diff --git a/CMakeLists.txt b/CMakeLists.txt
index fba8fd543c5e3b08574b0e7b29f2356b3e75898f..e85e030914f16a4f017af71db0a176646cb0b798 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -322,7 +322,7 @@ message(STATUS
" Info support (-DENABLE_INFO) : ${_INFO}\n"
" Graphical interface (-DENABLE_GUI) : ${_UI}\n"
" OpenGL support (-DENABLE_GFX) : ${_OPENGL}\n"
- " OpenGL via Mesa (-DUSE_MESA) : ${_USE_MESA}\n"
+ " OpenGL via Mesa (-DUSE_MESA) : ${_USE_MESA}\n"
" Image Processing support (-DENABLE_IMG) : ${_IMG}\n"
" Shader support (-DUSE_SHADER) : ${_SHADER}\n"
" Numpy support (-DUSE_NUMPY) : ${_NUMPY}\n"
@@ -333,6 +333,9 @@ message(STATUS
" Compound Lib (-DCOMPOUND_LIB) : ${_COMP_LIB}\n"
" TMAlign and TMScore (-DCOMPILE_TMTOOLS) : ${_TM_TOOLS}\n"
" Static Libraries (-DENABLE_STATIC) : ${ENABLE_STATIC}\n"
- " Debian-style 'libexec' (-DDEBIAN_STYLE_LIBEXEC) : ${_DEBIAN_STYLE_LIBEXEC}\n"
- " Hidden object visibility (-DHIDDEN_VISIBILITY) : ${_HIDDEN_VIS}")
+ " Debian-style 'libexec' (-DDEBIAN_STYLE_LIBEXEC) : ${_DEBIAN_STYLE_LIBEXEC}")
+if (CMAKE_COMPILER_IS_GNUCXX)
+ message(STATUS
+ " Hidden object visibility (-DHIDDEN_VISIBILITY) : ${_HIDDEN_VIS}")
+endif()
diff --git a/cmake_support/OST.cmake b/cmake_support/OST.cmake
index 70305fbb0142eccdf605611d1e68f702cd0bd756..902619dd345b360595f97de19053c7393e09dcb8 100644
--- a/cmake_support/OST.cmake
+++ b/cmake_support/OST.cmake
@@ -69,7 +69,6 @@ endmacro()
# content changed.
#-------------------------------------------------------------------------------
macro(copy_if_different FROM_DIR TO_DIR FILES TARGETS TARGET)
- set(ADD_TARGETS "")
foreach(SRC ${FILES})
set(SRCFILE ${SRC})
if("${FROM_DIR}" STREQUAL "" OR "${FROM_DIR}" STREQUAL "./")
@@ -86,14 +85,8 @@ macro(copy_if_different FROM_DIR TO_DIR FILES TARGETS TARGET)
file(MAKE_DIRECTORY ${TO_DIR})
add_custom_command(TARGET "${TARGET}" PRE_BUILD
DEPENDS ${FROM}
- COMMAND ${CMAKE_COMMAND} -E copy_if_different ${FROM} ${TO}
- COMMENT ""
- )
- list(APPEND ADD_TARGETS ${TO})
+ COMMAND ${CMAKE_COMMAND} -E copy_if_different ${FROM} ${TO})
endforeach()
- if (TARGETS)
- set(${TARGETS} ${ADD_TARGETS})
- endif()
endmacro()
#-------------------------------------------------------------------------------
@@ -101,11 +94,14 @@ endmacro()
#-------------------------------------------------------------------------------
macro(stage_headers HEADERS HEADER_INSTALL_DIR TARGET SUB)
set(FROM_DIR "./")
+ set(_HDR_SOURCE_DIR "${CMAKE_CURRENT_SOURCE_DIR}/${SUB}")
+ foreach(_HDR ${HEADERS})
+ list(APPEND _ABS_HEADER_NAMES ${_HDR_SOURCE_DIR}/${_HDR})
+ endforeach()
# introduce a helper target to make sure the headers are staged before
# building the library
string(REPLACE "/" "_" _SUB_NO_SLASH "${SUB}")
string(REPLACE "${PREFIX}_" "" _TARGET "${TARGET}")
- #message("target before: ${TARGET} after: ${_TARGET}")
set(_TARGET_NAME ${_TARGET}_${_SUB_NO_SLASH}_headers)
set(_SUB ${SUB})
if (NOT _SUB)
@@ -113,12 +109,10 @@ macro(stage_headers HEADERS HEADER_INSTALL_DIR TARGET SUB)
endif()
add_custom_target("${_TARGET_NAME}" COMMENT "")
set(HEADER_DIR "${HEADER_STAGE_PATH}/${HEADER_INSTALL_DIR}")
- copy_if_different("${FROM_DIR}" "${HEADER_DIR}"
- "${HEADERS}" ""
+ copy_if_different("" "${HEADER_DIR}"
+ "${_ABS_HEADER_NAMES}" ""
"${_TARGET_NAME}")
- add_dependencies("${TARGET}" "${_TARGET_NAME}")
- set_target_properties("${_TARGET_NAME}" PROPERTIES
- EchoString "Staging headers ${TARGET}")
+ add_dependencies(${TARGET} ${_TARGET_NAME})
endmacro()
#-------------------------------------------------------------------------------
@@ -269,7 +263,7 @@ macro(module)
install(FILES ${_ABS_HEADER_NAMES} DESTINATION
"include/${_HEADER_OUTPUT_DIR}/${_DIR}")
set(_HDR_STAGE_DIR "${_HEADER_OUTPUT_DIR}/${_DIR}")
- stage_headers("${_ABS_HEADER_NAMES}" "${_HDR_STAGE_DIR}"
+ stage_headers("${_HEADERS}" "${_HDR_STAGE_DIR}"
"${_LIB_NAME}" "${_DIR}")
set(_HEADERS)
else()
@@ -287,7 +281,7 @@ macro(module)
install(FILES ${_ABS_HEADER_NAMES} DESTINATION
"include/${_HEADER_OUTPUT_DIR}")
set(_HDR_STAGE_DIR "${_HEADER_OUTPUT_DIR}")
- stage_headers("${_ABS_HEADER_NAMES}" "${_HDR_STAGE_DIR}"
+ stage_headers("${_HEADERS}" "${_HDR_STAGE_DIR}"
"${_LIB_NAME}" "")
endif()
endif()
@@ -415,7 +409,7 @@ macro(script)
if (NOT _ARG_INPUT)
message(FATAL_ERROR "script() can only substitute when INPUT is present.")
endif()
- substitute(IN_FILE ${_INPUT} OUT_FILE ${_ARG_NAME}
+ substitute(IN_FILE "${CMAKE_CURRENT_SOURCE_DIR}/${_INPUT}" OUT_FILE ${_ARG_NAME}
DICT ${_ARG_SUBSTITUTE})
endif()
install(FILES ${_ARG_NAME} DESTINATION ${_ARG_OUTPUT_DIR}
@@ -501,9 +495,9 @@ macro(pymod)
return()
endif()
if (_ARG_OUTPUT_DIR)
- set(PYMOD_DIR "openstructure/${_ARG_OUTPUT_DIR}")
+ set(PYMOD_DIR "python${PYTHON_VERSION}/site-packages/${_ARG_OUTPUT_DIR}")
else()
- set(PYMOD_DIR "openstructure/${_ARG_PREFIX}/${_ARG_NAME}")
+ set(PYMOD_DIR "python${PYTHON_VERSION}/site-packages/${_ARG_PREFIX}/${_ARG_NAME}")
endif()
set(_LIB_NAME ${_ARG_PREFIX}_${_ARG_NAME})
set(PYMOD_STAGE_DIR "${LIB_STAGE_PATH}/${PYMOD_DIR}")
@@ -600,7 +594,12 @@ macro(pymod)
if (_ARG_UI)
add_dependencies("${_LIB_NAME}_pymod" "${_LIB_NAME}_ui"})
endif()
- copy_if_different("./" "${PYMOD_STAGE_DIR}" "${_PY_FILES}" "TARGETS"
+ set(_ABS_PY_FILES)
+ set(_PY_SOURCE_DIR "${CMAKE_CURRENT_SOURCE_DIR}")
+ foreach(_PY ${_PY_FILES})
+ list(APPEND _ABS_PY_FILES "${_PY_SOURCE_DIR}/${_PY}")
+ endforeach()
+ copy_if_different("./" "${PYMOD_STAGE_DIR}" "${_ABS_PY_FILES}" "TARGETS"
"${_LIB_NAME}_pymod")
add_dependencies("_${_LIB_NAME}" "${_LIB_NAME}_pymod")
compile_py_files(_${_LIB_NAME} ${PYMOD_STAGE_DIR} ${_PY_FILES})
diff --git a/deployment/CMakeLists.txt b/deployment/CMakeLists.txt
index 96945a7a51098cc736114b57998297735b3ad3d6..1a55585477a522275cc23467e5a91f5e99fb984c 100644
--- a/deployment/CMakeLists.txt
+++ b/deployment/CMakeLists.txt
@@ -3,6 +3,6 @@
include(Deployment)
set(SUBST_DIC OST_VERSION="${OST_VERSION}")
add_custom_target(deploymnt ALL)
-substitute(IN_FILE README.html.in OUT_FILE README.html
+substitute(IN_FILE ${CMAKE_CURRENT_SOURCE_DIR}/README.html.in OUT_FILE README.html
DICT ${SUBST_DIC})
add_subdirectory(win)
diff --git a/deployment/macos/deps.py b/deployment/macos/deps.py
index 2693db881eac8a5c648019ae79d56c46846aa43a..91ef55c9ada53c569dcf76fde350f57f8161f9e6 100644
--- a/deployment/macos/deps.py
+++ b/deployment/macos/deps.py
@@ -27,7 +27,7 @@ def _deps_for_lib(lib, pool, recursive=True):
return
def collect_deps(stage_dir, components, binaries, libexec_binaries,
- site_packages, site_packages_dir):
+ site_packages, site_packages_dir, libexec_path='openstructure'):
"""
Collect the dependencies for the given components and returns a list of
frameworks/libraries that the component depends on.
@@ -239,7 +239,8 @@ def make_standalone(stage_dir, outdir, no_includes, force_no_rpath=False,
# when running in non-gui mode, we are most likely missing the boost
# python library. Let's add it to the list of dependencies by
# inspecting "_ost_base.so".
- _deps_for_lib(os.path.join(stage_dir, 'lib/openstructure/ost/_ost_base.so'),
+ 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'
copy_deps(deps, outdir)
@@ -249,8 +250,8 @@ def make_standalone(stage_dir, outdir, no_includes, force_no_rpath=False,
print 'copying binaries'
copy_binaries(stage_dir, outdir, binaries, scripts, 'bin')
print 'copying pymod'
- shutil.copytree(os.path.join(stage_dir, 'lib/openstructure'),
- os.path.join(outdir, 'lib/openstructure'))
+ shutil.copytree(os.path.join(stage_dir,pymod_dir),
+ os.path.join(outdir, pymod_dir))
copied_py_framework=False
non_std_python=False
if os.path.exists(os.path.join(outdir, 'lib/Python.framework')):
@@ -310,9 +311,9 @@ def make_standalone(stage_dir, outdir, no_includes, force_no_rpath=False,
for sp in SITE_PACKAGES:
src=get_python_module_path(sp)
if os.path.isdir(src):
- shutil.copytree(src, os.path.join(outdir, 'lib/openstructure', sp))
+ shutil.copytree(src, os.path.join(outdir, pymod_dir, sp))
else:
- shutil.copy(src, os.path.join(outdir, 'lib/openstructure', sp))
+ shutil.copy(src, os.path.join(outdir, pymod_dir, sp))
print 'updating link commands of python shared objects'
os.path.walk(os.path.join(outdir, 'lib'),
update_pymod_shared_objects,
diff --git a/deployment/macos/pack.py b/deployment/macos/pack.py
new file mode 100644
index 0000000000000000000000000000000000000000..d849446be5d0f2e01d2ff27bed4c958cf5e7d16d
--- /dev/null
+++ b/deployment/macos/pack.py
@@ -0,0 +1,357 @@
+"""
+deploy.py helps you package your code into a standalone application.
+
+for now, MacOS X and Linux are supported...
+"""
+import os
+import subprocess
+import shutil
+import sys
+import glob
+
+def _lib_name(component):
+ return 'lib%s.dylib' % component
+
+def _deps_for_lib(lib, pool, recursive=True):
+ if lib in pool:
+ return
+ otool=subprocess.Popen(['otool', '-L', lib], stdout=subprocess.PIPE)
+ output=otool.communicate()[0]
+ lines=output.split('\n')[1:]
+ for line in lines:
+ d=line.split(' ')[0].strip()
+ if len(d)>0:
+ if d==lib:
+ continue
+ if d not in pool:
+ if d.startswith('/System') or d.startswith('/usr/lib'):
+ continue
+ if recursive:
+ _deps_for_lib(d, pool)
+ pool.add(d)
+ return
+
+def collect_deps(stage_dir, components, binaries, libexec_binaries,
+ site_packages, site_packages_dir, libexec_path='openstructure'):
+ """
+ Collect the dependencies for the given components and returns a list of
+ frameworks/libraries that the component depends on.
