.cc | 2 +-
modules/mol/mm/src/interaction.hh | 2 +-
modules/mol/mm/src/modeller.cc | 2 +-
modules/mol/mm/src/modeller.hh | 2 +-
modules/mol/mm/src/observer.cc | 2 +-
modules/mol/mm/src/observer.hh | 2 +-
modules/mol/mm/src/settings.hh.in | 2 +-
modules/mol/mm/src/simulation.cc | 2 +-
modules/mol/mm/src/simulation.hh | 2 +-
modules/mol/mm/src/state_extractor.cc | 2 +-
modules/mol/mm/src/state_extractor.hh | 2 +-
modules/mol/mm/src/steep.cc | 2 +-
modules/mol/mm/src/steep.hh | 2 +-
modules/mol/mm/src/system_creator.cc | 2 +-
modules/mol/mm/src/system_creator.hh | 2 +-
modules/mol/mm/src/topology.cc | 2 +-
modules/mol/mm/src/topology.hh | 2 +-
modules/mol/mm/src/topology_creator.cc | 2 +-
modules/mol/mm/src/topology_creator.hh | 2 +-
modules/mol/mm/tests/test_block.cc | 2 +-
modules/mol/mm/tests/test_block_modifiers.cc | 2 +-
modules/mol/mm/tests/test_forcefield.cc | 2 +-
modules/mol/mm/tests/test_interaction.cc | 2 +-
modules/mol/mm/tests/test_simulation.cc | 2 +-
modules/mol/mm/tests/test_topology.cc | 2 +-
modules/mol/mm/tests/tests.cc | 2 +-
modules/seq/alg/pymod/wrap_seq_alg.cc | 2 +-
modules/seq/alg/src/alignment_opts.hh | 2 +-
modules/seq/alg/src/clip_alignment.cc | 2 +-
modules/seq/alg/src/clip_alignment.hh | 2 +-
modules/seq/alg/src/conservation.cc | 2 +-
modules/seq/alg/src/conservation.hh | 2 +-
modules/seq/alg/src/contact_prediction_score.cc | 2 +-
modules/seq/alg/src/contact_prediction_score.hh | 2 +-
modules/seq/alg/src/contact_weight_matrix.cc | 2 +-
modules/seq/alg/src/contact_weight_matrix.hh | 2 +-
modules/seq/alg/src/distance_map.cc | 2 +-
modules/seq/alg/src/distance_map.hh | 2 +-
modules/seq/alg/src/entropy.cc | 2 +-
modules/seq/alg/src/entropy.hh | 2 +-
modules/seq/alg/src/global_align.cc | 2 +-
modules/seq/alg/src/global_align.hh | 2 +-
modules/seq/alg/src/impl/align_impl.hh | 2 +-
modules/seq/alg/src/ins_del.cc | 2 +-
modules/seq/alg/src/ins_del.hh | 2 +-
modules/seq/alg/src/local_align.cc | 2 +-
modules/seq/alg/src/local_align.hh | 2 +-
modules/seq/alg/src/merge_pairwise_alignments.cc | 2 +-
modules/seq/alg/src/merge_pairwise_alignments.hh | 2 +-
modules/seq/alg/src/module_config.hh | 2 +-
modules/seq/alg/src/pair_subst_weight_matrix.cc | 2 +-
modules/seq/alg/src/pair_subst_weight_matrix.hh | 2 +-
modules/seq/alg/src/semiglobal_align.cc | 2 +-
modules/seq/alg/src/semiglobal_align.hh | 2 +-
modules/seq/alg/src/sequence_identity.cc | 2 +-
modules/seq/alg/src/sequence_identity.hh | 2 +-
modules/seq/alg/src/sequence_similarity.cc | 2 +-
modules/seq/alg/src/sequence_similarity.hh | 2 +-
modules/seq/alg/src/subst_weight_matrix.cc | 2 +-
modules/seq/alg/src/subst_weight_matrix.hh | 2 +-
modules/seq/alg/src/variance_map.cc | 2 +-
modules/seq/alg/src/variance_map.hh | 2 +-
modules/seq/alg/tests/test_distance_analysis.cc | 2 +-
modules/seq/alg/tests/test_merge_pairwise_alignments.cc | 2 +-
modules/seq/alg/tests/test_sequence_identity.cc | 2 +-
modules/seq/alg/tests/tests.cc | 2 +-
modules/seq/base/pymod/__init__.py | 2 +-
modules/seq/base/pymod/const_seq_list_export_def.hh | 2 +-
modules/seq/base/pymod/export_profile_handle.cc | 2 +-
modules/seq/base/pymod/export_sequence.cc | 2 +-
modules/seq/base/pymod/wrap_seq.cc | 2 +-
modules/seq/base/src/aligned_column.cc | 2 +-
modules/seq/base/src/aligned_column.hh | 2 +-
modules/seq/base/src/aligned_column_iterator.hh | 2 +-
modules/seq/base/src/aligned_region.cc | 2 +-
modules/seq/base/src/aligned_region.hh | 2 +-
modules/seq/base/src/alignment_handle.cc | 2 +-
modules/seq/base/src/alignment_handle.hh | 2 +-
modules/seq/base/src/impl/sequence_impl.cc | 2 +-
modules/seq/base/src/impl/sequence_impl.hh | 2 +-
modules/seq/base/src/impl/sequence_impl_fw.hh | 2 +-
modules/seq/base/src/impl/sequence_list_impl.cc | 2 +-
modules/seq/base/src/impl/sequence_list_impl.hh | 2 +-
modules/seq/base/src/impl/sequence_list_impl_fw.hh | 2 +-
modules/seq/base/src/impl/sequence_list_iterator.hh | 2 +-
modules/seq/base/src/invalid_sequence.hh | 2 +-
modules/seq/base/src/module_config.hh | 2 +-
modules/seq/base/src/profile_handle.cc | 2 +-
modules/seq/base/src/profile_handle.hh | 2 +-
modules/seq/base/src/sequence_handle.cc | 2 +-
modules/seq/base/src/sequence_handle.hh | 2 +-
modules/seq/base/src/sequence_list.cc | 2 +-
modules/seq/base/src/sequence_list.hh | 2 +-
modules/seq/base/src/sequence_op.cc | 2 +-
modules/seq/base/src/sequence_op.hh | 2 +-
modules/seq/base/src/views_from_sequences.cc | 2 +-
modules/seq/base/src/views_from_sequences.hh | 2 +-
modules/seq/base/tests/test_aligned_column.cc | 2 +-
modules/seq/base/tests/test_aligned_region.cc | 2 +-
modules/seq/base/tests/test_alignment.cc | 2 +-
modules/seq/base/tests/test_profile.cc | 2 +-
modules/seq/base/tests/test_sequence.cc | 2 +-
modules/seq/base/tests/tests.cc | 2 +-
scripts/dng.bat.in | 2 +-
scripts/dng.in | 2 +-
scripts/ost.bat.in | 2 +-
scripts/ost.in | 2 +-
scripts/ost_config.in | 2 +-
1463 files changed, 1463 insertions(+), 1463 deletions(-)
diff --git a/deployment/CMakeLists.txt b/deployment/CMakeLists.txt
index 7f455981b..59e6f0867 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 2201c8d3d..23893a86c 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/win/dng.bat b/deployment/win/dng.bat
index f16b3c4bd..366d4b07d 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 8da3b5569..498170b99 100644
--- a/doc/conf/conf.py
+++ b/doc/conf/conf.py
@@ -49,7 +49,7 @@ master_doc = 'index'
# General information about the project.
project = 'OpenStructure'
-copyright = '2019, OpenStructure authors'
+copyright = '2020, OpenStructure authors'
# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
diff --git a/examples/code_fragments/ui/mdi_example.py b/examples/code_fragments/ui/mdi_example.py
index d6cd2abe2..4309979a0 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 52000903c..e46db7c82 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 ae9f73be7..94c0ff2d1 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
diff --git a/modules/base/pymod/__init__.py.in b/modules/base/pymod/__init__.py.in
index 2676aa771..7b39730af 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
diff --git a/modules/base/pymod/export_generic_property.cc b/modules/base/pymod/export_generic_property.cc
index b5fab8c7a..0102ba6b0 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 1434b4f67..61b5d3f2a 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 6aea1e0c1..aa9294b5b 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 80fa61862..83016d643 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/wrap_base.cc b/modules/base/pymod/wrap_base.cc
index 2b43f842e..2c4877911 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
diff --git a/modules/base/src/boost_filesystem_helper.cc b/modules/base/src/boost_filesystem_helper.cc
index b235b0498..0bd4af2e7 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 03a9786e7..1e58965c4 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 c5c5c6253..683157ae1 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 ff02641c5..0311ec2ad 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 887a80567..cacc8d8f8 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 0220885ae..f8900bf47 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 d537009e5..fb71af0f9 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 7c0ba516a..ff479e27b 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 ca6b01616..3a7acf14f 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 314d23cd4..bd3cf2cfb 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 ff752c24f..3e0633582 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 934ee37bb..c75256de1 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 4521e74a3..4b2a0fa77 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 f06d4ae1c..1bb25e5ed 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 572480206..7519c1e01 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 5dd148264..1f6d24ab0 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 6a4c6adf4..4b40fc211 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 66f96b827..48605adb4 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 57af6e9b5..07ad202f7 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 5e45bd2f8..e299a265f 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 1a3bae89c..4162bf79b 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 a255bfce2..d9854c471 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 4b98e1fd5..f04dad9f1 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 64f78a183..bed05bf30 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 03209b11f..a46245a27 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 38ab290bf..f7dfe59e4 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 13dac63ad..265914ca1 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 15edfa7c6..57ab1f6c2 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 cb0f7dc55..28648bb02 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 65dcd8004..2b1cb7d0c 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 c30c1fc6f..8846978a3 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 3cf34fc4c..e500db587 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 7ef5b6776..ea6b8d0cb 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
diff --git a/modules/base/tests/tests.cc b/modules/base/tests/tests.cc
index 8bf9b0a23..60e7ed62d 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/pymod/cadscore.py b/modules/bindings/pymod/cadscore.py
index 193bfc87f..5d931b04f 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
diff --git a/modules/bindings/pymod/dssp.py b/modules/bindings/pymod/dssp.py
index 36c5d1af2..a31a6cebe 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
diff --git a/modules/bindings/pymod/export_tmalign.cc b/modules/bindings/pymod/export_tmalign.cc
index f416d8c2a..aefe33ec7 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/ialign.py b/modules/bindings/pymod/ialign.py
index aa7105cd6..8409b9863 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
diff --git a/modules/bindings/pymod/tmtools.py b/modules/bindings/pymod/tmtools.py
index 3c1ef12c8..94fc4ceed 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
diff --git a/modules/bindings/pymod/wrap_bindings.cc b/modules/bindings/pymod/wrap_bindings.cc
index 364a543a3..c60893f21 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/wrap_tmalign.cc b/modules/bindings/src/wrap_tmalign.cc
index 5a7071396..bbc2eb506 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 124f51f05..4163d4644 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/config/base.hh b/modules/config/base.hh
index b10638e7e..a3aada65d 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 7e8a96579..9cc959a36 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 3cacc7c0b..7471428dc 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 94948475f..fc132e164 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/pymod/__init__.py b/modules/conop/pymod/__init__.py
index b70493ec9..96f2130d7 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
diff --git a/modules/conop/pymod/export_amino_acids.cc b/modules/conop/pymod/export_amino_acids.cc
index b1422c409..8b4f0525f 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 661fa9db1..400fad773 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 9f72861bd..3ffbbad53 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 c50c92cce..acb8e406f 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 66e5a894f..275245a7e 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 37e4d8bfc..262a1dfff 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 7f48ced62..559455755 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 053cfd75c..7b22b6d2d 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 04bcfce14..bc5257573 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 2ce42a485..cf11ae0a8 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 f79bb68ac..85aef0487 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 9cd043f00..0286e525f 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 6e496ad10..10c330192 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 dff839494..948cecee5 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 8c901e1ec..7c3fc9eeb 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 e7192c51e..2199c1c60 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 7ca7d961d..2bdd6e3b1 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 69a4c9220..abf43ca1c 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 cf7147ede..3d0838170 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 ba7297dd6..75c13630d 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 a2f931848..b69317c8f 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 40dbdb878..2b70864aa 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 224a38c88..ce6369d3e 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 7727bd704..844256a3c 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 65d340ecc..81add923d 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 04351f1d4..0af0dd06c 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 e617e85c1..6697c76ab 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 fe2013e25..47dae10ed 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 719ba7803..cea8d5fd3 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 58c842a57..2b05d2a0c 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
diff --git a/modules/conop/tests/test_heuristic_builder.cc b/modules/conop/tests/test_heuristic_builder.cc
index cf6efa96f..8ec8b697c 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 65e0a7fc2..d6ba9f058 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 485454611..4e5222242 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 21dd70140..a7b157852 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 38881c6df..5133a9694 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
diff --git a/modules/db/src/module_config.hh b/modules/db/src/module_config.hh
index cdc876ae1..03b1a0834 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/sqlite_conv.hh b/modules/db/src/sqlite_conv.hh
index 8e4cf959d..136c5ff64 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 f67d85cb0..8c626ee83 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 db9a8d352..a40c72509 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/geom/pymod/__init__.py b/modules/geom/pymod/__init__.py
index 88ad89786..4a8e70608 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
diff --git a/modules/geom/pymod/export_composite2.cc b/modules/geom/pymod/export_composite2.cc
index d208ab107..c4748c037 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 2ea8462b1..334f5532b 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 4a37c79f7..14fb9d4de 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 ba6faf85f..50414ed43 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 446aca95c..0dcce1b07 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 c12f6402c..53910aa0b 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 c457eb261..b152e1904 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 7e233f69c..c9f1b5656 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 b2f921246..9c9b59464 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 f760d7e70..77c660178 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 8adf113fc..7d7aba3f9 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 810c9de1c..c089319a8 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 8f594681f..34f9f11f5 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 0cdc3e373..f90b24cdd 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 af64cef74..31895316e 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 fa687fa24..70c8175fb 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 14df2fa8b..8abd01c72 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 ebd772733..9e9c840d3 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 9d2298942..6a4a6c9d1 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 2e8755944..58d47ab46 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 6d1ad48c1..f374e970c 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 8a6aec909..7bfd58e9a 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 bcbc9a779..13c3f80a7 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 ad25008f8..a31f5f76c 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 71eb1b3c6..86281e1c5 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 b2d795247..5abcd778a 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 8e8805036..02f1c7d61 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 09fb2c72e..283659e39 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 23bdf3e5e..00dfd14ee 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 b81c5a32d..ab3b016d7 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 45b8b111e..e00404ea4 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 fb100fa79..6fe7306d1 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 0c4390030..9d7f636bc 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 0062db1f7..48d19131c 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 2bf028ab5..255839d94 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 8127088ac..e0ef21819 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 d0bf5809d..3b6804879 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 b7743dfc0..9e6524a6d 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 edf414eb8..7b1a502c3 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 35cae2f03..1a24ce73b 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 c43780e0a..c082bcd8a 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 3888fa873..67cef15c0 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 760e1ae87..525726e3f 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 72a755200..218af5f40 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 6188dbf26..1707b622f 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 84fcb872a..99a7a7246 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 881f69b5b..edae2c187 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 9c00d5e8c..4b064aca8 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 6965c4843..40e764fcb 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 70871d227..e31b363fb 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 b0191ac7f..83ea4a0de 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 a69b2682d..0bda96a8b 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 6ce79ff3d..527928f45 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
diff --git a/modules/geom/src/vec4.hh b/modules/geom/src/vec4.hh
index 5947a1c06..f003002cf 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 bbe639f3b..64542ec0b 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 221a6bbf2..ef9a90323 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 65a027f74..ac8e9332a 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 f476eca30..f29419223 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 d7762cccf..c4378d166 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 b1bce87d4..a1e791ce6 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 a3cbf8531..bd823cb7e 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 400d5f1aa..f8664f1a5 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 a459f74d1..cd6110af4 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 48309acd0..13450ded0 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 f84daaa84..d076c9c94 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
diff --git a/modules/geom/tests/test_mat2.cc b/modules/geom/tests/test_mat2.cc
index 944de8e9a..7316b929f 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 2d4ce923e..eb8f65f80 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 bee468108..d51c49ba8 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 3805cc879..5d96e51c9 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 519b19f8e..63ec98bd3 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 96edec917..db6edc4d4 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 158f44d1e..c1c5d7a67 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 f52a47628..104905acb 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 3ea6090b2..ff561e774 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 b7c03ff7f..97cb8906d 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 44b87bcf1..ad493244a 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 c0b2b3030..87cf43c09 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 8c87ec211..1d84a86c4 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
diff --git a/modules/gfx/pymod/color_by_def.hh b/modules/gfx/pymod/color_by_def.hh
index 41436d833..86938289d 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 d8e944d21..d5a6f1e79 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 e67321250..009255bad 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 fd974b22d..c77458b67 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 0a3ca8362..334a96c5b 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 22c9a9743..2cfefea29 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 9a1ed0c5e..43dde9fb4 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 68e88f901..6952ddab0 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 a2cb803ba..6772994d8 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 fa09e623b..cfff11ac0 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 ea334ead8..0cfee858a 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 01b328d72..5762646ce 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 ba586fe62..4538f366e 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
diff --git a/modules/gfx/pymod/export_render_options.cc b/modules/gfx/pymod/export_render_options.cc
index 4f1de36c4..8116d84fb 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 746c958f7..d3982dfa9 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 b954a414a..f6b8efa5d 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 f89d54a4b..b97f30902 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 557e645ec..33dcb5361 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
