diff --git a/.gitignore b/.gitignore
index 56410cfa551dd48078e87a6a355fa7eadf1823ab..05c992e3f9ddc3fb38323fbdc356c996822989a0 100644
--- a/.gitignore
+++ b/.gitignore
@@ -24,6 +24,8 @@ pov_*test.inc
*-out.pdb
*-out.sdf
*-out.crd
+*-out.pqr
+*-out.png
CMakeLists.txt.user
OpenStructure.cbp
DartConfiguration.tcl
@@ -53,4 +55,8 @@ Debug
/deployment/win/create_archive.bat
/install_manifest.txt
*_out.csv
+*_out.tab
+*_out.pickle
/modules/io/tests/temp_img.tmp
+PYTEST-*.xml
+ost_*_tests_log.xml
diff --git a/CMakeLists.txt b/CMakeLists.txt
index da42bdb5f5cd2ea93ada1a91137b0685b6220a18..e65ba23237b81453d88e1b85698992d6ca26588f 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -12,9 +12,18 @@ set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${PROJECT_SOURCE_DIR}/cmake_support)
include(OST)
+if (CMAKE_COMPILER_IS_GNUCXX)
+ exec_program(gcc ARGS --version OUTPUT_VARIABLE CMAKE_C_COMPILER_VERSION)
+ if(CMAKE_C_COMPILER_VERSION MATCHES ".*4\\.[5-9].*")
+ set(OST_GCC_45 true)
+ else()
+ set(OST_GCC_45 false)
+ endif()
+endif()
+
option(USE_SHADER "whether to compile with shader support"
OFF)
-option(SET_RPATH "embed rpath upon make install"
+option(USE_RPATH "embed rpath upon make install"
OFF)
option(COMPILE_TMTOOLS "whether to compile the tmalign and tmscore programs"
OFF)
@@ -26,6 +35,8 @@ option(ENABLE_GFX "whether graphics support should be enabled"
ON)
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"
+ ON)
option(USE_NUMPY "whether numpy support is added"
OFF)
option(USE_DOUBLE_PRECISION "whether to compile in double precision"
@@ -51,6 +62,7 @@ if (FORTRAN_COMPILER)
endif()
+
if (PREFIX)
set(CMAKE_INSTALL_PREFIX ${PREFIX})
endif()
@@ -74,10 +86,20 @@ else()
set(_DOUBLE_PREC OFF)
endif()
+if (NOT ENABLE_INFO)
+ set(ENABLE_GFX OFF)
+endif()
+
if (NOT ENABLE_GFX)
set(ENABLE_GUI OFF)
endif()
+if (ENABLE_INFO)
+ set(_INFO ON)
+else()
+ set(_INFO OFF)
+endif()
+
if (ENABLE_GUI)
set(_UI ON)
else()
@@ -154,11 +176,26 @@ setup_compiler_flags()
set(CMAKE_LIBRARY_OUTPUT_DIRECTORY)
+if (ENABLE_STATIC AND UNIX AND NOT APPLE)
+ set (CMAKE_FIND_LIBRARY_SUFFIXES .a)
+endif()
+
setup_boost()
-
-find_package(Qt4 4.5.0 REQUIRED)
-find_package(OpenGL REQUIRED)
-find_package(PNG REQUIRED)
+
+if (ENABLE_INFO)
+ find_package(Qt4 4.5.0 REQUIRED)
+endif()
+
+if (ENABLE_GFX)
+ find_package(OpenGL REQUIRED)
+endif()
+
+if (ENABLE_IMG OR ENABLE_GFX)
+ find_package(PNG REQUIRED)
+else()
+ set (PNG_LIBRARY "")
+endif()
+
find_package(Eigen 2.0.0 REQUIRED)
find_package(Python 2.4 REQUIRED)
@@ -177,10 +214,15 @@ if (ENABLE_STATIC)
set(Boost_USE_STATIC_LIBS ON)
find_package(Boost ${_BOOST_MIN_VERSION}
COMPONENTS filesystem system iostreams regex REQUIRED)
- message(${Boost_LIBRARIES})
find_package(ZLIB REQUIRED)
- set(STATIC_LIBRARIES ${Boost_LIBRARIES} ${FFTW_LIBRARIES} ${TIFF_LIBRARIES}
- ${PNG_LIBRARIES} ${ZLIB_LIBRARIES})
+
+ if (UNIX AND NOT APPLE)
+ set(STATIC_LIBRARIES ${Boost_LIBRARIES} ${FFTW_LIBRARIES} ${TIFF_LIBRARIES}
+ ${PNG_LIBRARY} ${ZLIB_LIBRARY})
+ else ()
+ set(STATIC_LIBRARIES ${Boost_LIBRARIES} ${FFTW_LIBRARIES} ${TIFF_LIBRARIES}
+ ${PNG_LIBRARY} ${ZLIB_LIBRARY})
+ endif()
endif()
if (ENABLE_GUI)
@@ -218,13 +260,19 @@ if (UNIX)
endif()
endif()
+if (ENABLE_STATIC)
+ SET(CMAKE_SKIP_BUILD_RPATH TRUE)
+ SET(LINK_SEARCH_END_STATIC TRUE)
+endif()
add_subdirectory(modules)
add_subdirectory(scripts)
add_subdirectory(deployment)
-set(FILES_TO_BE_REMOVED CMakeFiles stage tests)
+
+set(FILES_TO_BE_REMOVED ${CMAKE_SOURCE_DIR}/stage tests)
set_directory_properties(PROPERTIES ADDITIONAL_MAKE_CLEAN_FILES
- "${FILES_TO_BE_REMOVED}")
+ "${FILES_TO_BE_REMOVED}")
+
#ost_match_boost_python_version(${PYTHON_LIBRARIES})
@@ -232,6 +280,7 @@ message(STATUS
"OpenStructure will be built with the following options:\n"
" Install Prefix (-DPREFIX) : ${CMAKE_INSTALL_PREFIX}\n"
" RPath in install (-DUSE_RPATH) : ${_USE_RPATH}\n"
+ " Info support (-DENABLE_INFO) : ${_INFO}\n"
" Graphical interface (-DENABLE_GUI) : ${_UI}\n"
" OpenGL support (-DENABLE_GFX) : ${_OPENGL}\n"
" Image Processing support (-DENABLE_IMG) : ${_IMG}\n"
@@ -243,4 +292,5 @@ 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}")
\ No newline at end of file
+ " Debian-style 'libexec' (-DDEBIAN_STYLE_LIBEXEC) : ${_DEBIAN_STYLE_LIBEXEC}" )
+
diff --git a/build_configs/buildconfig_arch b/build_configs/buildconfig_arch
new file mode 100644
index 0000000000000000000000000000000000000000..b0a6494db8715e33c8f0ae7a2f9cfb63c2f97392
--- /dev/null
+++ b/build_configs/buildconfig_arch
@@ -0,0 +1 @@
+set(PYTHON_BINARY "/usr/bin/python2" CACHE PATH "")
diff --git a/build_configs/buildconfig_arch_static b/build_configs/buildconfig_arch_static
new file mode 100644
index 0000000000000000000000000000000000000000..15c3ef31600755c4b217e623492e06b58bb44b5e
--- /dev/null
+++ b/build_configs/buildconfig_arch_static
@@ -0,0 +1,4 @@
+set(PYTHON_BINARY "/usr/bin/python2" CACHE PATH "")
+set(ZLIB_LIBRARY "/usr/lib/libz.a" CACHE PATH "")
+set(PNG_LIBRARY "/usr/lib/libpng12.a" CACHE PATH "")
+set(FFTW_LIBRARIES "/usr/lib/libfftw3f.a" CACHE PATH "")
diff --git a/build_configs/buildconfig_bc2_locallibs b/build_configs/buildconfig_bc2_locallibs
new file mode 100644
index 0000000000000000000000000000000000000000..fbc7a614754b8fba6a35957ba4d71bbb4061380d
--- /dev/null
+++ b/build_configs/buildconfig_bc2_locallibs
@@ -0,0 +1,11 @@
+set(FFTW_INCLUDE_PATH "/import/bc2/soft/app/FFTW/current/Linux/include/" CACHE PATH "")
+set(FFTW_LIBRARIES "/import/bc2/soft/app/FFTW/current/Linux/lib/libfftw3f.so" CACHE PATH "")
+set(Boost_COMPILER "-gcc41" CACHE PATH "")
+set(PYTHON_ROOT "/import/bc2/soft/app/Python/current/Linux/" CACHE PATH "")
+set(EIGEN2_INCLUDE_DIR "/import/bc2/soft/app/eigen/current/Linux/include/eigen2" CACHE PATH "")
+set(BOOST_ROOT "/import/bc2/soft/app/boost/current/Linux" CACHE PATH "")
+set(QT_QMAKE_EXECUTABLE "/import/bc2/soft/app/Qt/current/Linux/bin/qmake" CACHE PATH "")
+set(COMPOUND_LIB "/import/bc2/home/schwede/GROUP/OpenStructure/ChemLib/compounds.chemlib" CACHE PATH "")
+set(TIFF_LIBRARY "${OST_LOCAL_LIBS}/lib/libtiff.so" CACHE PATH "")
+set(TIFF_INCLUDE_DIR "${OST_LOCAL_LIBS}/include/" CACHE PATH "")
+set (CMAKE_BUILD_TYPE "Release" CACHE PATH "")
diff --git a/build_configs/buildconfig_bc2_static b/build_configs/buildconfig_bc2_static
new file mode 100644
index 0000000000000000000000000000000000000000..c26933d8ce996f93da782e919544f06312d57ff3
--- /dev/null
+++ b/build_configs/buildconfig_bc2_static
@@ -0,0 +1,11 @@
+set(FFTW_INCLUDE_PATH "/import/bc2/soft/app/FFTW/current/Linux/include/" CACHE PATH "")
+set(FFTW_LIBRARIES "/import/bc2/soft/app/FFTW/current/Linux/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 "/usr/lib64/libz.a" CACHE PATH "")
+set(Boost_COMPILER "-gcc41" CACHE PATH "")
+set(PYTHON_ROOT "/import/bc2/soft/app/Python/current/Linux/" CACHE PATH "")
+set(EIGEN2_INCLUDE_DIR "/import/bc2/soft/app/eigen/current/Linux/include/eigen2" CACHE PATH "")
+set(QT_QMAKE_EXECUTABLE "/import/bc2/soft/app/Qt/current/Linux/bin/qmake" CACHE PATH "")
+set(COMPOUND_LIB "/import/bc2/home/schwede/GROUP/OpenStructure/ChemLib/compounds.chemlib" CACHE PATH "")
+set (CMAKE_BUILD_TYPE "Release" CACHE PATH "")
diff --git a/build_configs/buildconfig_bc2_static_locallibs b/build_configs/buildconfig_bc2_static_locallibs
new file mode 100644
index 0000000000000000000000000000000000000000..c4ac3df6f76cfc58b2bfc41e5afcdb6a41edfddf
--- /dev/null
+++ b/build_configs/buildconfig_bc2_static_locallibs
@@ -0,0 +1,13 @@
+set(FFTW_INCLUDE_PATH "/import/bc2/soft/app/FFTW/current/Linux/include/" CACHE PATH "")
+set(FFTW_LIBRARIES "/import/bc2/soft/app/FFTW/current/Linux/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 "/usr/lib64/libz.a" CACHE PATH "")
+set(Boost_COMPILER "-gcc41" CACHE PATH "")
+set(PYTHON_ROOT "/import/bc2/soft/app/Python/current/Linux/" CACHE PATH "")
+set(EIGEN2_INCLUDE_DIR "/import/bc2/soft/app/eigen/current/Linux/include/eigen2" CACHE PATH "")
+set(QT_QMAKE_EXECUTABLE "/import/bc2/soft/app/Qt/current/Linux/bin/qmake" CACHE PATH "")
+set(COMPOUND_LIB "/import/bc2/home/schwede/GROUP/OpenStructure/ChemLib/compounds.chemlib" CACHE PATH "")
+set(TIFF_LIBRARY "${OST_LOCAL_LIBS}/lib/libtiff.a" CACHE PATH "")
+set(TIFF_INCLUDE_DIR "${OST_LOCAL_LIBS}/include/" CACHE PATH "")
+set (CMAKE_BUILD_TYPE "Release" CACHE PATH "")
diff --git a/cmake_support/FindBoost.cmake b/cmake_support/FindBoost.cmake
index e5cc004e34fa69b3be7fcb72cb741cefd6e145f8..47019edeb51ac0d09aecbe6859e1bc34d3253f9b 100644
--- a/cmake_support/FindBoost.cmake
+++ b/cmake_support/FindBoost.cmake
@@ -649,7 +649,6 @@ ${BOOST_ROOT}/lib
${BOOST_ROOT}/lib/boost-${Boost_MAJOR_VERSION}.${Boost_MINOR_VERSION}.${Boost_SUBMINOR_VERSION}
${BOOST_ROOT}/stage/lib
${_boost_LIBRARIES_SEARCH_DIRS})
-message("boost searchdirs:${_boost_LIBRARIES_SEARCH_DIRS}")
ENDIF( BOOST_ROOT )
IF( BOOST_LIBRARYDIR )
diff --git a/cmake_support/OST.cmake b/cmake_support/OST.cmake
index 297696f4ce0d1468309feed082bc96c68f0fa302..06457ad71f30651589b40be1b94fe7a710b243e4 100644
--- a/cmake_support/OST.cmake
+++ b/cmake_support/OST.cmake
@@ -142,7 +142,9 @@ macro(module)
"invalid use of module(): a module name must be provided")
endif()
-
+ if (ENABLE_STATIC AND _ARG_NO_STATIC)
+ return()
+ endif()
if (_ARG_HEADER_OUTPUT_DIR)
set(_HEADER_OUTPUT_DIR ${_ARG_HEADER_OUTPUT_DIR})
else()
@@ -162,6 +164,17 @@ macro(module)
# create library
#-----------------------------------------------------------------------------
file(MAKE_DIRECTORY ${LIB_STAGE_PATH})
+ file(MAKE_DIRECTORY ${EXECUTABLE_OUTPUT_PATH})
+ file(MAKE_DIRECTORY ${LIBEXEC_STAGE_PATH})
+ if (NOT TARGET make_stage_lib_dir)
+ add_custom_target(make_stage_lib_dir COMMAND ${CMAKE_COMMAND} -E make_directory ${LIB_STAGE_PATH})
+ endif()
+ if (NOT TARGET make_executable_output_dir)
+ add_custom_target(make_executable_output_dir COMMAND ${CMAKE_COMMAND} -E make_directory ${EXECUTABLE_OUTPUT_PATH})
+ endif()
+ if (NOT TARGET make_libexec_dir)
+ add_custom_target(make_libexec_dir COMMAND ${CMAKE_COMMAND} -E make_directory ${LIBEXEC_STAGE_PATH})
+ endif()
if (WIN32)
set(_ABS_FILE_PATTERN "^[A-Z]:/")
else()
@@ -177,14 +190,20 @@ macro(module)
list(APPEND _ABS_SOURCE_NAMES "${CMAKE_CURRENT_SOURCE_DIR}/${_SOURCE}")
endif()
endforeach()
- add_library(${_LIB_NAME} SHARED ${_ABS_SOURCE_NAMES})
-
+ if (ENABLE_STATIC AND NOT _ARG_NO_STATIC)
+ add_library(${_LIB_NAME} STATIC ${_ABS_SOURCE_NAMES})
+ else()
+ add_library(${_LIB_NAME} SHARED ${_ABS_SOURCE_NAMES})
+ endif()
set_target_properties(${_LIB_NAME}
PROPERTIES OUTPUT_NAME ${_LIB_NAME}
PROJECT_LABEL ${_ARG_NAME}
EchoString ${_ARG_NAME}
MODULE_DEPS "${_ARG_DEPENDS_ON}")
get_target_property(_DEFS ${_LIB_NAME} COMPILE_DEFINITIONS)
+ add_dependencies(${_LIB_NAME} make_stage_lib_dir)
+ add_dependencies(${_LIB_NAME} make_executable_output_dir)
+ add_dependencies(${_LIB_NAME} make_libexec_dir)
set_target_properties(${_LIB_NAME} PROPERTIES
COMPILE_DEFINITIONS OST_MODULE_${_UPPER_LIB_NAME})
set_target_properties(${_LIB_NAME} PROPERTIES
@@ -194,25 +213,6 @@ macro(module)
LIBRARY_OUTPUT_DIRECTORY ${LIB_STAGE_PATH}
ARCHIVE_OUTPUT_DIRECTORY ${LIB_STAGE_PATH}
RUNTIME_OUTPUT_DIRECTORY ${LIB_STAGE_PATH})
- if (ENABLE_STATIC AND NOT _ARG_NO_STATIC)
- add_library(${_LIB_NAME}_static STATIC ${_ABS_SOURCE_NAMES})
- set_target_properties(${_LIB_NAME}_static
- PROPERTIES OUTPUT_NAME ${_LIB_NAME}
- PROJECT_LABEL ${_ARG_NAME}
- EchoString ${_ARG_NAME}
- MODULE_DEPS "${_ARG_DEPENDS_ON}")
- get_target_property(_DEFS ${_LIB_NAME}_static COMPILE_DEFINITIONS)
- set_target_properties(${_LIB_NAME}_static PROPERTIES
- COMPILE_DEFINITIONS OST_MODULE_${_UPPER_LIB_NAME})
- set_target_properties(${_LIB_NAME}_static PROPERTIES
- LIBRARY_OUTPUT_DIRECTORY ${LIB_STAGE_PATH}
- ARCHIVE_OUTPUT_DIRECTORY ${LIB_STAGE_PATH}
- RUNTIME_OUTPUT_DIRECTORY ${LIB_STAGE_PATH})
- foreach(_DEPENDENCY ${_ARG_DEPENDS_ON})
- target_link_libraries(${_LIB_NAME}_static ${_DEPENDENCY}_static)
- endforeach()
- target_link_libraries(${_LIB_NAME} ${ZLIB_LIBRARIES})
- endif()
if (APPLE)
set_target_properties(${_LIB_NAME} PROPERTIES
LINK_FLAGS "-Wl,-rpath,@@loader_path"
@@ -222,7 +222,11 @@ macro(module)
#set_target_properties(${_LIB_NAME} PROPERTIES PREFIX "../")
install(TARGETS ${_LIB_NAME} ARCHIVE DESTINATION "${LIB_DIR}")
else()
- install(TARGETS ${_LIB_NAME} LIBRARY DESTINATION "${LIB_DIR}")
+ if (ENABLE_STATIC)
+ install(TARGETS ${_LIB_NAME} ARCHIVE DESTINATION "${LIB_DIR}")
+ else()
+ install(TARGETS ${_LIB_NAME} LIBRARY DESTINATION "${LIB_DIR}")
+ endif()
endif()
if (_ARG_LINK)
target_link_libraries(${_LIB_NAME} ${_ARG_LINK})
@@ -230,6 +234,10 @@ macro(module)
foreach(_DEPENDENCY ${_ARG_DEPENDS_ON})
target_link_libraries(${_LIB_NAME} ${_DEPENDENCY})
endforeach()
+ if (ENABLE_STATIC)
+ target_link_libraries(${_LIB_NAME} ${STATIC_LIBRARIES})
+ endif()
+
else()
add_custom_target("${_LIB_NAME}" ALL)
set_target_properties("${_LIB_NAME}" PROPERTIES HEADER_ONLY 1
@@ -302,13 +310,23 @@ macro(executable)
if (_ARG_LINK)
target_link_libraries(${_ARG_NAME} ${_ARG_LINK})
endif()
+ foreach(_DEP ${_ARG_DEPENDS_ON})
+ target_link_libraries(${_ARG_NAME} ${_DEP})
+ endforeach()
if (ENABLE_STATIC AND _ARG_STATIC)
- set(TARGET_SUFFIX _static)
target_link_libraries(${_ARG_NAME} ${STATIC_LIBRARIES})
+ if (UNIX AND NOT APPLE)
+ if (OST_GCC_45)
+ set_target_properties(${_ARG_NAME}
+ PROPERTIES LINK_SEARCH_END_STATIC TRUE
+ LINK_FLAGS "-static-libgcc -static-libstdc++ -static -pthread")
+ else()
+ set_target_properties(${_ARG_NAME}
+ PROPERTIES LINK_SEARCH_END_STATIC TRUE
+ LINK_FLAGS "-static-libgcc -static -pthread")
+ endif()
+ endif()
endif()
- foreach(_DEP ${_ARG_DEPENDS_ON})
- target_link_libraries(${_ARG_NAME} ${_DEP}${TARGET_SUFFIX})
- endforeach()
install(TARGETS ${_ARG_NAME} DESTINATION bin)
endmacro()
@@ -338,11 +356,13 @@ macro(executable_libexec)