+ """
+ pool=set()
+ for component in components:
+ 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'
+ if lib_name not in pool:
+ _deps_for_lib(lib_name, pool)
+ pool.add(lib_name)
+ for bin in 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'
+ continue
+ if bin_name not in pool:
+ _deps_for_lib(bin_name, pool)
+ for bin in 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'
+ 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
+ if not os.path.exists(full_path):
+ 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')):
+ _deps_for_lib(so_file, pool)
+ return pool
+
+LIBEXEC_SCRIPTS=['ost_config']
+LIBEXEC_BINARIES=[]
+GUI_LIBEXEC_BINARIES=['gosty']
+BINARIES=['ldt', 'chemdict_tool', 'tmalign', 'tmscore']
+GUI_BINARIES=[]
+GUI_COMPONENTS=['gfx', 'gui', 'info']
+COMPONENTS=['mol', 'geom', 'conop', 'seq_alg', 'seq',
+ 'img', 'img_alg', 'io', 'db', 'base']
+GUI_SCRIPTS=['dng']
+SCRIPTS=['ost']
+CHANGE_ID_RPATH='install_name_tool -id @rpath/%s %s'
+CHANGE_ID='install_name_tool -id @rpath/%s %s'
+CHANGE_LOAD_CMD_RPATH='install_name_tool -change %s @rpath/%s %s'
+CHANGE_LOAD_CMD='install_name_tool -change %s @executable_path/%s %s'
+ADD_RPATH='install_name_tool -add_rpath %s %s 2> /dev/null'
+SITE_PACKAGES=[]
+GUI_SITE_PACKAGES=['sip.so', 'sipconfig.py', 'sipdistutils.py', 'PyQt4']
+REMOVE_HEADERS='rm -rf `find %s/lib -type d -name Headers`'
+REMOVE_CURRENT='rm -rf `find %s/lib -type d -name Current`'
+# collect libs of non-standard libraries/frameworks we depend on
+
+def copy_binaries(stage_dir, outdir, binary_names, scripts, bin_dir,
+ append_bin=True):
+
+ exe_path=os.path.abspath(os.path.join(outdir, bin_dir))
+ for binary_name in binary_names:
+ if append_bin:
+ bin_name=os.path.join(stage_dir, bin_dir, binary_name)
+ else:
+ bin_name=os.path.join(stage_dir, binary_name)
+ if not os.path.exists(bin_name):
+ 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)
+ update_load_commands(dst_name, True, exe_path)
+ for script in scripts:
+ shutil.copy(os.path.join(stage_dir, bin_dir, script),
+ os.path.join(outdir,bin_dir, script))
+
+def split_framework_components(abs_path):
+ """
+ Splits the path pointing to a dynamic library within a framework
+
+ '/System/Frameworks/A.framework/Versions/4/A' =>
+ ['/System/Frameworks/A.framework', 'Versions/4/A']
+ """
+ parts=abs_path.split('/')
+ for i, s in enumerate(parts):
+ if s.endswith('.framework'):
+ lead=os.path.join('/', *parts[:i+1])
+ trail=os.path.join(*parts[i+1:])
+ return lead, trail
+
+def change_id(id, lib):
+ os.chmod(lib, 0666)
+ os.system(CHANGE_ID_RPATH % (id,lib))
+ os.chmod(lib, 0444)
+
+def update_load_commands(lib, exe, exe_path):
+ direct_deps=set()
+ _deps_for_lib(lib, direct_deps, recursive=False)
+ os.chmod(lib, 0666)
+ for direct_dep in direct_deps:
+ if direct_dep.endswith('.dylib'):
+ new_name=os.path.basename(direct_dep)
+ os.system(CHANGE_LOAD_CMD_RPATH % (direct_dep, new_name, lib))
+ else:
+ assert direct_dep.find('.framework/')>=0
+ framework_path, rel_path=split_framework_components(direct_dep)
+ framework_name=os.path.basename(framework_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)
+ else:
+ os.chmod(lib, 0444)
+
+def copy_deps(dependencies, outdir):
+ exe_path=os.path.join(outdir, 'bin')
+ for dep in dependencies:
+ if dep.endswith('.dylib'):
+ dst_name=os.path.join(outdir, 'lib', os.path.basename(dep))
+ if not os.path.exists(dep):
+ continue
+ if os.path.exists(dst_name):
+ continue
+ shutil.copy(dep, dst_name)
+ change_id(os.path.basename(dep), dst_name)
+ update_load_commands(dst_name, False, exe_path)
+ else:
+ assert dep.find('.framework/')>=0
+ framework_path, rel_path=split_framework_components(dep)
+ framework_name=os.path.basename(framework_path)
+ dst_name=os.path.join(outdir, 'lib', framework_name)
+ shutil.copytree(framework_path, dst_name)
+ change_id(os.path.join(dst_name, rel_path),
+ os.path.join(dst_name, rel_path))
+ os.unlink(os.path.join(dst_name, os.path.splitext(framework_name)[0]))
+ update_load_commands(os.path.join(dst_name, rel_path), False,
+ exe_path)
+
+def update_pymod_shared_objects(lib_path, path, files):
+ exe_path=os.path.abspath(os.path.join(lib_path, '../bin'))
+ for f in files:
+ if not os.path.exists(os.path.join(path, f)):
+ continue
+ base, ext=os.path.splitext(f)
+ if ext=='.so':
+ path_to_lib_path=os.path.relpath(lib_path, path)
+ abs_name=os.path.join(path, f)
+ os.system(ADD_RPATH % (path_to_lib_path, abs_name))
+ update_load_commands(abs_name, False, exe_path)
+ elif ext in ('.pyc', '.pyo'):
+ os.unlink(os.path.join(path, f))
+
+def merge_tree(src, dst):
+ """
+ Similar to shutil.copytree, but does not complain when the destination
+ directory already exists.
+ """
+ names = os.listdir(src)
+ if not os.path.exists(dst):
+ os.makedirs(dst)
+ errors = []
+ for name in names:
+ srcname = os.path.join(src, name)
+ dstname = os.path.join(dst, name)
+ try:
+ if os.path.islink(srcname):
+ linkto = os.readlink(srcname)
+ os.symlink(linkto, dstname)
+ elif os.path.isdir(srcname):
+ merge_tree(srcname, dstname)
+ else:
+ shutil.copy2(srcname, dstname)
+ except (IOError, os.error), why:
+ errors.append((srcname, dstname, str(why)))
+ except shutil.Error, err:
+ errors.extend(err.args[0])
+ try:
+ shutil.copystat(src, dst)
+ except OSError, 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
+
+def get_site_package_dir():
+ """
+ Get site-package directory of this python installation. This assumes
+ that ost was linked against the same version of Python (which is a very
+ reasonable thing to do, as this script is most likely run with ost).
+ """
+ for p in sys.path:
+ pattern='/site-packages'
+ index=p.find(pattern)
+ if index>=0:
+ return p[:index+len(pattern)]
+ raise RuntimeError("Couldn't determine site-packages location")
+
+def get_python_module_path(module):
+ for path in sys.path:
+ full_path=os.path.join(path, module)
+ if os.path.exists(full_path):
+ return full_path
+ return None
+
+
+def get_python_home():
+ """
+ Derive Python home by looking at the location of the os module
+ """
+ return os.path.dirname(sys.modules['os'].__file__)
+
+
+class Package(object):
+ def __init__(self, name, root_dir, binaries=[], scripts=[],
+ modules=[], libraries=[], libexec_dir=None, libexec_scripts=[]):
+ self.root_dir=root_dir
+ self.name=name
+ self.binaries=binaries
+ self.scripts=scripts
+ self.libraries=libraries
+ self.libexec_dir=libexec_dir
+ self.libexec_scripts=libexec_scripts
+ self.pymod_dir=os.path.join('lib', 'python%d.%d' % sys.version_info[0:2],
+ 'site-packages')
+ self.modules=modules
+ self.libexec_binaries=[]
+ self.site_packages=[]
+ self.site_packages_dir=''
+ def status(self, message):
+ print '%s: %s' % (self.name, message)
+
+ def _prepare_output_dir(self, output_dir):
+ """
+ Prepares the output directory structure, including lib, bin and an optional
+ libexec directory.
+ """
+ #if os.path.exists(output_dir):
+ # shutil.rmtree(output_dir)
+ if not os.path.exists(output_dir):
+ os.makedirs(output_dir)
+ if not os.path.exists(os.path.join(output_dir, 'bin')):
+ os.makedirs(os.path.join(output_dir, 'bin'))
+ if not os.path.exists(os.path.join(output_dir, 'lib')):
+ os.makedirs(os.path.join(output_dir, 'lib'))
+ 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
+ os.makedirs(out_exec_dir)
+ def _copy_site_packages(self, output_dir):
+ for sp in SITE_PACKAGES:
+ src=get_python_module_path(sp)
+ if os.path.isdir(src):
+ 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'
+ os.path.walk(os.path.join(output_dir, 'lib'),
+ update_pymod_shared_objects,
+ os.path.join(output_dir, 'lib'))
+
+ def ship(self, output_dir):
+ self._prepare_output_dir(output_dir)
+ if os.path.exists(os.path.join(self.root_dir, 'share')):
+ self.status('copying shared data files')
+ merge_tree(os.path.join(self.root_dir, 'share'),
+ os.path.join(output_dir, 'share'))
+ self.status('collecting dependencies')
+ deps=collect_deps(self.root_dir, self.libraries, self.binaries,
+ self.libexec_binaries, self.site_packages,
+ self.site_packages_dir)
+ # when running in non-gui mode, we are most likely missing the boost
+ # python library. Let's add it to the list of dependencies by
+ # inspecting "_ost_base.so".
+ pymod_dir='lib/python%d.%d/site-packages' % sys.version_info[0:2]
+ _deps_for_lib(os.path.join(self.root_dir, pymod_dir, 'ost/_ost_base.so'),
+ deps, recursive=False)
+ self.status('copying dependencies')
+ copy_deps(deps, output_dir)
+ if self.libexec_dir:
+ self.status('copying libexec binaries')
+ copy_binaries(self.root_dir, output_dir, self.libexec_binaries,
+ self.libexec_scripts,
+ os.path.join('libexec', self.libexec_dir))
+ self.status('copying binaries')
+ copy_binaries(self.root_dir, output_dir, self.binaries,
+ self.scripts, 'bin')
+ self.status('copying pymod')
+ merge_tree(os.path.join(self.root_dir,self.pymod_dir),
+ os.path.join(output_dir, self.pymod_dir))
+ self._copy_site_packages(output_dir)
+
+class OpenStructure(Package):
+ def __init__(self, stage_dir, minimal=True):
+ libs=['ost_mol', 'ost_geom', 'ost_conop', 'ost_seq_alg',
+ 'ost_io', 'ost_db', 'ost_base', 'ost_seq', 'ost_mol_alg']
+ super(OpenStructure, self).__init__('OpenStructure', stage_dir,
+ binaries=['ldt', 'chemdict_tool'],
+ libexec_scripts=['ost_config'],
+ scripts=['ost'],
+ libraries=libs,
+ libexec_dir='openstructure')
+
+class Qmean(Package):
+ def __init__(self, stage_dir):
+ super(Qmean, self).__init__('Qmean', stage_dir,
+ scripts=['qmean'],
+ libexec_scripts=['qmean_script.py'],
+ libexec_dir='qmean',
+ libraries=['qmean'])
+ost=OpenStructure('../../stage')
+qmean=Qmean('../../../../../qmean/stage')
+ost.ship('qmean')
+qmean.ship('qmean')
+
diff --git a/doc/conf/conf.py b/doc/conf/conf.py
index b2d284a53bf8f2843ea9a25b8b0828af9ccc2865..e87782b4c33be7d3f95160d365b9f600743470ad 100644
--- a/doc/conf/conf.py
+++ b/doc/conf/conf.py
@@ -13,13 +13,12 @@
import sys, os
-# If extensions (or modules to document with autodoc) are in another directory,
-# add these directories to sys.path here. If the directory is relative to the
-# documentation root, use os.path.abspath to make it absolute, like shown here.