diff --git a/modules/gfx/pymod/wrap_gfx.cc b/modules/gfx/pymod/wrap_gfx.cc
index b28c49659..10967df66 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 4245c32ec..8437de397 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 dacb9dbe3..68111dd7e 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 d2b45c21e..02c692326 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 7a05417c6..d7ddc4b5f 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 60607ad0e..a98e961d6 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 1340967f9..458f39fce 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 397ed3d41..49ba30e4d 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 6da2b9006..4024fa3ce 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 d2c6789f9..53bf367f5 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 58485af37..5f06c7079 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 031fe5e32..e5ff19c17 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 0ad7c60d8..0fe606ef3 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 514650f84..670bd8add 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 7e9e433a7..e51678417 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 de44bf1a0..fc412439a 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 49e6e294b..1995f7266 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 0a9e95952..7ac2bb99c 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 9c7f37345..97b611f35 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 32429a095..f3501d98e 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 1b453a48f..282c25800 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 d09be806c..1f580bf49 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 b0d1c15fb..bca982bb3 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 844731706..b76ecff61 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 518fc5792..c322cb4e5 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 6b8468a24..1d1f232ba 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 9106e2607..f16fe3292 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 192ad3913..b877a0ff1 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 5100490c1..88bd074cd 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 1780851eb..a663bde27 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 499248014..c0c9fe4ff 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 2a0d2303d..dfc2e55eb 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 e5efaacf9..d87ad16e3 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 657068c9e..716523f1d 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 6cff83885..d3c01d425 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 744b350ef..b265f1ac9 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 5b1d49a6b..ff41b28f3 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 97e235f41..dbfe17cdd 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 03d76a8c4..4049eb77f 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 07e49a92e..c2072ab89 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 73118a522..8bc44c1f6 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 a5af981b1..8d55b87d0 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 cb5454254..fa050c68a 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 7e60ab6d8..381f3c19a 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 8d878d7c2..9053101aa 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 773460563..82aa63038 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 69761cce0..ec4028e35 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
diff --git a/modules/gfx/src/glext_include.hh b/modules/gfx/src/glext_include.hh
index 874b70a31..3c39256db 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 77d30ee76..9bcaed92c 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 525a70aba..5be10034e 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 03f47680e..509dca86c 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 0018f3aa6..4f3fd3eba 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 e08a24eda..ae1efbdcf 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 ab807ad18..7f8894a09 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 fe73bbe19..756ee127d 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 da56ae179..26bd1e1ff 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 677f02f12..7eca13bbb 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 3dfedd484..87ba15c42 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 1d60eec76..220dcecd5 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 fa56d00ce..29d255c80 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 17d7854cb..619b60654 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 5f0ed4a6b..51afae44f 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 0f4c7f237..bcf8691ea 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 f780647b7..46cf90c10 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 1a6dcd2dc..e5090aa7e 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 ec3195464..cedd9567e 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 8c5c1bd3d..245fbbd09 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 3ff579078..1c2752714 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 22a6d432c..f8ea2f078 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 7e7f65989..b597ee31d 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 12412f680..932d6a0b4 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 9b623cc11..dc6f056f7 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 14c0332c3..0157c5b08 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 f07fbd625..fdecafc73 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 905791c34..5a5cae22f 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 72402ef9b..e6374352b 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 74a9f58db..5c655aeda 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 41bca43a3..0f4e691d8 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 e089e8ace..304b5b68c 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 bb6622ac8..e953f034a 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 110492ccd..b880f8b4a 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 603a7a0dd..ada35ee1a 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 cd3f937c6..6a9cfddb2 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 50bae81d5..eeb6c071d 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 64e9cac07..476e23825 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 c16461c69..1dab8b44c 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 c0a925b84..ca98facf4 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 c4520e078..1f93463d2 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 3190ff74c..f6cff0a99 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 0666880c1..60b06da8d 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 26b08d653..bb6dbf378 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 096e77566..bc380f068 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 39ed73b5c..98f62a3a0 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 5ed38b942..62a371ddf 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 2fccd83d8..ff82c50dc 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 b6c277ffb..47c04356e 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 ad8d2a787..7da2ee0f1 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 97d2e50bc..7e36c9606 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 95fd8bf03..df5ec2ca7 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 eae42acad..42bfca1fb 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 88c03e5b3..cc52307f1 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 d46059c08..ca7d9c2ad 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 673f4e20b..1afa4054d 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 f901c77cd..940a0f2a2 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 380572adc..2cad26f71 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 1b4c47fe5..b78dad0ab 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 7cba4e752..d8f4acdeb 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 f9420de62..40ce2b04b 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 7874e838a..caec031f2 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 5c6773226..be69ad680 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 128358cda..c3a640b8b 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 fdcf0a3fe..8d29f50fd 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 cee9025fa..6edb51cf7 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 3aa49b707..68021b6b6 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 3af16f422..46b0618c3 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 c38a88864..2f8c361b1 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 b0e039471..28454d43e 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 12e67481a..8054fc465 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 0deb63147..90949b4ec 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 f62319062..a2c282995 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 f630974d7..e50c4ad6f 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 c8ef79461..d1a998afb 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 a2c0c58a6..ff14bd8c1 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 0b06442fd..16840a3b1 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 84247aa78..7fadee42a 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 46552aa58..71758da14 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 04ce67de9..fefff8842 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 06c275632..92eb300cb 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 4b20f63d7..2a8801e53 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 f279d0026..5b50613a9 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 93f0206e5..b9626a567 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 abc469cc1..882ae2512 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 1712c0243..1a9920242 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 dfd7ddd4c..e9b275bea 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 fbc42af37..a9fd4746c 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 ea6865040..fdb5be5c5 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 2029ab482..a702da10a 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 96e1532bc..ab1243241 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 12690d820..591437815 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 ce9dfc602..4aae7e034 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 72ad4e829..33bac6f8e 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 1817ea62a..74c9bb255 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 a3c663838..215ec030e 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 fcd336de1..df814fab9 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 e5e9c0263..615f38b0b 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 e8817ed3e..d32523e28 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 badbebe30..2c00c9e18 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 1ce2a44eb..f53323a54 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 c10bec64d..714e60a63 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 6e9eea0fc..810103839 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 ab0d2c6b5..a204c40f6 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 41d0b02d9..10aa33aa9 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 03f88696b..211d9d244 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 149c8fc86..6520f0570 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 390f2d27a..c0adbef6c 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 ff3ea292c..52b7166f1 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 266f008d6..86dc6d909 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 7298a19e8..80946172e 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 cf25b9d4f..731f3185e 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 89dbaa728..566d289c7 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 ac24ef85a..69c8b3dbd 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 4354996e8..ea8020a60 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 f810c511c..0ec375b4d 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 21f82f2c3..630260542 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 c7730806a..83a42917d 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 3889c8e2f..2baf689d8 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
diff --git a/modules/gfx/tests/test_gfx_node.cc b/modules/gfx/tests/test_gfx_node.cc
index 95e7e222f..2d38d7e13 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_map_octree.cc b/modules/gfx/tests/test_map_octree.cc
index 41bfba860..245817b54 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 bb712952e..50c8c17ce 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/pymod/__init__.py b/modules/gui/pymod/__init__.py
index 68b4a7300..78c1617af 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
diff --git a/modules/gui/pymod/data_viewer_proxy.cc b/modules/gui/pymod/data_viewer_proxy.cc
index d4d418e1f..84930db5c 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 096485b40..bfacf0c05 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/superpositiondialog.py b/modules/gui/pymod/dng/superpositiondialog.py
index a6851c372..351cf4f97 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 1d6e22bfd..2a8cee63b 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 d5e03fe5e..3ce93fe74 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 b39d6dadd..4bef89833 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 66b704d84..e92246cb1 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 daf2eec4e..93f6cbd3d 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 044cf417a..ec0fae15d 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 ef7ee6777..18f945e2e 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 b6ecb5c0b..06846fc98 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 bc3adaa08..84d18c6c1 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 35220c966..9bb9c118b 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 69dd6bb38..cd3ffcc4c 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
diff --git a/modules/gui/pymod/export_overlay.cc b/modules/gui/pymod/export_overlay.cc
index 4b95814e2..11db3c6e8 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 71920ef1a..9f9880005 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 fbc5b6c59..20af5c8bd 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 84dfbe16d..ea7d4d02c 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 7b05d2bf8..a74d3155e 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 b814c257e..3ef9546b5 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 caecdc4d6..c4f68a758 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 6606e7875..40c01dc8a 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 3d968fd88..5a9f83469 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 fe6bd46fb..9393b6919 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/init_menubar.py b/modules/gui/pymod/init_menubar.py
index 03930fc53..c245f0f3c 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 24d53b8e5..f7c7f85e8 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 4d1c51119..18460a92a 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 da2deb806..5cf29fab3 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
diff --git a/modules/gui/pymod/scene/color_select_widget.py b/modules/gui/pymod/scene/color_select_widget.py
index 737fd8c48..25547e708 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 b15a8a490..4fda5cb17 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
diff --git a/modules/gui/pymod/scene/cpk_widget.py b/modules/gui/pymod/scene/cpk_widget.py
index 3ce8d05a2..408cde497 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
diff --git a/modules/gui/pymod/scene/custom_widget.py b/modules/gui/pymod/scene/custom_widget.py
index 2319e066c..be2e434a3 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
diff --git a/modules/gui/pymod/scene/file_loader.py b/modules/gui/pymod/scene/file_loader.py
index fedca4543..adf747d10 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 17ea07f0d..2b5a69f22 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
diff --git a/modules/gui/pymod/scene/gradient_info_handler.py b/modules/gui/pymod/scene/gradient_info_handler.py
index 5c7414504..eac8de236 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
diff --git a/modules/gui/pymod/scene/gradient_preset_widget.py b/modules/gui/pymod/scene/gradient_preset_widget.py
index e1717c98f..fd22117cc 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
diff --git a/modules/gui/pymod/scene/hsc_widget.py b/modules/gui/pymod/scene/hsc_widget.py
index 8ea2d4ede..ea6292258 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
diff --git a/modules/gui/pymod/scene/immutable_gradient_info_handler.py b/modules/gui/pymod/scene/immutable_gradient_info_handler.py
index 65ecf0d9c..ca59ac92d 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 e766c8402..d302f20d5 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 83dd1c741..e6882892f 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 0e2803dae..99fea817b 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 d3d78d034..f1d98d377 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
diff --git a/modules/gui/pymod/scene/line_trace_widget.py b/modules/gui/pymod/scene/line_trace_widget.py
index b9c6d7695..283ce9c66 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
diff --git a/modules/gui/pymod/scene/map_level_widget.py b/modules/gui/pymod/scene/map_level_widget.py
index e9a890be8..32b083e55 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
diff --git a/modules/gui/pymod/scene/preset.py b/modules/gui/pymod/scene/preset.py
index f06a477df..de2a9524a 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
diff --git a/modules/gui/pymod/scene/preset_editor_widget.py b/modules/gui/pymod/scene/preset_editor_widget.py
index 5c3ce6aa6..f3cb3f509 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
diff --git a/modules/gui/pymod/scene/preset_info_handler.py b/modules/gui/pymod/scene/preset_info_handler.py
index de1331668..cc0c5867e 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
diff --git a/modules/gui/pymod/scene/preset_widget.py b/modules/gui/pymod/scene/preset_widget.py
index 878e5268c..34f6bccb1 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
diff --git a/modules/gui/pymod/scene/render_mode_widget.py b/modules/gui/pymod/scene/render_mode_widget.py
index 520f6be65..72100a950 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
diff --git a/modules/gui/pymod/scene/render_op.py b/modules/gui/pymod/scene/render_op.py
index ea2b54263..3ce5c9da9 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 069b87dda..7367cecfe 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
diff --git a/modules/gui/pymod/scene/scene_observer_impl.py b/modules/gui/pymod/scene/scene_observer_impl.py
index b4a0096fa..987662ab5 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 80d35b9b4..91686daf2 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 198426dd1..0811a4c21 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
diff --git a/modules/gui/pymod/scene/sline_widget.py b/modules/gui/pymod/scene/sline_widget.py
index 890506bed..74ddaed10 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
diff --git a/modules/gui/pymod/scene/toolbar_options_widget.py b/modules/gui/pymod/scene/toolbar_options_widget.py
index 638ee2228..0113f9dc0 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
diff --git a/modules/gui/pymod/scene/trace_widget.py b/modules/gui/pymod/scene/trace_widget.py
index b68663e70..b0eaf20c2 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
diff --git a/modules/gui/pymod/scene/tube_widget.py b/modules/gui/pymod/scene/tube_widget.py
index 2d7538f4d..3413373d9 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
diff --git a/modules/gui/pymod/scene/uniform_color_widget.py b/modules/gui/pymod/scene/uniform_color_widget.py
index fb97cb853..4f4f8ccc0 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
diff --git a/modules/gui/pymod/scene/visibility_op.py b/modules/gui/pymod/scene/visibility_op.py
index 4b5fc7fb8..51874f02c 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 76f2662f3..d729f56c1 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
diff --git a/modules/gui/pymod/sip_handler.hh b/modules/gui/pymod/sip_handler.hh
index a244bdf82..c2f9c189a 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/trajectory_viewer.py b/modules/gui/pymod/trajectory_viewer.py
index 32960ffa1..ece7a3bc5 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
diff --git a/modules/gui/pymod/wrap_gui.cc b/modules/gui/pymod/wrap_gui.cc
index 64952c829..3dc805887 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
diff --git a/modules/gui/src/admin.cc b/modules/gui/src/admin.cc