target_link_libraries(${_ARG_NAME} ${_ARG_LINK})
endif()
if (ENABLE_STATIC AND _ARG_STATIC)
- set(TARGET_SUFFIX _static)
target_link_libraries(${_ARG_NAME} ${STATIC_LIBRARIES})
+ set_target_properties(${_ARG_NAME}
+ PROPERTIES LINK_SEARCH_END_STATIC TRUE)
+
endif()
foreach(_DEP ${_ARG_DEPENDS_ON})
- target_link_libraries(${_ARG_NAME} ${_DEP}${TARGET_SUFFIX})
+ target_link_libraries(${_ARG_NAME} ${_DEP})
endforeach()
install(TARGETS ${_ARG_NAME} DESTINATION ${LIBEXEC_PATH})
endmacro()
@@ -472,6 +492,9 @@ macro(pymod)
if (NOT _ARG_NAME)
message(FATAL_ERROR "invalid use of pymod(): a name must be provided")
endif()
+ if (ENABLE_STATIC)
+ return()
+ endif()
if (_ARG_OUTPUT_DIR)
set(PYMOD_DIR "openstructure/${_ARG_OUTPUT_DIR}")
else()
@@ -499,14 +522,18 @@ macro(pymod)
endif()
target_link_libraries("_${_LIB_NAME}" ${_PARENT_LIB_NAME}
${PYTHON_LIBRARIES} ${BOOST_PYTHON_LIBRARIES})
- if (_USE_RPATH)
- set_target_properties("_${_LIB_NAME}"
- PROPERTIES LIBRARY_OUTPUT_DIRECTORY ${PYMOD_STAGE_DIR}
- INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/${LIB_DIR}")
- else()
- set_target_properties("_${_LIB_NAME}"
- PROPERTIES LIBRARY_OUTPUT_DIRECTORY ${PYMOD_STAGE_DIR}
- INSTALL_RPATH "")
+
+ set_target_properties("_${_LIB_NAME}"
+ PROPERTIES LIBRARY_OUTPUT_DIRECTORY ${PYMOD_STAGE_DIR})
+
+ if (NOT ENABLE_STATIC)
+ if (_USE_RPATH)
+ set_target_properties("_${_LIB_NAME}"
+ PROPERTIES INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/${LIB_DIR}")
+ else()
+ set_target_properties("_${_LIB_NAME}"
+ PROPERTIES INSTALL_RPATH "")
+ endif()
endif()
if (APPLE)
file(RELATIVE_PATH _REL_PATH "${PYMOD_STAGE_DIR}" "${LIB_STAGE_PATH}")
@@ -582,12 +609,13 @@ macro(pymod)
add_dependencies("_${_LIB_NAME}" "_${dep}")
endforeach()
endif()
-
endmacro()
add_custom_target(check)
+add_custom_target(check_xml)
if (WIN32)
set_target_properties(check PROPERTIES EXCLUDE_FROM_ALL "1")
+ set_target_properties(check_xml PROPERTIES EXCLUDE_FROM_ALL "1")
endif()
#-------------------------------------------------------------------------------
@@ -630,7 +658,12 @@ macro(ost_unittest)
target_link_libraries(${_test_name} ${BOOST_UNIT_TEST_LIBRARIES}
"${_ARG_PREFIX}_${_ARG_MODULE}")
add_custom_target("${_test_name}_run"
- COMMAND OST_ROOT=${STAGE_DIR} ${CMAKE_CURRENT_BINARY_DIR}/${_test_name} || echo
+ COMMAND OST_ROOT=${STAGE_DIR} ${CMAKE_CURRENT_BINARY_DIR}/${_test_name} || echo
+ WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+ COMMENT "running checks for module ${_ARG_MODULE}"
+ DEPENDS ${_test_name})
+ add_custom_target("${_test_name}_run_xml"
+ COMMAND OST_ROOT=${STAGE_DIR} ${CMAKE_CURRENT_BINARY_DIR}/${_test_name} --log_format=xml --log_level=all > ${_test_name}_log.xml || echo
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
COMMENT "running checks for module ${_ARG_MODULE}"
DEPENDS ${_test_name})
@@ -642,6 +675,7 @@ macro(ost_unittest)
endif()
add_dependencies(check "${_test_name}_run")
+ add_dependencies(check_xml "${_test_name}_run_xml")
set_target_properties(${_test_name}
PROPERTIES RUNTIME_OUTPUT_DIRECTORY
"${CMAKE_CURRENT_BINARY_DIR}")
@@ -662,9 +696,15 @@ macro(ost_unittest)
sh -c "${PY_TESTS_CMD} ${CMAKE_CURRENT_SOURCE_DIR}/${py_test} || echo"
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
COMMENT "running checks ${py_test}" VERBATIM)
+ add_custom_target("${py_test}_run_xml"
+ sh -c "${PY_TESTS_CMD} ${CMAKE_CURRENT_SOURCE_DIR}/${py_test} xml || echo"
+ WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+ COMMENT "running checks ${py_test}" VERBATIM)
endif()
add_dependencies("${py_test}_run" ost_scripts "_${_ARG_PREFIX}_${_ARG_MODULE}")
+ add_dependencies("${py_test}_run_xml" ost_scripts "_${_ARG_PREFIX}_${_ARG_MODULE}")
add_dependencies(check "${py_test}_run")
+ add_dependencies(check_xml "${py_test}_run_xml")
if (WIN32)
set_target_properties("${py_test}_run" PROPERTIES EXCLUDE_FROM_ALL "1")
endif()
@@ -832,7 +872,7 @@ macro(setup_compiler_flags)
endif()
endif()
endmacro()
-set(_BOOST_MIN_VERSION 1.37)
+set(_BOOST_MIN_VERSION 1.31)
macro(setup_boost)
find_package(Boost ${_BOOST_MIN_VERSION} COMPONENTS python REQUIRED)
diff --git a/examples/dssp_sa.py b/examples/dssp_sa.py
new file mode 100644
index 0000000000000000000000000000000000000000..23369a99e7d18b74c2623150773687823666827a
--- /dev/null
+++ b/examples/dssp_sa.py
@@ -0,0 +1,7 @@
+from ost.bindings import dssp
+ent=io.LoadMMCIF('1ake.cif')
+dssp.AssignDSSP(ent, extract_burial_status=True)
+for chain in ent.chains:
+ if chain.is_polypeptide:
+ for res in chain.residues:
+ print res.GetFloatProp('relative_solvent_accessibility')
diff --git a/modules/base/doc/base.rst b/modules/base/doc/base.rst
index 6e0a6caf5f16b2367498e4284a98a1f067be92dd..72d9ed9dcc547e63247afb10905942c1be04a8b0 100644
--- a/modules/base/doc/base.rst
+++ b/modules/base/doc/base.rst
@@ -5,3 +5,4 @@
logging
settings
+ testutils
diff --git a/modules/base/doc/logging.rst b/modules/base/doc/logging.rst
index 1a81d479490ced8accd47006543a4c9c247b6749..2637bd9e2822a32618b15fc341163b17da63325c 100644
--- a/modules/base/doc/logging.rst
+++ b/modules/base/doc/logging.rst
@@ -14,7 +14,17 @@ OpenStructure has a logging system going beyond what print statements can offer.
see :ref:`picking-logging-level`.
:param message: The message to be logged
- :type message: str
+ :type message: convertible to string
+
+ Similar to the built-int print function, several arguments can be passed to
+ the logging functions. The arguments will be converted to string and then
+ concatenated together, separated by space. For example:
+
+ .. code-block:: python
+
+ LogMessage('here be numbers', 1, 2)
+
+ will be converted to 'here be numbers 1 2'.
.. note::
@@ -125,6 +135,10 @@ To change the current log sink you can use the following methods:
Change the log sink back to the previous one. It is an error to pop the log
sink when there is only one log sink on the stack.
+.. method:: GetCurrentLogSink()
+
+ Get the current (active) log sink.
+
.. _picking-logging-level:
Guidelines for picking logging level
diff --git a/modules/base/doc/testutils.rst b/modules/base/doc/testutils.rst
new file mode 100644
index 0000000000000000000000000000000000000000..649a0b3b350a2b30866f98a11873672acefdc5fa
--- /dev/null
+++ b/modules/base/doc/testutils.rst
@@ -0,0 +1,7 @@
+:mod:`~ost.testutils` -- Utils for Running Python Unittests
+================================================================================
+
+.. module:: ost.testutils
+ :synopsis: Helper Functions to Run Python Unittests
+
+.. autofunction:: ost.testutils.RunTests
\ No newline at end of file
diff --git a/modules/base/pymod/CMakeLists.txt b/modules/base/pymod/CMakeLists.txt
index 3f4f748a509f9e43796cb4bde0edf2c5cc162fc8..6a011018fb032d44e07680e214e9bfcb5c14e454 100644
--- a/modules/base/pymod/CMakeLists.txt
+++ b/modules/base/pymod/CMakeLists.txt
@@ -4,7 +4,8 @@ set(OST_BASE_PYMOD_SOURCES
export_range.cc
export_units.cc
)
-
-pymod(NAME base OUTPUT_DIR ost
- CPP ${OST_BASE_PYMOD_SOURCES}
- PY __init__.py settings.py stutil.py table.py)
+if (NOT ENABLE_STATIC)
+ pymod(NAME base OUTPUT_DIR ost
+ CPP ${OST_BASE_PYMOD_SOURCES}
+ PY __init__.py settings.py stutil.py table.py xmlrunner.py testutils.py)
+endif()
diff --git a/modules/base/pymod/export_logger.cc b/modules/base/pymod/export_logger.cc
index 91baeaea09d1681291592b39ecbc104f5f991d8d..91eccbdec2922ab4b5c1167ef48c3ef6d1d8e301 100644
--- a/modules/base/pymod/export_logger.cc
+++ b/modules/base/pymod/export_logger.cc
@@ -17,6 +17,7 @@
// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
//------------------------------------------------------------------------------
#include <boost/python.hpp>
+#include <boost/python/raw_function.hpp>
using namespace boost::python;
#include <ost/log.hh>
@@ -25,10 +26,11 @@ using namespace boost::python;
using namespace ost;
+struct PyLogSink: public LogSink {
-namespace {
+};
-struct WrappedLogSink : public LogSink {
+struct WrappedLogSink : public PyLogSink, public wrapper<PyLogSink> {
WrappedLogSink(PyObject* self): self_(self)
{ }
virtual void LogMessage(const String& message , int severity)
@@ -76,27 +78,72 @@ void pop_log_sink()
Logger::Instance().PopSink();
}
+LogSinkPtr get_log_sink()
+{
+ return Logger::Instance().GetCurrentSink();
+}
-void log_error(const String& m) {LOG_ERROR(m);}
-void log_warning(const String& m) {LOG_WARNING(m);}
-void log_script(const String& m) {LOG_SCRIPT(m);}
-void log_info(const String& m) {LOG_INFO(m);}
-void log_verbose(const String& m) {LOG_VERBOSE(m);}
+String args_to_string(tuple args, dict kwargs)
+{
+ std::stringstream ss;
+ bool empty=true;
+ for (size_t i=0, l=len(args); i<l; ++i) {
+ if (!empty) {
+ ss << " ";
+ }
+ empty=false;
+ String string_val;
+ try {
+ string_val=extract<String>(args[i]);
+ } catch (...) {
+ string_val=extract<String>(args[i].attr("__str__")());
+ }
+ ss << string_val;
+ }
+ return ss.str();
+}
+
+object log_error(tuple args, dict kwargs)
+{
+ LOG_ERROR(args_to_string(args, kwargs));
+ return object();
+}
+object log_warning(tuple args, dict kwargs)
+{
+ LOG_WARNING(args_to_string(args, kwargs));
+ return object();
+}
+object log_script(tuple args, dict kwargs)
+{
+ LOG_SCRIPT(args_to_string(args, kwargs));
+ return object();
+}
+object log_info(tuple args, dict kwargs)
+{
+ LOG_INFO(args_to_string(args, kwargs));
+ return object();
+}
+object log_verbose(tuple args, dict kwargs)
+{
+ LOG_VERBOSE(args_to_string(args, kwargs));
+ return object();
+}
void reset_sinks()
{
Logger::Instance().ResetSinks();
}
-}
void export_Logger()
{
- class_<LogSink, WrappedLogSinkPtr,
+ class_<LogSink, LogSinkPtr, boost::noncopyable>("_LogSink", no_init)
+ .def("LogMessage", &LogSink::LogMessage)
+ ;
+ class_<PyLogSink, WrappedLogSinkPtr, bases<LogSink>,
boost::noncopyable>("LogSink")
.def("LogMessage", &WrappedLogSink::LogMessageDefault)
;
-
class_<MultiLogSink, MultiLogSinkPtr, bases<LogSink>,
boost::noncopyable >("MultiLogSink", init<>())
.def("AddSink",&MultiLogSink::AddSink)
@@ -109,16 +156,23 @@ void export_Logger()
.def("LogMessage", &FileLogSink::LogMessage)
;
+ class_<StringLogSink, StringLogSinkPtr, bases<LogSink>,
+ boost::noncopyable >("StringLogSink", init<>())
+ .def("LogMessage", &StringLogSink::LogMessage)
+ .def("GetLog", &StringLogSink::GetLog)
+ ;
+
def("PushVerbosityLevel",push_verb);
def("PopVerbosityLevel",pop_verb);
def("GetVerbosityLevel",get_verb);
def("PushLogSink",push_log_sink);
+ def("GetCurrentLogSink",get_log_sink);
def("PopLogSink",pop_log_sink);
- def("LogError",log_error);
- def("LogWarning",log_warning);
- def("LogInfo",log_info);
- def("LogScript", log_script);
- def("LogVerbose", log_verbose);
+ def("LogError", raw_function(log_error, 1));
+ def("LogWarning",raw_function(log_warning, 1));
+ def("LogInfo", raw_function(log_info, 1));
+ def("LogScript", raw_function(log_script, 1));
+ def("LogVerbose", raw_function(log_verbose, 1));
// this relatively ugly construct is required to work around a problem with
// the "ost" command-line interpreter. If we don't remove all the sinks from
diff --git a/modules/base/pymod/export_units.cc b/modules/base/pymod/export_units.cc
index 1a50040f4ce41877e4cdf52faca60f1e81372553..80fa61862bd49513f2dfcc69013477479d07c59a 100644
--- a/modules/base/pymod/export_units.cc
+++ b/modules/base/pymod/export_units.cc
@@ -30,8 +30,7 @@ using namespace ost;
#ifdef OST_STATIC_PROPERTY_WORKAROUND
-namespace {
- struct Units_ {
+struct Units_ {
Real get_m() { return Units::m; }
Real get_mm() { return Units::mm; }
Real get_nm() { return Units::nm; }
@@ -53,9 +52,8 @@ namespace {
Real get_kDa() { return Units::kDa; }
Real get_Da() { return Units::Da; }
Real get_C() { return Units::C; }
- };
+};
-} //ns
#endif
diff --git a/modules/base/pymod/table.py b/modules/base/pymod/table.py
index 4d6f3bdd45a6cf0535813f2e576698fca75c9cee..4bd1a9999738a8814554997a7e7ceb6d4e7c6cfe 100644
--- a/modules/base/pymod/table.py
+++ b/modules/base/pymod/table.py
@@ -1,8 +1,10 @@
import csv
import re
+import math
from ost import stutil
import itertools
import operator
+import cPickle
from ost import LogError, LogWarning, LogInfo, LogVerbose
def MakeTitle(col_name):
@@ -16,7 +18,11 @@ def IsStringLike(value):
return True
except:
return False
-
+
+def IsNullString(value):
+ value=value.strip().upper()
+ return value in ('', 'NULL', 'NONE', 'NA')
+
def IsScalar(value):
if IsStringLike(value):
return True
@@ -28,6 +34,38 @@ def IsScalar(value):
except:
return True
+def GuessColumnType(iterator):
+ empty=True
+ possibilities=set(['bool', 'int', 'float'])
+ for ele in iterator:
+ str_ele=str(ele).upper()
+ if IsNullString(str_ele):
+ continue
+ empty=False
+ if 'int' in possibilities:
+ try:
+ int(str_ele)
+ except ValueError:
+ possibilities.remove('int')
+
+ if 'float' in possibilities:
+ try:
+ float(str_ele)
+ except ValueError:
+ possibilities.remove('float')
+ if 'bool' in possibilities:
+ if str_ele not in set(['YES', 'NO', 'TRUE', 'FALSE']):
+ possibilities.remove('bool')
+
+ if len(possibilities)==0:
+ return 'string'
+ if len(possibilities)==2:
+ return 'int'
+ if empty:
+ return 'string'
+ # return the last element available
+ return possibilities.pop()
+
class BinaryColExpr:
def __init__(self, op, lhs, rhs):
self.op=op
@@ -85,7 +123,7 @@ class TableCol:
return BinaryColExpr(operator.div, self, rhs)
-class Table:
+class Table(object):
"""
The table class provides convenient access to data in tabular form. An empty
@@ -96,7 +134,7 @@ class Table:
tab=Table()
If you want to add columns directly when creating the table, column names
- and column types can be specified as follows
+ and *column types* can be specified as follows
.. code-block:: python
@@ -106,6 +144,17 @@ class Table:
float and bool, respectively. There will be no data in the table and thus,
the table will not contain any rows.