+site_packs='python%d.%d/site-packages' % sys.version_info[0:2]
sys.path.append(os.path.join(os.path.abspath('../..'),
- 'stage/lib/openstructure'))
+ 'stage/lib', site_packs))
sys.path.append(os.path.join(os.path.abspath('../..'),
- 'stage/lib64/openstructure'))
+ 'stage/lib64', site_packs))
+print site_packs
import ost
# -- General configuration -----------------------------------------------------
diff --git a/examples/code_fragments/dokk/ligand.py b/examples/code_fragments/dokk/ligand.py
index 4fc297ebc0f961e1e7e13db2bd43f18b8fd8cdcf..2683aaddb139c60ea561964057774079c4c72cb7 100644
--- a/examples/code_fragments/dokk/ligand.py
+++ b/examples/code_fragments/dokk/ligand.py
@@ -100,7 +100,7 @@ class Ligand:
shift_vec = geom.Vec3(float(self.config.start["POSX"]),
float(self.config.start["POSY"]),
float(self.config.start["POSZ"]))
- transf = mol.Transform()
+ transf = geom.Transform()
transf.SetTrans(shift_vec)
edi.SetTransform(transf.GetMatrix())
self.RotateAxis(geom.Vec3(1,0,0), float(self.config.start["ROTX"]))
@@ -123,4 +123,4 @@ class Ligand:
if dot>0:
vec-=dot*p.GetNormal()
return vec
- return vec
\ No newline at end of file
+ return vec
diff --git a/examples/code_fragments/dokk/spnav_input.py b/examples/code_fragments/dokk/spnav_input.py
index e51798578ed9842c8d4a75ec8b22481d997fa426..6f1a9de953ef00196588011c823b3cfe5744096a 100644
--- a/examples/code_fragments/dokk/spnav_input.py
+++ b/examples/code_fragments/dokk/spnav_input.py
@@ -39,7 +39,7 @@ class SpnavInputDevice(QtCore.QObject):
def InputChanged(self, tx,ty,tz,rx,ry,rz):
if (not self._lock_input) and (self.level is not None):
ligand = self.level.ligand
- transf = mol.Transform()
+ transf = geom.Transform()
if(self.trans):
delta = geom.Vec3 ((tx/480.0)*self._trans_factor, (ty/480.0)*self._trans_factor, (-tz/480.0)*self._trans_factor)
transf.SetTrans(delta)
diff --git a/modules/geom/pymod/CMakeLists.txt b/modules/geom/pymod/CMakeLists.txt
index f79aeac4c2f9c8c127e28b0071c0ef502ba0ac38..5988cc95b1235d1b578e74b738469d002d3b2f0b 100644
--- a/modules/geom/pymod/CMakeLists.txt
+++ b/modules/geom/pymod/CMakeLists.txt
@@ -14,6 +14,7 @@ set(OST_GEOM_PYMOD_SOURCES
export_composite2_op.cc
export_composite3_op.cc
export_quat.cc
+ export_transform.cc
)
if (NOT ENABLE_STATIC)
diff --git a/modules/mol/base/pymod/export_transform.cc b/modules/geom/pymod/export_transform.cc
similarity index 91%
rename from modules/mol/base/pymod/export_transform.cc
rename to modules/geom/pymod/export_transform.cc
index 1dc8bdc16bb6df0ba9f55693ebd0866da449400e..b2f921246bd2b6bedc90fa786aaa58f58b045ac5 100644
--- a/modules/mol/base/pymod/export_transform.cc
+++ b/modules/geom/pymod/export_transform.cc
@@ -18,14 +18,10 @@
//------------------------------------------------------------------------------
#include <boost/python.hpp>
-#include <ost/mol/transform.hh>
-#if(OST_INFO_ENABLED)
-#include <ost/info/info.hh>
-#endif
+#include <ost/geom/transform.hh>
using namespace boost::python;
-using namespace ost;
-using namespace ost::mol;
+using namespace geom;
void export_Transform()
{
@@ -56,8 +52,4 @@ void export_Transform()
.def("ApplyZAxisTranslation",&Transform::ApplyZAxisTranslation)
.def("ApplyAxisRotation",&Transform::ApplyAxisRotation)
;
-#if(OST_INFO_ENABLED)
- def("TransformToInfo", &TransformToInfo);
- def("TransformFromInfo", &TransformFromInfo);
-#endif
}
diff --git a/modules/geom/pymod/wrap_geom.cc b/modules/geom/pymod/wrap_geom.cc
index 76bb7930057165463a426f60e133f15314b00618..14df2fa8b1fc2dbcff97f1f9913ca2861bc584e7 100644
--- a/modules/geom/pymod/wrap_geom.cc
+++ b/modules/geom/pymod/wrap_geom.cc
@@ -35,6 +35,7 @@ extern void export_Composite3();
extern void export_Composite2_op();
extern void export_Composite3_op();
extern void export_Quat();
+extern void export_Transform();
namespace details {
#if (defined(OST_STATIC_PROPERTY_WORKAROUND))
@@ -64,6 +65,7 @@ BOOST_PYTHON_MODULE(_ost_geom)
export_Composite2_op();
export_Composite3_op();
export_Quat();
+ export_Transform();
#if (defined(OST_STATIC_PROPERTY_WORKAROUND))
// workaround for a problem with boost python and python 2.6.3/4
diff --git a/modules/geom/src/CMakeLists.txt b/modules/geom/src/CMakeLists.txt
index b20b7d2439b5f58f2d5e2f936513fb4cda16dd8d..40f33282a196138eda009046a886606702360a9f 100644
--- a/modules/geom/src/CMakeLists.txt
+++ b/modules/geom/src/CMakeLists.txt
@@ -25,7 +25,7 @@ composite3_op.hh
aligned_cuboid.hh
vec_mat_predicates.hh
quat.hh
-
+transform.hh
point_cloud.hh
module_config.hh
)
@@ -43,6 +43,7 @@ composite3.cc
composite2_op.cc
composite3_op.cc
quat.cc
+transform.cc
aligned_cuboid.cc
point_cloud.cc
)
diff --git a/modules/geom/src/geom.hh b/modules/geom/src/geom.hh
index 138e8da92f7e78a45051f0123a4e6301c5ad9a6f..2bf028ab5b825a8a9eb100ba1c4d35e27626a640 100644
--- a/modules/geom/src/geom.hh
+++ b/modules/geom/src/geom.hh
@@ -29,5 +29,6 @@
#include "composite_op.hh"
#include "quat.hh"
#include "aligned_cuboid.hh"
+#include "transform.hh"
#endif
diff --git a/modules/mol/base/src/transform.cc b/modules/geom/src/transform.cc
similarity index 78%
rename from modules/mol/base/src/transform.cc
rename to modules/geom/src/transform.cc
index ba1e59258299ca1f6011ddc1ebe1582aafba222b..d2a07f6ab0a701d0194bdcd1a4d300f039017f1f 100644
--- a/modules/mol/base/src/transform.cc
+++ b/modules/geom/src/transform.cc
@@ -18,18 +18,13 @@
//------------------------------------------------------------------------------
#include <ost/config.hh>
-#if(OST_INFO_ENABLED)
-#include <ost/info/info.hh>
-#include <ost/info/geom_info_conversion.hh>
-#endif
#include <ost/log.hh>
-#include "transform.hh"
-
-namespace ost {
-using namespace geom;
+#include "transform.hh"
+#include "vecmat3_op.hh"
+#include "vecmat4_op.hh"
-namespace mol {
+namespace geom {
Transform::Transform():
rot_(Mat3(1,0,0, 0,1,0, 0,0,1)),
@@ -207,7 +202,7 @@ void Transform::update_tm()
try {
itm_ = Invert(tm_);
} catch (GeomException& e) {
- LOG_WARNING("caught GeomException in Transform::update_tm: " << e.what());
+ std::cerr << "caught GeomException in Transform::update_tm: " << e.what() << std::endl;
itm_=geom::Mat4();
}
}
@@ -221,36 +216,4 @@ void Transform::update_components()
trans_[2] = tm_(3,2);
}
-#if(OST_INFO_ENABLED)
-Transform TransformFromInfo(const info::InfoGroup& group)
-{
- if (!group.HasItem("center")) {
- throw info::InfoError("Error while loading transform from info: "
- "Group does not contain a center element");
- }
- if (!group.HasGroup("rotation")) {
- throw info::InfoError("Error while loading transform from info: "
- "Group does not contain a rotation element");
- }
- if (!group.HasItem("translation")) {
- throw info::InfoError("Error while loading transform from info: "
- "Group does not contain a translation element");
- }
- Transform tf;
- tf.SetCenter(group.GetItem("center").AsVector());
- tf.SetTrans(group.GetItem("translation").AsVector());
- tf.SetRot(info::Mat3FromInfo(group.GetGroup("rotation")));
- return tf;
-}
-
-void TransformToInfo(const Transform& transform, info::InfoGroup& group)
-{
- Transform tf;
- group.CreateItem("center", transform.GetCenter());
- group.CreateItem("translation", transform.GetTrans());
- info::InfoGroup rot=group.CreateGroup("rotation");
- info::Mat3ToInfo(transform.GetRot(), rot);
-}
-#endif
-
-}} // ns
+} // ns
diff --git a/modules/geom/src/transform.hh b/modules/geom/src/transform.hh
new file mode 100644
index 0000000000000000000000000000000000000000..997f763950d7f94a7f7c6df35ea11f210b40847d
--- /dev/null
+++ b/modules/geom/src/transform.hh
@@ -0,0 +1,100 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2011 by the OpenStructure authors
+//
+// This library is free 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
+//------------------------------------------------------------------------------
+#ifndef OST_GEOM_TRANSFORM_HH
+#define OST_GEOM_TRANSFORM_HH
+
+/*
+ Author: Ansgar Philippsen
+*/
+
+#include <ost/config.hh>
+
+#include "module_config.hh"
+#include "vec3.hh"
+#include "vec4.hh"
+#include "mat3.hh"
+#include "mat.hh"
+#include "aligned_cuboid.hh"
+
+namespace geom {
+
+/// \brief basic and essential transformation class, including translation,
+/// rotation and center of rotation
+class DLLEXPORT_OST_GEOM Transform {
+public:
+ Transform();
+
+ /// \brief retrieve transformation matrix
+ Mat4 GetMatrix() const {return tm_;}
+ /// \brief retrieve transposed transformation matrix
+ Mat4 GetTransposedMatrix() const {return ttm_;}
+ /// \brief retrieve inverted transformation matrix
+ Mat4 GetInvertedMatrix() const {return itm_;}
+
+ /// \brief set center of rotation
+ void SetCenter(const Vec3& c);
+ /// \brief retrieve center of rotation
+ Vec3 GetCenter() const;
+
+ // directly set tm, messing up rot/trans/cen !