index d82e384bd..057048429 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 cfaa482be..0b9019339 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 f53fb0fed..077f8fe0a 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 8f09c2414..c1c04fc40 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 5a75d5181..be46724af 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 c1f18847e..7146a1732 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 9de780147..8f2967c9d 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 71fe55351..77f06107e 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 3f145e555..f946bc5c8 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 be3ac007e..68ffa086e 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 86c05bb07..2d362a23d 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 8ec433c4d..33487455c 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 f27b3eb0d..ff0393f14 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 0d94bd69b..2b73ede45 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 554cc67c2..c519ff6bd 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 ac0df0f56..5fdf759c5 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 fdf5b8cb4..9b104aed6 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 3088a2f3e..bf2aeecbd 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 a593884b1..f21fc3571 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 69f125d61..6ff4ced57 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 dc18830de..1a9dd9531 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 a6ee6bc2b..4f7b26132 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 1fa56b5e6..e273de13b 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 59cbce5b9..b6ed1d3ba 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 96d440a27..b1c0238ac 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 c1505e2d9..3de2f4de3 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 b64475e6c..b0e71c2c0 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 7a38205b8..5c87342ff 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 ac2a709fb..f3da58534 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 2a3bb7657..fa21eeaf0 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 a80d843da..ba266f041 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 69bb6a5dd..cfb85454f 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 13ba39f87..b356d31d0 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 a4bf9b058..825ac242c 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 84f10563f..06db7a9d1 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 9244f4457..15d635e5c 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 3bf47d6d9..05b23eb4e 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 43e82562a..4a7702e56 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 e78a71837..b60394185 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 a37f3f8ef..5f42db711 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 f66a4e66a..217a3097c 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 09a21eaf5..ad20766cd 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 63b78a188..071dc27fc 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 53b7d7ea7..edf2a1d94 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 4bb5f3c73..5cebbc73c 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 7c33f7d1f..b390e9111 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 b68b837fe..04d1cb420 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 476c6e89f..0aef38717 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 8e2e50758..805fa5cab 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 ed226aba8..01cac724d 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 270d35131..3b650a925 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 3d64433a9..4234bf81c 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 d82217ccd..6f3510be3 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 8bec7a907..1dfdbdb7d 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 36d74b2a7..4a85adb43 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 ee29b1f71..f6d00bfb5 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 2daf43d3d..2b003ca9d 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 350b1f520..689cbf9ee 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
diff --git a/modules/gui/src/gosty.hh b/modules/gui/src/gosty.hh
index a4c3f25ba..ebebdbc80 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 de0b008cc..58bd7dd89 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 5398c01c8..0831e1316 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 10022c6ae..36c700294 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 fe6eec7e6..5d15bb9cc 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 e68f5fcf8..3de15cda8 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 86105fb96..2ead5affd 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 3c931ca8e..bdfb45195 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 9e03d53a0..76ac61168 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 2ddeea9f7..b7eee29ab 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 61c6055d1..56f956000 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 33ad612ba..b41b949ad 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 95c8e035e..8fd500aea 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 2af0d5e01..26a8ddc4c 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 60d0e7bb7..82680d349 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 b16df9afe..714c5f0c8 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 e9c0d224e..2d48e79aa 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 a45752148..baac49c7a 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 5a19dc358..508cddf5c 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 e1927445c..ab88057c8 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 72f3eebf9..ea2e31ff7 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 987d66709..e255e4497 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 318e4f3b4..ec52d04fe 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 e65cea90d..880f6a774 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 d81a44cd7..57b7c0dda 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 a474c0608..285794a3d 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 3c7896440..a01a2f882 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 f3763a1b6..f880d2040 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 81312afb1..865405616 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 463641357..abb98607c 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 0d979e822..a3866207e 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 8aea1cbdc..8cf6cbf9d 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 1c30ad993..8bbf2f179 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 e35feb059..37847c6fa 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 5b1e03313..06996c8a2 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 1b05717e2..d1a1d5867 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 92025d0b0..3b7dd73ab 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 879807a96..5a152a4eb 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 dacc1ec21..63b752188 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 8f20c9b75..e42b1aed5 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 b02550762..125815578 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 32237a89b..9b0a7f347 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 318f01f2c..5cfb399b9 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 573133e73..d9debf2a9 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 292657027..738527d29 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 8699aab5a..f60a030b4 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 1add06e69..4dce53f9b 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 ea882f6b4..524a74edb 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 eed96f457..ae6f900d9 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 57df03470..b3962c859 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 4dcb382da..67eb9bd2a 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 97c818762..9c3b56769 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 39195d850..01fbb205c 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 99057d7e8..c440a2d24 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 922e88d98..86c62358c 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 fbca0a890..f9b527ba9 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 af7f93d38..bd548d143 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 a2fcedbcc..216fe915a 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 944951114..18008a10c 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 0e5df593f..e8c483f74 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 08b0c3471..93c9af99b 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
diff --git a/modules/gui/src/python_shell/python_interpreter.hh b/modules/gui/src/python_shell/python_interpreter.hh
index 3cbe055cb..43083cc61 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 693273bc2..37b2216af 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 4dfd0f3ba..67991a6c0 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 5f7fb42a6..c65a6d002 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 66639a2cd..c8dc4ba3f 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
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 e03444f69..1524d17e9 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 c1cee49ef..c0c359141 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 6b05294f8..1d3694e54 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 21b283e6b..79e88e3b2 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 b651747b8..b9c0d0dd3 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 11cc3fad0..38bdf9445 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 9abb7cae1..492d833f9 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 bb95922f0..4f3375466 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 903867a3f..6cb32f768 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 93d3f3896..023bdb22f 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 090272bbb..3b246addf 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 72ab4be2a..b4ae78bda 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 aaa97a529..6280ac72c 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 3c6b2d3d8..a44f0c60c 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 49dc6c5c9..8b2f43467 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 08d96cd6e..7a687c301 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 87e082af6..8c5982cb1 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 f5b7c5223..26566ae7f 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 679542078..88543975d 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 048ed68eb..82d8ee15a 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 8db26c10a..197317ec9 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 d1dd8ce5c..f14d4a025 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 d7d9e17d2..79711be96 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 1dda3afbb..9fb389b64 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 444092c07..9d1913e7c 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 991665771..140e0fbe4 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 a3550f428..97ed93c8f 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 acf6ff2c9..d01fdfad6 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 c3b20201a..514bf979b 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 1d33e6d0b..a066325d0 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 814616697..9dc1647af 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 5412441a1..e300b61b3 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 bedcf0df4..bd1adb113 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 68fc6421f..7bf862a31 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 be66a8399..7057b6a9d 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 53419a3ae..70ce89365 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 70a8c2bdc..aae03ae53 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 56ca0929a..12c844b18 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 d10da3813..8f006a982 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 45d97225c..0d9fa0049 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 e18e6d62c..9dc79522b 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 9c9eba9f4..be5ceb9f9 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 1fa74f165..216723b05 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 a9e589124..638f8ea47 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 bc1fb5a9f..c5994b8fc 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 2eb308cbe..c25c9d487 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 ca06e19c8..8a8c01823 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 9d779dcb7..882bc5ba6 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 f71c83268..4f5dd843b 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 4a9722f7f..a449492d0 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 bba7f59ab..1f789ac86 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 45984b7ce..4b08a8d82 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 68661b097..bb4420cdb 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 024d45f8e..dd574f97d 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 6c61c775d..dbe8956fb 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 ef2292c4d..e9b32b5f2 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 3e99b51cc..c63619d9d 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 6b183788d..cf370596f 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 2e8375075..f3601709f 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 d84669079..644672914 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 c9cf6d681..144d36600 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 338233164..35808af61 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 c761267e4..fdf9256ab 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 50a36a11c..90ac3c7da 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 9084ee7fa..1fd0526bb 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 9c96d31c5..78646d8ce 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 b2c86168f..7d7ccfdf1 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 ec496675b..b013214a9 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 c4c2a76ae..15cf1f6c9 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 544a7d755..1782e2f3a 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 5f567bab7..70277b361 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 80842f877..fab8435ff 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 91babf268..d4247c441 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 849c09c63..ee7c0f884 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 26303e0cf..a6aac62db 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 502393434..5d9c73f8b 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 cdfebf148..48ffaea33 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 8d07b4dd0..25ebf9254 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 0d9e36a3b..c65b72603 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 2ca4ad9ce..e48380938 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 bef7ab1da..b52926bf0 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 157c97a04..8ebe532bd 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 771acdc6a..63b68dbf8 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 46cfbe05e..77e9603da 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 491669d47..09727b32c 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 d64020ad9..dad4e1c66 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 ce605c8f4..de2f1256d 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 1d431cbae..21f741943 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 cbe6e2855..fd903dbc4 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 d367b56ed..0feab0cf7 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 13e4f0fd0..197e59eac 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 9a7020ff9..2a8868582 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 24c743b64..d7f4354af 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 97993f0cd..16a39a7dd 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 c3addfe40..e3e043aba 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 85ff6ece6..b04299a13 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 bd780a3b9..d8bb59c8b 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 4c1558a5a..13658f819 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 e2c842616..26615cecf 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 d4dd16fa5..9e38897b1 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 8cc3d9abb..0a805765c 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 ba425ffa8..74860e2a6 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 2014121b6..3f940ea96 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 ee663099d..1144c0646 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 78a6f88dc..baa17d250 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 96e622a3d..b9dd7f1ec 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 e7ed5b61e..bed8c99f8 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 730fffa94..b3329bf6b 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 86effde21..98ebd79f3 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 8c620c8a7..7fd2accc4 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 c46f17916..bd08115d5 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 348b308c4..d03216871 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 faa680936..9c8e8e83c 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 4792763f3..cd8a12dfc 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 945855cca..975889779 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 aeac798a4..72948ee93 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 e904821c9..67b5873ed 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 55cd23137..9c9faaa86 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 85e051a9c..a404eb7a5 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 542c99ccd..219abf4ab 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 7851000cd..013c11200 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 df5d8dcd5..156d817ca 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 3be9a7681..6f2660761 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 a8b1557dc..5b1e3b35d 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 47e178324..83c255164 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 879868555..6438831bf 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 24e309f56..132835611 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 61fa450c8..e2e7d6f1c 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 eb90f5f9a..74729397d 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 809dc477b..5473f01d8 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 c52d396c9..5399c6692 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 efb6d752a..b68f8f793 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 e1f664c08..524f68dd3 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 f19735efe..50b3b3371 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 bc480825a..8b04a6e0b 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 b9c20757d..f567bf7f8 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 643e5fa54..035b5352e 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 a02863f59..75b6dc541 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 cf5e0a8f5..fb10f73d7 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 805731f76..2ec19a679 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
diff --git a/modules/img/alg/pymod/export_filter.cc b/modules/img/alg/pymod/export_filter.cc
index f1bf0f779..06a0ecfda 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 de8a3f016..1e7d334db 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 f41aae120..f7c53bdf4 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 3f0a638c2..ca6d56d38 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 b024609d3..a4c9e2d61 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 cee27ebf1..4778e020b 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 8b92849a6..1a8e216ec 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 b2a0cb099..040ed827e 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 f39a5b4ef..35af08953 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 7519c57b3..428d8382a 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
diff --git a/modules/img/alg/src/alg_transform.cc b/modules/img/alg/src/alg_transform.cc
index f0dadad3d..36b76edd3 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 372943799..3c52caf1b 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 3ed2d1f47..8fe67ae8b 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 53b6e1ca0..30498be68 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 5256ff368..6e61f90d1 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 420d98297..5b72520f7 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 bf05037fe..76e4e53a1 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 e44a3e4c3..73e52e74b 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 9a8e4a225..79409ecf5 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 70543151b..51deeb200 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 a55a292e3..54ab0a7c0 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 b473e20c0..d7f8a4b15 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 a88ea5664..ccd96d534 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 7df974ebe..e2adc5827 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 17a2a7b94..3b0686392 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 6f783e83a..cd8451f68 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 8e2798d6c..9ec3ab424 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 dc5cedf7f..48c45a53e 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 ef2d07714..3d5559431 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 b5ca096d0..783ae8c49 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 8265dcc10..299c9de65 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 6aef59bcf..c592937c5 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 29bbfe561..6772f9c95 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 61cc3199c..1c88ab34d 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 c8b3ccfc9..e47724049 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 b1b6066aa..8f01fc4ad 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 34e50e72e..60a881161 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
diff --git a/modules/img/alg/src/filter.hh b/modules/img/alg/src/filter.hh