+ The following *column types* are supported:
+
+ ======= ========
+ name abbrev
+ ======= ========
+ string s
+ float f
+ int i
+ bool b
+ ======= ========
+
If you want to add data to the table in addition, use the following:
.. code-block:: python
@@ -232,11 +281,25 @@ class Table:
raise ValueError('Unknown type %s' % ty)
def GetColIndex(self, col):
+ '''
+ Returns the column index for the column with the given name.
+
+ :raises: ValueError if no column with the name is found
+ '''
if col not in self.col_names:
raise ValueError('Table has no column named "%s"' % col)
return self.col_names.index(col)
+ def GetColNames(self):
+ '''
+ Returns a list containing all column names.
+ '''
+ return self.col_names
+
def HasCol(self, col):
+ '''
+ Checks if the column with a given name is present in the table.
+ '''
return col in self.col_names
def __getitem__(self, k):
@@ -255,6 +318,14 @@ class Table:
r[col_index]=v
def ToString(self, float_format='%.3f', int_format='%d', rows=None):
+ '''
+ Convert the table into a string representation.
+ The output format can be modified for int and float type columns by
+ specifying a formatting string for the parameters 'float_format' and
+ 'int_format'.
+ The option 'rows' specify the range of rows to be printed. The parameter
+ must be a iterable containing two elements, e.g. [start_row, end_row].
+ '''
widths=[len(cn) for cn in self.col_names]
sel_rows=self.rows
if rows:
@@ -294,7 +365,7 @@ class Table:
def __str__(self):
return self.ToString()
- def _AddRowsFromDict(self, d, merge=False):
+ def _AddRowsFromDict(self, d, overwrite=False):
# get column indices
idxs = [self.GetColIndex(k) for k in d.keys()]
@@ -317,11 +388,11 @@ class Table:
new_row[idx] = self._Coerce(v, self.col_types[idx])
# partially overwrite existing row with new data
- if merge:
- merge_idx = self.GetColIndex(merge)
+ if overwrite:
+ overwrite_idx = self.GetColIndex(overwrite)
added = False
for i,r in enumerate(self.rows):
- if r[merge_idx]==new_row[merge_idx]:
+ if r[overwrite_idx]==new_row[overwrite_idx]:
for j,e in enumerate(self.rows[i]):
if new_row[j]==None:
new_row[j] = e
@@ -329,40 +400,49 @@ class Table:
added = True
break
- # if not merge or merge did not find appropriate row
- if not merge or not added:
+ # if not overwrite or overwrite did not find appropriate row
+ if not overwrite or not added:
self.rows.append(new_row)
- def AddRow(self, data, merge=None):
+ def AddRow(self, data, overwrite=None):
"""
- Add a row to the table. *row* may either a dictionary in which case the keys
- in the dictionary must match the column names. Columns not found in the dict
- will be initialized to None. Alternatively, if data is a list-like object,
- the row is initialized from the values in data. The number of items in data
- must match the number of columns in the table. A :class:`ValuerError` is
- raised otherwise.
+ Add a row to the table.
+
+ *row* may either be a dictionary or a list-like object.
+ In the case of a dictionary the keys in the dictionary must match the column
+ names. Columns not found in the dict will be initialized to None.
+ Alternatively, if data is a list-like object, the row is initialized from
+ the values in data. The number of items in data must match the number of
+ columns in the table. A :class:`ValuerError` is raised otherwise. The values
+ are added in the order specified in the list, thus, the order of the data
+ must match the columns.
+
+ If *overwrite* is set and not None (must be set to an existing column name),
+ an existing row is overwritten if the value of column *overwrite* matches.
+ If no matching row is found, a new row is appended to the table.
"""
if type(data)==dict:
- self._AddRowsFromDict(data, merge)
+ self._AddRowsFromDict(data, overwrite)
else:
if len(data)!=len(self.col_names):
+ print data, self.col_names
msg='data array must have %d elements, not %d'
- raise ValueError(msg % (len(self.col_names), len(self.data)))
+ raise ValueError(msg % (len(self.col_names), len(data)))
new_row = [self._Coerce(v, t) for v, t in zip(data, self.col_types)]
# fully overwrite existing row with new data
- if merge:
- merge_idx = self.GetColIndex(merge)
+ if overwrite:
+ overwrite_idx = self.GetColIndex(overwrite)
added = False
for i,r in enumerate(self.rows):
- if r[merge_idx]==new_row[merge_idx]:
+ if r[overwrite_idx]==new_row[overwrite_idx]:
self.rows[i] = new_row
added = True
break
- # if not merge or merge did not find appropriate row
- if not merge or not added:
+ # if not overwrite or overwrite did not find appropriate row
+ if not overwrite or not added:
self.rows.append(new_row)
def RemoveCol(self, col):
@@ -448,22 +528,9 @@ class Table:
return filt_tab
@staticmethod
- def Load(stream_or_filename):
- """
- Load table from stream or file with given name. The file must contain a
- header line of the form
-
- col_name1[type1] <col_name2[type2]>...
-
- The types given in brackets must be one of the data types the :class:`Table`
- class understands. Each following line in the file then must contains exactly
- the same number of data items as listed in the header. The data items are
- automatically converted to the column format. Lines starting with a '#' and
- empty lines are ignored.
-
- :returns: A new :class:`Table` instance
- """
- fieldname_pattern=re.compile(r'(?P<name>[A-Za-z0-9_]+)(\[(?P<type>\w+)\])?')
+ def _LoadOST(stream_or_filename):
+ fieldname_pattern=re.compile(r'(?P<name>[^[]+)(\[(?P<type>\w+)\])?')
+ values_pattern=re.compile("([^\" ]+|\"[^\"]*\")+")
if not hasattr(stream_or_filename, 'read'):
stream=open(stream_or_filename, 'r')
else:
@@ -486,16 +553,104 @@ class Table:
if match.group('type'):
fieldtypes.append(match.group('type'))
else:
- fieldtypes.append('str')
+ fieldtypes.append('string')
fieldnames.append(match.group('name'))
tab=Table(fieldnames, fieldtypes)
header=True
continue
- tab.AddRow(line.split())
+ tab.AddRow([x.strip('"') for x in values_pattern.findall(line)])
if num_lines==0:
raise IOError("Cannot read table from empty stream")
return tab
+ def _GuessColumnTypes(self):
+ for col_idx in range(len(self.col_names)):
+ self.col_types[col_idx]=GuessColumnType(self[self.col_names[col_idx]])
+ for row in self.rows:
+ for idx in range(len(row)):
+ row[idx]=self._Coerce(row[idx], self.col_types[idx])
+
+ @staticmethod
+ def _LoadCSV(stream_or_filename, sep):
+ if not hasattr(stream_or_filename, 'read'):
+ stream=open(stream_or_filename, 'r')
+ else:
+ stream=stream_or_filename
+ reader=csv.reader(stream, delimiter=sep)
+ first=True
+ for row in reader:
+ if first:
+ header=row
+ types='s'*len(row)
+ tab=Table(header, types)
+ first=False
+ else:
+ tab.AddRow(row)
+ if first:
+ raise IOError('trying to load table from empty CSV stream/file')
+
+ tab._GuessColumnTypes()
+ return tab
+
+ @staticmethod
+ def _LoadPickle(stream_or_filename):
+ if not hasattr(stream_or_filename, 'read'):
+ stream=open(stream_or_filename, 'rb')
+ else:
+ stream=stream_or_filename
+ return cPickle.load(stream)
+
+ @staticmethod
+ def Load(stream_or_filename, format='ost', sep=','):
+ """
+ Load table from stream or file with given name.
+
+ By default, the file format is *ost* (see below) and is *not* automatically
+ determined (e.g. from file extension). Thus, it *format* must be specified
+ for reading other file formats.
+
+ The following file formats are understood:
+
+ - ost
+
+ This is an ost-specific, but still human readable file format. The file
+ (stream) must start with header line of the form
+
+ col_name1[type1] <col_name2[type2]>...
+
+ The types given in brackets must be one of the data types the
+ :class:`Table` class understands. Each following line in the file then must
+ contains exactly the same number of data items as listed in the header. The
+ data items are automatically converted to the column format. Lines starting
+ with a '#' and empty lines are ignored.
+
+ - pickle
+
+ Deserializes the table from a pickled byte stream
+
+ - csv
+
+ Reads the table from comma separated values stream. Since there is no
+ explicit type information in the csv file, the column types are guessed,
+ using the following simple rules:
+
+ * if all values are either NA/NULL/NONE the type is set to string
+ * if all non-null values are convertible to float/int the type is set to
+ float/int
+ * if all non-null values are true/false/yes/no, the value is set to bool
+ * for all other cases, the column type is set to string
+
+ :returns: A new :class:`Table` instance
+ """
+ format=format.lower()
+ if format=='ost':
+ return Table._LoadOST(stream_or_filename)
+ if format=='csv':
+ return Table._LoadCSV(stream_or_filename, sep=sep)
+ if format=='pickle':
+ return Table._LoadPickle(stream_or_filename)
+ raise ValueError('unknown format ""' % format)
+
def Sort(self, by, order='+'):
"""
Performs an in-place sort of the table, based on column.
@@ -508,19 +663,34 @@ class Table:
return sign*cmp(lhs[key_index], rhs[key_index])
self.rows=sorted(self.rows, _key_cmp)
+ def GetUnique(self, col, ignore_nan=True):
+ """
+ Extract a list of all unique values from one column
+ """
+ idx = self.GetColIndex(col)
+ seen = {}
+ result = []
+ for row in self.rows:
+ item = row[idx]
+ if item!=None or ignore_nan==False:
+ if item in seen: continue
+ seen[item] = 1
+ result.append(item)
+ return result
+
def Zip(self, *args):
"""
Allows to conveniently iterate over a selection of columns, e.g.
- .. code-block::python
+ .. code-block:: python
tab=Table.Load('...')
- for col1, col in tab.Zip('col1', 'col2'):
+ for col1, col2 in tab.Zip('col1', 'col2'):
print col1, col2
is a shortcut for
- .. code-block::python
+ .. code-block:: python
tab=Table.Load('...')
for col1, col2 in zip(tab['col1'], tab['col2']):
@@ -530,8 +700,9 @@ class Table:
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,
- num_z_levels=10, diag_line=False, labels=None, title=None,
- clear=True, save=False):
+ color=None, plot_if=None, legend=None,
+ num_z_levels=10, diag_line=False, labels=None, max_num_labels=None,
+ title=None, clear=True, save=False, **kwargs):
"""
Plot x against y using matplot lib
"""
@@ -543,9 +714,9 @@ class Table:
xs = []
ys = []
zs = []
-
+
if clear:
- plt.clf()
+ plt.figure(figsize=[8, 6])
if x_title:
nice_x=x_title
@@ -567,12 +738,17 @@ class Table:
nice_z = MakeTitle(z)
else:
nice_z = None
-
+ if color:
+ kwargs['color']=color
+ if legend:
+ kwargs['label']=legend
if y and z:
idx3 = self.GetColIndex(z)
idx2 = self.GetColIndex(y)
for row in self.rows:
if row[idx1]!=None and row[idx2]!=None and row[idx3]!=None:
+ if plot_if and not plot_if(self, row):
+ continue
xs.append(row[idx1])
ys.append(row[idx2])
zs.append(row[idx3])
@@ -590,7 +766,7 @@ class Table:
xi = np.linspace(min(xs)-0.1,max(xs)+0.1,len(xs)*10)
yi = np.linspace(min(ys)-0.1,max(ys)+0.1,len(ys)*10)
- zi = mlab.griddata(xs, ys, zs, xi, yi, interp='linear')
+ zi = mlab.griddata(xs, ys, zs, xi, yi)
plt.contour(xi,yi,zi,levels,linewidths=0.5,colors='k')
plt.contourf(xi,yi,zi,levels,cmap=plt.cm.jet)
@@ -600,9 +776,11 @@ class Table:
idx2=self.GetColIndex(y)
for row in self.rows:
if row[idx1]!=None and row[idx2]!=None:
+ if plot_if and not plot_if(self, row):
+ continue
xs.append(row[idx1])
ys.append(row[idx2])
- plt.plot(xs, ys, style)
+ plt.plot(xs, ys, style, **kwargs)
else:
label_vals=[]
@@ -611,14 +789,22 @@ class Table:
label_idx=self.GetColIndex(labels)
for row in self.rows:
if row[idx1]!=None:
+ if plot_if and not plot_if(self, row):
+ continue
xs.append(row[idx1])
if labels:
label_vals.append(row[label_idx])
- plt.plot(xs, style)
+ plt.plot(xs, style, **kwargs)
if labels:
- plt.xticks(np.arange(len(xs)), label_vals, rotation=45, size='x-small')
+ interval = 1
+ if max_num_labels:
+ if len(label_vals)>max_num_labels:
+ interval = int(math.ceil(float(len(label_vals))/max_num_labels))
+ label_vals = label_vals[::interval]
+ plt.xticks(np.arange(0, len(xs), interval), label_vals, rotation=45,
+ size='x-small')
- if not title:
+ if title==None:
if nice_z:
title = '%s of %s vs. %s' % (nice_z, nice_x, nice_y)
elif nice_y:
@@ -626,7 +812,12 @@ class Table:
else:
title = nice_x
- plt.title(title, size='x-large', fontweight='bold')
+ plt.title(title, size='x-large', fontweight='bold',
+ verticalalignment='bottom')
+
+ if legend:
+ plt.legend(loc=0)
+
if x and y:
plt.xlabel(nice_x, size='x-large')
if x_range:
@@ -638,7 +829,11 @@ class Table:
plt.ylabel(nice_y, size='x-large')
else:
- plt.ylabel(nice_x, size='x-large')
+ if y_range:
+ plt.ylim(y_range[0], y_range[1])
+ if x_title:
+ plt.xlabel(x_title, size='x-large')
+ plt.ylabel(nice_y, size='x-large')
if save:
plt.savefig(save)
return plt
@@ -650,8 +845,8 @@ class Table:
histtype='stepfilled', align='mid', x_title=None,
y_title=None, title=None, clear=True, save=False):
"""
- Create a histogram of the data in col for the range x_range, split into
- num_bins bins and plot it using matplot lib
+ Create a histogram of the data in col for the range *x_range*, split into
+ *num_bins* bins and plot it using matplot lib.
"""
try:
import matplotlib.pyplot as plt
@@ -788,11 +983,12 @@ class Table:
def Sum(self, col):
"""
Returns the sum of the given column. Cells with None are ignored. Returns
- 0.0, if the column doesn't contain any elements.
+ 0.0, if the column doesn't contain any elements. Col must be of numeric
+ column type ('float', 'int') or boolean column type.
"""
idx = self.GetColIndex(col)
col_type = self.col_types[idx]
- if col_type!='int' and col_type!='float':
+ if col_type!='int' and col_type!='float' and col_type!='bool':
raise TypeError("Sum can only be used on numeric column types")
s = 0.0
for r in self.rows:
@@ -803,12 +999,16 @@ class Table:
def Mean(self, col):
"""
Returns the mean of the given column. Cells with None are ignored. Returns
- None, if the column doesn't contain any elements.
+ None, if the column doesn't contain any elements. Col must be of numeric
+ ('float', 'int') or boolean column type.
+
+ If column type is *bool*, the function returns the ratio of
+ number of 'Trues' by total number of elements.
"""
idx = self.GetColIndex(col)
col_type = self.col_types[idx]
- if col_type!='int' and col_type!='float':
- raise TypeError("Mean can only be used on numeric column types")
+ if col_type!='int' and col_type!='float' and col_type!='bool':
+ raise TypeError("Mean can only be used on numeric or bool column types")
vals=[]
for v in self[col]:
@@ -819,15 +1019,81 @@ class Table:
except:
return None
+ def RowMean(self, mean_col_name, cols):
+ """
+ Adds a new column of type 'float' with a specified name (mean_col),
+ containing the mean of all specified columns for each row.
+
+ Cols are specified by their names and must be of numeric column
+ type ('float', 'int') or boolean column type.. Cells with None are ignored.
+ Adds None if the row doesn't contain any values.
+
+
+ == Example ==
+
+ Staring with the following table:
+
+ ==== ==== ====
+ x y u
+ ==== ==== ====
+ 1 10 100
+ 2 15 None
+ 3 20 400
+ ==== ==== ====
+
+ the code here adds a column with the name 'mean' to yield the table below:
+
+ .. code-block::python
+
+ tab.RowMean('mean', 'x', 'u')
+
+
+ ==== ==== ==== =====
+ x y u mean
+ ==== ==== ==== =====
+ 1 10 100 50.5
+ 2 15 None 2
+ 3 20 400 201.5
+ ==== ==== ==== =====
+
+ """
+
+ if IsScalar(cols):
+ cols = [cols]
+
+ cols_idxs = []
+ for col in cols:
+ idx = self.GetColIndex(col)
+ col_type = self.col_types[idx]
+ if col_type!='int' and col_type!='float' and col_type!='bool':
+ raise TypeError("RowMean can only be used on numeric column types")
+ cols_idxs.append(idx)
+
+ mean_rows = []
+ for row in self.rows:
+ vals = []
+ for idx in cols_idxs:
+ v = row[idx]
+ if v!=None:
+ vals.append(v)
+ try:
+ mean = stutil.Mean(vals)
+ mean_rows.append(mean)
+ except:
+ mean_rows.append(None)
+
+ self.AddCol(mean_col_name, 'f', mean_rows)
+
def Median(self, col):
"""
Returns the median of the given column. Cells with None are ignored. Returns
- None, if the column doesn't contain any elements.
+ None, if the column doesn't contain any elements. Col must be of numeric
+ column type ('float', 'int') or boolean column type.
"""
idx = self.GetColIndex(col)
col_type = self.col_types[idx]
- if col_type!='int' and col_type!='float':
- raise TypeError("Mean can only be used on numeric column types")
+ if col_type!='int' and col_type!='float' and col_type!='bool':
+ raise TypeError("Median can only be used on numeric column types")
vals=[]
for v in self[col]:
@@ -842,12 +1108,13 @@ class Table:
def StdDev(self, col):
"""
Returns the standard deviation of the given column. Cells with None are
- ignored. Returns None, if the column doesn't contain any elements.
+ ignored. Returns None, if the column doesn't contain any elements. Col must
+ be of numeric column type ('float', 'int') or boolean column type.
"""
idx = self.GetColIndex(col)
col_type = self.col_types[idx]
- if col_type!='int' and col_type!='float':
- raise TypeError("Mean can only be used on numeric column types")
+ if col_type!='int' and col_type!='float' and col_type!='bool':
+ raise TypeError("StdDev can only be used on numeric column types")
vals=[]
for v in self[col]:
@@ -879,6 +1146,9 @@ class Table:
there are not enough data points to calculate a correlation coefficient,
None is returned.
"""
+ if IsStringLike(col1) and IsStringLike(col2):
+ col1 = self.GetColIndex(col1)
+ col2 = self.GetColIndex(col2)
vals1, vals2=([],[])
for v1, v2 in zip(self[col1], self[col2]):
if v1!=None and v2!=None:
@@ -889,10 +1159,72 @@ class Table:
except:
return None
- def Save(self, stream):
+ def SpearmanCorrel(self, col1, col2):
+ """
+ Calculate the Spearman correlation coefficient between col1 and col2, only
+ taking rows into account where both of the values are not equal to None. If
+ there are not enough data points to calculate a correlation coefficient,
+ None is returned.