+ void SetMatrix(const Mat4& m);
+
+ /// \name rotation
+ //@{
+ /// \brief rotate around x-axis
+ void ApplyXAxisRotation(float delta);
+ void ApplyYAxisRotation(float delta);
+ void ApplyZAxisRotation(float delta);
+ void ApplyAxisRotation(float delta, const Vec3& axis);
+
+ Mat3 GetXAxisRotation(float delta);
+ Mat3 GetYAxisRotation(float delta);
+ Mat3 GetZAxisRotation(float delta);
+
+ Mat3 GetRot() const;
+ void SetRot(const Mat3& r);
+ //@}
+ /// \brief translation
+ //@{
+ void ApplyXAxisTranslation(float delta);
+ void ApplyYAxisTranslation(float delta);
+ void ApplyZAxisTranslation(float delta);
+ void SetTrans(const Vec3& t);
+ Vec3 GetTrans() const;
+ //@}
+
+ Vec3 Apply(const Vec3& v) const;
+ Vec4 Apply(const Vec4& v) const;
+ AlignedCuboid Apply(const AlignedCuboid& c) const;
+
+private:
+ Mat3 rot_;
+ Vec3 trans_;
+ Vec3 cen_;
+ Mat4 tm_;
+ Mat4 ttm_;
+ Mat4 itm_;
+
+ void update_tm();
+ void update_components();
+};
+
+} // ns
+
+#endif
diff --git a/modules/geom/tests/CMakeLists.txt b/modules/geom/tests/CMakeLists.txt
index 027a167490b6256249a53a4cf1e569a237f3c8af..e4056c27878386828af14e91f2c56ee40e1566a6 100644
--- a/modules/geom/tests/CMakeLists.txt
+++ b/modules/geom/tests/CMakeLists.txt
@@ -11,6 +11,7 @@ set(GEOM_UNITTESTS
test_vec2.cc
test_vec3.cc
test_vec4.cc
+ test_transform.cc
tests.cc
test_geom.py
)
diff --git a/modules/mol/base/tests/test_transform.cc b/modules/geom/tests/test_transform.cc
similarity index 92%
rename from modules/mol/base/tests/test_transform.cc
rename to modules/geom/tests/test_transform.cc
index 5c950acc5a170448290be09dde71d76fad5e8e66..5f4a543fd8ecfa21c3a3ac78a0a4b88d24ee36f9 100644
--- a/modules/mol/base/tests/test_transform.cc
+++ b/modules/geom/tests/test_transform.cc
@@ -22,14 +22,11 @@
#define BOOST_TEST_DYN_LINK
#include <boost/test/unit_test.hpp>
#include <boost/test/auto_unit_test.hpp>
-#include <ost/mol/mol.hh>
-#include <ost/mol/transform.hh>
#include <ost/geom/geom.hh>
-using namespace ost;
-using namespace ost::mol;
+using namespace geom;
-BOOST_AUTO_TEST_SUITE( mol_base );
+BOOST_AUTO_TEST_SUITE( geom_base );
BOOST_AUTO_TEST_CASE(test_transform)
{
diff --git a/modules/gfx/pymod/CMakeLists.txt b/modules/gfx/pymod/CMakeLists.txt
index a3d8b251dda72f07f6e7394ad4fb3d0996fb4bd4..0ee14167c4f19232a7e4ecbdda746ab6c1b6a2a9 100644
--- a/modules/gfx/pymod/CMakeLists.txt
+++ b/modules/gfx/pymod/CMakeLists.txt
@@ -26,7 +26,7 @@ pymod(NAME gfx CPP ${OST_GFX_PYMOD_SOURCES} PY __init__.py py_gfx_obj.py)
set(GRADIENT_FILE
gradients.xml
)
-copy_if_different("./" "${STAGE_DIR}/share/openstructure/scene"
+copy_if_different("${CMAKE_CURRENT_SOURCE_DIR}" "${STAGE_DIR}/share/openstructure/scene"
"${GRADIENT_FILE}" "PRESET GRADIENTS" _ost_gfx)
install(FILES ${GRADIENT_FILE} DESTINATION "share/openstructure/scene")
\ No newline at end of file
diff --git a/modules/gfx/pymod/export_scene.cc b/modules/gfx/pymod/export_scene.cc
index 18728c2cf3feee60f5727efffd5a61c098f4151b..39d1fde6bde504a407dea60247b7cadf01fb5b8a 100644
--- a/modules/gfx/pymod/export_scene.cc
+++ b/modules/gfx/pymod/export_scene.cc
@@ -60,7 +60,7 @@ geom::AlignedCuboid scene_get_bb2(Scene* scene, bool use_tf)
return scene->GetBoundingBox(use_tf);
}
-geom::AlignedCuboid scene_get_bb3(Scene* scene, const mol::Transform& tf)
+geom::AlignedCuboid scene_get_bb3(Scene* scene, const geom::Transform& tf)
{
return scene->GetBoundingBox(tf);
}
diff --git a/modules/gfx/src/CMakeLists.txt b/modules/gfx/src/CMakeLists.txt
index 7a92969a95edb65706c9ecf012960c48eeae932e..57cf1601f715667068611be5abaa0559efaf7165 100644
--- a/modules/gfx/src/CMakeLists.txt
+++ b/modules/gfx/src/CMakeLists.txt
@@ -269,7 +269,7 @@ if (USE_SHADER)
shader/material_toon1.glsl
shader/material_toon2.glsl
)
- copy_if_different("./" "${SHARED_DATA_PATH}/shader" "${SHADER_FILES}"
+ copy_if_different("${CMAKE_CURRENT_SOURCE_DIR}" "${SHARED_DATA_PATH}/shader" "${SHADER_FILES}"
"SHADER_TARGETS" ost_gfx)
install(FILES ${SHADER_FILES} DESTINATION "share/openstructure/shader")
endif(USE_SHADER)
@@ -277,7 +277,7 @@ set(TEXTURE_FILES
test_texture.png
glyph_texture.png
)
-copy_if_different("./" "${SHARED_DATA_PATH}/textures" "${TEXTURE_FILES}"
+copy_if_different("${CMAKE_CURRENT_SOURCE_DIR}" "${SHARED_DATA_PATH}/textures" "${TEXTURE_FILES}"
"TEXTURE_TARGETS" ost_gfx)
install(FILES ${TEXTURE_FILES} DESTINATION "share/openstructure/textures")
diff --git a/modules/gfx/src/entity.cc b/modules/gfx/src/entity.cc
index 3aec22fe5eaee632938be7b74ba4bc97342db774..df1ad6bfc08fc8b9b7d421653eca750d7f0469cd 100644
--- a/modules/gfx/src/entity.cc
+++ b/modules/gfx/src/entity.cc
@@ -231,7 +231,7 @@ void Entity::Rebuild()
// update center in transformation
geom::Vec3 center=this->GetCenter();
- Transform tf=this->GetTF();
+ geom::Transform tf=this->GetTF();
tf.SetCenter(center);
tf.SetTrans(center+GetTF().GetTrans()-GetTF().GetCenter());
this->SetTF(tf);
diff --git a/modules/gfx/src/gfx_object.cc b/modules/gfx/src/gfx_object.cc
index d527ceffabf5b805535a0dc1c796cd74b82ab19b..f7e3b06a5af9a5b1962156db728b4556e331c98c 100644
--- a/modules/gfx/src/gfx_object.cc
+++ b/modules/gfx/src/gfx_object.cc
@@ -400,7 +400,7 @@ geom::AlignedCuboid GfxObj::GetBoundingBox(bool use_tf) const
}
void GfxObj::ProcessLimits(geom::Vec3& minc, geom::Vec3& maxc,
- const mol::Transform& tf) const
+ const geom::Transform& tf) const
{
try {
geom::AlignedCuboid coord_limits=tf.Apply(this->GetBoundingBox(true));
@@ -476,13 +476,13 @@ void GfxObj::OnInput(const InputEvent& e)
}
}
-const mol::Transform& GfxObj::GetTF() const
+const geom::Transform& GfxObj::GetTF() const
{
return transform_;
}
-void GfxObj::SetTF(const mol::Transform& tf)
+void GfxObj::SetTF(const geom::Transform& tf)
{
transform_=tf;
}
diff --git a/modules/gfx/src/gfx_object.hh b/modules/gfx/src/gfx_object.hh
index 8809e1046fe10d15c410bc51f86545cc1bc32cf1..fc906c35c9fdb7c563417c6785e5023d2dabe594 100644
--- a/modules/gfx/src/gfx_object.hh
+++ b/modules/gfx/src/gfx_object.hh
@@ -33,7 +33,7 @@
#include <ost/config.hh>
#include <ost/gfx/module_config.hh>
-#include <ost/mol/transform.hh>
+#include <ost/geom/transform.hh>
#include "gfx_object_fw.hh"
#include "gfx_object_base.hh"
@@ -123,7 +123,7 @@ public:
will be adjusted based on the Cuboid returned by GetBoundingBox(true)
*/
virtual void ProcessLimits(geom::Vec3& minc, geom::Vec3& maxc,
- const mol::Transform& tf) const;
+ const geom::Transform& tf) const;
// implemented in derived classes for the actual GL rendering
/*
@@ -168,9 +168,9 @@ public:
void Clear();
/// \brief get transform
- const mol::Transform& GetTF() const;
+ const geom::Transform& GetTF() const;
/// \brief set transform
- void SetTF(const mol::Transform& tf);
+ void SetTF(const geom::Transform& tf);
// add a label at the given position
void AddLabel(const String& s, const geom::Vec3& pos, const Color& col, float psize);
@@ -225,7 +225,7 @@ public:
RenderMode::Type render_mode_;
unsigned int debug_flags_;
- mol::Transform transform_;
+ geom::Transform transform_;
bool rebuild_;
bool refresh_;
float line_width_;
diff --git a/modules/gfx/src/impl/entity_detail.cc b/modules/gfx/src/impl/entity_detail.cc
index 02e40b2138edee1e989c80a6680fee04fedbc897..407654cfcfa514cc379a240ac1a68bc6d131a077 100644
--- a/modules/gfx/src/impl/entity_detail.cc
+++ b/modules/gfx/src/impl/entity_detail.cc
@@ -57,7 +57,7 @@ void DoRenderBlur(BondEntryList& bl, float bf1, float bf2)
{
// add blur for this particular orientation!
// don't use vertex array, but on-the-fly oriented and z-sorted quads
- mol::Transform tf = Scene::Instance().GetTransform();
+ geom::Transform tf = Scene::Instance().GetTransform();
std::vector<BlurQuadEntry> bql;
for (BondEntryList::iterator it=bl.begin(); it!=bl.end();++it) {
diff --git a/modules/gfx/src/impl/scene_fx.cc b/modules/gfx/src/impl/scene_fx.cc
index 8979d96441fc5367ec6cf223266654949683bee4..de0000484bf41a13d91220a312e54013ac643922 100644
--- a/modules/gfx/src/impl/scene_fx.cc
+++ b/modules/gfx/src/impl/scene_fx.cc
@@ -406,7 +406,7 @@ void SceneFX::prep_shadow_map()
#endif
// modelview transform for the lightsource pov
- mol::Transform ltrans(Scene::Instance().GetTransform());
+ geom::Transform ltrans(Scene::Instance().GetTransform());
ltrans.SetRot(Scene::Instance().GetLightRot()*ltrans.GetRot());
// calculate encompassing box for ortho projection
diff --git a/modules/gfx/src/map_iso.cc b/modules/gfx/src/map_iso.cc
index 5dbd4d3907c57964a3b21c0d9183e3e1917ccf2e..7a2c5160c435badb6bd25267759c6fd9a119ebed 100644
--- a/modules/gfx/src/map_iso.cc
+++ b/modules/gfx/src/map_iso.cc
@@ -86,7 +86,7 @@ MapIso::MapIso(const String& name, const img::MapHandle& mh,
SetMatDiff(Color(1,1,1));
SetMatSpec(Color(0.1,0.1,0.1));
SetMatShin(32);
- mol::Transform tf=this->GetTF();
+ geom::Transform tf=this->GetTF();
tf.SetCenter(this->GetCenter());
tf.SetTrans(this->GetCenter());
this->SetTF(tf);
diff --git a/modules/gfx/src/povray.hh b/modules/gfx/src/povray.hh
index b647420a148964a96a26abe3b73b264b74316116..c8ef79461b8380c9c870d547fe1f6e26b180d0eb 100644
--- a/modules/gfx/src/povray.hh
+++ b/modules/gfx/src/povray.hh
@@ -26,7 +26,7 @@
#include <string>
#include <fstream>
-#include <ost/mol/transform.hh>
+#include <ost/geom/transform.hh>
#include "color.hh"
@@ -63,7 +63,7 @@ public:
public:
bool use_tf;
- mol::Transform tf;
+ geom::Transform tf;
private:
std::string pov_file_;
diff --git a/modules/gfx/src/prim_list.cc b/modules/gfx/src/prim_list.cc
index b531ba2796a597b8e8eb9d171c6a49d9d87a1e42..e07820e6bc6c15af276b8a7012baa21b00545eb3 100644
--- a/modules/gfx/src/prim_list.cc
+++ b/modules/gfx/src/prim_list.cc
@@ -65,12 +65,12 @@ geom::AlignedCuboid PrimList::GetBoundingBox() const
geom::Vec3 maxc(-std::numeric_limits<float>::max(),
-std::numeric_limits<float>::max(),
-std::numeric_limits<float>::max());
- ProcessLimits(minc,maxc,mol::Transform());
+ ProcessLimits(minc,maxc,geom::Transform());
return geom::AlignedCuboid(minc,maxc);
}
void PrimList::ProcessLimits(geom::Vec3& minc, geom::Vec3& maxc,