index 3cd7399de..bbeddccbd 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 a130b6f4c..a0c98cdea 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 3f3fa9303..a38bde19d 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 c9ac40bc9..7e39fc655 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 ad787c1dd..780e59d02 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 9c8e7880f..474a8b4f5 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 cad9f81d6..0c1214de8 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 b8c760be6..6c3f45fd1 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 f366b07eb..51af3ae6c 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 fbe042644..bd3675d29 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 5efe73b4f..2b7efb1f9 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 16d90f351..ba11a81ad 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 c930ba43a..619a9f845 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 45e38d7a7..50223addf 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 fece6ef10..281134b58 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 782b2fc3e..d271e1e3f 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 a42a5d822..9d787dd02 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 062d60d55..1c8e19102 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 f66cea6ec..ef72f460d 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 44e8637ba..9c2ebeb2e 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 de1d8ca44..980471283 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 974944052..0aae3d3b1 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 b61642fc5..6d888333e 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 6e4c54980..b62bd5d86 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 4619ab86b..ab2562b2d 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 9f7c1dbf8..0dcf7f0ad 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 739d3a6d1..755885ec6 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 4452404c2..6d45b6cad 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 75b1a2770..63ff35bd7 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 21c22d45c..5ce238421 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 0aab1c74d..a9d9d1737 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 ab4ba6a16..a46f86554 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 0fef98f0f..f56eee431 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 e830ed0de..8e3201f5d 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 aa5fa3745..366f39280 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 c24b3f670..8f01d972d 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 488a188d7..42deac2aa 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 fd8696581..1bb5674ef 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 e23dc471d..6af6bbb70 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 cc3fc20d6..a37fadfa5 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 037c0f6ed..bf2e32db9 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 cc8eaddb5..d5f425ab6 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 f4c8a506c..1384b5242 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 d2c7f59cc..bf0ef9fc3 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 262314998..ec030d9af 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 ba1861621..080c5adbb 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 cb4530eac..077127072 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 c69638644..177806049 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 15d7300bc..b62d0069a 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 1437c53de..cba8f11df 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 490fd514e..4a66c4d52 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 60c1f6bcf..cc936d131 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 e2603bd6e..b538283d8 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 b4c780402..d786e411c 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 2aa29ed4f..2c311287e 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 3adf0c1ba..20dbe18f8 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 a99805445..8304bc5ca 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 83c17ed7e..9021a4cf2 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 8a2fed0b8..2c78e31d1 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 d5df2f79c..2eedb2ec9 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 6ed68a277..4d87b0442 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 ce85c2d91..60e071a93 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 7d8d0a1d1..18f25b236 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 c476a32db..77b2bfd9c 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 af9ca66cd..aef7f63c8 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 c5382ce88..71e08ceef 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 ed6a9ff42..c94b9fa0e 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 fe0546004..12840d64c 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 2b13c649f..14534d06b 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 21108200d..a5e71cd48 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 70a51626e..3c32046dc 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 7e202193f..1ea096343 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 62a12549d..6087074e4 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 98b617900..577a73a7a 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 d3db88c2f..d7d4d2508 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 698e7a515..e9d4b8054 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/pymod/__init__.py b/modules/img/base/pymod/__init__.py
index 398809616..f78f0f7ad 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
diff --git a/modules/img/base/pymod/export_data.cc b/modules/img/base/pymod/export_data.cc
index 24f72acb3..f96e6932a 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 4fe222395..167f5c789 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 57e3c6f1b..ae0a14bbb 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
diff --git a/modules/img/base/pymod/export_image_handle.cc b/modules/img/base/pymod/export_image_handle.cc
index 1c6481b87..fe9c08250 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 f1fb6a6cf..a725befd8 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 f7b46a93d..64bcd01a3 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 40f42e9b0..add09cd7c 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 540745ca5..74e1bf13b 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 147f22c92..d65b81737 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 53047e6e8..10a0e838c 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 ecb187e81..9bd7d75e0 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 0c4604767..8e4f561a2 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 8206e36a7..7fdd4f791 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 fb782d513..805ce6468 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 f89f14e95..26c1608c2 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 4b00bc044..e19024a8a 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 f5d73f5f4..eb08e7e2a 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 501177b93..8ec006054 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 922920079..36e8c74b6 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 80a0a57cd..eeb3553b9 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 64d04fd13..fc67a847b 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 47c00ba80..65bdea8c0 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 3ab5d6063..8c7f492d3 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 cb581c5f6..3cfe86026 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 02e05ff4c..0509b9893 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 4d42d6621..c8854576b 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 0d369a2bd..c061a97c3 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 234cfaade..ae1563cc5 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 13b90f4d3..b6ee88dd1 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 3f32d13d8..f6ceff5da 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 492c4ccb0..608c9892f 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 7d6d0afad..16978d96e 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 238b680b8..e1e566bfa 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 56b2f68b9..e2349c1c3 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 bf8fbb453..b3674bf65 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 bbc17548c..1e6220e70 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 dba4fd758..79bdc308a 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 e3838fd6b..6e15920b2 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 101a562a2..ad921f7d9 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 03b877c11..6bbf1bda6 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 fe84239cd..9303835bf 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 847d897c4..3d7261f9c 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 f91784055..3e88fbbdd 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 6feb304b1..f1e4bd278 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 3b885a0fb..6cd6f15c6 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 522e5f7af..74fe70e1a 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 433147013..1b2248f04 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 6a519b9bf..1bcecb2bd 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 c0dd86303..3e6fcb3a3 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 28dab6fdf..0dc05b585 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 12da6444f..cdcde6836 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 54a4b939e..3b3027d1f 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 2c96b2f86..c829d841d 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 34fc74e61..394fb0d64 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 d32edb98d..5be50dc60 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 0749e4be2..f4c291e48 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 32d00ed40..60b4cc967 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 67e729574..15bdd7a2f 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 37120dd31..b7b774e07 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 50ef49fed..d77a3cd36 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 0b5e4e601..5faf04b64 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 3783caec5..7f6b2af98 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 2726358d6..2628e7695 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 352d710f6..d743f9235 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 0f8dad75b..ca5eb5717 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 3d0a8472b..a00d58da2 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 a8b22ff5e..3d70607d9 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 64fdadb3f..c5a74904d 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 a83820aa1..3607590af 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 27974200e..13fdb9ac9 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 8f7e8c6ee..a33e9d350 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 37a3cbd90..4544b49dc 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 2e59892bd..81e082340 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 1eaf3c77a..003b68470 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 05f9cb384..22c7023bb 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 12be417ee..3c5492f08 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 b38bfe57f..a680121a5 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 a4dfd4774..6401257ea 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 8f1a0a087..1a946efb2 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 231a4d1d1..8a8959a0d 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 feb22bacb..1f5278f0c 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 6d96125c2..45822e163 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 5f26dc729..9e7c29410 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 4cd5287ea..d13d9a773 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 cf3879f87..21d7effdc 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 847c47d80..e6e2746ca 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 f25b37a22..2c1b3f37e 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 434f2abb6..1cfdbdad8 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 5de7c61e4..9342cc52a 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 76f6ad8f1..8b2214a00 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 0387491ff..db482e194 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 e602ede1b..510c9cd08 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 0a68b3851..ca0655a18 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 3a2d3a864..4099a9ea8 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 36d520094..ef8ad6bec 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 7b8ca63b8..6329873ff 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 c3f5840b7..c7b7e9c81 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 700a786cd..865d72e04 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 329bd9c7c..417fdc342 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 fd1131ec6..42e25b7a8 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 b50eab440..8c61d6e34 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 73bb6a409..94ad9d50c 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 01d0f22cd..82671d206 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 caf0fdda2..ee3a6c1fa 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 2c790e421..08eda0161 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 731875450..7101fd04f 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 94d1d2914..2de59687d 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 0d9f307e7..757a2d18b 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 559f787b6..3fcde1f7a 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 ca287cb88..d4aa34bea 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 72b9be47e..917694895 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 8b8d6827f..3d5b0eda0 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 380f93ea1..7eebf7651 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 4af9cfc6b..0342b50fd 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 44cfdf1a9..b51683848 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 f27ad4c2a..9c99d6af8 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 97e1fa460..09b609dc8 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 e648d11f2..ef44bca55 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 26258de74..0790879d6 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 fae8e0183..5785cc5aa 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 bbe25ac0c..b8a081326 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 8436553fc..0e10a2e3e 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 045ccf97f..a475cc1cb 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 92815608b..b7508ce90 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 fc6591133..066e033bb 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 4ae6cb1b2..64456854b 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 b9700fc81..af7313be4 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 cd87ed0e7..c8adeae84 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 00357322c..099fec5c6 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 c6430782f..78cbafb45 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 2018095cc..5bbe985fe 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 8d5d2e1db..a038c2b6e 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 9dcc187e3..e7533359d 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 07324c71c..c62385413 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 053a7ecfa..9a1489dc2 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 47a290b7e..979758618 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 0a8f99622..3f4d1b4e8 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 a093c3efa..57cd30af3 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 4ae162a7b..1581c5907 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 3fa1490c4..dab46136a 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 dced5481d..001bfb4d4 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 2a7891c32..6ad97d530 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 f7aca6252..743c1acf7 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 9da221259..7d85b2cd1 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 dea44e1d6..9774715f1 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 6ad36ac83..2269a5d28 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 9840cee0c..25d2d0c86 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 9f76073d4..fa41d8652 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 6af2dd3c0..465c6bae0 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 bd0cacbd6..36ed0c9e3 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 ab1e6d879..eb422652d 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 161687ebe..2040417cb 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 5d78be195..a46082e98 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
diff --git a/modules/info/pymod/wrap_info.cc b/modules/info/pymod/wrap_info.cc
index cf15c736d..1a6bf1248 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 8e5711904..e73b9e652 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 bab90abec..83584eda9 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 fdb365a7f..1981f7a6c 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 6464cbb38..7d74b3f86 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 2483d6487..8250d8afd 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 2ed933084..023cef910 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 d0823edf8..449ce728d 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 263ae222c..cc7ce7188 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 30aeda562..99dc7e671 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 e556e79ba..d91552d4a 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 4b3c46be3..40aa9f7ed 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 9e24085f0..95155280d 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 d3317eb00..8eb5d393f 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 9036727c5..2a1e25514 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 24e862d72..1091a106f 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 2cca7e5fd..78a12b06e 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 9cfd9d6ac..573aa8c6b 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 fe8421a8f..1a985760a 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 cf778aae9..a94e2b984 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 6e68fde8f..a7b34d206 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 164681270..84c071f29 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 2db767667..a78bf4911 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 132034406..509f22fbd 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 0b364d575..605b5a115 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 ec6c38ef1..c52301847 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/pymod/__init__.py b/modules/io/pymod/__init__.py
index dbc139f63..a71fe0d18 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
diff --git a/modules/io/pymod/export_map_io.cc b/modules/io/pymod/export_map_io.cc
index ab195ef2d..0b730140d 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 0252c5532..fa63ed244 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 6aa26d96f..addb94f3b 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 d23770774..42fee8bc7 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
diff --git a/modules/io/pymod/wrap_io.cc b/modules/io/pymod/wrap_io.cc
index 55e0dd61c..0cf910a43 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 3062fa1db..00d57b6c7 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 f610f376d..7a417dc3a 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 88cbb7e71..ffe36c6f4 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 cc42070f0..b30501291 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
diff --git a/modules/io/src/convert.hh b/modules/io/src/convert.hh
index c5002ea0b..7224f6986 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 b45176918..47ee2a5af 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/image_format.hh b/modules/io/src/img/image_format.hh
index 95a611367..97603f918 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
index 2fa3ddc99..8ce7122fc 100644
--- a/modules/io/src/img/image_format_conversion.cc
+++ b/modules/io/src/img/image_format_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
// Copyright (C) 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_io_plugin.hh b/modules/io/src/img/image_io_plugin.hh