+
+ The function depends on the following module: *scipy.stats.mstats*
+ """
+ try:
+ import scipy.stats.mstats
+
+ if IsStringLike(col1) and IsStringLike(col2):
+ col1 = self.GetColIndex(col1)
+ col2 = self.GetColIndex(col2)
+ vals1, vals2=([],[])
+ for v1, v2 in zip(self[col1], self[col2]):
+ if v1!=None and v2!=None:
+ vals1.append(v1)
+ vals2.append(v2)
+ try:
+ correl = scipy.stats.mstats.spearmanr(vals1, vals2)[0]
+ if scipy.isnan(correl):
+ return None
+ return correl
+ except:
+ return None
+
+ except ImportError:
+ LogError("Function needs scipy.stats.mstats, but I could not import it.")
+ raise
+
+
+ def Save(self, stream_or_filename, format='ost', sep=','):
"""
- Save the table to stream or filename
+ Save the table to stream or filename. For supported file formats, see
+ :meth:`Load`
"""
+ format=format.lower()
+ if format=='ost':
+ return self._SaveOST(stream_or_filename)
+ if format=='csv':
+ return self._SaveCSV(stream_or_filename, sep=sep)
+ if format=='pickle':
+ return self._SavePickle(stream_or_filename)
+ raise ValueError('unknown format "%s"' % format)
+
+ def _SavePickle(self, stream):
+ if not hasattr(stream, 'write'):
+ stream=open(stream, 'wb')
+ cPickle.dump(self, stream, cPickle.HIGHEST_PROTOCOL)
+
+ def _SaveCSV(self, stream, sep):
+ if not hasattr(stream, 'write'):
+ stream=open(stream, 'wb')
+
+ writer=csv.writer(stream, delimiter=sep)
+ writer.writerow(['%s' % n for n in self.col_names])
+ for row in self.rows:
+ row=list(row)
+ for i, c in enumerate(row):
+ if c==None:
+ row[i]='NA'
+ writer.writerow(row)
+
+ def _SaveOST(self, stream):
if hasattr(stream, 'write'):
writer=csv.writer(stream, delimiter=' ')
else:
@@ -1020,7 +1352,9 @@ class Table:
style='-', title=None, x_title=None, y_title=None,
clear=True, save=None):
'''
- Plot an enrichment curve using matplotlib
+ Plot an enrichment curve using matplotlib.
+
+ For more information about parameters, see :meth:`ComputeEnrichment`
'''
try:
@@ -1120,7 +1454,9 @@ class Table:
class_dir='-', class_cutoff=2.0):
'''
Computes the area under the curve of the enrichment using the trapezoidal
- rule
+ rule.
+
+ For more information about parameters, see :meth:`ComputeEnrichment`
'''
try:
import numpy as np
@@ -1133,6 +1469,242 @@ class Table:
LogError("Function needs numpy, but I could not import it.")
raise
+ def ComputeROC(self, score_col, class_col, score_dir='-',
+ class_dir='-', class_cutoff=2.0):
+ '''
+ Computes the receiver operating characteristics of one column (e.g. score)
+ over all data points.
+
+ For this it is necessary, that the datapoints are classified into positive
+ and negative points. This can be done in two ways:
+
+ - by using one 'bool' column (*class_col*) which contains True for positives
+ and False for negatives
+ - by using a non-bool column (*class_col*), a cutoff value (*class_cutoff*)
+ and the classification columns direction (*class_dir*). This will generate
+ the classification on the fly
+
+ - if *class_dir* =='-': values in the classification column that are
+ less than or equal to *class_cutoff* will be counted
+ as positives
+ - if *class_dir* =='+': values in the classification column that are
+ larger than or equal to *class_cutoff* will be
+ counted as positives
+
+ During the calculation, the table will be sorted according to *score_dir*,
+ where a '-' values means smallest values first and therefore, the smaller
+ the value, the better.
+
+ If *class_col* does not contain any positives (i.e. value is True (if column
+ is of type bool) or evaluated to True (if column is of type int or float
+ (depending on *class_dir* and *class_cutoff*))) the ROC is not defined and
+ the function will return *None*.
+ '''
+
+ ALLOWED_DIR = ['+','-']
+
+ score_idx = self.GetColIndex(score_col)
+ score_type = self.col_types[score_idx]
+ if score_type!='int' and score_type!='float':
+ raise TypeError("Score column must be numeric type")
+
+ class_idx = self.GetColIndex(class_col)
+ class_type = self.col_types[class_idx]
+ if class_type!='int' and class_type!='float' and class_type!='bool':
+ raise TypeError("Classifier column must be numeric or bool type")
+
+ if (score_dir not in ALLOWED_DIR) or (class_dir not in ALLOWED_DIR):
+ raise ValueError("Direction must be one of %s"%str(ALLOWED_DIR))
+
+ self.Sort(score_col, score_dir)
+
+ x = [0]
+ y = [0]
+ tp = 0
+ fp = 0
+ old_score_val = None
+
+ for i,row in enumerate(self.rows):
+ class_val = row[class_idx]
+ score_val = row[score_idx]
+ if class_val!=None:
+ if old_score_val==None:
+ old_score_val = score_val
+ if score_val!=old_score_val:
+ x.append(fp)
+ y.append(tp)
+ old_score_val = score_val
+ if class_type=='bool':
+ if class_val==True:
+ tp += 1
+ else:
+ fp += 1
+ else:
+ if (class_dir=='-' and class_val<=class_cutoff) or (class_dir=='+' and class_val>=class_cutoff):
+ tp += 1
+ else:
+ fp += 1
+ x.append(fp)
+ y.append(tp)
+
+ # if no false positives or false negatives values are found return None
+ if x[-1]==0 or y[-1]==0:
+ return None
+
+ x = [float(v)/x[-1] for v in x]
+ y = [float(v)/y[-1] for v in y]
+ return x,y
+
+ def ComputeROCAUC(self, score_col, class_col, score_dir='-',
+ class_dir='-', class_cutoff=2.0):
+ '''
+ Computes the area under the curve of the receiver operating characteristics
+ using the trapezoidal rule.
+
+ For more information about parameters, see :meth:`ComputeROC`
+ '''
+ try:
+ import numpy as np
+
+ roc = self.ComputeROC(score_col, class_col, score_dir,
+ class_dir, class_cutoff)
+
+ if not roc:
+ return None
+ return np.trapz(roc[1], roc[0])
+ except ImportError:
+ LogError("Function needs numpy, but I could not import it.")
+ raise
+
+ def PlotROC(self, score_col, class_col, score_dir='-',
+ class_dir='-', class_cutoff=2.0,
+ style='-', title=None, x_title=None, y_title=None,
+ clear=True, save=None):
+ '''
+ Plot an ROC curve using matplotlib.
+
+ For more information about parameters, see :meth:`ComputeROC`
+ '''
+
+ try:
+ import matplotlib.pyplot as plt
+
+ roc = self.ComputeROC(score_col, class_col, score_dir,
+ class_dir, class_cutoff)
+
+ if not roc:
+ return None
+
+ enrx, enry = roc
+
+ if not title:
+ title = 'ROC of %s'%score_col
+
+ if not x_title:
+ x_title = 'false positive rate'
+
+ if not y_title:
+ y_title = 'true positive rate'
+
+ if clear:
+ plt.clf()
+
+ plt.plot(enrx, enry, style)
+
+ plt.title(title, size='x-large', fontweight='bold')
+ plt.ylabel(y_title, size='x-large')
+ plt.xlabel(x_title, size='x-large')
+
+ if save:
+ plt.savefig(save)
+
+ return plt
+ except ImportError:
+ LogError("Function needs matplotlib, but I could not import it.")
+ raise
+
+ def ComputeMCC(self, score_col, class_col, score_dir='-',
+ class_dir='-', score_cutoff=2.0, class_cutoff=2.0):
+ '''
+ Compute Matthews correlation coefficient (MCC) for one column (*score_col*)
+ with the points classified into true positives, false positives, true
+ negatives and false negatives according to a specified classification
+ column (*class_col*).
+
+ The datapoints in *score_col* and *class_col* are classified into
+ positive and negative points. This can be done in two ways:
+
+ - by using 'bool' columns which contains True for positives and False
+ for negatives
+
+ - by using 'float' or 'int' columns and specifying a cutoff value and the
+ columns direction. This will generate the classification on the fly
+
+ * if *class_dir*/*score_dir*=='-': values in the classification column
+ that are less than or equal to
+ *class_cutoff*/*score_cutoff* will be
+ counted as positives
+ * if *class_dir*/*score_dir*=='+': values in the classification column
+ that are larger than or equal to
+ *class_cutoff*/*score_cutoff* will be
+ counted as positives
+
+ The two possibilities can be used together, i.e. 'bool' type for one column
+ and 'float'/'int' type and cutoff/direction for the other column.
+ '''
+ ALLOWED_DIR = ['+','-']
+
+ score_idx = self.GetColIndex(score_col)
+ score_type = self.col_types[score_idx]
+ if score_type!='int' and score_type!='float' and score_type!='bool':
+ raise TypeError("Score column must be numeric or bool type")
+
+ class_idx = self.GetColIndex(class_col)
+ class_type = self.col_types[class_idx]
+ if class_type!='int' and class_type!='float' and class_type!='bool':
+ raise TypeError("Classifier column must be numeric or bool type")
+
+ if (score_dir not in ALLOWED_DIR) or (class_dir not in ALLOWED_DIR):
+ raise ValueError("Direction must be one of %s"%str(ALLOWED_DIR))
+
+ tp = 0
+ fp = 0
+ fn = 0
+ tn = 0
+
+ for i,row in enumerate(self.rows):
+ class_val = row[class_idx]
+ score_val = row[score_idx]
+ if class_val!=None:
+ if (class_type=='bool' and class_val==True) or (class_type!='bool' and ((class_dir=='-' and class_val<=class_cutoff) or (class_dir=='+' and class_val>=class_cutoff))):
+ if (score_type=='bool' and score_val==True) or (score_type!='bool' and ((score_dir=='-' and score_val<=score_cutoff) or (score_dir=='+' and score_val>=score_cutoff))):
+ tp += 1
+ else:
+ fn += 1
+ else:
+ if (score_type=='bool' and score_val==False) or (score_type!='bool' and ((score_dir=='-' and score_val>score_cutoff) or (score_dir=='+' and score_val<score_cutoff))):
+ tn += 1
+ else:
+ fp += 1
+
+ mcc = None
+ msg = None
+ if (tp+fn)==0:
+ msg = 'factor (tp + fn) is zero'
+ elif (tp+fp)==0:
+ msg = 'factor (tp + fp) is zero'
+ elif (tn+fn)==0:
+ msg = 'factor (tn + fn) is zero'
+ elif (tn+fp)==0:
+ msg = 'factor (tn + fp) is zero'
+
+ if msg:
+ LogWarning("Could not compute MCC: MCC is not defined since %s"%msg)
+ else:
+ mcc = ((tp*tn)-(fp*fn)) / math.sqrt((tp+fn)*(tp+fp)*(tn+fn)*(tn+fp))
+ return mcc
+
+
def IsEmpty(self, col_name=None, ignore_nan=True):
'''
Checks if a table is empty.
@@ -1169,12 +1741,52 @@ class Table:
return False
return True
+ def Extend(self, tab, overwrite=None):
+ """
+ Append each row of *tab* to the current table. The data is appended based
+ on the column names, thus the order of the table columns is *not* relevant,
+ only the header names.
+
+ If there is a column in *tab* that is not present in the current table,
+ it is added to the current table and filled with *None* for all the rows
+ present in the current table.
+
+ If the type of any column in *tab* is not the same as in the current table
+ a *TypeError* is raised.
+
+ If *overwrite* is set and not None (must be set to an existing column name),
+ an existing row is overwritten if the value of column *overwrite* matches.
+ If no matching row is found, a new row is appended to the table.
+ """
+ # add column to current table if it doesn't exist
+ for name,typ in zip(tab.col_names, tab.col_types):
+ if not name in self.col_names:
+ self.AddCol(name, typ)
+
+ # check that column types are the same in current and new table
+ for name in self.col_names:
+ if name in tab.col_names:
+ curr_type = self.col_types[self.GetColIndex(name)]
+ new_type = tab.col_types[tab.GetColIndex(name)]
+ if curr_type!=new_type:
+ raise TypeError('cannot extend table, column %s in new '%name +\
+ 'table different type (%s) than in '%new_type +\
+ 'current table (%s)'%curr_type)
+
+ num_rows = len(tab.rows)
+ for i in range(0,num_rows):
+ row = tab.rows[i]
+ data = dict(zip(tab.col_names,row))
+ self.AddRow(data, overwrite)
+
def Merge(table1, table2, by, only_matching=False):
"""
Returns a new table containing the data from both tables. The rows are
- combined based on the common values in the column by. For example, the two
- tables below
+ combined based on the common values in the column(s) by. The option 'by' can
+ be a list of column names. When this is the case, merging is based on
+ multiple columns.
+ For example, the two tables below
==== ====
x y
@@ -1269,4 +1881,4 @@ def Merge(table1, table2, by, only_matching=False):
new_tab.AddRow(row)
return new_tab
-
\ No newline at end of file
+
diff --git a/modules/base/pymod/testutils.py b/modules/base/pymod/testutils.py
new file mode 100644
index 0000000000000000000000000000000000000000..fe3e7a024d0c19baea30fa663549f5513489870a
--- /dev/null
+++ b/modules/base/pymod/testutils.py
@@ -0,0 +1,54 @@
+def RunTests():
+ '''
+ This function behaves as a custom TestLoader for python unittests.
+
+ With no system arguments, the default unittest TestRunner is used.
+
+ If the first system argument (sys.argv[1]) is set to 'xml', a XMLTestRunner
+ is used, which produces a JUnit compatible XML output file. Within the current
+ module, each function is identified which is a subclass of unittest.TestCase
+ and for each TestCase, a test suite is executed, producing an individual
+ output file for each TestCase. The output file has the name,
+ 'PYTEST-<TestCaseName>.xml'.
+
+ Example of a Python testcase:
+
+ .. code-block:: python
+
+ import unittest
+
+ class TestRenumber(unittest.TestCase):
+
+ def setUp(self):
+ # prepare stuff"
+ pass
+
+ def testSomeFunction(self):
+ # do some asserts
+ pass
+
+ if __name__ == "__main__":
+ from ost import testutils
+ testutils.RunTests()
+
+ '''
+ import unittest
+ import sys
+ try:
+ if len(sys.argv)>1 and sys.argv[1]=='xml':
+ import inspect
+ import types
+ import __main__
+ from ost import xmlrunner
+ for name, obj in inspect.getmembers(__main__):
+ if (isinstance(obj, (type, types.ClassType)) and
+ issubclass(obj, unittest.TestCase)):
+ suite = unittest.TestLoader().loadTestsFromTestCase(obj)
+ stream = open('PYTEST-%s.xml'%name, 'w')
+ xmlrunner.XMLTestRunner(stream).run(suite)
+ stream.close()
+
+ else:
+ unittest.main()
+ except Exception, e:
+ print e
\ No newline at end of file
diff --git a/modules/base/pymod/wrap_base.cc b/modules/base/pymod/wrap_base.cc
index 1ba0b15718baec2fbf014e9301583d052a3d2205..40ad33717f79c38e58c21624b87736f387016f3c 100644
--- a/modules/base/pymod/wrap_base.cc
+++ b/modules/base/pymod/wrap_base.cc
@@ -21,6 +21,7 @@
#include <vector>
#include <ost/geom/export_helper/vector.hh>
#include <ost/base.hh>
+#include <ost/string_ref.hh>
#include <ost/platform.hh>
#include <ost/message.hh>
#include <ost/version.hh>
@@ -38,8 +39,48 @@ void translator(const ost::Error& x) {
}
+struct stringref_to_python_string
+{
+ static PyObject* convert(ost::StringRef const& s)
+ {
+ return boost::python::incref(boost::python::object(s.str()).ptr());
+ }
+};
+
+struct stringref_from_python_string
+{
+ stringref_from_python_string()
+ {
+ boost::python::converter::registry::push_back(&convertible,
+ &construct,
+ boost::python::type_id<ost::StringRef>());
+ }
+
+ static void* convertible(PyObject* obj_ptr)
+ {
+ if (!PyString_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();
+ void* storage = (
+ (boost::python::converter::rvalue_from_python_storage<ost::StringRef>*)
+ data)->storage.bytes;
+ new (storage) ost::StringRef(value, strlen(value));
+ data->convertible = storage;
+ }
+};
+
+
BOOST_PYTHON_MODULE(_ost_base)
{
+ boost::python::to_python_converter<ost::StringRef,
+ stringref_to_python_string>();
+ stringref_from_python_string();
register_exception_translator<ost::Error>(&translator);
def("SetPrefixPath", &ost::SetPrefixPath);
@@ -50,6 +91,7 @@ BOOST_PYTHON_MODULE(_ost_base)
scope().attr("VERSION_MAJOR")=OST_VERSION_MAJOR;
scope().attr("VERSION_MINOR")=OST_VERSION_MINOR;
scope().attr("VERSION_PATCH")=OST_VERSION_PATCH;
+ scope().attr("WITH_NUMPY")= OST_NUMPY_SUPPORT_ENABLED;
export_Logger();
export_Range();
export_Units();
@@ -67,5 +109,5 @@ BOOST_PYTHON_MODULE(_ost_base)
class_<std::vector<int> >("IntList", init<>())
.def(vector_indexing_suite<std::vector<int> >())
.def(geom::VectorAdditions<IntList>())
- ;
+ ;
}
diff --git a/modules/base/pymod/xmlrunner.py b/modules/base/pymod/xmlrunner.py
new file mode 100644
index 0000000000000000000000000000000000000000..e2bcae76df26efef15363d6775dca6b8bbd0bc34
--- /dev/null
+++ b/modules/base/pymod/xmlrunner.py
@@ -0,0 +1,390 @@
+"""
+XML Test Runner for PyUnit
+"""
+
+# Written by Sebastian Rittau <srittau@jroger.in-berlin.de> and placed in
+# the Public Domain. With contributions by Paolo Borelli and others.
+
+__version__ = "0.1"
+
+import os.path
+import re
+import sys
+import time
+import traceback
+import unittest
+from xml.sax.saxutils import escape
+
+try:
+ from StringIO import StringIO
+except ImportError:
+ from io import StringIO
+
+
+class _TestInfo(object):
+
+ """Information about a particular test.
+
+ Used by _XMLTestResult.
+
+ """
+
+ def __init__(self, test, time):
+ (self._class, self._method) = test.id().rsplit(".", 1)
+ self._time = time
+ self._error = None
+ self._failure = None
+
+ @staticmethod
+ def create_success(test, time):
+ """Create a _TestInfo instance for a successful test."""