- const mol::Transform& tf) const
+ const geom::Transform& tf) const
{
for(SpherePrimList::const_iterator it=points_.begin();it!=points_.end();++it) {
geom::Vec3 tpos = tf.Apply(it->position);
diff --git a/modules/gfx/src/prim_list.hh b/modules/gfx/src/prim_list.hh
index 395e53e2ad22ce359b37281caead22cad1a423e9..afc999a7febc930495d2f7620c7795295293be42 100644
--- a/modules/gfx/src/prim_list.hh
+++ b/modules/gfx/src/prim_list.hh
@@ -64,7 +64,7 @@ class DLLEXPORT_OST_GFX PrimList: public GfxObj
virtual geom::AlignedCuboid GetBoundingBox() const;
virtual void ProcessLimits(geom::Vec3& minc, geom::Vec3& maxc,
- const mol::Transform& tf) const;
+ const geom::Transform& tf) const;
/// \brief get center
virtual geom::Vec3 GetCenter() const;
diff --git a/modules/gfx/src/scene.cc b/modules/gfx/src/scene.cc
index fde6ad665d0ce3537bf9c97d5e3d26d1055bb62a..2650eea5b09f5169bee74a9e984437573619aa3c 100644
--- a/modules/gfx/src/scene.cc
+++ b/modules/gfx/src/scene.cc
@@ -699,13 +699,13 @@ float Scene::GetDefaultTextSize()
namespace {
-void draw_lightdir(const Vec3& ldir, const mol::Transform& tf)
+void draw_lightdir(const Vec3& ldir, const geom::Transform& tf)
{
glPushAttrib(GL_ENABLE_BIT);
glMatrixMode(GL_MODELVIEW);
glPushMatrix();
glLoadIdentity();
- mol::Transform tmpt(tf);
+ geom::Transform tmpt(tf);
tmpt.SetRot(Mat3::Identity());
glMultMatrix(tmpt.GetTransposedMatrix().Data());
glDisable(GL_NORMALIZE);
@@ -1216,7 +1216,7 @@ namespace {
class BBCalc: public GfxNodeVisitor
{
public:
- BBCalc(const geom::Vec3& mmin, const geom::Vec3& mmax, const mol::Transform& tf):
+ BBCalc(const geom::Vec3& mmin, const geom::Vec3& mmax, const geom::Transform& tf):
minc(mmin),maxc(mmax),tf(tf),valid(false) {}
bool VisitNode(GfxNode* node, const Stack& st) {
@@ -1235,7 +1235,7 @@ public:
}
Vec3 minc,maxc;
- mol::Transform tf;
+ geom::Transform tf;
bool valid;
};
@@ -1243,10 +1243,10 @@ public:
geom::AlignedCuboid Scene::GetBoundingBox(bool use_tf) const
{
- return GetBoundingBox(use_tf ? transform_ : mol::Transform());
+ return GetBoundingBox(use_tf ? transform_ : geom::Transform());
}
-geom::AlignedCuboid Scene::GetBoundingBox(const mol::Transform& tf) const
+geom::AlignedCuboid Scene::GetBoundingBox(const geom::Transform& tf) const
{
BBCalc bbcalc(Vec3(std::numeric_limits<float>::max(),
std::numeric_limits<float>::max(),
@@ -1264,12 +1264,12 @@ geom::AlignedCuboid Scene::GetBoundingBox(const mol::Transform& tf) const
return geom::AlignedCuboid(geom::Vec3(),geom::Vec3());
}
-mol::Transform Scene::GetTransform() const
+geom::Transform Scene::GetTransform() const
{
return transform_;
}
-void Scene::SetTransform(const mol::Transform& t)
+void Scene::SetTransform(const geom::Transform& t)
{
transform_=t;
this->RequestRedraw();
@@ -1721,7 +1721,7 @@ public:
}
}
Vec3 minc,maxc;
- mol::Transform transform;
+ geom::Transform transform;
bool valid;
};
diff --git a/modules/gfx/src/scene.hh b/modules/gfx/src/scene.hh
index 62630ced64dd95afd7b36957e2a97d6f35a3ba61..4edc6663770bbdb3c047382f04e925474bd06baf 100644
--- a/modules/gfx/src/scene.hh
+++ b/modules/gfx/src/scene.hh
@@ -30,7 +30,7 @@
#include <boost/shared_array.hpp>
#include <ost/gfx/module_config.hh>
-#include <ost/mol/transform.hh>
+#include <ost/geom/transform.hh>
#include <ost/mol/atom_handle.hh>
#include "gl_include.hh"
@@ -84,7 +84,7 @@ class DLLEXPORT_OST_GFX Scene {
// refactoring of the scene it into a management
// and a view part
struct SceneViewStackEntry {
- mol::Transform transform;
+ geom::Transform transform;
float fov;
float znear,zfar;
};
@@ -363,13 +363,13 @@ class DLLEXPORT_OST_GFX Scene {
geom::AlignedCuboid GetBoundingBox(bool use_tf=true) const;
/// \brief return bounding box of with a given transform
- geom::AlignedCuboid GetBoundingBox(const mol::Transform& tf) const;
+ geom::AlignedCuboid GetBoundingBox(const geom::Transform& tf) const;
/// \brief get full underlying transformation
- mol::Transform GetTransform() const;
+ geom::Transform GetTransform() const;
/// \brief set transform
- void SetTransform(const mol::Transform& t);
+ void SetTransform(const geom::Transform& t);
/// \brief returns a compact, internal representation of the scene orientation
geom::Mat4 GetRTC() const;
@@ -513,7 +513,7 @@ private:
mutable GfxNodeP root_node_; // mutable is slightly hackish
SceneObserverList observers_;
- mol::Transform transform_; // overall modelview transformation
+ geom::Transform transform_; // overall modelview transformation
bool gl_init_;
diff --git a/modules/gui/pymod/CMakeLists.txt b/modules/gui/pymod/CMakeLists.txt
index cf4ea93cd6db34bc3764c2132c0836266f2ddc9c..4ac7f7cfe75a5fe6a0e843a4389e64e02e8228ed 100644
--- a/modules/gui/pymod/CMakeLists.txt
+++ b/modules/gui/pymod/CMakeLists.txt
@@ -105,7 +105,7 @@ set(PRESET_FILES
scene/presets.xml
scene/loaders.xml
)
-copy_if_different("./" "${STAGE_DIR}/share/openstructure/scene"
+copy_if_different("${CMAKE_CURRENT_SOURCE_DIR}" "${STAGE_DIR}/share/openstructure/scene"
"${PRESET_FILES}" "IMMUTABLE_FILES" _ost_gui)
install(FILES ${PRESET_FILES} DESTINATION "share/openstructure/scene")
@@ -115,7 +115,7 @@ set(INSPECTOR_ICONS
scene/icons/render_icon.png
scene/icons/tool_icon.png
)
-copy_if_different("./" "${STAGE_DIR}/share/openstructure/scene/icons"
+copy_if_different("${CMAKE_CURRENT_SOURCE_DIR}" "${STAGE_DIR}/share/openstructure/scene/icons"
"${INSPECTOR_ICONS}" "ICONS_FOR_INSPECTOR" _ost_gui)
install(FILES ${INSPECTOR_ICONS} DESTINATION "share/openstructure/scene/icons")
diff --git a/modules/gui/share/CMakeLists.txt b/modules/gui/share/CMakeLists.txt
index 816af7f807240d1d363ada12768a7d9d6c8f1f37..de3daf8d83caa584ae0cd072ae6aeefb8ffa4b2e 100644
--- a/modules/gui/share/CMakeLists.txt
+++ b/modules/gui/share/CMakeLists.txt
@@ -23,11 +23,11 @@ set(GUI_IMAGES
)
add_custom_target(scene_icons ALL)
-copy_if_different("./" "${STAGE_DIR}/share/openstructure/gui/icons"
+copy_if_different("${CMAKE_CURRENT_SOURCE_DIR}" "${STAGE_DIR}/share/openstructure/gui/icons"
"${GUI_ICONS}" "ICONS_FOR_GUI" scene_icons)
install(FILES ${GUI_ICONS} DESTINATION "share/openstructure/gui/icons")
add_custom_target(gui_images ALL)
-copy_if_different("./" "${STAGE_DIR}/share/openstructure/gui/images"
+copy_if_different("${CMAKE_CURRENT_SOURCE_DIR}" "${STAGE_DIR}/share/openstructure/gui/images"
"${GUI_IMAGES}" "IMAGES_FOR_GUI" gui_images)
install(FILES ${GUI_IMAGES} DESTINATION "share/openstructure/gui/images")
\ No newline at end of file
diff --git a/modules/gui/src/dock_widget.cc b/modules/gui/src/dock_widget.cc
index 9ba553ca55d551e6c669150cf222e7e9967df800..53b7d7ea70f32d44f965a0f1d65de3029ebc3c1a 100644
--- a/modules/gui/src/dock_widget.cc
+++ b/modules/gui/src/dock_widget.cc
@@ -35,4 +35,4 @@ void DockWidget::closeEvent(QCloseEvent* e)
emit OnClose(this);
}
-}} // ns
\ No newline at end of file
+}} // ns
diff --git a/modules/gui/src/gosty.cc b/modules/gui/src/gosty.cc
index 49750b9dca33c65e927d52dad461d5973b96fc80..670c454c1886f0c1c2013954d3996a38060781b6 100644
--- a/modules/gui/src/gosty.cc
+++ b/modules/gui/src/gosty.cc
@@ -108,13 +108,20 @@ String get_ost_root()
void setup_python_search_path(const String& root, PythonInterpreter& pi)
{
+ std::stringstream site_pkgs;
+ site_pkgs << "python" << PY_MAJOR_VERSION << "." << PY_MINOR_VERSION;
#ifdef _MSC_VER
- pi.AppendModulePath(QString::fromStdString(root+"\\lib\\openstructure"));
+ pi.AppendModulePath(QString::fromStdString(root+"\\lib\\"+site_pkgs.str()
+ +"\\site-packages"));
#else
# if (defined(__ppc64__) || defined(__x86_64__)) && !defined(__APPLE__)
- pi.AppendModulePath(QString::fromStdString(root+"/lib64/openstructure"));
+ pi.AppendModulePath(QString::fromStdString(root+"/lib64/"+
+ site_pkgs.str()+
+ "site-packages"));
# else
- pi.AppendModulePath(QString::fromStdString(root+"/lib/openstructure"));
+ pi.AppendModulePath(QString::fromStdString(root+"/lib/"+
+ site_pkgs.str()+
+ "/site-packages"));
# endif
#endif
pi.AppendModulePath(".");
diff --git a/modules/gui/src/tools/map_tool.cc b/modules/gui/src/tools/map_tool.cc
index e16895621fabc2ca32c2797dd395a00fc8b936af..96e622a3d39b914a37f6e2c87a9ec0ddcfeb72ee 100644
--- a/modules/gui/src/tools/map_tool.cc
+++ b/modules/gui/src/tools/map_tool.cc
@@ -56,7 +56,7 @@ void MapTool::MouseMove(const MouseEvent& event)
gfx::Scene::Instance().StatusMessage(s.str());
}
} else if(gfx::MapSlab* ms = dynamic_cast<gfx::MapSlab*>(np.get())) {
- mol::Transform tf = gfx::Scene::Instance().GetTransform();
+ geom::Transform tf = gfx::Scene::Instance().GetTransform();
geom::Plane plane = ms->GetPlane();
if(event.GetButtons()==MouseEvent::LeftButton) {
if (event.IsShiftPressed()) {
diff --git a/modules/img/alg/pymod/wrap_alg.cc b/modules/img/alg/pymod/wrap_alg.cc
index c141fe11310076374194677f601e98a1929eb446..7185f34021a1b70e7f6a8f380896ec7feeafcdc6 100644
--- a/modules/img/alg/pymod/wrap_alg.cc
+++ b/modules/img/alg/pymod/wrap_alg.cc
@@ -54,7 +54,7 @@
using namespace ost;
using namespace ost::img;
-using namespace ost::img::alg;
+//using namespace ost::img::alg;
using namespace boost::python;
// fw decl
@@ -63,11 +63,8 @@ void export_Normalizer();
void export_Transcendentals();
void export_Polar();
-using namespace ost::img;
-using namespace ost::img::alg;
-
namespace {
-list get_histo_bins(const Histogram& hist) {
+list get_histo_bins(const alg::Histogram& hist) {
list result;
const std::vector<int>& bins = hist.GetBins();
for(std::vector<int>::const_iterator it=bins.begin();it!=bins.end();++it) {
@@ -76,32 +73,32 @@ list get_histo_bins(const Histogram& hist) {
return result;
}
-void frac_shift0(FractionalShift* s)
+void frac_shift0(alg::FractionalShift* s)
{
s->SetShift();
}
-void frac_shift1(FractionalShift* s, Real sx)
+void frac_shift1(alg::FractionalShift* s, Real sx)
{
s->SetShift(sx);
}
-void frac_shift2(FractionalShift* s, Real sx, Real sy)
+void frac_shift2(alg::FractionalShift* s, Real sx, Real sy)
{
s->SetShift(sx,sy);
}
-void frac_shift3(FractionalShift* s, Real sx, Real sy, Real sz)