index 2700d4509..0fcc421fb 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 b0bcf89da..f704ba421 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 dfb61702b..4256e2bf0 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 5f012919f..0a7e60c59 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 4fdd6e285..e599bf51c 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 4bc8ce268..906149503 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 f035b5ccc..2f49ab461 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 53fb9bfd1..48d7e6f41 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 6e7e56816..c7b3351ec 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 97191f67e..0d48a3265 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 4c823edc1..ef43ef502 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 ca4ee55c2..2c3883d8d 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 163d02413..4cab4e891 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 a61715908..13749047f 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 3e76ac989..97de7c67c 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 609250349..3225ef871 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 aeaf2c54e..7ee93968f 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 9d1740abb..65ce4691a 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 d8e2e9710..9c5f90a96 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 64f7c17af..f0abdd712 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 35bfea611..f4bae5260 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 61156a58b..345796c07 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 337ccc1df..dac33489a 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 5de368e2a..1ff47c99f 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 4b5a1a360..77ab77640 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 ad261daf9..36a08bb3a 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 aa6f9a438..e0170d851 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 cd0ad364c..5de5b240f 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 c3efe9017..715743c05 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 053f17976..701b94e49 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 76de383f7..81b72d2d7 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 782565d2c..0547519a6 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 cfd288c75..61f880d46 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 18297af6d..4a6e9d266 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 d47cc94fd..7db9a10c3 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 aafd33a79..af15c1235 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 83f2f1a1b..1d12e0b52 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 16c968252..d42fe9a22 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 e81d31351..ec31b4bbf 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 dded28a46..2afd163e3 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 3d858fcc6..1c2c2327e 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 3781fcda4..b12cb5187 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 709b07623..78116c81b 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 ca9590169..98e4a830f 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 7f923d345..6c032dc32 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 a86d1dceb..68955f3fd 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 e55a409b8..7fefdc890 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 69e466a23..f9f76eca6 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 07bfca81e..f1fbfbb00 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 f1efaee3c..ada62fb92 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 0b48e50be..ff2512b12 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 e99933ec3..a9dced835 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 55c20fc96..d5b4aef15 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 4f14b35e3..22060e8c6 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 4ce5f94b7..a9d34c3eb 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 80ff0bb49..b6e18a132 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 5312ae716..838f24a3c 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 5b3a9388a..e27761948 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 3e0fa3537..25c58ff9c 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 22e3e33a8..c152229ef 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 9e8413853..6392ef4b1 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 e7d0e6bcb..925dfde23 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 bf0a3a8a0..14acca8ca 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 f360b974e..df98fa2dd 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 3884fb268..a0dfa38ec 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 a2f070850..2bab0097e 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 181c2ad8a..7b28c8b2a 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 d12b3219f..ed7bea103 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 23aa19782..5e0e1c529 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 033890c96..7ac15b694 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 6a2603d0d..f402fc3c0 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 d90bb9d1a..e7a478b7a 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 45bc1867a..8089d7ac1 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 02e294649..8ca166d97 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 214eb626c..da9c087c6 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 139c39a84..bc6a3947a 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 0201caf57..3737b6ade 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 a5d33acce..6ef348fbc 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 6f198b7f3..a63ab720c 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 5ed6ceb39..25c45b925 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 8053a0c1a..4f11b5967 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 309ab98f2..8eb8eb650 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 81a6acb2c..69fb8907c 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 0b55a73f1..c15f6debb 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 e89a0dc6d..6926421c5 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 b524f3161..d8f7403b9 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 a3acd275c..97fe449cf 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 9bca49efe..e652b845a 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 a72cee4b2..6c623241a 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 be4798d76..a84710b7c 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 90ed88622..418413295 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 783d69762..19c78de8b 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 9312ed0c4..612ca2b10 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 1be00a1e2..74aa87f98 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 746bae322..2dff01015 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 87a00673b..ae8350731 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 d023c1361..461d457cb 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 843e7eeba..4ca0c06f0 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 5fb188ad3..564ffe488 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 915a45e60..de540f6be 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 c6cb21c58..93d4ccb13 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 1a2befe05..4d1a139b7 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 f51d67af1..4f229bed1 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 1ae165d16..73b8f24c8 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
diff --git a/modules/io/tests/test_io_img.cc b/modules/io/tests/test_io_img.cc
index 11821e11f..bb7f541b1 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_pdb.cc b/modules/io/tests/test_io_pdb.cc
index 4cfc22492..400034f9b 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_sdf.cc b/modules/io/tests/test_io_sdf.cc
index 1aa5faf28..0dcbf5fd6 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 a99b93c9c..b866c3949 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 7cc80671b..a6c1b543a 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 ecd3e3f67..efb35d54f 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 b3c9d7c23..21efd569f 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 7c4c67d97..10961781c 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 86edfe272..c97140079 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 faa6774fc..f06c51adb 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/pymod/export_accessibility.cc b/modules/mol/alg/pymod/export_accessibility.cc
index 789c8f8da..ebafe3635 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 0720999be..5e78f6cbc 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 ee122d2da..256c3e219 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 fe8ebe52d..51f6b7510 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 c626a6ce3..5578bd050 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 8d485b169..ccb6053ab 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 6191b6921..d79dea60c 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 2714f5847..a81965889 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 8f03153e5..0dcfd0e5e 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 87e4cbbc7..ffe803a0a 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 4db2668e9..d006ca09d 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/wrap_mol_alg.cc b/modules/mol/alg/pymod/wrap_mol_alg.cc
index 1c42af212..f00a537c5 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
diff --git a/modules/mol/alg/src/accessibility.hh b/modules/mol/alg/src/accessibility.hh
index 2ed83cc53..d942ff3b4 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 e117e0864..d7204be01 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 c42ca2ef6..797ac4b3f 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 ba1700295..6dbe03ca9 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 bdc0ab646..ddbecd43d 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
diff --git a/modules/mol/alg/src/consistency_checks.hh b/modules/mol/alg/src/consistency_checks.hh
index 34eb4568b..23038e366 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 f67d3556d..7a5c7b9be 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 bd583ed02..8a1f47c9a 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 22bc3fe8b..53ecaba15 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 8623d8779..84df0f665 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 fe6d12c75..0365a2826 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 c2e00d87a..f8e5331cd 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 8f592a37f..4b913efdb 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 916fe4fac..794c671e0 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 2ab0ff089..592eda0bf 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 f021ef7ec..0dae68b93 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 b51c582ad..ef878cbc8 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
diff --git a/modules/mol/alg/src/nonstandard.hh b/modules/mol/alg/src/nonstandard.hh
index 1dce74fd4..06a9149aa 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 e9265312c..0eea5cb94 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 b344cfca4..1ddf66fc5 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 198efee76..6a6b35cd8 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 4c156ba1f..506ac2b7d 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 7874c2454..958c28520 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 b561b0a7f..e1b36a0b3 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 2f450f692..2de4d70fd 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 ef8ebe921..b2cbbf9c0 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 8a75ef9aa..3f85c5c27 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 b8f775939..6780213cf 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 72719c2e6..c7c1f74ab 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 359530f7c..38678d797 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 f32e4a85a..623b344f6 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_consistency_checks.cc b/modules/mol/alg/tests/test_consistency_checks.cc
index 927b9d1ef..ffc21d43c 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
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 56d247515..11a194b2a 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_superposition.cc b/modules/mol/alg/tests/test_superposition.cc
index ba35aa122..1ea1edbee 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/tests.cc b/modules/mol/alg/tests/tests.cc
index 4308786c1..1631a0299 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/pymod/__init__.py b/modules/mol/base/pymod/__init__.py
index e6dd8d59a..7e8bf1eb6 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
diff --git a/modules/mol/base/pymod/export_atom.cc b/modules/mol/base/pymod/export_atom.cc
index d623fffba..343833440 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 7f38fc562..5af079a44 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 c95268df4..5dc6e6503 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 58a464e1a..84ff717b6 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 557e62297..de8e69302 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 70ee5d1d1..4ca48fe52 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 566f0a43c..82aa5e45e 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 46a435ad4..de040484a 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 ebdbcf2b2..3c5ab7900 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
diff --git a/modules/mol/base/pymod/export_entity.cc b/modules/mol/base/pymod/export_entity.cc
index 62d26b5b5..c0b54781a 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
diff --git a/modules/mol/base/pymod/export_entity_view.cc b/modules/mol/base/pymod/export_entity_view.cc
index fb969ce46..0db065a07 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 274742c6f..a9b8c0824 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 8f1fc9460..f4c87ab88 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 f16c0c3cd..3d92274da 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 fad1a74bd..02f2c8457 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 79d167996..a3a7f16ea 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 c6defa5de..d826f3e2a 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 fbf9e2b72..dcf27a5ff 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 3a6d1e328..2ad23ea9e 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 0c1281ad8..dacc39183 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 a24ca3abb..b1547fb51 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 c3ec3777d..b69c8ceb0 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 cb2a219c2..25eba43f8 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 c0effc863..1dbdf09d5 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 ed16ac0f8..2bd424c8e 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 5016e1587..a853669c1 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 9a68a860d..9dd04ca12 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 ea4425add..76acfff53 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 0ddd6d0fe..b7c1f6592 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 85c40ed1a..98eb33a23 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 069ff39b9..755b54b22 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 d46ed485b..a4b72c6bc 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 bbf0cfdad..4114a1462 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 984c948fd..5463ef0a8 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 b15f431e0..90a213870 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 5ab00787c..9e79f2b75 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 0c292fb8d..2e553cff8 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 a195a4042..3338db7fe 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 8f8d2c0e1..96c038460 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 3f9ea30ba..c107261d3 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 97f80f23e..efd838679 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 ff3a6b059..afd4788a0 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 49c294fce..8fb7a39cf 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 33d24d1d4..7317bb5a4 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 53f31d9ae..196efa167 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 edce072cb..20e77064f 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 f3c0e13c9..e83bc8c2a 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 b58e3e98c..21bed68dd 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 fcc5bd330..0f36572b7 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 22ca4a561..5a08d2309 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 f1effeb78..683b659fb 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 838b9afc4..847bc9305 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 b00ac720e..26136abd3 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 a463aa851..b17d23f0b 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 cb0ab5f0f..18383529a 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 ddbe254a2..ee5f15eb5 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 25370fe25..7e35c794d 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 043c8388a..bab2bd72d 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 fdece1e73..dfff46212 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 eaa947a5e..b80804665 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 c5b9c2ca5..26cfa75e3 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 e88845d8b..5e0243b0c 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 0a9f1a28e..8852ec2c9 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 2cd6b3a82..53b3b810f 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 c4ea3aebd..d2c614bb0 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 cfeb00e5d..a5f5d6e0b 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 910c7fd85..f16dbdcf7 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 eb5180743..8bb9231f0 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 50a7c6338..72625a0d1 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 f0852b738..73d0d5e6a 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 b342c526a..c229a2d33 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 ab2be2112..33cd7df9c 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 ebf27f7d6..a9f774964 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 b592f18e0..8debefa0c 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 48b41bac3..d07bc6436 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 b6a4a34a6..feb03df4e 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 124a24ba3..0ed6d4697 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 3a5a61532..0c7243445 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 acb50b57a..ec7b52885 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 aa5bbf690..cb9aa522e 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 15b3b6e51..cbf411af9 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 74e659a6b..7b96659cf 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 cac771039..ee26230be 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 a722c93e6..4699a96da 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 90ef2ad75..db0731f27 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 7a1e3a303..56a2b6ffb 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 5fedf1484..f0ef0caad 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 63459aee4..1f0248755 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 71df89405..84c7b1e41 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 8d8b0f4a0..592e74a57 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 9e170f26d..b8c679df8 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 26e99bed2..63882ff44 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 610521393..7cf5fae60 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 3d0f106b5..52c4553e4 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 733999f26..a7c2cfb95 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 4b81bc3db..a70322975 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 f29b7f136..d681ec3ab 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 3cf659196..c4ddfbe36 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 91b6843e7..fea1b0a6f 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 de5d67f88..4184a9cc2 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 3a1d796b2..e2719f368 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 d8daf7f8f..b20010988 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 a5ff121d2..ab7ba4274 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 9f9ffcdd9..553209a6b 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 e6d441e5d..11d6e9173 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 88892cdae..9e4a54498 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 6b6d15f6a..a240650e7 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 995db6ddb..a5aa7b210 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 5e7b7a333..19fdf0d4d 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 43e31f731..f6be45e5f 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 ac736c74e..ab8e5829f 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 2f80a94cf..467227294 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 981b747cf..7fec20853 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 4359cc26b..a1672b362 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 4ab52ac98..0519c296b 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 34bb3b83c..9f7ad521d 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 84d016499..c8a092cc9 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 639306c90..2b18845d3 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 f2d8edfdd..c1957baf9 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 068a1013b..2aca92a79 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 7b2418431..8996574a0 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 07950307d..b788d7c2e 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 30e174b24..0011a962a 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 117979652..a355f7fcf 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 6462036c8..1772cfc41 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 ff1c5c11b..0efb534ac 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 15caa6bd5..ee463fe1a 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 289096413..518de3f1a 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 f76b0e5f9..52ff4a501 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 6e2c72f8d..a6ba51de3 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 bf1f12de5..1fec95006 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 eb7a09d3d..e379dcafb 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 0e9dce740..413bc6af4 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 336acdbe7..d5ccc42a3 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 69cf67e4d..9636269e8 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 d7199d1b2..f15ec326c 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 6fb69167f..a0ce21c18 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 a11b3a91e..9a329cdc7 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 5031b5236..d33c277e8 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 2830bc821..ad991fbd1 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 06f7e7bf0..34fadd033 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 38b1d6f15..b7536f487 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 e46691cd2..8268c4041 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 83e02b41c..4b37c4c32 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 dea7c29ab..4c719b0d4 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 cab4b81d0..235545309 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 4b793d33e..860fbbd6f 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 fc992d8c9..680448623 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 1bfe911ab..774252ca1 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 71898da71..d65fd864e 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 30e8bdcdd..d3b5ce903 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 c1442dd45..3fca04ca0 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 140682182..4a7527de4 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 39be2c38c..ec0136f42 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 4f7b8dbb2..dfb90a80c 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 7d8ea3485..c09285839 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 73358b98d..3a78a1f34 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 cfd61c509..23e904e85 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_query.cc b/modules/mol/base/tests/test_query.cc