+ return _TestInfo(test, time)
+
+ @staticmethod
+ def create_failure(test, time, failure):
+ """Create a _TestInfo instance for a failed test."""
+ info = _TestInfo(test, time)
+ info._failure = failure
+ return info
+
+ @staticmethod
+ def create_error(test, time, error):
+ """Create a _TestInfo instance for an erroneous test."""
+ info = _TestInfo(test, time)
+ info._error = error
+ return info
+
+ def print_report(self, stream):
+ """Print information about this test case in XML format to the
+ supplied stream.
+
+ """
+ stream.write(' <testcase classname="%(class)s" name="%(method)s" time="%(time).4f">' % \
+ {
+ "class": self._class,
+ "method": self._method,
+ "time": self._time,
+ })
+ if self._failure is not None:
+ self._print_error(stream, 'failure', self._failure)
+ if self._error is not None:
+ self._print_error(stream, 'error', self._error)
+ stream.write('</testcase>\n')
+
+ def _print_error(self, stream, tagname, error):
+ """Print information from a failure or error to the supplied stream."""
+ text = escape(str(error[1]))
+ stream.write('\n')
+ stream.write(' <%s type="%s">%s\n' \
+ % (tagname, _clsname(error[0]), text))
+ tb_stream = StringIO()
+ traceback.print_tb(error[2], None, tb_stream)
+ stream.write(escape(tb_stream.getvalue()))
+ stream.write(' </%s>\n' % tagname)
+ stream.write(' ')
+
+
+def _clsname(cls):
+ return cls.__module__ + "." + cls.__name__
+
+
+class _XMLTestResult(unittest.TestResult):
+
+ """A test result class that stores result as XML.
+
+ Used by XMLTestRunner.
+
+ """
+
+ def __init__(self, classname):
+ unittest.TestResult.__init__(self)
+ self._test_name = classname
+ self._start_time = None
+ self._tests = []
+ self._error = None
+ self._failure = None
+
+ def startTest(self, test):
+ unittest.TestResult.startTest(self, test)
+ self._error = None
+ self._failure = None
+ self._start_time = time.time()
+
+ def stopTest(self, test):
+ time_taken = time.time() - self._start_time
+ unittest.TestResult.stopTest(self, test)
+ if self._error:
+ info = _TestInfo.create_error(test, time_taken, self._error)
+ elif self._failure:
+ info = _TestInfo.create_failure(test, time_taken, self._failure)
+ else:
+ info = _TestInfo.create_success(test, time_taken)
+ self._tests.append(info)
+
+ def addError(self, test, err):
+ unittest.TestResult.addError(self, test, err)
+ self._error = err
+
+ def addFailure(self, test, err):
+ unittest.TestResult.addFailure(self, test, err)
+ self._failure = err
+
+ def print_report(self, stream, time_taken, out, err):
+ """Prints the XML report to the supplied stream.
+
+ The time the tests took to perform as well as the captured standard
+ output and standard error streams must be passed in.a
+
+ """
+ stream.write('<testsuite errors="%(e)d" failures="%(f)d" ' % \
+ { "e": len(self.errors), "f": len(self.failures) })
+ stream.write('name="%(n)s" tests="%(t)d" time="%(time).3f">\n' % \
+ {
+ "n": self._test_name,
+ "t": self.testsRun,
+ "time": time_taken,
+ })
+ for info in self._tests:
+ info.print_report(stream)
+ stream.write(' <system-out><![CDATA[%s]]></system-out>\n' % out)
+ stream.write(' <system-err><![CDATA[%s]]></system-err>\n' % err)
+ stream.write('</testsuite>\n')
+
+
+class XMLTestRunner(object):
+
+ """A test runner that stores results in XML format compatible with JUnit.
+
+ XMLTestRunner(stream=None) -> XML test runner
+
+ The XML file is written to the supplied stream. If stream is None, the
+ results are stored in a file called TEST-<module>.<class>.xml in the
+ current working directory (if not overridden with the path property),
+ where <module> and <class> are the module and class name of the test class.
+
+ """
+
+ def __init__(self, stream=None):
+ self._stream = stream
+ self._path = "."
+
+ def run(self, test):
+ """Run the given test case or test suite."""
+ class_ = test.__class__
+ classname = class_.__module__ + "." + class_.__name__
+ if self._stream == None:
+ filename = "TEST-%s.xml" % classname
+ stream = file(os.path.join(self._path, filename), "w")
+ stream.write('<?xml version="1.0" encoding="utf-8"?>\n')
+ else:
+ stream = self._stream
+
+ result = _XMLTestResult(classname)
+ start_time = time.time()
+
+ try:
+ self._orig_stdout = sys.stdout
+ self._orig_stderr = sys.stderr
+ sys.stdout = StringIO()
+ sys.stderr = StringIO()
+ test(result)
+ try:
+ out_s = sys.stdout.getvalue()
+ except AttributeError:
+ out_s = ""
+ try:
+ err_s = sys.stderr.getvalue()
+ except AttributeError:
+ err_s = ""
+ finally:
+ sys.stdout = self._orig_stdout
+ sys.stderr = self._orig_stderr
+
+
+ time_taken = time.time() - start_time
+ result.print_report(stream, time_taken, out_s, err_s)
+ if self._stream is None:
+ stream.close()
+
+ return result
+
+ def _set_path(self, path):
+ self._path = path
+
+ path = property(lambda self: self._path, _set_path, None,
+ """The path where the XML files are stored.
+
+ This property is ignored when the XML file is written to a file
+ stream.""")
+
+
+class _fake_std_streams(object):
+
+ def __enter__(self):
+ self._orig_stdout = sys.stdout
+ self._orig_stderr = sys.stderr
+ sys.stdout = StringIO()
+ sys.stderr = StringIO()
+
+ def __exit__(self, exc_type, exc_val, exc_tb):
+ sys.stdout = self._orig_stdout
+ sys.stderr = self._orig_stderr
+
+
+class XMLTestRunnerTest(unittest.TestCase):
+
+ def setUp(self):
+ self._stream = StringIO()
+
+ def _try_test_run(self, test_class, expected):
+
+ """Run the test suite against the supplied test class and compare the
+ XML result against the expected XML string. Fail if the expected
+ string doesn't match the actual string. All time attributes in the
+ expected string should have the value "0.000". All error and failure
+ messages are reduced to "Foobar".
+
+ """
+
+ runner = XMLTestRunner(self._stream)
+ runner.run(unittest.makeSuite(test_class))
+
+ got = self._stream.getvalue()
+ # Replace all time="X.YYY" attributes by time="0.000" to enable a
+ # simple string comparison.
+ got = re.sub(r'time="\d+\.\d+"', 'time="0.000"', got)
+ # Likewise, replace all failure and error messages by a simple "Foobar"
+ # string.
+ got = re.sub(r'(?s)<failure (.*?)>.*?</failure>', r'<failure \1>Foobar</failure>', got)
+ got = re.sub(r'(?s)<error (.*?)>.*?</error>', r'<error \1>Foobar</error>', got)
+ # And finally Python 3 compatibility.
+ got = got.replace('type="builtins.', 'type="exceptions.')
+
+ self.assertEqual(expected, got)
+
+ def test_no_tests(self):
+ """Regression test: Check whether a test run without any tests
+ matches a previous run.
+
+ """
+ class TestTest(unittest.TestCase):
+ pass
+ self._try_test_run(TestTest, """<testsuite errors="0" failures="0" name="unittest.TestSuite" tests="0" time="0.000">
+ <system-out><![CDATA[]]></system-out>
+ <system-err><![CDATA[]]></system-err>
+</testsuite>
+""")
+
+ def test_success(self):
+ """Regression test: Check whether a test run with a successful test
+ matches a previous run.
+
+ """
+ class TestTest(unittest.TestCase):
+ def test_foo(self):
+ pass
+ self._try_test_run(TestTest, """<testsuite errors="0" failures="0" name="unittest.TestSuite" tests="1" time="0.000">
+ <testcase classname="__main__.TestTest" name="test_foo" time="0.000"></testcase>
+ <system-out><![CDATA[]]></system-out>
+ <system-err><![CDATA[]]></system-err>
+</testsuite>
+""")
+
+ def test_failure(self):
+ """Regression test: Check whether a test run with a failing test
+ matches a previous run.
+
+ """
+ class TestTest(unittest.TestCase):
+ def test_foo(self):
+ self.assert_(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>
+ </testcase>
+ <system-out><![CDATA[]]></system-out>
+ <system-err><![CDATA[]]></system-err>
+</testsuite>
+""")
+
+ def test_error(self):
+ """Regression test: Check whether a test run with a erroneous test
+ matches a previous run.
+
+ """
+ class TestTest(unittest.TestCase):
+ def test_foo(self):
+ raise IndexError()
+ self._try_test_run(TestTest, """<testsuite errors="1" failures="0" name="unittest.TestSuite" tests="1" time="0.000">
+ <testcase classname="__main__.TestTest" name="test_foo" time="0.000">
+ <error type="exceptions.IndexError">Foobar</error>
+ </testcase>
+ <system-out><![CDATA[]]></system-out>
+ <system-err><![CDATA[]]></system-err>
+</testsuite>
+""")
+
+ def test_stdout_capture(self):
+ """Regression test: Check whether a test run with output to stdout
+ matches a previous run.
+
+ """
+ class TestTest(unittest.TestCase):
+ def test_foo(self):
+ sys.stdout.write("Test\n")
+ self._try_test_run(TestTest, """<testsuite errors="0" failures="0" name="unittest.TestSuite" tests="1" time="0.000">
+ <testcase classname="__main__.TestTest" name="test_foo" time="0.000"></testcase>
+ <system-out><![CDATA[Test
+]]></system-out>
+ <system-err><![CDATA[]]></system-err>
+</testsuite>
+""")
+
+ def test_stderr_capture(self):
+ """Regression test: Check whether a test run with output to stderr
+ matches a previous run.
+
+ """
+ class TestTest(unittest.TestCase):
+ def test_foo(self):
+ sys.stderr.write("Test\n")
+ self._try_test_run(TestTest, """<testsuite errors="0" failures="0" name="unittest.TestSuite" tests="1" time="0.000">
+ <testcase classname="__main__.TestTest" name="test_foo" time="0.000"></testcase>
+ <system-out><![CDATA[]]></system-out>
+ <system-err><![CDATA[Test
+]]></system-err>
+</testsuite>
+""")
+
+ class NullStream(object):
+ """A file-like object that discards everything written to it."""
+ def write(self, buffer):
+ pass
+
+ def test_unittests_changing_stdout(self):
+ """Check whether the XMLTestRunner recovers gracefully from unit tests
+ that change stdout, but don't change it back properly.
+
+ """
+ class TestTest(unittest.TestCase):
+ def test_foo(self):
+ sys.stdout = XMLTestRunnerTest.NullStream()
+
+ runner = XMLTestRunner(self._stream)
+ runner.run(unittest.makeSuite(TestTest))
+
+ def test_unittests_changing_stderr(self):
+ """Check whether the XMLTestRunner recovers gracefully from unit tests
+ that change stderr, but don't change it back properly.
+
+ """
+ class TestTest(unittest.TestCase):
+ def test_foo(self):
+ sys.stderr = XMLTestRunnerTest.NullStream()
+
+ runner = XMLTestRunner(self._stream)
+ runner.run(unittest.makeSuite(TestTest))
+
+
+if __name__ == "__main__":
+ unittest.main()
diff --git a/modules/base/src/log_sink.hh b/modules/base/src/log_sink.hh
index f4b14d00752935fe7fb307d465d44c5b7f52598c..f06d4ae1c6221c0691a5715cc60bc355b4344431 100644
--- a/modules/base/src/log_sink.hh
+++ b/modules/base/src/log_sink.hh
@@ -20,6 +20,7 @@
#define OST_LOG_SINK_HH
#include <ostream>
+#include <sstream>
#include <iostream>
#include <fstream>
#include <stack>
@@ -35,7 +36,7 @@ class DLLEXPORT LogSink {
public:
LogSink(){};
virtual ~LogSink() { }
- virtual void LogMessage(const String& message, int severity=0)=0;
+ virtual void LogMessage(const String& message, int severity=0) {};
};
typedef boost::shared_ptr<LogSink> LogSinkPtr;
@@ -51,6 +52,23 @@ private:
std::ostream& stream_;
};
+class DLLEXPORT StringLogSink : public LogSink {
+public:
+ StringLogSink():LogSink(),stream_(){}
+ virtual void LogMessage(const String& message, int severity){
+ stream_ << message;
+ }
+ String GetLog() const
+ {
+ return stream_.str();
+ }
+
+private:
+ std::ostringstream stream_;
+};
+
+typedef boost::shared_ptr<StringLogSink> StringLogSinkPtr;
+
class DLLEXPORT FileLogSink : public LogSink {
public:
FileLogSink(const String& file_name):stream_(file_name.c_str(), std::ios::out){}
diff --git a/modules/base/src/string_ref.cc b/modules/base/src/string_ref.cc
index 5cc42986b497f65cd9899b971eafbd3bbdd93a45..03209b11fabacadbff82daae3f36c80b1140f898 100644
--- a/modules/base/src/string_ref.cc
+++ b/modules/base/src/string_ref.cc
@@ -18,6 +18,7 @@
//------------------------------------------------------------------------------
#include <ost/string_ref.hh>
+#include <math.h>
namespace ost {
@@ -53,6 +54,11 @@ std::pair<bool, float> StringRef::to_float() const
int sig=1;
bool after_dot=false;
float factor=0.1;
+ bool after_exponent=false;
+ float exponent=0.0;
+ int exponent_sig=1;
+ bool after_exponent_sign=false;
+
for (const char* c=begin_; c!=end_; ++c) {
if (*c=='-' && empty) {
empty=false;
@@ -71,17 +77,41 @@ std::pair<bool, float> StringRef::to_float() const
if (after_dot==true) {
n+=factor*int(*c-'0');
factor*=0.1;
+ } else if (after_exponent==true) {
+ exponent=exponent*10+int(*c-'0');
} else {
n=n*10+int(*c-'0');
}
continue;
}
+ if ((*c=='+' || *c=='-') && after_exponent==true) {
+ if (after_exponent_sign==true) {
+ return std::make_pair(false, 0.0f);
+ }
+ if (*c=='-') {
+ exponent_sig=-1;
+ }
+ after_exponent_sign=true;
+ continue;
+ }
+ if (*c=='e' || *c=='E') {
+ if (after_exponent==true) {
+ return std::make_pair(false, 0.0f);
+ }
+ after_exponent=true;
+ after_dot=false;
+ continue;
+ }
return std::make_pair(false, 0.0f);
}
if (empty) {
return std::make_pair(false, 0.0f);
}
- return std::make_pair(true, sig*n);
+ if (after_exponent==false) {
+ return std::make_pair(true, sig*n);
+ } else {
+ return std::make_pair(true, sig*n*float(pow(10,exponent_sig*exponent)));
+ }
}
std::ostream& operator<<(std::ostream& stream, const StringRef& strref)
@@ -113,4 +143,37 @@ std::vector<StringRef> StringRef::split(char p) const
return result;
}
+std::vector<StringRef> StringRef::split() const
+{
+ std::vector<StringRef> result;
+ const char* s=begin_;
+ const char* l=begin_;
+ while (s!=end_) {
+ if (isspace(*s)) {
+ if (l!=s) {
+ result.push_back(StringRef(l, s-l));
+ }
+ l=s+1;
+ }
+ ++s;
+ }
+ if (l!=s) {
+ result.push_back(StringRef(l, s-l));
+ }
+ return result;
+}
+
+std::string StringRef::str_no_whitespace() const
+{
+ std::string whitespaceless_string;
+ whitespaceless_string.reserve(this->size());
+ for (const char* s=begin_; s!=end_; ++s) {
+ if (isspace(*s)) {
+ continue;
+ }
+ whitespaceless_string.push_back(*s);
+
+ }
+ return whitespaceless_string;
+}
}
diff --git a/modules/base/src/string_ref.hh b/modules/base/src/string_ref.hh
index cc5661ebaa2c15dc96818d8fb86fbb8a3a7b4696..802dd594069257ba17213a02d73144018e635b32 100644
--- a/modules/base/src/string_ref.hh
+++ b/modules/base/src/string_ref.hh
@@ -28,7 +28,6 @@
#include <ost/base.hh>
#include <string.h>
#include <vector>
-#include <ost/message.hh>
#include <ost/module_config.hh>
@@ -60,8 +59,9 @@ public:
assert(!this->empty());
return *begin_;
}
- /// \brief find character in StringRef
- /// \return iterator position when found, else iterator pointing to the end
+
+ /// \brief find character in StringRef
+ /// \return iterator position when found, else iterator pointing to the end
const_iterator find(char p) const {
const char* s=begin_;
while (s!=end_) {
@@ -72,7 +72,7 @@ public:
}
return s;
}
-
+
/// \brief returns a substring of the string
///
/// \param pos the starting position of the substring
@@ -147,10 +147,16 @@ public:
/// \brief split string into chunks delimited by \p p
std::vector<StringRef> split(char p) const;
+
+ /// \brief split string into chunks delimited by whitespace
+ std::vector<StringRef> split() const;
+
+ /// \brief returns a new string with all whitespace removed from
+ /// this StringRef
+ std::string str_no_whitespace() const;
private:
const char* begin_;
- const char* end_;
-
+ const char* end_;
};
//std::stringstream& operator<<(std::stringstream& stream, const StringRef& strref);
diff --git a/modules/base/tests/CMakeLists.txt b/modules/base/tests/CMakeLists.txt
index c18fcda10eef03664e59767ce1659004689188c1..5a5bce51ae28460c28bc807e824f52af8f593f7a 100644
--- a/modules/base/tests/CMakeLists.txt
+++ b/modules/base/tests/CMakeLists.txt
@@ -4,6 +4,7 @@ set(OST_BASE_UNIT_TESTS
test_pod_vector.cc
test_stutil.py
test_table.py
+ test_log.py
tests.cc
)
diff --git a/modules/base/tests/test_log.py b/modules/base/tests/test_log.py
new file mode 100644
index 0000000000000000000000000000000000000000..cec9378edc965174e460c392ee8bf28a69d106e8
--- /dev/null
+++ b/modules/base/tests/test_log.py
@@ -0,0 +1,43 @@
+import unittest
+import ost
+
+# Altough the logging system might appear to be too simple to be worth writing a
+# specific test case for, it actually isn't. The python export is very fragile
+# and seemingly trivial changes can break the code in unexpected ways. So let's
+# check for some invariants