+void frac_shift3(alg::FractionalShift* s, Real sx, Real sy, Real sz)
{
s->SetShift(sx,sy,sz);
}
-void frac_shift4(FractionalShift* s, const Vec2& v)
+void frac_shift4(alg::FractionalShift* s, const Vec2& v)
{
s->SetShift(v);
}
-void frac_shift5(FractionalShift* s, const Vec3& v)
+void frac_shift5(alg::FractionalShift* s, const Vec3& v)
{
s->SetShift(v);
}
@@ -109,7 +106,7 @@ void frac_shift5(FractionalShift* s, const Vec3& v)
Real real_spatial_cross_correlation_1(const ConstImageHandle& image1,
const ConstImageHandle& image2)
{
- return RealSpatialCrossCorrelation(image1,image2);
+ return alg::RealSpatialCrossCorrelation(image1,image2);
}
@@ -117,94 +114,94 @@ Real real_spatial_cross_correlation_2(const ConstImageHandle& image1,
const ConstImageHandle& image2,
const Extent& extent)
{
- return RealSpatialCrossCorrelation(image1,image2,extent);
+ return alg::RealSpatialCrossCorrelation(image1,image2,extent);
}
} //anon ns
BOOST_PYTHON_MODULE(_ost_img_alg)
{
- class_<AutoCorrelate, bases<ConstModOPAlgorithm> >("AutoCorrelate",init<>());
+ class_<alg::AutoCorrelate, bases<ConstModOPAlgorithm> >("AutoCorrelate",init<>());
- class_<Clear,bases<ConstModIPAlgorithm> >("Clear", init<>());
+ class_<alg::Clear,bases<ConstModIPAlgorithm> >("Clear", init<>());
- class_<Conj,bases<ConstModIPAlgorithm> >("Conj", init<>());
+ class_<alg::Conj,bases<ConstModIPAlgorithm> >("Conj", init<>());
- class_<ExplicitConvolute,bases<ConstModOPAlgorithm> >("ExplicitConvolute", init<const ConstImageHandle&,optional<bool> >());
+ class_<alg::ExplicitConvolute,bases<ConstModOPAlgorithm> >("ExplicitConvolute", init<const ConstImageHandle&,optional<bool> >());
- class_<ExplicitCorrelate,bases<ConstModOPAlgorithm> >("ExplicitCorrelate", init<const ConstImageHandle&>());
+ class_<alg::ExplicitCorrelate,bases<ConstModOPAlgorithm> >("ExplicitCorrelate", init<const ConstImageHandle&>());
- class_<CrossCorrelate,bases<ConstModIPAlgorithm> >("CrossCorrelate", init<const ConstImageHandle&>());
+ class_<alg::CrossCorrelate,bases<ConstModIPAlgorithm> >("CrossCorrelate", init<const ConstImageHandle&>());
- class_<DFT,bases<ConstModOPAlgorithm> >("DFT", init<>());
+ class_<alg::DFT,bases<ConstModOPAlgorithm> >("DFT", init<>());
- class_<FFT,bases<ConstModOPAlgorithm> >("FFT", init<>());
+ class_<alg::FFT,bases<ConstModOPAlgorithm> >("FFT", init<>());
- class_<PowerSpectrum,bases<ConstModOPAlgorithm> >("PowerSpectrum",init<>());
+ class_<alg::PowerSpectrum,bases<ConstModOPAlgorithm> >("PowerSpectrum",init<>());
- class_<Fill,bases<ConstModIPAlgorithm> >("Fill", init<const Complex&>())
+ class_<alg::Fill,bases<ConstModIPAlgorithm> >("Fill", init<const Complex&>())
.def(init<Real>())
;
- class_<Threshold,bases<ConstModIPAlgorithm> >("Threshold", init<const Complex&>())
+ class_<alg::Threshold,bases<ConstModIPAlgorithm> >("Threshold", init<const Complex&>())
.def(init<Real>())
;
- class_<DensitySlice,bases<ConstModIPAlgorithm> >("DensitySlice",
+ class_<alg::DensitySlice,bases<ConstModIPAlgorithm> >("DensitySlice",
init<const Complex&,const Complex&>())
.def(init<Real,Real>())
;
- class_<ClipMinMax,bases<ConstModIPAlgorithm> >("ClipMinMax",
+ class_<alg::ClipMinMax,bases<ConstModIPAlgorithm> >("ClipMinMax",
init<const Complex&,const Complex&>())
.def(init<Real,Real>())
;
- class_<Histogram, bases<NonModAlgorithm> >("Histogram", init<int,Real,Real>() )
+ class_<alg::Histogram, bases<NonModAlgorithm> >("Histogram", init<int,Real,Real>() )
.def("GetBins",get_histo_bins)
;
- class_<Negate,bases<ConstModIPAlgorithm> >("Negate", init<>());
-
- class_<Stat, bases<NonModAlgorithm> >("Stat", init<>() )
- .def("GetMean",&Stat::GetMean)
- .def("SetMean",&Stat::SetMean)
- .def("GetMinimum",&Stat::GetMinimum)
- .def("GetMinimumPosition",&Stat::GetMinimumPosition)
- .def("SetMinimum",&Stat::SetMinimum)
- .def("GetMaximum",&Stat::GetMaximum)
- .def("GetMaximumPosition",&Stat::GetMaximumPosition)
- .def("SetMaximum",&Stat::SetMaximum)
- .def("GetSum",&Stat::GetSum)
- .def("GetRootMeanSquare",&Stat::GetRootMeanSquare)
- .def("GetSkewness",&Stat::GetSkewness)
- .def("GetKurtosis",&Stat::GetKurtosis)
- .def("GetVariance",&Stat::GetVariance)
- .def("SetVariance",&Stat::SetVariance)
- .def("GetStandardDeviation",&Stat::GetStandardDeviation)
- .def("SetStandardDeviation",&Stat::SetStandardDeviation)
- .def("GetCenterOfMass",&Stat::GetCenterOfMass)
+ class_<alg::Negate,bases<ConstModIPAlgorithm> >("Negate", init<>());
+
+ class_<alg::Stat, bases<NonModAlgorithm> >("Stat", init<>() )
+ .def("GetMean",&alg::Stat::GetMean)
+ .def("SetMean",&alg::Stat::SetMean)
+ .def("GetMinimum",&alg::Stat::GetMinimum)
+ .def("GetMinimumPosition",&alg::Stat::GetMinimumPosition)
+ .def("SetMinimum",&alg::Stat::SetMinimum)
+ .def("GetMaximum",&alg::Stat::GetMaximum)
+ .def("GetMaximumPosition",&alg::Stat::GetMaximumPosition)
+ .def("SetMaximum",&alg::Stat::SetMaximum)
+ .def("GetSum",&alg::Stat::GetSum)
+ .def("GetRootMeanSquare",&alg::Stat::GetRootMeanSquare)
+ .def("GetSkewness",&alg::Stat::GetSkewness)
+ .def("GetKurtosis",&alg::Stat::GetKurtosis)
+ .def("GetVariance",&alg::Stat::GetVariance)
+ .def("SetVariance",&alg::Stat::SetVariance)
+ .def("GetStandardDeviation",&alg::Stat::GetStandardDeviation)
+ .def("SetStandardDeviation",&alg::Stat::SetStandardDeviation)
+ .def("GetCenterOfMass",&alg::Stat::GetCenterOfMass)
.def(self_ns::str(self))
;
- class_<StatMinMax, bases<NonModAlgorithm> >("StatMinMax", init<>() )
- .def("GetMinimum",&StatMinMax::GetMinimum)
- .def("GetMinimumPosition",&StatMinMax::GetMinimumPosition)
- .def("SetMinimum",&StatMinMax::SetMinimum)
- .def("GetMaximum",&StatMinMax::GetMaximum)
- .def("GetMaximumPosition",&StatMinMax::GetMaximumPosition)
- .def("SetMaximum",&StatMinMax::SetMaximum)
+ class_<alg::StatMinMax, bases<NonModAlgorithm> >("StatMinMax", init<>() )
+ .def("GetMinimum",&alg::StatMinMax::GetMinimum)
+ .def("GetMinimumPosition",&alg::StatMinMax::GetMinimumPosition)
+ .def("SetMinimum",&alg::StatMinMax::SetMinimum)
+ .def("GetMaximum",&alg::StatMinMax::GetMaximum)
+ .def("GetMaximumPosition",&alg::StatMinMax::GetMaximumPosition)
+ .def("SetMaximum",&alg::StatMinMax::SetMaximum)
.def(self_ns::str(self))
;
- class_<Randomize,bases<ConstModIPAlgorithm> >("Randomize", init<>());
+ class_<alg::Randomize,bases<ConstModIPAlgorithm> >("Randomize", init<>());
- class_<MaskImage, bases<ConstModIPAlgorithm> >("MaskImage",init<const MaskPtr&,optional<bool> >())
+ class_<alg::MaskImage, bases<ConstModIPAlgorithm> >("MaskImage",init<const MaskPtr&,optional<bool> >())
;
- class_<SmoothMaskImage, bases<ModIPAlgorithm> >("SmoothMaskImage",init<const MaskPtr&, Real, optional<bool> >())
+ class_<alg::SmoothMaskImage, bases<ModIPAlgorithm> >("SmoothMaskImage",init<const MaskPtr&, Real, optional<bool> >())
;
- class_<LocalSigmaThreshold, bases<ConstModOPAlgorithm> >("LocalSigmaThreshold", init<int,Real>() );
+ class_<alg::LocalSigmaThreshold, bases<ConstModOPAlgorithm> >("LocalSigmaThreshold", init<int,Real>() );
export_Filter();
export_Normalizer();
@@ -212,34 +209,34 @@ BOOST_PYTHON_MODULE(_ost_img_alg)
export_Transcendentals();
- class_<Transformation>("Transformation", init<>())
+ class_<alg::Transformation>("Transformation", init<>())
.def(init<const Mat4&>())
.def(init<const Mat4&, const Mat4&>())
;
- class_<Rotate2D, bases<Transformation> >("Rotate2D", init<Real>() );
- class_<Rotate2D90, bases<Transformation> >("Rotate2D90", init<int>() );
- class_<Scale, bases<Transformation> >("Scale", init<Real>() );
- class_<Translate, bases<Transformation> >("Translate", init<const Vec3&>() );
+ class_<alg::Rotate2D, bases<alg::Transformation> >("Rotate2D", init<Real>() );
+ class_<alg::Rotate2D90, bases<alg::Transformation> >("Rotate2D90", init<int>() );
+ class_<alg::Scale, bases<alg::Transformation> >("Scale", init<Real>() );
+ class_<alg::Translate, bases<alg::Transformation> >("Translate", init<const Vec3&>() );
- class_<Transform,bases<ConstModOPAlgorithm> >("Transform",init<>())
- .def(init<const Transformation&, optional<const Vec3&> >())
+ class_<alg::Transform,bases<ConstModOPAlgorithm> >("Transform",init<>())
+ .def(init<const alg::Transformation&, optional<const Vec3&> >())
;
- class_<Shift,bases<ConstModOPAlgorithm> >("Shift",init<>())
+ class_<alg::Shift,bases<ConstModOPAlgorithm> >("Shift",init<>())
.def(init<const Point&>())
;
- class_<Mirror,bases<ConstModOPAlgorithm> >("Mirror",init<>())
+ class_<alg::Mirror,bases<ConstModOPAlgorithm> >("Mirror",init<>())
.def(init<int>())
;
- class_<DiscreteShrink, bases<ConstModOPAlgorithm> >("DiscreteShrink",init<optional<const Size&> >())
- .def("SetBlocksize",&DiscreteShrink::SetBlocksize)
- .def("GetBlocksize",&DiscreteShrink::GetBlocksize)
+ class_<alg::DiscreteShrink, bases<ConstModOPAlgorithm> >("DiscreteShrink",init<optional<const Size&> >())
+ .def("SetBlocksize",&alg::DiscreteShrink::SetBlocksize)
+ .def("GetBlocksize",&alg::DiscreteShrink::GetBlocksize)
;
- class_<FractionalShift, bases<ModIPAlgorithm> >("FractionalShift", init<optional <Real,Real,Real> >() )
+ class_<alg::FractionalShift, bases<ModIPAlgorithm> >("FractionalShift", init<optional <Real,Real,Real> >() )
.def(init<const Vec3&>())
.def("SetShift",frac_shift0)
.def("SetShift",frac_shift1)
@@ -247,22 +244,22 @@ BOOST_PYTHON_MODULE(_ost_img_alg)
.def("SetShift",frac_shift3)
.def("SetShift",frac_shift4)
.def("SetShift",frac_shift5)
- .def("GetShift",&FractionalShift::GetShift)
+ .def("GetShift",&alg::FractionalShift::GetShift)
;
- class_<LineAverage, bases<ConstModOPAlgorithm> >("LineAverage", init<>() )
+ class_<alg::LineAverage, bases<ConstModOPAlgorithm> >("LineAverage", init<>() )
.def(init<unsigned int>())
- .def("GetGeometry",&LineAverage::GetGeometry)
- .def("SetGeometry",&LineAverage::SetGeometry)
+ .def("GetGeometry",&alg::LineAverage::GetGeometry)
+ .def("SetGeometry",&alg::LineAverage::SetGeometry)
;
def("RealSpatialCrossCorrelation",real_spatial_cross_correlation_1);