index 185b0f168..0d8b318cb 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 a06c6a6cf..17ef6ee59 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 ecc8d40b1..8df3e10b1 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 1bb37feed..36ad6dc2c 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 2aee173d3..703de4518 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 f61f5d5bc..45a762f5e 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 117985fd0..574260406 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 ac671a2b6..0310464f7 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
diff --git a/modules/mol/mm/pymod/antechamber.py b/modules/mol/mm/pymod/antechamber.py
index 0092f406c..258aa974d 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
diff --git a/modules/mol/mm/pymod/export_block_modifiers.cc b/modules/mol/mm/pymod/export_block_modifiers.cc
index 08287f08f..0a42e7b2b 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 514b7919b..295c3f189 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 b8a4fa6a8..8337e7eea 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 82c74c6d7..8c8b5f90c 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 240f22f4b..09f66a1ee 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 57dc7a911..aa2e7114a 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 c0f71609d..5c91b9703 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 47a023612..3ef812c9c 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 38a09d305..7d9c6573f 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 7e38401d6..88c6fc4bc 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 b4611a680..2845dc271 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 fa5320904..c4749abe2 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
diff --git a/modules/mol/mm/pymod/wrap_mol_mm.cc b/modules/mol/mm/pymod/wrap_mol_mm.cc
index 32e36e04b..c7648fa8b 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/block_modifiers.hh b/modules/mol/mm/src/block_modifiers.hh
index 4212e496b..de201bfb7 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 2077880c7..1e05f944c 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 aa28327d4..37edf7ab4 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 c7cb9244d..f4ea82960 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 957e44579..649cbfb9a 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 c323277a7..ab9291c61 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 6435226e0..b99ffc0b3 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 08e4bfefe..9818c87b3 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 8ee115a3b..4f0b8ee65 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 09734d1dc..a34c75d12 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 facf818e5..375eb1e74 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 93e9d2311..d5829fdb0 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 72f6ba8f0..4675dc7b3 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 12762e244..4a8863718 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 1a9da3094..ac1ec34b1 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 2ec09e194..8c97de897 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 0364715c4..90a862083 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 e9103cea3..cdc2a391c 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/settings.hh.in b/modules/mol/mm/src/settings.hh.in
index d94e51642..d379447ff 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 dea985213..5e7f179a0 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 7cbf06d1a..c10487ae7 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 478174f7f..ae5e5a83f 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 38ecece64..3cb830344 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 94d987d2c..d32a23a2f 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 1d5826710..1c1c7cd00 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 7d51c905e..5f1029330 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
diff --git a/modules/mol/mm/src/system_creator.hh b/modules/mol/mm/src/system_creator.hh
index 274c9453b..b0dc6d748 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 d9810ce34..836bf4a9f 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
diff --git a/modules/mol/mm/src/topology.hh b/modules/mol/mm/src/topology.hh
index 501d4e901..e7c8e70ec 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
diff --git a/modules/mol/mm/src/topology_creator.cc b/modules/mol/mm/src/topology_creator.cc
index 453bf132f..c80ec9da4 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 026abdc5c..04be4684a 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 93826f825..b0f0613a6 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 46b9c03c6..493e1842b 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 45b658a1d..89bc16b03 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 5c1980790..6223cfe7d 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 4836f2f2a..ba9c282d6 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 e74b79a4b..e7d56a66b 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 973da7b13..95e3ae428 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/pymod/wrap_seq_alg.cc b/modules/seq/alg/pymod/wrap_seq_alg.cc
index 30909790c..9df107976 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 38aaa1154..84687af40 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 02ff9c14b..18b31c1a8 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 7af6abf5b..d5f568476 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 e80077efd..30253a37b 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 651b5bdd1..b9d7a2673 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 c01653c2f..892aecd5c 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 c88001e1d..a22eecaa7 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 fd1701827..fa1c9a1b8 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 7039690b7..19822d9d7 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/distance_map.cc b/modules/seq/alg/src/distance_map.cc
index 57a172913..0dbcb0400 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 faf1f553c..bfb85b54a 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 ed4f091d6..ed608776f 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 85ec4ac0d..b336ed00a 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 ad8275c9c..2c5de2629 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 a920832d7..b664cd625 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 33c1afe76..c31b76bb9 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 50e915990..6996e5697 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 eb4bfe396..572cb5b88 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 bea994306..fdcdd662e 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 14b8f9af5..49ebdaf11 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 aa90c1359..a3e4ebfcc 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 04bc8832d..eb75c7c7b 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 b111b7ece..3a9da2e0c 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 2d1f0705b..050408ff4 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 6c0a247ae..598985060 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 4b89fd15c..07bd59dc7 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 6d1ca5002..39439fec5 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 ed88a5048..080dc3810 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 93d233213..a1f81b6fd 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 67f2e0637..4d20e7134 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 daaa09a7b..222567b18 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 315b00f10..8f05ba92c 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
diff --git a/modules/seq/alg/src/subst_weight_matrix.hh b/modules/seq/alg/src/subst_weight_matrix.hh
index c3bb6d605..25f74dc1a 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 c3c214f83..c50527ac3 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 0c7e02824..6bf4780f9 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/test_distance_analysis.cc b/modules/seq/alg/tests/test_distance_analysis.cc
index 928c00ead..9be0d6fe0 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 bcdca910f..649735af8 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_sequence_identity.cc b/modules/seq/alg/tests/test_sequence_identity.cc
index 87bd3f33e..0f0d44be8 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 5a9ec9d00..ffa56935c 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/pymod/__init__.py b/modules/seq/base/pymod/__init__.py
index 2e45c5a10..726f3f5af 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
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 cd1f52853..e6320c15f 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 101446d45..2458a4355 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 e881187c5..2b23ef15a 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
diff --git a/modules/seq/base/pymod/wrap_seq.cc b/modules/seq/base/pymod/wrap_seq.cc
index 1dbc2ba17..e2b107792 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 5960a04ee..2e9c5a0ef 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 5b197d733..554a14523 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 95bef716e..72fba01a8 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 50b358c64..0abbecf03 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 2c197d35c..280ac151d 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 8b8f2fc28..06cb9d5bf 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 6ac044cfd..bd268a0d3 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 9864fe8e5..d95cb9d72 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 ccb64b775..1e851c417 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 233afacba..38d185c01 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 6580aac92..8349210d3 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 cb69e41ea..3910ed9e7 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 095d21b30..dba2686bc 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 9af6bbaab..c798e92ab 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 da74ebd9c..b7162169f 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 e01b2e96f..e977356b6 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 c6aee7a58..7fc378575 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 4a06461b8..dcbe4d332 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 f57a624e7..22ba482c2 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 cf9aa732d..4e91befaf 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 1242720cd..01fef4a20 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 2e6895c6e..89d302f4b 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 17e36da50..b6a5dfda5 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 d3f9fc6a1..5f24281d9 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 1ef113248..65afd7e58 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 363319d4a..14e328da5 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 73e75310c..678933eba 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 27ddc299b..ab0277827 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 05a405b37..1018310eb 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 252add767..44338d0aa 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 b18855bdd..f731b8db6 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 4d3b8b161..aac4b1128 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/dng.bat.in b/scripts/dng.bat.in
index 202d75f67..b40ba5b68 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
diff --git a/scripts/dng.in b/scripts/dng.in
index c04f6b307..93e7d862e 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.bat.in b/scripts/ost.bat.in
index 006fffe52..77056f5c4 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 6da63bda4..ee1f600a6 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
diff --git a/scripts/ost_config.in b/scripts/ost_config.in
index cda517095..c8a170a32 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
--
GitLab
From 90d766f89b32622bf470830addc3c36c49f888fc Mon Sep 17 00:00:00 2001
From: Gerardo Tauriello <gerardo.tauriello@unibas.ch>
Date: Thu, 13 Feb 2020 16:02:03 +0100
Subject: [PATCH 105/142] Fix doc typo
---
modules/conop/doc/aminoacid.rst | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/modules/conop/doc/aminoacid.rst b/modules/conop/doc/aminoacid.rst
index a33104ca6..7867e8a0c 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
--
GitLab
From ad684fdb3c739ca305cbe208c02bc965595d1348 Mon Sep 17 00:00:00 2001
From: Gerardo Tauriello <gerardo.tauriello@unibas.ch>
Date: Thu, 13 Feb 2020 17:21:00 +0100
Subject: [PATCH 106/142] SCHWED-949: Updated tests for non-standard amino
acids.
---
modules/conop/tests/test_amino_acids.cc | 18 ++++++++++++++----
1 file changed, 14 insertions(+), 4 deletions(-)
diff --git a/modules/conop/tests/test_amino_acids.cc b/modules/conop/tests/test_amino_acids.cc
index 2b05d2a0c..60b8ee3b9 100644
--- a/modules/conop/tests/test_amino_acids.cc
+++ b/modules/conop/tests/test_amino_acids.cc
@@ -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);
--
GitLab
From 002d97351b1ac37eeec17cce38e5d2f95fc27de5 Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Fri, 14 Feb 2020 14:05:46 +0100
Subject: [PATCH 107/142] Adapt new C/ CXX_FLAGS into the CI YAML file
---
.gitlab-ci.yml | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 755fed9fc..0fafefeb2 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -71,8 +71,8 @@ test:centos7.3:
-DZLIB_INCLUDE_DIR=$EBROOTZLIB/include
-DZLIB_LIBRARY=$EBROOTZLIB/lib/libz.so
-DOPTIMIZE=1
- -DCMAKE_C_FLAGS='-L/scicore/soft/apps/libpng/1.6.34-GCCcore-7.3.0/lib/ -L/scicore/soft/apps/LibTIFF/4.0.9-GCCcore-7.3.0/lib/ -L/scicore/soft/apps/zlib/1.2.11-GCCcore-7.3.0/lib/ -isystem ${EBROOTBOOST}/include -isystem ${EBROOTOPENMM}/include'
- -DCMAKE_CXX_FLAGS='-L/scicore/soft/apps/libpng/1.6.34-GCCcore-7.3.0/lib/ -L/scicore/soft/apps/LibTIFF/4.0.9-GCCcore-7.3.0/lib/ -L/scicore/soft/apps/zlib/1.2.11-GCCcore-7.3.0/lib/ -isystem ${EBROOTBOOST}/include -isystem ${EBROOTOPENMM}/include'
+ -DCMAKE_C_FLAGS='-L${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."
--
GitLab
From 90c9ad165392b4082fd9d3950225c512914380c2 Mon Sep 17 00:00:00 2001
From: Bienchen <stefanbienert@me.com>
Date: Mon, 17 Feb 2020 10:56:20 +0100
Subject: [PATCH 108/142] SCHWED-4649: Enforce new policy to get rid of -L in
CMake calls
---
CMakeLists.txt | 14 ++++++++++++--
modules/doc/install.rst | 12 +++++++-----
2 files changed, 19 insertions(+), 7 deletions(-)
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 3908e11f6..f49d1ba83 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -2,7 +2,15 @@
# Author: Marco Biasini
#-------------------------------------------------------------------------------
-cmake_minimum_required(VERSION 2.6.4 FATAL_ERROR)
+cmake_minimum_required(VERSION 3.12.1 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)
@@ -262,7 +270,7 @@ 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.sip)
ost_find_python_module(PyQt5)
endif()
@@ -362,3 +370,5 @@ message(STATUS
" Debian/Ubuntu directory layout (-DUBUNTU_LAYOUT) : ${_UBUNTU_LAYOUT}"
${HIDDEN_VIS_MSG})
+
+# LocalWords: CMake CMP
diff --git a/modules/doc/install.rst b/modules/doc/install.rst
index 7d342fd6f..9d59fbed5 100644
--- a/modules/doc/install.rst
+++ b/modules/doc/install.rst
@@ -28,7 +28,7 @@ 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)
+* `CMake <http://cmake.org>`_ (3.12.1)
* `Python3 <http://python.org>`_ (3.6)
* `Boost <http://boost.org>`_ (1.65)
* `zlib <https://zlib.net/>`_ (usually comes with Boost or system)
@@ -317,11 +317,13 @@ version of OpenStructure.
-DOPTIMIZE=ON
-**macOS (Mojave/ High Sierra) with Homebrew**
+**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
@@ -398,4 +400,4 @@ 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
--
GitLab
From 1de6649a292cb53ba2eff9912be28009ed2b1b71 Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Mon, 17 Feb 2020 13:19:48 +0100
Subject: [PATCH 109/142] SCHWED-4612: Set OpenGL GL preferences, new Python
module name for sip in check if sip is installed.
---
CMakeLists.txt | 9 ++++++++-
1 file changed, 8 insertions(+), 1 deletion(-)
diff --git a/CMakeLists.txt b/CMakeLists.txt
index f49d1ba83..e42ceeb00 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -31,7 +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(ENABLE_GFX "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"
@@ -221,6 +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()
--
GitLab
From f2f934e42ff00b00039d525c6c75481a3c6875cd Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Mon, 17 Feb 2020 15:34:09 +0100
Subject: [PATCH 110/142] Fixe doption name
---
CMakeLists.txt | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/CMakeLists.txt b/CMakeLists.txt
index e42ceeb00..1eb22ab60 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -32,7 +32,7 @@ option(ENABLE_GUI "whether the graphical user interface should be enabled"
ON)
option(ENABLE_GFX "whether graphics support should be enabled"
ON)
-option(ENABLE_GFX "whether to use the OpenGL Legacy GL implementation"
+option(OPENGLPREFERENCE_LEGACY "whether to use the OpenGL Legacy GL implementation"
OFF)
option(ENABLE_IMG "whether the image processing module should be compiled"
ON)
--
GitLab
From f621e39141afef65fb504cd8a8a9d30fe96b1e53 Mon Sep 17 00:00:00 2001
From: Gerardo Tauriello <gerardo.tauriello@unibas.ch>
Date: Mon, 17 Feb 2020 18:53:10 +0100
Subject: [PATCH 111/142] Get rid of unused VAX conversion files.
Relevant VAX conversion code is in convert.cc.
---
modules/io/src/convert.cc | 3 +
modules/io/src/img/CMakeLists.txt | 3 -
modules/io/src/img/convert_vax_data.c | 1408 -----------------
modules/io/src/img/convert_vax_data.h | 263 ---
modules/io/src/img/image_format_conversion.cc | 110 --
5 files changed, 3 insertions(+), 1784 deletions(-)
delete mode 100755 modules/io/src/img/convert_vax_data.c
delete mode 100755 modules/io/src/img/convert_vax_data.h
delete mode 100644 modules/io/src/img/image_format_conversion.cc
diff --git a/modules/io/src/convert.cc b/modules/io/src/convert.cc
index b30501291..19a7bfe65 100644
--- a/modules/io/src/convert.cc
+++ b/modules/io/src/convert.cc
@@ -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/img/CMakeLists.txt b/modules/io/src/img/CMakeLists.txt
index d17f46e8e..d3fea543a 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 cab50f2ae..000000000
--- 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 e8e057780..000000000
--- 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_conversion.cc b/modules/io/src/img/image_format_conversion.cc
deleted file mode 100644
index 8ce7122fc..000000000
--- 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) 2008-2020 by the 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
--
GitLab
From 229e0b46787a05ff71b9eab6336dc4cbdec384f9 Mon Sep 17 00:00:00 2001
From: Bienchen <stefanbienert@me.com>
Date: Tue, 18 Feb 2020 10:25:16 +0100
Subject: [PATCH 112/142] SCHWED-4512: Tell clang on macOS to ignore unknown
GCC warnings
---
CMakeLists.txt | 7 +++++++
1 file changed, 7 insertions(+)
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 1eb22ab60..09cde1148 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -304,6 +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}
--
GitLab
From 9cc1c3261494682d954ca207755d0f9959be8af5 Mon Sep 17 00:00:00 2001
From: Bienchen <stefanbienert@me.com>
Date: Wed, 19 Feb 2020 11:20:07 +0100
Subject: [PATCH 113/142] SCHWED-4612: silence a macOS specific warning about
OpenGL deprecation.