+class TestLog(unittest.TestCase):
+ def testGetLogSink(self):
+ logsink=ost.GetCurrentLogSink()
+ self.assertTrue(hasattr(logsink, 'LogMessage'))
+ # Check if the return type of logsink is sane
+ ost.PushLogSink(ost.GetCurrentLogSink())
+ def testPushPopLogSink(self):
+ class MyLogSink(ost.LogSink):
+ def __init__(self):
+ ost.LogSink.__init__(self)
+ ls=MyLogSink()
+ ost.PushLogSink(ls)
+ self.assertEqual(ls, ost.GetCurrentLogSink())
+ ost.PopLogSink()
+ self.assertNotEqual(ls, ost.GetCurrentLogSink())
+
+ def testLogMessage(self):
+ class CapturingLogSink(ost.LogSink):
+ def __init__(self):
+ ost.LogSink.__init__(self)
+ def LogMessage(self, message, severity):
+ self.message=message
+ self.severity=severity
+ ost.PushLogSink(ls)
+ ls=CapturingLogSink()
+ ost.PushLogSink(ls)
+ ost.LogError('error message')
+ self.assertEqual(ls.message, 'error message\n')
+ self.assertEqual(ls.severity, 0)
+ ost.LogWarning(1, 2, 3)
+ self.assertEqual(ls.message, '1 2 3\n')
+ self.assertEqual(ls.severity, 1)
+ ost.PopLogSink()
+if __name__ == "__main__":
+ from ost import testutils
+ testutils.RunTests()
\ No newline at end of file
diff --git a/modules/base/tests/test_string_ref.cc b/modules/base/tests/test_string_ref.cc
index 50793bff7f83bde41e88047717d31687b7fbe5f8..05ea7701ec963d2d89f0c6098c9272e2cd59d3f2 100644
--- a/modules/base/tests/test_string_ref.cc
+++ b/modules/base/tests/test_string_ref.cc
@@ -84,6 +84,55 @@ BOOST_AUTO_TEST_CASE( test_string_ref)
BOOST_CHECK(r2.first==false);
r2=StringRef("12.34.", 6).to_float();
BOOST_CHECK(r2.first==false);
+
+ // 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);
+ r3=StringRef("1.5", 3).to_float();
+ BOOST_CHECK(r3.first==true);
+ 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();
+ BOOST_CHECK(r3.first==false);
+ r3=StringRef("12.34.", 6).to_float();
+ BOOST_CHECK(r3.first==false);
+ r3=StringRef("12.34e5", 7).to_float();
+ BOOST_CHECK(r3.first==true);
+ r3=StringRef("12e4", 4).to_float();
+ BOOST_CHECK(r3.first==true);
+ BOOST_CHECK_CLOSE(Real(120000), Real(r3.second), Real(1e-4));
+ r3=StringRef("2e+4", 4).to_float();
+ BOOST_CHECK(r3.first==true);
+ BOOST_CHECK_CLOSE(Real(20000), Real(r3.second), Real(1e-4));
+ r3=StringRef("2.3E+4", 6).to_float();
+ BOOST_CHECK(r3.first==true);
+ BOOST_CHECK_CLOSE(Real(23000), Real(r3.second), Real(1e-4));
+ r3=StringRef("2.3E-4", 6).to_float();
+ BOOST_CHECK(r3.first==true);
+ BOOST_CHECK_CLOSE(Real(0.00023), Real(r3.second), Real(1e-4));
+ r3=StringRef("2.010000e+00", 12).to_float();
+ BOOST_CHECK(r3.first==true);
+ BOOST_CHECK_CLOSE(Real(2.01), Real(r3.second), Real(1e-4));
+ r3=StringRef("5e-34", 5).to_float();
+ BOOST_CHECK(r3.first==true);
+ r3=StringRef("5E-34", 5).to_float();
+ BOOST_CHECK(r3.first==true);
+ r3=StringRef("5.34e-34", 8).to_float();
+ BOOST_CHECK(r3.first==true);
+ r3=StringRef("5.34e-34e", 9).to_float();
+ BOOST_CHECK(r3.first==false);
+ r3=StringRef("5.34ee34", 8).to_float();
+ BOOST_CHECK(r3.first==false);
+ r3=StringRef("5.34e--34e", 10).to_float();
+ BOOST_CHECK(r3.first==false);
+ r3=StringRef("5.34e+3+4", 9).to_float();
+ BOOST_CHECK(r3.first==false);
+ r3=StringRef("5.34e-+34e", 10).to_float();
+ BOOST_CHECK(r3.first==false);
+ r3=StringRef("5.34e-3-4", 9).to_float();
+ BOOST_CHECK(r3.first==false);
}
BOOST_AUTO_TEST_SUITE_END()
diff --git a/modules/base/tests/test_stutil.py b/modules/base/tests/test_stutil.py
index 6cc4570b5605b5eb47c7507e0d0aa7f942f66496..7d5b9f98f9790db63846bfaa934fafa7de1d891b 100644
--- a/modules/base/tests/test_stutil.py
+++ b/modules/base/tests/test_stutil.py
@@ -86,7 +86,5 @@ class TestStUtils(unittest.TestCase):
(stutil.Correl(self.data3, self.data2), self.correl2)
if __name__ == "__main__":
- try:
- unittest.main()
- except Exception, e:
- print e
\ No newline at end of file
+ from ost import testutils
+ testutils.RunTests()
\ No newline at end of file
diff --git a/modules/base/tests/test_table.py b/modules/base/tests/test_table.py
index 2baf48934eb8e58f5a0696b48792c9237059033d..7b6b3be222600a86e534eb12c1b3d02cfe1da654 100644
--- a/modules/base/tests/test_table.py
+++ b/modules/base/tests/test_table.py
@@ -10,20 +10,37 @@ from ost.table import *
import ost
HAS_NUMPY=True
+HAS_SCIPY=True
HAS_MPL=True
+HAS_PIL=True
try:
import numpy as np
except ImportError:
HAS_NUMPY=False
+ print "Could not find numpy: ignoring some table class unit tests"
+try:
+ import scipy.stats.mstats
+except ImportError:
+ HAS_SCIPY=False
+ print "Could not find scipy.stats.mstats: ignoring some table class unit tests"
+
try:
import matplotlib
matplotlib.use('Agg')
except ImportError:
HAS_MPL=False
+ print "Could not find matplotlib: ignoring some table class unit tests"
+
+try:
+ import Image
+ import ImageChops
+except ImportError:
+ HAS_PIL=False
+ print "Could not find python imagine library: ignoring some table class unit tests"
class TestTable(unittest.TestCase):
-
+
def setUp(self):
ost.PushVerbosityLevel(3)
@@ -45,9 +62,9 @@ class TestTable(unittest.TestCase):
self.CompareColCount(tab, 3)
self.CompareRowCount(tab, 0)
self.CompareColTypes(tab, ['first','second', 'third'], 'sif')
- tab.AddRow(['x',3, None], merge=None)
- tab.AddRow(['foo',None, 2.2], merge=None)
- tab.AddRow([None,9, 3.3], merge=None)
+ tab.AddRow(['x',3, None], overwrite=None)
+ tab.AddRow(['foo',None, 2.2], overwrite=None)
+ tab.AddRow([None,9, 3.3], overwrite=None)
return tab
def CompareRowCount(self, t, row_count):
@@ -95,11 +112,18 @@ class TestTable(unittest.TestCase):
'''
self.CompareRowCount(t, len(ref_data))
idx = t.GetColIndex(col_name)
+ col_type = t.col_types[idx]
for i, (row, ref) in enumerate(zip(t.rows, ref_data)):
- self.assertEqual(row[idx],
- ref,
- "data (%s) in col (%s), row (%i) different from expected value (%s)" \
- %(row[idx], col_name, i, ref))
+ if (isinstance(ref, float) or isinstance(ref, int)) and (isinstance(row[idx], float) or isinstance(row[idx], int)):
+ self.assertAlmostEqual(row[idx],
+ ref,
+ msg="data (%s) in col (%s), row (%i) different from expected value (%s)" \
+ %(row[idx], col_name, i, ref))
+ else:
+ self.assertEqual(row[idx],
+ ref,
+ "data (%s) in col (%s), row (%i) different from expected value (%s)" \
+ %(row[idx], col_name, i, ref))
def CompareColTypes(self, t, col_names, ref_types):
'''
@@ -124,6 +148,17 @@ class TestTable(unittest.TestCase):
"column type (%s) at column %i, different from reference col type (%s)" \
%(t.col_types[idx], idx, ref_type))
+ def CompareImages(self, img1, img2):
+ '''
+ Compares two images based on all pixel values. This function needs the
+ python imaging library (PIL) package.
+ '''
+ if not HAS_PIL:
+ return
+ diff = ImageChops.difference(img1, img2)
+ self.assertEqual(diff.getbbox(),None)
+
+
def testZip(self):
tab=Table(['col1', 'col2', 'col3', 'col4'], 'sssi')
tab.AddRow(['a', 'b', 'c', 1])
@@ -162,6 +197,14 @@ class TestTable(unittest.TestCase):
self.CompareRowCount(tab, 0)
self.assertRaises(ValueError, tab.GetColIndex, 'a')
+ def testGuessColumnType(self):
+ self.assertEqual(GuessColumnType(['1', '1.3', '2']), 'float')
+ self.assertEqual(GuessColumnType(['1', '1', '2']), 'int')
+ self.assertEqual(GuessColumnType(['NONE', '1', '1', '2']), 'int')
+ self.assertEqual(GuessColumnType(['NONE', '1', '1', '2']), 'int')
+ self.assertEqual(GuessColumnType(['NONE', '1', '1', 'a']), 'string')
+ self.assertEqual(GuessColumnType(['NONE', 'TRUE', 'False']), 'bool')
+ self.assertEqual(GuessColumnType(['NONE']), 'string')
def testTableInitSingleColEmpty(self):
'''
empty table with one float column:
@@ -332,7 +375,7 @@ class TestTable(unittest.TestCase):
tab = Table(['first'],'i')
self.CompareColCount(tab, 1)
self.CompareRowCount(tab, 0)
- tab.AddRow([2], merge=None)
+ tab.AddRow([2], overwrite=None)
self.CompareColCount(tab, 1)
self.CompareRowCount(tab, 1)
self.CompareColNames(tab, ['first'])
@@ -351,7 +394,7 @@ class TestTable(unittest.TestCase):
tab.AddCol('first', 'int')
self.CompareColCount(tab, 1)
self.CompareRowCount(tab, 0)
- tab.AddRow([2], merge=None)
+ tab.AddRow([2], overwrite=None)
self.CompareColCount(tab, 1)
self.CompareRowCount(tab, 1)
self.CompareColNames(tab, ['first'])
@@ -371,7 +414,7 @@ class TestTable(unittest.TestCase):
self.CompareColCount(tab, 2)
self.CompareRowCount(tab, 0)
self.CompareColTypes(tab, ['first','second'], 'si')
- tab.AddRow(['x',3], merge=None)
+ tab.AddRow(['x',3], overwrite=None)
self.CompareColCount(tab, 2)
self.CompareRowCount(tab, 1)
tab.AddCol('third', 'float', 3.141)
@@ -398,9 +441,9 @@ class TestTable(unittest.TestCase):
self.CompareColCount(tab, 3)
self.CompareRowCount(tab, 0)
self.CompareColTypes(tab, ['first','second', 'third'], 'sif')
- tab.AddRow(['x',3, 1.0], merge=None)
- tab.AddRow(['foo',6, 2.2], merge=None)
- tab.AddRow(['bar',9, 3.3], merge=None)
+ tab.AddRow(['x',3, 1.0], overwrite=None)
+ tab.AddRow(['foo',6, 2.2], overwrite=None)
+ tab.AddRow(['bar',9, 3.3], overwrite=None)
self.CompareColCount(tab, 3)
self.CompareRowCount(tab, 3)
self.CompareDataFromDict(tab, {'second': [3,6,9], 'first': ['x','foo','bar'], 'third': [1,2.2,3.3]})
@@ -423,9 +466,9 @@ class TestTable(unittest.TestCase):
self.CompareColCount(tab, 3)
self.CompareRowCount(tab, 0)
self.CompareColTypes(tab, ['first','second', 'aaa'], 'sif')
- tab.AddRow({'first':'x','second':3, 'aaa':1.0}, merge=None)
- tab.AddRow({'aaa':2.2, 'second':6, 'first':'foo'}, merge=None)
- tab.AddRow({'second':9, 'aaa':3.3, 'first':'bar'}, merge=None)
+ tab.AddRow({'first':'x','second':3, 'aaa':1.0}, overwrite=None)
+ tab.AddRow({'aaa':2.2, 'second':6, 'first':'foo'}, overwrite=None)
+ tab.AddRow({'second':9, 'aaa':3.3, 'first':'bar'}, overwrite=None)
self.CompareColCount(tab, 3)
self.CompareRowCount(tab, 3)
self.CompareDataFromDict(tab, {'second': [3,6,9], 'first': ['x','foo','bar'], 'aaa': [1,2.2,3.3]})
@@ -447,9 +490,9 @@ class TestTable(unittest.TestCase):
self.CompareColCount(tab, 1)
self.CompareRowCount(tab, 0)
self.CompareColTypes(tab, ['first'], 's')
- tab.AddRow(['x'], merge=None)
- tab.AddRow(['foo'], merge=None)
- tab.AddRow(['bar'], merge=None)
+ tab.AddRow(['x'], overwrite=None)
+ tab.AddRow(['foo'], overwrite=None)
+ tab.AddRow(['bar'], overwrite=None)
tab.AddCol('second', 'int')
tab.AddCol('third', 'float', 3.141)
self.CompareColCount(tab, 3)
@@ -458,9 +501,9 @@ class TestTable(unittest.TestCase):
'first': ['x','foo','bar'],
'third': [3.141, 3.141, 3.141]})
- def testAddRowFromDictWithMerge(self):
+ def testAddRowFromDictWithOverwrite(self):
'''
- add rows from dictionary with merge (i.e. overwrite third row with additional data)
+ add rows from dictionary with overwrite (i.e. overwrite third row with additional data)
x foo bar
------------------
@@ -479,14 +522,14 @@ class TestTable(unittest.TestCase):
self.CompareDataFromDict(tab, {'x': ['row1', 'row2', 'row3'],
'foo': [True, None, False],
'bar': [1, 2, None]})
- tab.AddRow({'x':'row3', 'bar':3}, merge='x')
+ tab.AddRow({'x':'row3', 'bar':3}, overwrite='x')
self.CompareDataFromDict(tab, {'x': ['row1', 'row2', 'row3'],
'foo': [True, None, False],
'bar': [1, 2, 3]})
- def testAddRowFromListWithMerge(self):
+ def testAddRowFromListWithOverwrite(self):
'''
- add rows from list with merge (i.e. overwrite third row with additional data)
+ add rows from list with overwrite (i.e. overwrite third row with additional data)
x foo bar
------------------
@@ -506,7 +549,7 @@ class TestTable(unittest.TestCase):
self.CompareDataFromDict(tab, {'x': ['row1', 'row2', 'row3'],
'foo': [True, None, False],
'bar': [1, 2, None]})
- tab.AddRow(['row3', True, 3], merge='x')
+ tab.AddRow(['row3', True, 3], overwrite='x')
self.CompareDataFromDict(tab, {'x': ['row1', 'row2', 'row3'],
'foo': [True, None, True],
'bar': [1, 2, 3]})
@@ -677,21 +720,32 @@ class TestTable(unittest.TestCase):
tab.Sort('third', '+')
self.CompareDataFromDict(tab, {'first': [None,'foo','x'], 'second': [9,None,3], 'third': [3.3,2.2,None]})
- def testSaveLoadTable(self):
+ def testLoadTableOSTUnknownType(self):
+ self.assertRaises(ValueError, Table.Load, os.path.join('testfiles','ost-table-unknown-type.tab'))
+
+ def testLoadTableOSTNoType(self):
+ tab = Table.Load(os.path.join('testfiles','ost-table-notype.tab'))
+ self.CompareDataFromDict(tab, {'first': ['x','foo',None], 'second': [3,None,9], 'third': [None,2.2,3.3]})
+
+ 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'])
+
+ def testSaveLoadTableOST(self):
tab = self.CreateTestTable()
self.CompareDataFromDict(tab, {'first': ['x','foo',None], 'second': [3,None,9], 'third': [None,2.2,3.3]})
# write to disc
- tab.Save("saveloadtable_filename_out.csv")
- out_stream = open("saveloadtable_stream_out.csv", 'w')
+ tab.Save("saveloadtable_filename_out.tab")
+ out_stream = open("saveloadtable_stream_out.tab", 'w')
tab.Save(out_stream)
out_stream.close()
# read from disc
- in_stream = open("saveloadtable_stream_out.csv", 'r')
+ in_stream = open("saveloadtable_stream_out.tab", 'r')
tab_loaded_stream = Table.Load(in_stream)
in_stream.close()
- tab_loaded_fname = Table.Load('saveloadtable_filename_out.csv')
+ tab_loaded_fname = Table.Load('saveloadtable_filename_out.tab')
# check content
self.CompareDataFromDict(tab_loaded_stream, {'first': ['x','foo',None], 'second': [3,None,9], 'third': [None,2.2,3.3]})
@@ -699,10 +753,61 @@ class TestTable(unittest.TestCase):
# check Errors for empty/non existing files
self.assertRaises(IOError, Table.Load, 'nonexisting.file')
- self.assertRaises(IOError, Table.Load, os.path.join('testfiles','emptytable.csv'))
+ 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)
+ def testSaveLoadTableOSTWithSpaces(self):
+ tab = self.CreateTestTable()
+ tab.AddRow(['hello spaces',10, 10.1], overwrite=None)
+ self.CompareDataFromDict(tab, {'first': ['x','foo',None,'hello spaces'], 'second': [3,None,9,10], 'third': [None,2.2,3.3,10.1]})
+
+ # write to disc
+ tab.Save("saveloadtable_withspaces_filename_out.tab")
+
+ # read from disc
+ 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 testSaveLoadTableCSV(self):
+ tab = self.CreateTestTable()
+ self.CompareDataFromDict(tab, {'first': ['x','foo',None], 'second': [3,None,9], 'third': [None,2.2,3.3]})
+
+ # write to disc
+ tab.Save("saveloadtable_filename_out.csv", format='csv')
+ out_stream = open("saveloadtable_stream_out.csv", 'w')
+ tab.Save(out_stream, format='csv')
+ out_stream.close()
+
+ # read from disc
+ in_stream = open("saveloadtable_stream_out.csv", 'r')
+ tab_loaded_stream = Table.Load(in_stream, format='csv')
+ in_stream.close()
+ tab_loaded_fname = Table.Load('saveloadtable_filename_out.csv', format='csv')
+
+ # check content
+ self.CompareDataFromDict(tab_loaded_stream, {'first': ['x','foo',None], 'second': [3,None,9], 'third': [None,2.2,3.3]})
+ self.CompareDataFromDict(tab_loaded_fname, {'first': ['x','foo',None], 'second': [3,None,9], 'third': [None,2.2,3.3]})
+
+ def testSaveLoadTablePickle(self):
+ tab = self.CreateTestTable()
+ self.CompareDataFromDict(tab, {'first': ['x','foo',None], 'second': [3,None,9], 'third': [None,2.2,3.3]})
+ # write to disc
+ tab.Save("saveloadtable_filename_out.pickle", format='pickle')
+ out_stream = open("saveloadtable_stream_out.pickle", 'wb')
+ tab.Save(out_stream, format='pickle')
+ out_stream.close()
+
+ # read from disc
+ in_stream = open("saveloadtable_stream_out.pickle", 'rb')
+ tab_loaded_stream = Table.Load(in_stream, format='pickle')
+ in_stream.close()
+ tab_loaded_fname = Table.Load('saveloadtable_filename_out.pickle', format='pickle')
+
+ # check content
+ self.CompareDataFromDict(tab_loaded_stream, {'first': ['x','foo',None], 'second': [3,None,9], 'third': [None,2.2,3.3]})
+ self.CompareDataFromDict(tab_loaded_fname, {'first': ['x','foo',None], 'second': [3,None,9], 'third': [None,2.2,3.3]})
+
def testMergeTable(self):
'''
Merge the following two tables:
@@ -816,42 +921,72 @@ class TestTable(unittest.TestCase):
def testSumTable(self):
tab = self.CreateTestTable()
tab.AddCol('fourth','bool',[False,True,False])
+ 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.assertRaises(TypeError,tab.Sum,'fourth')
- self.assertRaises(ValueError,tab.Sum,'fifth')
+ self.assertEquals(tab.Sum('fourth'),1)
+ self.assertRaises(TypeError,tab.Sum,'fifth')
+ self.assertRaises(ValueError,tab.Sum,'sixth')
def testMedianTable(self):
tab = self.CreateTestTable()
tab.AddCol('fourth','bool',[False,True,False])