def("RealSpatialCrossCorrelation",real_spatial_cross_correlation_2);
- class_<HighestPeakSearch3D, bases<NonModAlgorithm> >("HighestPeakSearch3D" ,init<int,int,Real>())
+ class_<alg::HighestPeakSearch3D, bases<NonModAlgorithm> >("HighestPeakSearch3D" ,init<int,int,Real>())
.def(init<int,int>())
.def(init<int>())
.def(init<>())
- .def("GetPeakList",&HighestPeakSearch3D::GetPeakList)
- .def("ClearPeakList",&HighestPeakSearch3D::ClearPeakList)
+ .def("GetPeakList",&alg::HighestPeakSearch3D::GetPeakList)
+ .def("ClearPeakList",&alg::HighestPeakSearch3D::ClearPeakList)
;
}
diff --git a/modules/img/alg/tests/test_transform.cc b/modules/img/alg/tests/test_transform.cc
index 2721c3369d73805d7ec99675f08d085e74210d01..62a12549d8e66ea390c61ca8535f474d348d8af0 100644
--- a/modules/img/alg/tests/test_transform.cc
+++ b/modules/img/alg/tests/test_transform.cc
@@ -33,21 +33,20 @@
namespace {
using namespace ost::img;
-using namespace ost::img::alg;
void test()
{
alg::Randomize rnd;
- Transform transform;
+ alg::Transform transform;
}
void test_point()
{
Point p0(3,-2,1);
Point p1a(9,-6,3);
- Point p1b(Scale(3.0).Apply(p0));
+ Point p1b(alg::Scale(3.0).Apply(p0));
Point p2a(Point(2,3,1));
- Point p2b=Rotate2D(M_PI_2).Apply(p0);
+ Point p2b=alg::Rotate2D(M_PI_2).Apply(p0);
std::ostringstream msg;
msg << p1a << " != " << p1b;
@@ -61,9 +60,9 @@ void test_extent()
{
Extent e0(Point(0,0),Point(2,3));
Extent e1a(Point(-1,-1),Point(7,10));
- Extent e1b=Scale(3.0).Apply(e0);
+ Extent e1b=alg::Scale(3.0).Apply(e0);
Extent e2a(Point(-3,0),Point(0,2));
- Extent e2b=Rotate2D(M_PI_2).Apply(e0);
+ Extent e2b=alg::Rotate2D(M_PI_2).Apply(e0);
std::ostringstream msg;
msg << e1a << " != " << e1b;
@@ -74,10 +73,10 @@ void test_extent()
e0=Extent(Point(-3,-2),Size(8,10));
e1a=Extent(Point(-10,-7),Size(24,30));
- e1b=Scale(3.0).Apply(e0);
+ e1b=alg::Scale(3.0).Apply(e0);
e2a=Extent(Point(-7,-3),Size(10,8));
- e2b=Rotate2D(M_PI_2).Apply(e0);
+ e2b=alg::Rotate2D(M_PI_2).Apply(e0);
msg.str("");
msg << e1a << " != " << e1b;
diff --git a/modules/info/pymod/wrap_info.cc b/modules/info/pymod/wrap_info.cc
index 4af9741d63430f0964b415d83410641ab9d54762..cf15c736d937cccbd6f910e3646aba3c8448d97a 100644
--- a/modules/info/pymod/wrap_info.cc
+++ b/modules/info/pymod/wrap_info.cc
@@ -314,4 +314,8 @@ BOOST_PYTHON_MODULE(_ost_info)
class_<VerboseInfoVisitor, bases<InfoVisitor> >("VerboseInfoVisitor",init<>())
;
+
+ def("TransformToInfo", &TransformToInfo);
+ def("TransformFromInfo", &TransformFromInfo);
+
}
diff --git a/modules/info/src/geom_info_conversion.cc b/modules/info/src/geom_info_conversion.cc
index 8c7681be583ed4464f1e6460dcf32a3e541aa4c9..8e5711904bb103d9ce0237b051e7c799bb0071e9 100644
--- a/modules/info/src/geom_info_conversion.cc
+++ b/modules/info/src/geom_info_conversion.cc
@@ -80,4 +80,35 @@ geom::Mat4 Mat4FromInfo(const InfoGroup& group)
return mat;
}
-}}
+geom::Transform TransformFromInfo(const InfoGroup& group)
+{
+ if (!group.HasItem("center")) {
+ throw InfoError("Error while loading transform from info: "
+ "Group does not contain a center element");
+ }
+ if (!group.HasGroup("rotation")) {
+ throw InfoError("Error while loading transform from info: "
+ "Group does not contain a rotation element");
+ }
+ if (!group.HasItem("translation")) {
+ throw InfoError("Error while loading transform from info: "
+ "Group does not contain a translation element");
+ }
+ geom::Transform tf;
+ tf.SetCenter(group.GetItem("center").AsVector());
+ tf.SetTrans(group.GetItem("translation").AsVector());
+ tf.SetRot(Mat3FromInfo(group.GetGroup("rotation")));
+ return tf;
+}
+
+void TransformToInfo(const geom::Transform& transform, InfoGroup& group)
+{
+ geom::Transform tf;
+ group.CreateItem("center", transform.GetCenter());
+ group.CreateItem("translation", transform.GetTrans());
+ InfoGroup rot=group.CreateGroup("rotation");
+ Mat3ToInfo(transform.GetRot(), rot);
+}
+
+}} // ns
+
diff --git a/modules/info/src/geom_info_conversion.hh b/modules/info/src/geom_info_conversion.hh
index cb06e05ebeefa521ae05daab60c28c8f551663f4..bab90abec02b82cfbf701a75dcd258db88b9bbaa 100644
--- a/modules/info/src/geom_info_conversion.hh
+++ b/modules/info/src/geom_info_conversion.hh
@@ -53,6 +53,15 @@ void DLLEXPORT_OST_INFO Mat4ToInfo(const geom::Mat4& mat, InfoGroup& group);
///\brief load Mat4 from info
geom::Mat4 DLLEXPORT_OST_INFO Mat4FromInfo(const InfoGroup& group);
+
+/// \brief read transformation from info group
+/// \relates Transform
+geom::Transform DLLEXPORT_OST_INFO TransformFromInfo(const info::InfoGroup& group);
+/// \brief store transformation in info group
+/// \relates Transform
+void DLLEXPORT_OST_INFO TransformToInfo(const geom::Transform& transform,
+ info::InfoGroup& group);
+
//@}
}}
diff --git a/modules/mol/alg/src/CMakeLists.txt b/modules/mol/alg/src/CMakeLists.txt
index 146717ace4972b697c0ce160206b67749c029f2e..b91dd1e42a5f975e29a192666d847e1c56b33115 100644
--- a/modules/mol/alg/src/CMakeLists.txt
+++ b/modules/mol/alg/src/CMakeLists.txt
@@ -48,12 +48,12 @@ module(NAME mol_alg SOURCES ${OST_MOL_ALG_SOURCES}
DEPENDS_ON ${MOL_ALG_DEPS}
LINK ${BOOST_PROGRAM_OPTIONS})
-copy_if_different("." "${STAGE_DIR}/share/openstructure"
+copy_if_different("${CMAKE_CURRENT_SOURCE_DIR}" "${STAGE_DIR}/share/openstructure"
"atom_scattering_properties.txt" "ATOM_SCATTERING_PROPS"
"ost_mol_alg")
install(FILES "atom_scattering_properties.txt" DESTINATION "share/openstructure/")
-copy_if_different("." "${STAGE_DIR}/share/openstructure"
+copy_if_different("${CMAKE_CURRENT_SOURCE_DIR}" "${STAGE_DIR}/share/openstructure"
"stereo_chemical_props.txt" "STEREO_CHEMICAL_PROPS"
"ost_mol_alg")
install(FILES "stereo_chemical_props.txt" DESTINATION "share/openstructure/")
diff --git a/modules/mol/alg/src/lddt.cc b/modules/mol/alg/src/lddt.cc
index 2142989048973aaec76da73470c078e69e212c16..fdd70d953c802f7319611071b57ca1e30a2b5c32 100644
--- a/modules/mol/alg/src/lddt.cc
+++ b/modules/mol/alg/src/lddt.cc
@@ -283,6 +283,7 @@ int main (int argc, char **argv)
EntityView v=model.CreateFullView();
boost::filesystem::path pathstring(files[i]);
+
#if BOOST_FILESYSTEM_VERSION==3 || BOOST_VERSION<103400
String filestring=pathstring.string();
#else
diff --git a/modules/mol/base/pymod/CMakeLists.txt b/modules/mol/base/pymod/CMakeLists.txt
index 6e158771aa0c9e3b2608203469f9b3afc65e5708..3f514b2b8afba9e8f95473898b9649da2b3afcb7 100644
--- a/modules/mol/base/pymod/CMakeLists.txt
+++ b/modules/mol/base/pymod/CMakeLists.txt
@@ -18,7 +18,6 @@ export_bounding_box.cc
export_query_view_wrapper.cc
export_torsion.cc
export_visitor.cc
-export_transform.cc
wrap_mol.cc
export_entity_property_mapper.cc
)
diff --git a/modules/mol/base/pymod/__init__.py b/modules/mol/base/pymod/__init__.py
index 8eb77fa6d3055f6259d7d1aa4c31ccffb9da7098..c51905578ce1f422598c5769f2717f69c4039e0f 100644
--- a/modules/mol/base/pymod/__init__.py
+++ b/modules/mol/base/pymod/__init__.py
@@ -20,6 +20,17 @@ from _ost_mol import *
import ost.geom as _geom
from ost.mol import alg
+__transform_warning_flag=True
+
+def Transform(tf=None):
+ from ost import LogWarning
+ if __transform_warning_flag:
+ LogWarning("mol.Transform is deprecated, please use geom.Transform instead")
+ __transform_warning_flag=False
+ if tf:
+ return _geom.Transform(tf)
+ else:
+ return _geom.Transform()
def MergeCoordGroups(*coord_groups):
"""
diff --git a/modules/mol/base/pymod/wrap_mol.cc b/modules/mol/base/pymod/wrap_mol.cc
index 31cf8165b463460f346fc6d1ec820ceb317edb65..0c1281ad8f9b490790e32902e0f8822e559be33b 100644
--- a/modules/mol/base/pymod/wrap_mol.cc
+++ b/modules/mol/base/pymod/wrap_mol.cc
@@ -42,7 +42,6 @@ void export_PropertyID();
void export_BoundingBox();
void export_QueryViewWrapper();
void export_EntityPropertyMapper();
-void export_Transform();
BOOST_PYTHON_MODULE(_ost_mol)
{
@@ -71,5 +70,4 @@ BOOST_PYTHON_MODULE(_ost_mol)
export_BoundingBox();
export_QueryViewWrapper();
export_EntityPropertyMapper();
- export_Transform();
}
diff --git a/modules/mol/base/src/CMakeLists.txt b/modules/mol/base/src/CMakeLists.txt
index 7c92f9f45ca67bef9452a829ef6e6de6e933c5ff..8bb7187ebe9d229fe4aad338a71e53674e22ae3f 100644
--- a/modules/mol/base/src/CMakeLists.txt
+++ b/modules/mol/base/src/CMakeLists.txt
@@ -31,7 +31,6 @@ residue_view.cc
surface_builder.cc
surface_handle.cc
torsion_handle.cc
-transform.cc
query_view_wrapper.cc
view_op.cc
coord_source.cc
@@ -87,13 +86,13 @@ surface_builder.hh
surface_handle.hh
surface_prop.hh
torsion_handle.hh
-transform.hh
query_view_wrapper.hh
view_op.hh
view_type_fw.hh
view_op.hh
xcs_editor.hh
bounding_box.hh
+transform.hh
module_config.hh)
foreach(_impl_src ${OST_MOL_IMPL_SOURCES})
diff --git a/modules/mol/base/src/coord_group.cc b/modules/mol/base/src/coord_group.cc
index 4fe6677ee7da3981ee2bc3f9b48f2c26599820e4..5af231a559b8e07db90f6ec34d539aa238ed63ea 100644
--- a/modules/mol/base/src/coord_group.cc
+++ b/modules/mol/base/src/coord_group.cc
@@ -19,9 +19,10 @@
#include <ost/invalid_handle.hh>
#include <ost/integrity_error.hh>
#include <ost/log.hh>
-#include <ost/mol/in_mem_coord_source.hh>
-#include <ost/mol/view_op.hh>
-#include <ost/mol/mol.hh>
+#include <ost/geom/transform.hh>
+#include "in_mem_coord_source.hh"
+#include "view_op.hh"
+#include "mol.hh"
#include "coord_group.hh"
@@ -255,7 +256,7 @@ CoordGroupHandle CoordGroupHandle::Filter(const EntityView& selected, int first,
return filtered_cg;
}
-void CoordGroupHandle::ApplyTransform(const mol::Transform& tf)
+void CoordGroupHandle::ApplyTransform(const geom::Transform& tf)
{
this->CheckValidity();
if (source_->IsMutable()) {
diff --git a/modules/mol/base/src/coord_group.hh b/modules/mol/base/src/coord_group.hh
index 74fffcb6c45d47f2e0f0e3c469e5174a07a31cab..623f745efbb3bc37411d93279ee99baa5c5fb7f5 100644
--- a/modules/mol/base/src/coord_group.hh
+++ b/modules/mol/base/src/coord_group.hh
@@ -28,9 +28,12 @@
#include "atom_handle.hh"
#include "coord_source.hh"
-namespace ost { namespace mol {
+namespace geom {
+ // we should really have fw headers...