---
modules/gfx/src/gl_include.hh | 2 ++
1 file changed, 2 insertions(+)
diff --git a/modules/gfx/src/gl_include.hh b/modules/gfx/src/gl_include.hh
index ec4028e35..9ea90d473 100644
--- a/modules/gfx/src/gl_include.hh
+++ b/modules/gfx/src/gl_include.hh
@@ -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>
--
GitLab
From 2aad79ae07bcee5bf7ab43dcd078b165f6f715e2 Mon Sep 17 00:00:00 2001
From: Bienchen <stefanbienert@me.com>
Date: Wed, 19 Feb 2020 11:42:18 +0100
Subject: [PATCH 114/142] SCHWED-4612: Switch for CMake to toggle GL
implementation used by OpenGL
---
modules/doc/install.rst | 4 ++++
1 file changed, 4 insertions(+)
diff --git a/modules/doc/install.rst b/modules/doc/install.rst
index 9d59fbed5..28b34d60e 100644
--- a/modules/doc/install.rst
+++ b/modules/doc/install.rst
@@ -226,6 +226,10 @@ 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
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
--
GitLab
From f22f3839d6ab4f3d5554c40cdd5f5781b8cdac6d Mon Sep 17 00:00:00 2001
From: Bienchen <stefanbienert@me.com>
Date: Wed, 19 Feb 2020 12:07:00 +0100
Subject: [PATCH 115/142] SCHWED-4634: Updated the CMake call for macOS
---
modules/doc/install.rst | 36 +++++++++++++++++++++++++++---------
1 file changed, 27 insertions(+), 9 deletions(-)
diff --git a/modules/doc/install.rst b/modules/doc/install.rst
index 28b34d60e..81ddfa8b7 100644
--- a/modules/doc/install.rst
+++ b/modules/doc/install.rst
@@ -350,18 +350,36 @@ 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
--------------------------------------------------------------------------------
--
GitLab
From aa65a3cc11e4cdd52d9a6988d457311ca2aa5338 Mon Sep 17 00:00:00 2001
From: Gerardo Tauriello <gerardo.tauriello@unibas.ch>
Date: Wed, 19 Feb 2020 19:02:51 +0100
Subject: [PATCH 116/142] Allow short filenames in molck.
---
tools/molck/main.cc | 14 +++++++-------
1 file changed, 7 insertions(+), 7 deletions(-)
diff --git a/tools/molck/main.cc b/tools/molck/main.cc
index 8507a1895..2016019cf 100644
--- a/tools/molck/main.cc
+++ b/tools/molck/main.cc
@@ -56,15 +56,15 @@ 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);
--
GitLab
From ab13e8d4382aaed2da8afb26a91a8df87c9b401f Mon Sep 17 00:00:00 2001
From: Gerardo Tauriello <gerardo.tauriello@unibas.ch>
Date: Wed, 19 Feb 2020 19:28:51 +0100
Subject: [PATCH 117/142] SCHWED-4657: fix default MolckSettings in molck
binary.
---
modules/mol/alg/doc/molck.rst | 38 +++++++++++----------
tools/molck/main.cc | 62 +++++++++++++++++++----------------
2 files changed, 55 insertions(+), 45 deletions(-)
diff --git a/modules/mol/alg/doc/molck.rst b/modules/mol/alg/doc/molck.rst
index 7ffd414ae..286127b28 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 and 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/tools/molck/main.cc b/tools/molck/main.cc
index 2016019cf..53ff93f4d 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 and 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()
{
@@ -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);
--
GitLab
From 1324c0c425596cd27078dea1180ea6e8a8a37e34 Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Thu, 20 Feb 2020 12:01:43 +0100
Subject: [PATCH 118/142] SCHWED-4635: Changes to make the container work
---
CMakeLists.txt | 4 ++--
cmake_support/OST.cmake | 28 ++++++++++++++++++++++++++++
2 files changed, 30 insertions(+), 2 deletions(-)
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 09cde1148..727630fe5 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -2,7 +2,7 @@
# Author: Marco Biasini
#-------------------------------------------------------------------------------
-cmake_minimum_required(VERSION 3.12.1 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
@@ -277,8 +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(PyQt5.sip)
ost_find_python_module(PyQt5)
+ ost_find_python_module_alt("PyQt5.sip;sip")
endif()
if (ENABLE_SPNAV)
diff --git a/cmake_support/OST.cmake b/cmake_support/OST.cmake
index 41e8f7a78..3b6821210 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:
--
GitLab
From 172c0fa1b9583d191bfa38a4a21aa94e3cd95a14 Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Thu, 20 Feb 2020 14:09:52 +0100
Subject: [PATCH 119/142] SCHWED-4635: Add new compiler flags to container
compilation
---
docker/Dockerfile | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/docker/Dockerfile b/docker/Dockerfile
index 56d87ebcf..5dfd05ed7 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -84,7 +84,9 @@ RUN cd ${SRC_FOLDER} && \
-DOPEN_MM_INCLUDE_DIR=$OPENMM_INCLUDE_PATH \
-DOPEN_MM_PLUGIN_DIR=$OPENMM_LIB_PATH/plugins \
-DENABLE_GFX=ON \
- -DENABLE_GUI=ON && \
+ -DENABLE_GUI=ON \
+ -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 && \
--
GitLab
From f882c759b0f55e3f898d85710f727073413e9f15 Mon Sep 17 00:00:00 2001
From: Gerardo Tauriello <gerardo.tauriello@unibas.ch>
Date: Thu, 20 Feb 2020 10:49:14 +0100
Subject: [PATCH 120/142] Fix molck usage text
---
modules/mol/alg/doc/molck.rst | 2 +-
tools/molck/main.cc | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/modules/mol/alg/doc/molck.rst b/modules/mol/alg/doc/molck.rst
index 286127b28..7c4d9ee63 100644
--- a/modules/mol/alg/doc/molck.rst
+++ b/modules/mol/alg/doc/molck.rst
@@ -53,7 +53,7 @@ please find them following:
- oxt - Remove terminal oxygens
- nonstd - Remove all residues not one of the
20 standard amino acids
- - unk - Remove unknown and atoms not following
+ - unk - Remove unknown atoms not following
the nomenclature
Default: hyd
--fix-ele Clean up element column
diff --git a/tools/molck/main.cc b/tools/molck/main.cc
index 53ff93f4d..efed0e21f 100644
--- a/tools/molck/main.cc
+++ b/tools/molck/main.cc
@@ -38,7 +38,7 @@ const char* USAGE=
" - oxt - Remove terminal oxygens\n"
" - nonstd - Remove all residues not one of the\n"
" 20 standard amino acids\n"
-" - unk - Remove unknown and atoms not following\n"
+" - unk - Remove unknown atoms not following\n"
" the nomenclature\n"
" Default: hyd\n"
" --fix-ele Clean up element column\n"
--
GitLab
From 02c266d7af83a3903c78476f44207c6da5b2cc20 Mon Sep 17 00:00:00 2001
From: Gerardo Tauriello <gerardo.tauriello@unibas.ch>
Date: Thu, 20 Feb 2020 13:56:07 +0100
Subject: [PATCH 121/142] SCHWED-4658: mol.alg.CopyResidue can deal with bad
backbones now.
This is used in Molck's MapNonStandardResidues which used to fail if there
were missing (or unmappable) backbone atoms in modified residues.
---
modules/mol/alg/src/nonstandard.cc | 12 ++-
modules/mol/alg/tests/test_nonstandard.py | 75 +++++++++++++++----
.../mol/alg/tests/testfiles/cbeta_fail.pdb | 13 ++++
3 files changed, 83 insertions(+), 17 deletions(-)
create mode 100644 modules/mol/alg/tests/testfiles/cbeta_fail.pdb
diff --git a/modules/mol/alg/src/nonstandard.cc b/modules/mol/alg/src/nonstandard.cc
index ef878cbc8..f675cc974 100644
--- a/modules/mol/alg/src/nonstandard.cc
+++ b/modules/mol/alg/src/nonstandard.cc
@@ -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>
@@ -58,8 +59,15 @@ bool CopyResidue(ResidueHandle src_res, ResidueHandle dst_res,
}
// 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");
+ 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/tests/test_nonstandard.py b/modules/mol/alg/tests/test_nonstandard.py
index cbe8257a7..c7f49215e 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())
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 000000000..3c856297e
--- /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
--
GitLab
From 58a9a88a2881eaec7fd1de40265fae516b9da6fa Mon Sep 17 00:00:00 2001
From: Gerardo Tauriello <gerardo.tauriello@unibas.ch>
Date: Thu, 20 Feb 2020 14:24:23 +0100
Subject: [PATCH 122/142] Clarify doc for CopyResidue functions.
---
modules/mol/alg/doc/molalg.rst | 35 ++++++++++++++++++------------
modules/mol/alg/src/nonstandard.cc | 8 +++----
2 files changed, 25 insertions(+), 18 deletions(-)
diff --git a/modules/mol/alg/doc/molalg.rst b/modules/mol/alg/doc/molalg.rst
index 5262c236a..8c9322a30 100644
--- a/modules/mol/alg/doc/molalg.rst
+++ b/modules/mol/alg/doc/molalg.rst
@@ -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/src/nonstandard.cc b/modules/mol/alg/src/nonstandard.cc
index f675cc974..04d05720c 100644
--- a/modules/mol/alg/src/nonstandard.cc
+++ b/modules/mol/alg/src/nonstandard.cc
@@ -49,16 +49,16 @@ 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") {
+ 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");
--
GitLab
From 178103751dc8067758674c7f1cec26996c8214f1 Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Thu, 20 Feb 2020 15:46:51 +0100
Subject: [PATCH 123/142] SCHWED-4635: Updated Singularity documentation &
container build instructions
---
singularity/README.rst | 4 ++--
singularity/Singularity | 2 +-
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/singularity/README.rst b/singularity/README.rst
index 69daf50bc..b831f76e5 100644
--- a/singularity/README.rst
+++ b/singularity/README.rst
@@ -38,13 +38,13 @@ 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 125f21324..5ebf34855 100644
--- a/singularity/Singularity
+++ b/singularity/Singularity
@@ -1,5 +1,5 @@
BootStrap: docker
-From: registry.scicore.unibas.ch/schwede/openstructure:python3_test
+From: registry.scicore.unibas.ch/schwede/openstructure:python3_test2
%post
--
GitLab
From 3e1654758d4812dafdc747be1502264d0f26b0f6 Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Thu, 20 Feb 2020 16:02:53 +0100
Subject: [PATCH 124/142] SCHWED-4638: Bump version numbers
---
CMakeLists.txt | 4 ++--
docker/Dockerfile | 2 +-
scripts/bump-version.py | 12 ------------
3 files changed, 3 insertions(+), 15 deletions(-)
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 727630fe5..91af96562 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -13,8 +13,8 @@ cmake_policy(SET CMP0060 NEW)
project(OpenStructure CXX C)
set (CMAKE_EXPORT_COMPILE_COMMANDS 1)
-set (OST_VERSION_MAJOR 1)
-set (OST_VERSION_MINOR 10)
+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)
diff --git a/docker/Dockerfile b/docker/Dockerfile
index 5dfd05ed7..63df3f9e4 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -2,7 +2,7 @@ FROM ubuntu:18.04
# ARGUMENTS
###########
-ARG OPENSTRUCTURE_VERSION="python3_port"
+ARG OPENSTRUCTURE_VERSION="2.0.0"
ARG SRC_FOLDER="/usr/local/src"
ARG CPUS_FOR_MAKE=2
ARG MSMS_VERSION="2.6.1"
diff --git a/scripts/bump-version.py b/scripts/bump-version.py
index 0df1088bf..367b3f635 100755
--- a/scripts/bump-version.py
+++ b/scripts/bump-version.py
@@ -1,10 +1,5 @@
-#!/usr/bin/env python
import sys
-raise RuntimeError("Many things have changed in the Python 3 port. " +
- "bump-version.py might require updates. " +
- "Only remove this error after careful checking!")
-
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)")
@@ -40,10 +35,3 @@ for i, line in enumerate(lines):
if line.startswith("ARG OPENSTRUCTURE_VERSION"):
lines[i] = 'ARG OPENSTRUCTURE_VERSION="%s"\n' % version_string
open("docker/Dockerfile", "w").writelines(lines)
-
-# fix Singularity recipe
-lines = open("singularity/Singularity").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)
--
GitLab
From 3d6d82334a96c02c83ea386a29c9d8f2b3dc448f Mon Sep 17 00:00:00 2001
From: Tauriello Gerardo <gerardo.tauriello@unibas.ch>
Date: Thu, 20 Feb 2020 17:25:21 +0100
Subject: [PATCH 125/142] Update GUI part of docker README.rst
---
docker/README.rst | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/docker/README.rst b/docker/README.rst
index bc6efa1ae..517345d9c 100644
--- a/docker/README.rst
+++ b/docker/README.rst
@@ -155,7 +155,9 @@ 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
--
GitLab
From 04003aa37dc055acbc8921b9c11fe92720cfefd9 Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Mon, 24 Feb 2020 09:56:21 +0100
Subject: [PATCH 126/142] Match the required CMake version to the one in
CMakeLists.txt
---
modules/doc/install.rst | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/modules/doc/install.rst b/modules/doc/install.rst
index 81ddfa8b7..e78a5b047 100644
--- a/modules/doc/install.rst
+++ b/modules/doc/install.rst
@@ -28,7 +28,7 @@ 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>`_ (3.12.1)
+* `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)
--
GitLab
From f5c0be2a36ea8d17ebcc9529336357d6203ab87e Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Mon, 24 Feb 2020 16:58:04 +0100
Subject: [PATCH 127/142] SCHWED-4633: Changed installation instructions
towards Debian 10.