+ 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.assertRaises(TypeError,tab.Median,'fourth')
- self.assertRaises(ValueError,tab.Median,'fifth')
+ self.assertEquals(tab.Median('fourth'),False)
+ self.assertRaises(TypeError,tab.Median,'fifth')
+ self.assertRaises(ValueError,tab.Median,'sixth')
def testMeanTable(self):
tab = self.CreateTestTable()
tab.AddCol('fourth','bool',[False,True,False])
+ 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.assertRaises(TypeError,tab.Mean,'fourth')
- self.assertRaises(ValueError,tab.Mean,'fifth')
+ self.assertAlmostEquals(tab.Mean('fourth'),0.33333333)
+ self.assertRaises(TypeError,tab.Mean,'fifth')
+ self.assertRaises(ValueError,tab.Mean,'sixth')
+
+ def testRowMeanTable(self):
+ '''
+ first second third fourth
+ -----------------------------
+ x 3 NA 1
+ foo NA 2.200 2
+ NA 9 3.300 3
+ NA NA NA NA
+ '''
+ tab = self.CreateTestTable()
+ tab.AddCol('fourth','float',[1,2,3])
+ tab.AddRow([None, None, None, None])
+
+ self.assertRaises(TypeError, tab.RowMean, 'mean', ['first', 'second'])
+ tab.RowMean('mean', ['third', 'second', 'fourth'])
+ self.CompareDataFromDict(tab, {'mean': [2,2.1,5.1,None],
+ 'first': ['x','foo',None,None],
+ 'second': [3,None,9,None],
+ 'third': [None,2.2,3.3,None],
+ 'fourth': [1,2,3,None]})
+
def testStdDevTable(self):
tab = self.CreateTestTable()
tab.AddCol('fourth','bool',[False,True,False])
+ 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.assertRaises(TypeError,tab.StdDev,'fourth')
- self.assertRaises(ValueError,tab.StdDev,'fifth')
+ self.assertAlmostEquals(tab.StdDev('fourth'),0.47140452079)
+ self.assertRaises(TypeError,tab.StdDev,'fifth')
+ self.assertRaises(ValueError,tab.StdDev,'sixth')
def testCountTable(self):
tab = self.CreateTestTable()
@@ -914,7 +1049,7 @@ class TestTable(unittest.TestCase):
class_dir='y')
def testPlotEnrichment(self):
- if not HAS_MPL:
+ if not HAS_MPL or not HAS_PIL:
return
tab = Table(['score', 'rmsd', 'classific'], 'ffb',
score=[2.64,1.11,2.17,0.45,0.15,0.85,1.13,2.90,0.50,1.03,1.46,2.83,1.15,2.04,0.67,1.27,2.22,1.90,0.68,0.36,1.04,2.46,0.91,0.60],
@@ -923,7 +1058,11 @@ class TestTable(unittest.TestCase):
pl = tab.PlotEnrichment(score_col='score', score_dir='-',
class_col='rmsd', class_cutoff=2.0,
- class_dir='-')
+ class_dir='-',
+ save=os.path.join("testfiles","enrichment-out.png"))
+ img1 = Image.open(os.path.join("testfiles","enrichment-out.png"))
+ #img2 = Image.open(os.path.join("testfiles","enrichment.png"))
+ #self.CompareImages(img1, img2)
#pl.show()
def testCalcEnrichmentAUC(self):
@@ -940,7 +1079,121 @@ class TestTable(unittest.TestCase):
class_dir='-')
self.assertAlmostEquals(auc, auc_ref)
-
+
+ def testPlotROC(self):
+ if not HAS_MPL or not HAS_PIL:
+ return
+ tab = Table(['classific', 'score'], 'bf',
+ 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])
+ pl = tab.PlotROC(score_col='score', score_dir='+',
+ class_col='classific',
+ save=os.path.join("testfiles","roc-out.png"))
+ img1 = Image.open(os.path.join("testfiles","roc-out.png"))
+ #img2 = Image.open(os.path.join("testfiles","roc.png"))
+ #self.CompareImages(img1, img2)
+
+ # 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])
+ pl = tab.PlotROC(score_col='score', score_dir='+',
+ class_col='classific',
+ save=os.path.join("testfiles","roc-out.png"))
+ self.assertEquals(pl, None)
+
+ def testPlotROCSameValues(self):
+ if not HAS_MPL or not HAS_PIL:
+ return
+ tab = Table(['classific', 'score'], 'bf',
+ 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])
+ pl = tab.PlotROC(score_col='score', score_dir='+',
+ class_col='classific',
+ save=os.path.join("testfiles","roc-same-val-out.png"))
+ img1 = Image.open(os.path.join("testfiles","roc-same-val-out.png"))
+ #img2 = Image.open(os.path.join("testfiles","roc-same-val.png"))
+ #self.CompareImages(img1, img2)
+ #pl.show()
+
+ def testCalcROCAUC(self):
+ if not HAS_NUMPY:
+ return
+ auc_ref = 0.68
+ tab = Table(['classific', 'score'], 'bf',
+ 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)
+
+ # 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)
+
+ def testCalcROCAUCWithCutoff(self):
+ if not HAS_NUMPY:
+ return
+ tab = Table(['classific', 'score'], 'ff',
+ 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)
+
+ # no true positives
+ auc = tab.ComputeROCAUC(score_col='score', class_col='classific', class_cutoff=1.0)
+ self.assertEquals(auc, None)
+
+ def testCalcROCFromFile(self):
+ 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)
+
+
+ def testCalcROCAUCSameValues(self):
+ if not HAS_NUMPY:
+ return
+ auc_ref = 0.685
+ tab = Table(['classific', 'score'], 'bf',
+ 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)
+
+ def testCalcMCC(self):
+ tab = Table(['score', 'rmsd', 'class_rmsd', 'class_score', 'class_wrong'], 'ffbbb',
+ score= [2.64, 1.11, 2.17, 0.45,0.15,0.85, 1.13, 2.90, 0.50, 1.03, 1.46, 2.83, 1.15, 2.04, 0.67, 1.27, 2.22, 1.90, 0.68, 0.36,1.04, 2.46, 0.91,0.60],
+ rmsd=[9.58,1.61,7.48,0.29,1.68,3.52,3.34,8.17,4.31,2.85,6.28,8.78,0.41,6.29,4.89,7.30,4.26,3.51,3.38,0.04,2.21,0.24,7.58,8.40],
+ class_rmsd= [False,True, False,True,True,False,False,False,False,False,False,False,True, False,False,False,False,False,False,True,False,True,False,False],
+ class_score=[False,False,False,True,True,True, False,False,True, False,False,False,False,False,True, False,False,False,True, True,False,False,True,True],
+ 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)
+ mcc = tab.ComputeMCC(score_col='class_score', class_col='class_rmsd')
+ self.assertAlmostEquals(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)
+ 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)
+ 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)
+ mcc = tab.ComputeMCC(score_col='class_wrong', class_col='class_rmsd')
+ self.assertEquals(mcc,None)
+
+
+ def testCalcMCCPreclassified(self):
+ tab = Table(['reference', 'prediction1', 'prediction2'],'bbb',
+ reference= [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, False, True, False, False, False, False, False, False, False, False, False, False, True, False, False, True, False, False, False, False, False, False, False, False],
+ 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)
+ mcc = tab.ComputeMCC(score_col='prediction2', class_col='reference')
+ self.assertAlmostEquals(mcc, 0.882089673321)
+
def testTableAsNumpyMatrix(self):
'''
@@ -1057,9 +1310,131 @@ class TestTable(unittest.TestCase):
self.assertFalse(tab.IsEmpty('a', ignore_nan=False))
self.assertFalse(tab.IsEmpty('b', ignore_nan=False))
self.assertFalse(tab.IsEmpty('c', ignore_nan=False))
-
+
+ def testUnique(self):
+ 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])
+
+ def testCorrel(self):
+ tab = self.CreateTestTable()
+ self.assertEquals(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)
+
+ def testSpearmanCorrel(self):
+ if not HAS_SCIPY:
+ return
+ tab = self.CreateTestTable()
+ self.assertEquals(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)
+
+ def testExtend(self):
+ '''
+ first second third
+ ----------------------
+ x 3 NA
+ foo NA 2.200
+ NA 9 3.300
+ '''
+
+ # simple extend of the same table
+ tab = self.CreateTestTable()
+ self.CompareDataFromDict(tab, {'first': ['x','foo',None],
+ 'second': [3,None,9],
+ 'third': [None,2.2,3.3]})
+
+ tab.Extend(tab)
+ self.CompareDataFromDict(tab, {'first': ['x','foo',None,'x','foo',None],
+ 'second': [3,None,9,3,None,9],
+ 'third': [None,2.2,3.3,None,2.2,3.3]})
+
+ # simple extend of different tables with the same data
+ tab = self.CreateTestTable()
+ tab2 = self.CreateTestTable()
+ tab.Extend(tab2)
+ self.CompareDataFromDict(tab, {'first': ['x','foo',None,'x','foo',None],
+ 'second': [3,None,9,3,None,9],
+ 'third': [None,2.2,3.3,None,2.2,3.3]})
+ self.CompareDataFromDict(tab2, {'first': ['x','foo',None],
+ 'second': [3,None,9],
+ 'third': [None,2.2,3.3]})
+
+ # add additional columns to current table
+ tab = self.CreateTestTable()
+ tab2 = self.CreateTestTable()
+ tab2.AddCol('foo','i',[1,2,3])
+ tab.Extend(tab2)
+ self.CompareDataFromDict(tab, {'first': ['x','foo',None,'x','foo',None],
+ 'second': [3,None,9,3,None,9],
+ 'third': [None,2.2,3.3,None,2.2,3.3],
+ 'foo': [None,None,None,1,2,3]})
+
+ # different order of the data
+ tab = self.CreateTestTable()
+ tab2 = Table(['third','second','first'],
+ 'fis',
+ third=[None,2.2,3.3],
+ first=['x','foo',None],
+ second=[3, None, 9])
+ self.CompareDataFromDict(tab2, {'first': ['x','foo',None],
+ 'second': [3,None,9],
+ 'third': [None,2.2,3.3]})
+ tab.Extend(tab2)
+ self.CompareDataFromDict(tab, {'first': ['x','foo',None,'x','foo',None],
+ 'second': [3,None,9,3,None,9],
+ 'third': [None,2.2,3.3,None,2.2,3.3]})
+
+ # with overwrite (additional column)
+ tab = self.CreateTestTable()
+ tab2 = self.CreateTestTable()
+ tab2.AddCol('foo','i',[1,2,3])
+ tab.Extend(tab2, overwrite='first')
+ self.CompareDataFromDict(tab, {'first': ['x','foo',None],
+ 'second': [3,None,9],
+ 'third': [None,2.2,3.3],
+ 'foo': [1,2,3]})
+
+ # with overwrite (no matching value)
+ tab = self.CreateTestTable()
+ tab2 = Table(['third','second','first'],
+ 'fis',
+ third=[None,2.2,3.3],
+ first=['a','bar','bla'],
+ second=[3, None, 9])
+ tab.Extend(tab2, overwrite='first')
+ self.CompareDataFromDict(tab, {'first': ['x','foo',None,'a','bar','bla'],
+ 'second': [3,None,9,3,None,9],
+ 'third': [None,2.2,3.3,None,2.2,3.3]})
+
+ # with overwrite (with matching values)
+ tab = self.CreateTestTable()
+ tab2 = Table(['third','second','first'],
+ 'fis',
+ third=[None,2.2,3.4],
+ first=['a','bar','bla'],
+ second=[3, None, 9])
+ tab.Extend(tab2, overwrite='third')
+ self.CompareDataFromDict(tab, {'first': ['a','bar',None,'bla'],
+ 'second': [3,None,9,9],
+ 'third': [None,2.2,3.3,3.4]})
+
+ # cannot extend if types are different
+ tab = Table('aaa','s',a=['a','b'])
+ tab2 = Table('aaa','i',a=[1,2])
+ self.assertRaises(TypeError, tab.Extend, tab2)
+
if __name__ == "__main__":
- try:
- unittest.main()
- except Exception, e:
- print e
+ from ost import testutils
+ testutils.RunTests()
diff --git a/modules/base/tests/testfiles/enrichment.png b/modules/base/tests/testfiles/enrichment.png
new file mode 100644
index 0000000000000000000000000000000000000000..6fa5157f913a556a3d27eccf63479d92f4eb806d
Binary files /dev/null and b/modules/base/tests/testfiles/enrichment.png differ
diff --git a/modules/base/tests/testfiles/ost-table-difficult-headers.tab b/modules/base/tests/testfiles/ost-table-difficult-headers.tab
new file mode 100644
index 0000000000000000000000000000000000000000..792a25971450fa7150964dc540539b8a24cfaf49
--- /dev/null
+++ b/modules/base/tests/testfiles/ost-table-difficult-headers.tab
@@ -0,0 +1,8 @@
+cut-off[float] a_sangle[float] smoo:thing[float] 3O89.pdb.gz[float] 3P0K;pdbgz[float]
+1.0 20.0 0.0 0.5 0.5
+1.0 20.0 2.0 0.600685362782 0.774702862809
+1.0 20.0 4.0 0.749697277923 0.872928615954
+1.0 20.0 6.0 0.775949336433 0.864866900109
+1.0 20.0 8.0 0.673823016565 0.818450326527
+1.0 20.0 10.0 0.528419548581 0.779631093875
+1.0 20.0 12.0 0.463080015499 0.761846789747
diff --git a/modules/base/tests/testfiles/ost-table-notype.tab b/modules/base/tests/testfiles/ost-table-notype.tab
new file mode 100644
index 0000000000000000000000000000000000000000..10f59019bc567304bf57520c2f6c0e8f99d308f4
--- /dev/null
+++ b/modules/base/tests/testfiles/ost-table-notype.tab
@@ -0,0 +1,4 @@
+first second[int] third[float]
+x 3 NA
+foo NA 2.2
+NA 9 3.3
diff --git a/modules/base/tests/testfiles/ost-table-unknown-type.tab b/modules/base/tests/testfiles/ost-table-unknown-type.tab
new file mode 100644
index 0000000000000000000000000000000000000000..69c79442b33df285507c7f42845f73aa09663ed0
--- /dev/null
+++ b/modules/base/tests/testfiles/ost-table-unknown-type.tab
@@ -0,0 +1,4 @@
+first[unknown] second[int] third[float]
+x 3 NA
+foo NA 2.2
+NA 9 3.3
diff --git a/modules/base/tests/testfiles/roc-same-val.png b/modules/base/tests/testfiles/roc-same-val.png
new file mode 100644
index 0000000000000000000000000000000000000000..b459c553da696100743b9b41dc09e8dcbeaef5a3
Binary files /dev/null and b/modules/base/tests/testfiles/roc-same-val.png differ
diff --git a/modules/base/tests/testfiles/roc.png b/modules/base/tests/testfiles/roc.png
new file mode 100644
index 0000000000000000000000000000000000000000..d02985dacd945e6dfc57301d99994b098c0879dd
Binary files /dev/null and b/modules/base/tests/testfiles/roc.png differ
diff --git a/modules/base/tests/testfiles/roc_table.dat b/modules/base/tests/testfiles/roc_table.dat
new file mode 100644
index 0000000000000000000000000000000000000000..2de91a2691f99683a6f86658e6f71b136cc57a6d
--- /dev/null
+++ b/modules/base/tests/testfiles/roc_table.dat
@@ -0,0 +1,152 @@
+rnum[int] reference[float] prediction[float]
+1 0.0 0.0
+2 0.0 0.0
+3 0.0 0.0
+4 0.0 0.0
+5 0.2 0.2
+6 0.0 0.0
+7 0.0 0.0
+8 1.0 1.0
+9 0.2 0.2
+10 0.2 0.2
+11 0.2 0.2
+12 1.0 1.0
+13 0.0 0.0
+14 0.0 0.0
+15 0.0 0.0
+16 0.0 0.0
+17 0.0 0.0
+18 0.0 0.0
+19 0.0 0.0
+20 0.0 0.0
+21 0.0 0.0
+22 0.0 0.0
+23 0.0 0.0
+24 0.0 0.0
+25 0.0 0.0
+26 0.0 0.0
+27 0.0 0.0
+28 0.0 0.0
+29 0.0 0.0
+30 0.0 0.0
+31 0.0 0.0
+32 0.2 0.2
+33 0.0 0.0
+34 0.0 0.0
+35 0.0 0.0
+36 0.0 0.0
+37 0.0 0.0
+38 0.0 0.0
+39 0.0 0.0
+40 0.0 0.0
+41 0.0 0.0
+42 0.0 0.0
+43 0.0 0.0
+44 0.0 0.0
+45 0.0 0.0
+46 0.0 0.0
+47 0.0 0.0
+48 0.0 0.0
+49 0.0 0.0
+50 0.0 0.0
+51 0.0 0.0
+52 0.0 0.0
+53 0.0 0.0
+54 0.0 0.0
+55 0.0 0.0
+56 0.0 0.0
+57 0.0 0.0
+58 0.0 0.0
+59 0.0 0.0
+60 0.0 0.0
+61 0.0 0.0
+62 0.0 0.0
+63 0.0 0.0
+64 0.0 0.0
+65 0.0 0.0
+66 0.0 0.0
+67 0.0 0.0
+68 0.0 0.0
+69 0.0 0.0
+70 0.0 0.0
+71 0.2 0.2
+72 0.0 0.0
+73 0.2 0.2
+74 0.0 0.0
+75 0.0 0.0
+76 0.0 0.0
+77 0.0 0.0
+78 0.0 0.0
+79 0.0 0.0
+80 0.0 0.0
+81 0.0 0.0
+82 0.0 0.0
+83 0.0 0.0
+84 0.0 0.0
+85 0.0 0.0
+86 0.0 0.0
+87 0.0 0.0
+88 0.0 0.0
+89 0.0 0.0
+90 0.0 0.0
+91 0.2 0.2
+92 0.0 0.0
+93 0.0 0.0
+94 0.0 0.0
+95 0.0 0.0
+96 0.0 0.0
+97 0.0 0.0
+98 0.0 0.0
+99 0.0 0.0
+100 0.0 0.0
+101 0.0 0.0
+102 0.0 0.0
+103 0.2 0.2
+104 0.2 0.2
+105 0.5 0.5
+106 0.0 0.0
+107 0.0 0.0
+108 0.0 0.0
+109 0.0 0.0
+110 0.0 0.0
+111 0.2 0.2
+112 0.0 0.0
+113 0.5 0.5
+114 0.2 0.2
+115 1.0 1.0
+116 0.5 0.5
+117 0.5 0.5
+118 0.5 0.5
+119 1.0 1.0
+120 0.0 0.0
+121 0.0 0.0
+122 0.0 0.0
+123 0.0 0.0
+124 0.0 0.0
+125 0.0 0.0
+126 0.0 0.0
+127 0.0 0.0
+128 0.0 0.0
+129 0.0 0.0
+130 0.0 0.0
+131 0.0 0.0
+132 0.0 0.0
+133 0.0 0.0
+134 0.0 0.0
+135 0.0 0.0
+136 0.0 0.0
+137 0.0 0.0
+138 0.0 0.0
+139 0.0 0.0
+140 0.0 0.0
+141 0.0 0.0
+142 0.0 0.0
+143 0.0 0.0
+144 0.0 0.0
+145 0.0 0.0
+146 0.0 0.0
+147 0.0 0.0
+148 0.0 0.0
+149 0.0 0.0
+150 0.0 0.0
+151 0.0 0.0
diff --git a/modules/bindings/doc/bindings.rst b/modules/bindings/doc/bindings.rst
index fc5357608c5a09becf40ba13b0ebed59fe634769..744f6059c6d736c6a2c2eaa57bdae979b9c7c286 100644
--- a/modules/bindings/doc/bindings.rst
+++ b/modules/bindings/doc/bindings.rst
@@ -17,3 +17,4 @@ So far, the binding module includes:
blast
msms
tmtools
+ clustalw
diff --git a/modules/bindings/doc/clustalw.rst b/modules/bindings/doc/clustalw.rst
new file mode 100644
index 0000000000000000000000000000000000000000..a7f738d5e5e3a2fe71e48cb9a07874cc4078ded1
--- /dev/null
+++ b/modules/bindings/doc/clustalw.rst
@@ -0,0 +1,8 @@
+:mod:`~ost.bindings.clustalw` - Perform multiple sequence alignment
+================================================================================
+
+.. module:: ost.bindings.clustalw
+ :synopsis: Perform multiple sequence alignment
+
+
+.. autofunction:: ost.bindings.clustalw.ClustalW
diff --git a/modules/bindings/doc/dssp.rst b/modules/bindings/doc/dssp.rst
index 61de495e34f920e85bc801800feb24c4ca5a3305..bb9d2b57b0f081bd0f6ec0d7b82e0ef9bcf59089 100644
--- a/modules/bindings/doc/dssp.rst
+++ b/modules/bindings/doc/dssp.rst
@@ -2,19 +2,22 @@
================================================================================
.. module:: ost.bindings.dssp
- :synopsis: Interface to the DSSP commandline utility
+ :synopsis: Interface to the DSSP command line utility
Introduction
--------------------------------------------------------------------------------
-DSSP is a program developed by Wolfgang Kabsch and Chris Sander to assign secondary structure states to protein structures. The assignment is based on hydrogen bonding patterns and geometric features.