+ class Transform;
+}
-class Transform;
+namespace ost { namespace mol {
/// \brief coordinate group, for trajectories and such
class DLLEXPORT_OST_MOL CoordGroupHandle {
@@ -109,7 +112,7 @@ public:
CoordGroupHandle Filter(const EntityView& selected,int first=0,int last=-1) const;
/// \brief apply in-place transform to each coordinate in each frame
- void ApplyTransform(const Transform& tf);
+ void ApplyTransform(const geom::Transform& tf);
private:
diff --git a/modules/mol/base/src/coord_source.cc b/modules/mol/base/src/coord_source.cc
index 06b7864b7a831fa2fe8d0e144765b6bff2094b9e..fa58ce041c963aaac3dbf522be37533fb33e0b4a 100644
--- a/modules/mol/base/src/coord_source.cc
+++ b/modules/mol/base/src/coord_source.cc
@@ -21,10 +21,10 @@
Author: Marco Biasini
*/
#include <ost/log.hh>
+#include <ost/geom/transform.hh>
#include "atom_handle.hh"
#include "xcs_editor.hh"
#include "in_mem_coord_source.hh"
-#include "transform.hh"
#include "coord_source.hh"
namespace ost { namespace mol {
@@ -165,7 +165,7 @@ geom::Vec3 CoordSource::GetAtomPos(uint frame, AtomHandle atom) const
return geom::Vec3();
}
-void CoordSource::ApplyTransform(const Transform& tf)
+void CoordSource::ApplyTransform(const geom::Transform& tf)
{
if(!mutable_) return;
size_t frame_count=GetFrameCount();
diff --git a/modules/mol/base/src/coord_source.hh b/modules/mol/base/src/coord_source.hh
index a33162abc4e14a95a94e1414aa90401cb47bd0af..3f83e5a3e19800956364a2c679d38660412d0736 100644
--- a/modules/mol/base/src/coord_source.hh
+++ b/modules/mol/base/src/coord_source.hh
@@ -27,11 +27,14 @@
#include <ost/mol/coord_frame.hh>
#include <ost/mol/entity_handle.hh>
+namespace geom {
+ // we should really have fw headers...
+ class Transform;
+}
namespace ost { namespace mol {
class CoordSource;
-class Transform;
typedef boost::shared_ptr<CoordSource> CoordSourcePtr;
@@ -82,7 +85,7 @@ public:
virtual void AddFrame(const std::vector<geom::Vec3>& coords,const geom::Vec3& cell_size,const geom::Vec3& cell_angles) = 0;
virtual void InsertFrame(int pos, const std::vector<geom::Vec3>& coords) = 0;
- void ApplyTransform(const Transform& tf);
+ void ApplyTransform(const geom::Transform& tf);
protected:
void SetMutable(bool flag);
diff --git a/modules/mol/base/src/entity_handle.hh b/modules/mol/base/src/entity_handle.hh
index 67b2a847e4ab4050d9dfd9043e9fa3ab46ae0bd6..2783b404b75b11a1e31127017d8461b740752cf5 100644
--- a/modules/mol/base/src/entity_handle.hh
+++ b/modules/mol/base/src/entity_handle.hh
@@ -20,7 +20,6 @@
#define OST_ENTITY_HANDLE_HH
#include <ost/mol/module_config.hh>
-#include <ost/mol/transform.hh>
#include "impl/entity_impl_fw.hh"
#include "entity_visitor_fw.hh"
diff --git a/modules/mol/base/src/impl/entity_impl.hh b/modules/mol/base/src/impl/entity_impl.hh
index d1d1ca050f30a7fdee8d7ab5d64bf417ee183dc8..ccbf85b449cdf035493096c73157a485dc9baea8 100644
--- a/modules/mol/base/src/impl/entity_impl.hh
+++ b/modules/mol/base/src/impl/entity_impl.hh
@@ -31,7 +31,6 @@
#include <ost/mol/entity_view.hh>
-#include <ost/mol/transform.hh>
#include <ost/mol/residue_prop.hh>
#include <ost/mol/impl/atom_impl_fw.hh>
#include <ost/mol/impl/residue_impl_fw.hh>
diff --git a/modules/mol/base/src/transform.hh b/modules/mol/base/src/transform.hh
index f9c59f6f5095256795b90e105d8067f20f1e6772..a3cad4c8ba2b2976644b7957f07a23ab735a3241 100644
--- a/modules/mol/base/src/transform.hh
+++ b/modules/mol/base/src/transform.hh
@@ -1,104 +1,6 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2011 by the OpenStructure authors
-//
-// This library is free 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
-//------------------------------------------------------------------------------
-#ifndef OST_MOL_BASE_TRANSFORM_HH
-#define OST_MOL_BASE_TRANSFORM_HH
-
-/*
- Author: Ansgar Philippsen
-*/
-
-#include <ost/config.hh>
-#include <ost/geom/geom.hh>
-#if(OST_INFO_ENABLED)
-#include <ost/info/info_fw.hh>
-#endif
-#include <ost/mol/module_config.hh>
+#include <ost/geom/transform.hh>
namespace ost { namespace mol {
-
-/// \brief basic and essential transformation class, including translation,
-/// rotation and center of rotation
-class DLLEXPORT_OST_MOL Transform {
-public:
- Transform();
-
- geom::Mat4 GetMatrix() const {return tm_;}
- geom::Mat4 GetTransposedMatrix() const {return ttm_;}
- geom::Mat4 GetInvertedMatrix() const {return itm_;}
-
- void SetCenter(const geom::Vec3& c);
- geom::Vec3 GetCenter() const;
-
- // directly set tm, messing up rot/trans/cen !
- void SetMatrix(const geom::Mat4& m);
-
- /// \name rotation
- //@{
- /// \brief rotate around x-axis
- void ApplyXAxisRotation(float delta);
- void ApplyYAxisRotation(float delta);
- void ApplyZAxisRotation(float delta);
- void ApplyAxisRotation(float delta, const geom::Vec3& axis);
-
- geom::Mat3 GetXAxisRotation(float delta);
- geom::Mat3 GetYAxisRotation(float delta);
- geom::Mat3 GetZAxisRotation(float delta);
-
- geom::Mat3 GetRot() const;
- void SetRot(const geom::Mat3& r);
- //@}
- /// \brief translation
- //@{
- void ApplyXAxisTranslation(float delta);
- void ApplyYAxisTranslation(float delta);
- void ApplyZAxisTranslation(float delta);
- void SetTrans(const geom::Vec3& t);
- geom::Vec3 GetTrans() const;
- //@}
-
- geom::Vec3 Apply(const geom::Vec3& v) const;
- geom::Vec4 Apply(const geom::Vec4& v) const;
- geom::AlignedCuboid Apply(const geom::AlignedCuboid& c) const;
-
-private:
- geom::Mat3 rot_;
- geom::Vec3 trans_;
- geom::Vec3 cen_;
- geom::Mat4 tm_;
- geom::Mat4 ttm_;
- geom::Mat4 itm_;
-
- void update_tm();
- void update_components();
-};
-
-
-
-#if(OST_INFO_ENABLED)
-/// \brief read transformation from info group
-/// \relates Transform
-Transform DLLEXPORT_OST_MOL TransformFromInfo(const info::InfoGroup& group);
-/// \brief store transformation in info group
-/// \relates Transform
-void DLLEXPORT_OST_MOL TransformToInfo(const Transform& transform,
- info::InfoGroup& group);
-#endif
-}} // ns
-
-#endif
+#warning mol::Transform is deprecated, use geom::Transform instead
+ typedef geom::Transform Transform;
+}}
diff --git a/modules/mol/base/tests/CMakeLists.txt b/modules/mol/base/tests/CMakeLists.txt
index c29dc6adfe3d5ec1bbe2e85a5a587940b35848c2..5085b0b10b257fab18361001a1cb7a55b796769d 100644
--- a/modules/mol/base/tests/CMakeLists.txt
+++ b/modules/mol/base/tests/CMakeLists.txt
@@ -10,7 +10,6 @@ set(OST_MOL_BASE_UNIT_TESTS
test_query.cc
test_surface.cc
test_residue.cc
- test_transform.cc
test_view.cc
test_view_op.cc
tests.cc
diff --git a/modules/mol/base/tests/test_coord_group.cc b/modules/mol/base/tests/test_coord_group.cc
index 3c0cdc18fbe5fe139c930d0e7f54ad26cb5941ea..a26f2e2bd7dcfb296a62922792408e4b4c2c4b97 100644
--- a/modules/mol/base/tests/test_coord_group.cc
+++ b/modules/mol/base/tests/test_coord_group.cc
@@ -81,7 +81,7 @@ BOOST_AUTO_TEST_CASE(coord_group)
BOOST_CHECK(ac.GetPos()==geom::Vec3(-17,-18,-19));
BOOST_CHECK(ad.GetPos()==geom::Vec3(9,10,11));
- Transform tf;
+ geom::Transform tf;
tf.ApplyXAxisRotation(17.0);
tf.ApplyYAxisRotation(-135.0);
tf.ApplyZAxisRotation(234.0);
diff --git a/modules/mol/base/tests/test_entity.cc b/modules/mol/base/tests/test_entity.cc
index 46a4de626f41d8a37c57c8b0292ab2e7605dca2b..d8ecd8f3b9a9007e84549d6b4a20e302a1a5fe67 100644
--- a/modules/mol/base/tests/test_entity.cc
+++ b/modules/mol/base/tests/test_entity.cc
@@ -181,7 +181,7 @@ BOOST_AUTO_TEST_CASE(transformation)
BOOST_CHECK(eh.IsTransformationIdentity()==true);
- Transform trans;
+ geom::Transform trans;
trans.ApplyZAxisRotation(90.0);
geom::Mat4 mat = trans.GetMatrix();
@@ -203,7 +203,7 @@ BOOST_AUTO_TEST_CASE(transformation)
CHECK_TRANSFORMED_ATOM_POSITION(atom3,tr_atom3);
CHECK_ORIGINAL_ATOM_POSITION(atom3,orig_atom3);
- Transform trans2;
+ geom::Transform trans2;
trans2.ApplyXAxisTranslation(3.5);
geom::Mat4 mat2 = trans2.GetMatrix();
diff --git a/scripts/CMakeLists.txt b/scripts/CMakeLists.txt
index 0b6b429a45beebc7c2233d65218dba89fa86f32d..12b81a310b570f6888852d04864af183022ce4f3 100644
--- a/scripts/CMakeLists.txt
+++ b/scripts/CMakeLists.txt
@@ -33,13 +33,13 @@ if (NOT ENABLE_STATIC)
set(INIT_SCRIPTS
init_cl.py
)
-
+ set(SPD "${LIB_DIR}/python${PYTHON_VERSION}/site-packages")
if (ENABLE_GUI)
list(APPEND INIT_SCRIPTS init.py)
endif()
- copy_if_different("./" "${STAGE_DIR}/${LIB_DIR}/openstructure"
+ copy_if_different("${CMAKE_CURRENT_SOURCE_DIR}" "${STAGE_DIR}/${SPD}"
"${INIT_SCRIPTS}" "python init scripts" ost_scripts)
- install(FILES ${INIT_SCRIPTS} DESTINATION "${LIB_DIR}/openstructure")
+ install(FILES ${INIT_SCRIPTS} DESTINATION "${SPD}")
endif()
diff --git a/scripts/init_cl.py b/scripts/init_cl.py
index 09b38ed9785b1075acbdc5dbfe8de8e1d14d21f3..d4a14df4cd339872dc62c2de5898b04f07e75c76 100644
--- a/scripts/init_cl.py
+++ b/scripts/init_cl.py
@@ -26,10 +26,11 @@ parser.add_option("-v", "--verbosity_level", action="store", type="int", dest="v
parser.disable_interspersed_args()
(options, args) = parser.parse_args()
+_site_packs='python%d.%d/site-packages' % sys.version_info[0:2]
if platform.machine()=='x86_64':
- sys.path.insert(0, os.getenv('DNG_ROOT')+'/lib64/openstructure')
+ sys.path.insert(0, os.path.join(os.getenv('DNG_ROOT'), 'lib64', _site_packs))
else:
- sys.path.insert(0,os.getenv('DNG_ROOT')+'/lib/openstructure')
+ sys.path.insert(0,os.path.join(os.getenv('DNG_ROOT'), 'lib', _site_packs))
from ost import *
import ost
diff --git a/scripts/ost.in b/scripts/ost.in
index 90c74f045e5ceff238b207c3043046d96546c57f..407daed10f8d2b6fed92f1724c9c4b369bef0244 100755
--- a/scripts/ost.in
+++ b/scripts/ost.in
@@ -31,6 +31,6 @@ BIN_DIR=`dirname "$SCRIPT_NAME"`
source $BIN_DIR/../@LIBEXEC_PATH@/ost_config
-$pyexec $interactive "$DNG_ROOT/@LIBDIR@/openstructure/init_cl.py" $opts
+$pyexec $interactive "$DNG_ROOT/@LIBDIR@/python@PYTHON_VERSION@/site-packages/init_cl.py" $opts
RC=$?
exit $RC
diff --git a/scripts/ost_config.in b/scripts/ost_config.in
index faaae8e264e655496fe35471dc0bb685c6a6f59b..5894bdb12c62241d556e04fb909eb9f83a17c5ef 100644
--- a/scripts/ost_config.in
+++ b/scripts/ost_config.in
@@ -24,7 +24,7 @@
export DNG_ROOT=`cd "$BIN_DIR/..";pwd`
export DNG_BINDIR="$DNG_ROOT/bin"
export DNG_LIBDIR="$DNG_ROOT/@LIBDIR@"
-export DNG_INITDIR="$DNG_LIBDIR/openstructure"
+export DNG_INITDIR="$DNG_LIBDIR/python@PYTHON_VERSION@/site-packages"
export PATH="$DNG_BINDIR:${PATH}"
export DYLD_FRAMEWORK_PATH="$DNG_LIBDIR:${DYLD_FRAMEWORK_PATH}"