---
modules/doc/install.rst | 6 ++++--
1 file changed, 4 insertions(+), 2 deletions(-)
diff --git a/modules/doc/install.rst b/modules/doc/install.rst
index e78a5b047..72e4e26e3 100644
--- a/modules/doc/install.rst
+++ b/modules/doc/install.rst
@@ -299,7 +299,7 @@ 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:
@@ -320,7 +320,9 @@ version of OpenStructure.
cmake . -DPYTHON_LIBRARIES=/usr/lib/x86_64-linux-gnu/libpython3.6m.so \
-DOPTIMIZE=ON
-
+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
--
GitLab
From 86dcab9ce7318e2063f627680eed2b09159a3ffe Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Tue, 25 Feb 2020 13:11:36 +0100
Subject: [PATCH 128/142] make sure we're actually looking at a boolean
comparison
---
modules/base/tests/test_string_ref.cc | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/modules/base/tests/test_string_ref.cc b/modules/base/tests/test_string_ref.cc
index ea6b8d0cb..6b75fd0f6 100644
--- a/modules/base/tests/test_string_ref.cc
+++ b/modules/base/tests/test_string_ref.cc
@@ -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();
--
GitLab
From 6fa44c03df340418261ee3e82d9ac2fb2106c2da Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Tue, 25 Feb 2020 14:46:50 +0100
Subject: [PATCH 129/142] Updated the Singularity README.md
---
singularity/README.rst | 5 ++---
1 file changed, 2 insertions(+), 3 deletions(-)
diff --git a/singularity/README.rst b/singularity/README.rst
index b831f76e5..3f0391c0f 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
--------------
--
GitLab
From 74704c02de7cfe364a539ead1f4f7cd0307d6058 Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Tue, 25 Feb 2020 15:23:10 +0100
Subject: [PATCH 130/142] Put SIngularity under bump_version.py control
---
scripts/bump-version.py | 10 ++++++++++
singularity/Singularity | 3 +--
2 files changed, 11 insertions(+), 2 deletions(-)
diff --git a/scripts/bump-version.py b/scripts/bump-version.py
index 367b3f635..361e78772 100755
--- a/scripts/bump-version.py
+++ b/scripts/bump-version.py
@@ -35,3 +35,13 @@ for i, line in enumerate(lines):
if line.startswith("ARG OPENSTRUCTURE_VERSION"):
lines[i] = 'ARG OPENSTRUCTURE_VERSION="%s"\n' % version_string
open("docker/Dockerfile", "w").writelines(lines)
+
+# fix Singularity recipe
+vfile = "singularity/Singularity"
+lines = open(vfile).readlines()
+for i, line in enumerate(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/singularity/Singularity b/singularity/Singularity
index 3a3889f20..9d1a3d96b 100644
--- a/singularity/Singularity
+++ b/singularity/Singularity
@@ -1,6 +1,5 @@
BootStrap: docker
-From: registry.scicore.unibas.ch/schwede/openstructure:python3_test2
-
+From: registry.scicore.unibas.ch/schwede/openstructure:"2.0.0"
%post
##############################################################################
--
GitLab
From 5eeb60630a21a9d54540be71b5493645e4b440ee Mon Sep 17 00:00:00 2001
From: Bienchen <stefan.bienert@unibas.ch>
Date: Wed, 26 Feb 2020 09:02:30 +0100
Subject: [PATCH 131/142] Fixed Jupyter in the Sungularity container
---
singularity/Singularity | 8 ++++++--
1 file changed, 6 insertions(+), 2 deletions(-)
diff --git a/singularity/Singularity b/singularity/Singularity
index 9d1a3d96b..222fe694e 100644
--- a/singularity/Singularity
+++ b/singularity/Singularity
@@ -35,7 +35,7 @@ locale-gen en_US.UTF-8
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 JUPYTER_RUNTIME_DIR="/tmp/jupyter_runtime"
mkdir -p /usr/local/share/ipython
mkdir -p $JUPYTER_PATH
@@ -68,10 +68,14 @@ jupyter nbextension enable nglview --py --sys-prefix
##############################################################################
# ENVIRONMENT
##############################################################################
+export TEMP="/tmp"
+export TEMPDIR="/tmp"
+export TMPDIR="/tmp"
+export TMP="/tmp"
export IPYTHONDIR="/usr/local/share/ipython"
export JUPYTER_CONFIG_DIR="/usr/local/etc/jupyter"
export JUPYTER_PATH="/usr/local/share/jupyter"
-export JUPYTER_RUNTIME_DIR="$JUPYTER_PATH/runtime"
+export JUPYTER_RUNTIME_DIR="$TMPDIR/jupyter_runtime"
%apprun ChemdictTool
##############################################################################
--
GitLab
From 253ab1315c66cc734b59e9c137292c25e28faebd Mon Sep 17 00:00:00 2001
From: Gerardo Tauriello <gerardo.tauriello@unibas.ch>
Date: Wed, 26 Feb 2020 11:14:45 +0100
Subject: [PATCH 132/142] Fix consistency reporting in ost-compare-structures.
---
actions/ost-compare-structures | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/actions/ost-compare-structures b/actions/ost-compare-structures
index 60a2b8c95..0ae1dad2d 100644
--- a/actions/ost-compare-structures
+++ b/actions/ost-compare-structures
@@ -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
--
GitLab
From 2a25ef9a96c5ad981e9a69f30e23f9d72576bd9a Mon Sep 17 00:00:00 2001
From: Gerardo Tauriello <gerardo.tauriello@unibas.ch>
Date: Wed, 26 Feb 2020 11:27:38 +0100
Subject: [PATCH 133/142] Cleaning up code/doc/tests of consistency checks.
---
modules/mol/alg/doc/molalg.rst | 2 +-
modules/mol/alg/src/consistency_checks.cc | 20 +++++--
.../mol/alg/tests/test_consistency_checks.cc | 59 ++++++++++---------
3 files changed, 46 insertions(+), 35 deletions(-)
diff --git a/modules/mol/alg/doc/molalg.rst b/modules/mol/alg/doc/molalg.rst
index 8c9322a30..d1957af34 100644
--- a/modules/mol/alg/doc/molalg.rst
+++ b/modules/mol/alg/doc/molalg.rst
@@ -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.)
diff --git a/modules/mol/alg/src/consistency_checks.cc b/modules/mol/alg/src/consistency_checks.cc
index ddbecd43d..f476f3ad6 100644
--- a/modules/mol/alg/src/consistency_checks.cc
+++ b/modules/mol/alg/src/consistency_checks.cc
@@ -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/tests/test_consistency_checks.cc b/modules/mol/alg/tests/test_consistency_checks.cc
index ffc21d43c..657c3076f 100644
--- a/modules/mol/alg/tests/test_consistency_checks.cc
+++ b/modules/mol/alg/tests/test_consistency_checks.cc
@@ -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();
--
GitLab
From e4388088bcf75dc4c8fdc4d426d815235010f489 Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Mon, 2 Mar 2020 17:07:15 +0100
Subject: [PATCH 134/142] Mention container registry in documentation/ REAMDE
---
docker/README.rst | 13 ++++++++++++-
modules/doc/install.rst | 6 ++++--
2 files changed, 16 insertions(+), 3 deletions(-)
diff --git a/docker/README.rst b/docker/README.rst
index 517345d9c..93e58eb30 100644
--- a/docker/README.rst
+++ b/docker/README.rst
@@ -6,10 +6,21 @@ 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 image from the OST registry
+----------------------------------
+
+OST has its own [container registry](https://git.scicore.unibas.ch/schwede/openstructure/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
diff --git a/modules/doc/install.rst b/modules/doc/install.rst
index 72e4e26e3..37af4de49 100644
--- a/modules/doc/install.rst
+++ b/modules/doc/install.rst
@@ -8,8 +8,10 @@ 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://sylabs.io/singularity/>`_.
-The latest recipes and instructions can be found on our GitLab site
-(`Docker instructions`_ and `Singularity instructions`_).
+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:
--
GitLab
From a4edc72775a11db708798fb5d819252baa398ec2 Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Mon, 2 Mar 2020 17:09:05 +0100
Subject: [PATCH 135/142] Cosmetics
---
docker/README.rst | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/docker/README.rst b/docker/README.rst
index 93e58eb30..3d3b410ca 100644
--- a/docker/README.rst
+++ b/docker/README.rst
@@ -6,10 +6,11 @@ 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 image from the OST registry
+Obtain Docker image from the OST registry
----------------------------------
-OST has its own [container registry](https://git.scicore.unibas.ch/schwede/openstructure/container_registry) inside GitLab. There we try to keep one image for the latest stable version of OST. You can import it by
+OST has its own `container registry https://git.scicore.unibas.ch/schwede/openstructure/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
--
GitLab
From 64503dbe4637d5bb584bbc3183bf9587bcbbcae4 Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Mon, 2 Mar 2020 17:10:05 +0100
Subject: [PATCH 136/142] Cosmetics
---
docker/README.rst | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/docker/README.rst b/docker/README.rst
index 3d3b410ca..974c4807b 100644
--- a/docker/README.rst
+++ b/docker/README.rst
@@ -7,10 +7,10 @@ OST Docker
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 https://git.scicore.unibas.ch/schwede/openstructure/container_registry`_ inside GitLab. There we try to keep one image for
-the latest stable version of OST. You can import it by
+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
--
GitLab
From dd3beeed84585e0dcf0c478c4975e77ed3cb7ea7 Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Tue, 3 Mar 2020 13:13:54 +0100
Subject: [PATCH 137/142] SCHWED-4632: Get rid of last traces of Python 2.7
---
build_configs/buildconfig_bc2 | 14 +++++++-------
build_configs/buildconfig_bc2_static | 14 +++++++-------
scripts/dng.bat.in | 2 +-
scripts/ost-nightly-build.sh | 6 +++---
4 files changed, 18 insertions(+), 18 deletions(-)
diff --git a/build_configs/buildconfig_bc2 b/build_configs/buildconfig_bc2
index ae7aa9384..5c8dccf19 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 d25730b34..bf27f7e8f 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/scripts/dng.bat.in b/scripts/dng.bat.in
index b40ba5b68..d012f7b74 100644
--- a/scripts/dng.bat.in
+++ b/scripts/dng.bat.in
@@ -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/ost-nightly-build.sh b/scripts/ost-nightly-build.sh
index b8c458661..6f6cbddfe 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)
}
--
GitLab
From 4ef866259d01894754b69c8766c449c62ae40c3e Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Tue, 3 Mar 2020 13:38:06 +0100
Subject: [PATCH 138/142] SCHWED-4637: Added version 2.0.0 to the changelog
---
CHANGELOG.txt | 9 +++++++++
1 file changed, 9 insertions(+)
diff --git a/CHANGELOG.txt b/CHANGELOG.txt
index ea3c60e1a..1fbce2364 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
--------------------------------------------------------------------------------
--
GitLab
From 840f98868591b5fc95b04f0a3409d6f3d760d897 Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavier.robin@unibas.ch>
Date: Fri, 6 Mar 2020 15:21:59 +0100
Subject: [PATCH 139/142] fix DeprecationWarning: invalid escape sequence
---
modules/base/pymod/table.py | 14 +++++++-------
modules/bindings/pymod/clustalw.py | 4 ++--
2 files changed, 9 insertions(+), 9 deletions(-)
diff --git a/modules/base/pymod/table.py b/modules/base/pymod/table.py
index 4277edf94..6c9a039f9 100644
--- a/modules/base/pymod/table.py
+++ b/modules/base/pymod/table.py
@@ -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
@@ -1137,7 +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`
@@ -1203,7 +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
@@ -2360,7 +2360,7 @@ Statistics for column %(col)s
deprecated in the future. Numpy itself suggests replacing numpy matrix by
numpy array.
- :param \*args: column names to include in numpy array
+ :param \\*args: column names to include in numpy array
:warning: The function depends on *numpy*
'''
@@ -2396,7 +2396,7 @@ Statistics for column %(col)s
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
+ :param \\*args: column names to include in numpy matrix
:warning: The function depends on *numpy*
'''
@@ -2487,7 +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.
@@ -2499,7 +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
diff --git a/modules/bindings/pymod/clustalw.py b/modules/bindings/pymod/clustalw.py
index aab374f07..f95422b79 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
======= ======================= ======= ============================
'''
--
GitLab
From 5ae2daca19cf92cac2a61939c466bee276b79ca9 Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Wed, 11 Mar 2020 11:57:05 +0100
Subject: [PATCH 140/142] Fix bump-cersion script and Singularity file
---
scripts/bump-version.py | 2 +-
singularity/Singularity | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/scripts/bump-version.py b/scripts/bump-version.py
index 361e78772..25873539b 100755
--- a/scripts/bump-version.py
+++ b/scripts/bump-version.py
@@ -42,6 +42,6 @@ lines = open(vfile).readlines()
for i, line in enumerate(lines):
if line.startswith("From: registry.scicore.unibas.ch/schwede/openstructure:"):
lines[i] = 'From: registry.scicore.unibas.ch/schwede/openstructure:'+\
- '"%s"' % version_string
+ '%s' % version_string
break
open(vfile, "w").writelines(lines)
diff --git a/singularity/Singularity b/singularity/Singularity
index 222fe694e..a9b790a9c 100644
--- a/singularity/Singularity
+++ b/singularity/Singularity
@@ -1,5 +1,5 @@
BootStrap: docker
-From: registry.scicore.unibas.ch/schwede/openstructure:"2.0.0"
+From: registry.scicore.unibas.ch/schwede/openstructure:2.0.0
%post
##############################################################################
--
GitLab
From b54d2d09c2e0eda9d7ed1a9a7c8b8e2263db1faf Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Mon, 16 Mar 2020 19:57:22 +0100
Subject: [PATCH 141/142] make blosum data reproducible
Reason for that effort was the detection of an error in one of the entries
in BLOSUM100 (a missing minus, see diff).
To guarantee reproducibility (and check all matrices for errors),
the blosum matrix files from NCBI at
ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/ have been downloaded and
the generate_blosum_data.py script spits out the required content
in subst_weight_matrix.cc.
---
modules/seq/alg/src/data/BLOSUM100 | 31 ++++++++++++
modules/seq/alg/src/data/BLOSUM45 | 31 ++++++++++++
modules/seq/alg/src/data/BLOSUM62 | 31 ++++++++++++
modules/seq/alg/src/data/BLOSUM80 | 31 ++++++++++++
.../seq/alg/src/data/generate_blosum_data.py | 47 +++++++++++++++++++
modules/seq/alg/src/subst_weight_matrix.cc | 7 ++-
6 files changed, 176 insertions(+), 2 deletions(-)
create mode 100644 modules/seq/alg/src/data/BLOSUM100
create mode 100644 modules/seq/alg/src/data/BLOSUM45
create mode 100644 modules/seq/alg/src/data/BLOSUM62
create mode 100644 modules/seq/alg/src/data/BLOSUM80
create mode 100644 modules/seq/alg/src/data/generate_blosum_data.py
diff --git a/modules/seq/alg/src/data/BLOSUM100 b/modules/seq/alg/src/data/BLOSUM100
new file mode 100644
index 000000000..46e9e8516
--- /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 000000000..18c332389
--- /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 000000000..205f139aa
--- /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 000000000..78172a359
--- /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 000000000..cb0dc1f60
--- /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/subst_weight_matrix.cc b/modules/seq/alg/src/subst_weight_matrix.cc
index 8f05ba92c..f382e4f8e 100644
--- a/modules/seq/alg/src/subst_weight_matrix.cc
+++ b/modules/seq/alg/src/subst_weight_matrix.cc
@@ -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},
--
GitLab
From 44275484239f37abf87be9030be3505a9fd3dd60 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Thu, 19 Mar 2020 17:32:08 +0100
Subject: [PATCH 142/142] Python export for estimating cbeta positions
---
modules/mol/alg/pymod/wrap_mol_alg.cc | 16 ++++++++++++++++
1 file changed, 16 insertions(+)
diff --git a/modules/mol/alg/pymod/wrap_mol_alg.cc b/modules/mol/alg/pymod/wrap_mol_alg.cc
index f00a537c5..fd5b6d94d 100644
--- a/modules/mol/alg/pymod/wrap_mol_alg.cc
+++ b/modules/mol/alg/pymod/wrap_mol_alg.cc
@@ -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));
}
--
GitLab