+DSSP is a program developed by Wolfgang Kabsch and Chris Sander to assign
+secondary structure states to protein structures. The assignment is based on
+hydrogen bonding patterns and geometric features.
The program can be downloaded from `<http://swift.cmbi.ru.nl/gv/dssp/>`_.
-Example
+Examples
--------------------------------------------------------------------------------
-The following example assigns secondary structure states to an entity by using the DSSP program.
+The following example assigns secondary structure states to an entity by using
+the DSSP program.
.. code-block:: python
@@ -23,9 +26,27 @@ The following example assigns secondary structure states to an entity by using t
ent=io.LoadPDB('1ake.pdb')
dssp.AssignDSSP(ent)
+
+Now we fetch structure information plus solvent accessibility for an entity
+using the mmCIF interface.
+
+
+.. code-block:: python
+
+ from ost.bindings import dssp
+ ent=io.LoadMMCIF('1ake.cif')
+ dssp.AssignDSSP(ent, extract_burial_status=True)
+ for chain in ent.chains:
+ if chain.is_polypeptide:
+ for res in chain.residues:
+ print res.GetFloatProp('relative_solvent_accessibility')
+
+
DSSP bindings Usage
--------------------------------------------------------------------------------
.. autofunction:: ost.bindings.dssp.AssignDSSP
.. autofunction:: ost.bindings.dssp.LoadDSSP
+
+.. LocalWords: dssp AssignDSSP ent GetFloatProp autofunction
diff --git a/modules/bindings/doc/msms.rst b/modules/bindings/doc/msms.rst
index 0085571c0a063b15bb78e7ecb6dded7a89ad24ef..d9ed150c26576990b22e7ad7005a5e28914aa701 100644
--- a/modules/bindings/doc/msms.rst
+++ b/modules/bindings/doc/msms.rst
@@ -6,6 +6,10 @@
.. autoclass:: ost.bindings.msms.MsmsProcessError
+.. autofunction:: ost.bindings.msms.CalculateSurface
+
.. autofunction:: ost.bindings.msms.CalculateSurfaceArea
-.. autofunction:: ost.bindings.msms.CalculateSurface
+.. autofunction:: ost.bindings.msms.CalculateSurfaceVolume
+
+.. autofunction:: ost.bindings.msms.GetVersion
\ No newline at end of file
diff --git a/modules/bindings/pymod/blast.py b/modules/bindings/pymod/blast.py
index 054bff58c0575848d08642a6f935c09c7912df98..8f14d64dc27f259c7bd7756d27c7d9313b5e6731 100644
--- a/modules/bindings/pymod/blast.py
+++ b/modules/bindings/pymod/blast.py
@@ -136,7 +136,8 @@ def Blast(query, database, gap_open=11, gap_ext=1, matrix='BLOSUM62',
:type query: :class:`seq.ConstSequenceHandle`
:param database: The filename of the sequence database. Make sure that
- formatdb has been run on the database and the <database>.pin file exists.
+ formatdb has been run on the database and the <database>.pin or
+ <database>.pal file exists.
:param matrix: The substitution matrix to be used. Must be one of 'BLOSUM45',
'BLOSUM62', 'BLOSUM80', 'PAM30', 'PAM70'.
:param gap_open: Gap opening penalty. Note that only a subset of gap opening
@@ -155,7 +156,7 @@ def Blast(query, database, gap_open=11, gap_ext=1, matrix='BLOSUM62',
subst_mats=('BLOSUM45', 'BLOSUM62', 'BLOSUM80', 'PAM30', 'PAM70',)
if matrix not in subst_mats:
raise ValueError('matrix must be one of %s' % ', '.join(subst_mats))
- if not os.path.exists('%s.pin' % database):
+ if not os.path.exists('%s.pin' % database) and not os.path.exists('%s.pal' % database):
raise IOError("Database %s does not exist" % database)
blastall_exe=settings.Locate('blastall', explicit_file_name=blast_location)
args=[blastall_exe, '-d', database, '-p', 'blastp',
diff --git a/modules/bindings/pymod/clustalw.py b/modules/bindings/pymod/clustalw.py
index 2c2fd6ebac5cf580dd1a259cb087a0ada9a127c4..0204cd8ccc9a51962ccbef257676341c43b4cd7c 100644
--- a/modules/bindings/pymod/clustalw.py
+++ b/modules/bindings/pymod/clustalw.py
@@ -5,6 +5,46 @@ import subprocess
def ClustalW(seq1, seq2=None, clustalw=None, keep_files=False, nopgap=False,
clustalw_option_string=False):
+ '''
+ Runs a clustalw multiple sequence alignment. The results are returned as a
+ :class:`~ost.seq.AlignmentHandle` instance.
+
+ There are two ways to use this function:
+
+ - align exactly two sequences:
+
+ :param seq1: sequence_one
+ :type seq1: :class:`~ost.seq.SequenceHandle` or :class:`str`
+
+ :param seq2: sequence_two
+ :type seq2: :class:`~ost.seq.SequenceHandle` or :class:`str`
+
+ The two sequences can be specified as two separate function parameters
+ (`seq1`, `seq2`). The type of both parameters can be either
+ :class:`~ost.seq.SequenceHandle` or :class:`str`, but must be the same for
+ both parameters.
+
+ - align two or more sequences:
+
+ :param seq1: sequence_list
+ :type seq1: :class:`~ost.seq.SequenceList`
+
+ :param seq2: must be :class:`None`
+
+ Two or more sequences can be specified by using a
+ :class:`~ost.seq.SequenceList`. It is then passed as the first function
+ parameter (`seq1`). The second parameter (`seq2`) must be :class:`None`.
+
+
+ :param clustalw: path to clustalw executable (used in :func:`~ost.settings.Locate`)
+ :type clustalw: :class:`str`
+ :param nopgap: turn residue-specific gaps off
+ :type nopgap: :class:`bool`
+ :param clustalw_option_string: additional clustalw flags (see http://toolkit.tuebingen.mpg.de/clustalw/help_params)
+ :type clustalw_option_string: :class:`str`
+ :param keep_files: do not delete temporary files
+ :type keep_files: :class:`bool`
+ '''
clustalw_path=settings.Locate(('clustalw', 'clustalw2'),
explicit_file_name=clustalw)
diff --git a/modules/bindings/pymod/dssp.py b/modules/bindings/pymod/dssp.py
index 1cb1db3aa9b21ea17f29aa0348a32d4fc32d1c14..f27aa9db9405357a3221adffb190921092febad5 100644
--- a/modules/bindings/pymod/dssp.py
+++ b/modules/bindings/pymod/dssp.py
@@ -88,7 +88,10 @@ def AssignDSSP(ent, pdb_path="", extract_burial_status=False, tmp_dir=None,
:param ent: The entity for which the secondary structure should be calculated
:type ent: :class:`~ost.mol.EntityHandle` or :class:`~ost.mol.EntityView`
- :param extract_burial_status: If true, also extract burial status
+ :param extract_burial_status: If true, also extract burial status and store
+ as float-property
+ ``relative_solvent_accessibility`` at residue
+ level
:param tmp_dir: If set, overrides the default tmp directory of the
operating system
:param dssp_bin: The path to the DSSP executable
diff --git a/modules/bindings/pymod/msms.py b/modules/bindings/pymod/msms.py
index fc50ff1c7b8081f1774d62fc36712bfb8487b4e7..60009f6070d2592ed6790521359a82684771f647 100644
--- a/modules/bindings/pymod/msms.py
+++ b/modules/bindings/pymod/msms.py
@@ -100,7 +100,7 @@ def _SetupFiles(entity, selection):
return (tmp_dir_name, tmp_file_name)
-def _ParseAreaFile(entity,file, asa_prop, esa_prop):
+def _ParseAreaFile(entity, selection, file, asa_prop, esa_prop):
"""
Reads Area file (-af) and attach sasa and sesa per atom to an entitiy
@@ -111,16 +111,17 @@ def _ParseAreaFile(entity,file, asa_prop, esa_prop):
:param esa_prop: Name of the float property for SESA
:raises: :class:`RuntimeError` if number of atoms in file != number of atoms in entity
"""
+ view=entity.Select(selection)
area_fh = open(file)
area_lines = area_fh.readlines()
area_fh.close()
# shift first line
area_lines = area_lines[1:]
- if entity.GetAtomCount() != len(area_lines):
- raise RuntimeError, "Atom count (%d) unequeal to number of atoms in area file (%d)" % (entity.GetAtomCount(), len(area_lines))
+ 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))
for l in area_lines:
atom_no, sesa, sasa = l.split()
- a = entity.atoms[int(atom_no)]
+ a = view.atoms[int(atom_no)]
if asa_prop:
a.SetFloatProp(asa_prop, float(sasa))
if esa_prop:
@@ -218,14 +219,14 @@ def CalculateSurfaceArea(entity, density=1.0, radius=1.5, all_surf=False,
(msms_executable, msms_data_file, msms_data_file, density, radius)
if all_surf:
command+=" -all"
- if attach_asa != None:
+ if attach_asa != None or attach_esa != None:
command+=" -af %s" % os.path.join(msms_data_dir, "asa_atom")
# run msms
stdout_value=_RunMSMS(command)
# add sesa and asa to entity if attach_asa is specified
- if attach_asa != None:
- _ParseAreaFile(entity, os.path.join(msms_data_dir, "asa_atom.area"),
+ if attach_asa != None or attach_esa != None:
+ _ParseAreaFile(entity, selection, os.path.join(msms_data_dir, "asa_atom.area"),
attach_asa, attach_esa)
# parse MSMS output
@@ -248,6 +249,84 @@ def CalculateSurfaceArea(entity, density=1.0, radius=1.5, all_surf=False,
return (msms_ases, msms_asas)
+def CalculateSurfaceVolume(entity, density=1.0, radius=1.5, all_surf=False,
+ no_hydrogens=False, no_hetatoms=False, no_waters=False,
+ selection='',
+ msms_exe=None, msms_env=None, keep_files=False,
+ attach_asa=None, attach_esa=None):
+ """
+ Calculates the volume of the solvent excluded surface by using the external MSMS program.
+
+ This method calculates the volume of the molecular surface by invoking the external
+ program MSMS. First, it is checked if the MSMS executable is present, then,
+ the necessary files are prepared in a temporary directory and MSMS is
+ executed. The last step is to remove the temporary directory.
+
+
+ :param entity: OST entity to calculate surface
+ :param density: Surface point density
+ :param radius: Surface probe radius
+ :param all_surf: Calculate surface area for all cavities (returns multiple
+ surfaces areas as a list)
+ :param no_hydrogens: Calculate surface only for hevy atoms
+ :param selection: Calculate surface for subset of entity
+ :param msms_exe: msms executable (full path to executable)
+ :param msms_env: msms environment variable
+ :param keep_files: Do not delete temporary files
+ :param attach_asa: Attaches per atom SASA to specified FloatProp at atom level
+ :param attach_esa: Attaches per atom SESA to specified FloatProp at atom level
+ :returns: Tuple of lists for (SES, SAS)
+ """
+ import re
+
+ # check if msms executable is specified
+ msms_executable=_GetExecutable(msms_exe, msms_env)
+
+ # parse selection
+ if no_hydrogens:
+ if selection!='':
+ selection+=" and "
+ selection+="ele!=H"
+
+ if no_hetatoms:
+ if selection!='':
+ selection+=" and "
+ selection+="ishetatm=False"
+
+ if no_waters:
+ if selection!='':
+ selection+=" and "
+ selection+="rname!=HOH"
+
+ # setup files for msms
+ (msms_data_dir, msms_data_file)=_SetupFiles(entity, selection)
+
+ # set command line
+ command="%s -if %s -of %s -density %s -probe_radius %s " % \
+ (msms_executable, msms_data_file, msms_data_file, density, radius)
+ if all_surf:
+ command+=" -all"
+ if attach_asa != None or attach_esa != None:
+ command+=" -af %s" % os.path.join(msms_data_dir, "asa_atom")
+ # run msms
+ stdout_value=_RunMSMS(command)
+
+ # add sesa and asa to entity if attach_asa is specified
+ if attach_asa != None or attach_esa != None:
+ _ParseAreaFile(entity, selection, os.path.join(msms_data_dir, "asa_atom.area"),
+ attach_asa, attach_esa)
+
+ # parse MSMS output
+ ses_volume=0
+ for line in stdout_value.splitlines():
+ if re.match(' Total ses_volume:', line):
+ ses_volume=float(line.split(':')[1])
+
+ # clean up
+ if not keep_files:
+ _CleanupFiles(msms_data_dir)
+
+ return ses_volume
def CalculateSurface(entity, density=1.0, radius=1.5, all_surf=False,
@@ -269,7 +348,7 @@ def CalculateSurface(entity, density=1.0, radius=1.5, all_surf=False,
:param radius: Surface probe radius
:param all_surf: Calculate surface for all cavities (returns multiple
surfaces as a list)
- :param no_hydrogens: Calculate surface only for hevy atoms
+ :param no_hydrogens: Calculate surface only for heavy atoms
:param selection: Calculate surface for subset of entity
:param msms_exe: msms executable (full path to executable)
:param msms_env: msms environment variable
diff --git a/modules/bindings/pymod/tmtools.py b/modules/bindings/pymod/tmtools.py
index 2f53fcb350285d907f945c17ef47fb71b8e34079..3c53b9975db978068aaa4397fca2f2e34be74813 100644
--- a/modules/bindings/pymod/tmtools.py
+++ b/modules/bindings/pymod/tmtools.py
@@ -34,8 +34,17 @@ from ost import settings, io, geom, seq
def _SetupFiles(models):
# create temporary directory
tmp_dir_name=tempfile.mkdtemp()
+ dia = 'PDB'
for index, model in enumerate(models):
- io.SavePDB(model, os.path.join(tmp_dir_name, 'model%02d.pdb' % (index+1)))
+ for chain in model.chains:
+ if len(chain.name) > 1:
+ dia = 'CHARMM'
+ break;
+ for res in chain.residues:
+ if len(res.name) > 3:
+ dia = 'CHARMM'
+ break;
+ io.SavePDB(model, os.path.join(tmp_dir_name, 'model%02d.pdb' % (index+1)), dialect=dia)
return tmp_dir_name
def _CleanupFiles(dir_name):
diff --git a/modules/bindings/tests/test_blast.py b/modules/bindings/tests/test_blast.py
index e8e151a4ec4a325658df4cee69c4b8d0b30feb47..8b4215faa45d71660a7799f3211885f519745a56 100644
--- a/modules/bindings/tests/test_blast.py
+++ b/modules/bindings/tests/test_blast.py
@@ -44,7 +44,5 @@ if __name__ == "__main__":
except(settings.FileNotFound):
print "Could not find blastall executable: ignoring unit tests"
sys.exit(0)
- try:
- unittest.main()
- except Exception, e:
- print e
+ from ost import testutils
+ testutils.RunTests()
diff --git a/modules/bindings/tests/test_clustalw.py b/modules/bindings/tests/test_clustalw.py
index 0fdb040db2b59f1a1a216a520059fb9d0f3faada..fa5a5e6b5eb44cbe11a0a11a68dc93d7d64cf123 100644
--- a/modules/bindings/tests/test_clustalw.py
+++ b/modules/bindings/tests/test_clustalw.py
@@ -68,7 +68,5 @@ if __name__ == "__main__":
except(settings.FileNotFound):
print "Could not find clustalw executable: ignoring unit tests"
sys.exit(0)
- try:
- unittest.main()
- except Exception, e:
- print e
+ from ost import testutils
+ testutils.RunTests()
diff --git a/modules/bindings/tests/test_msms.py b/modules/bindings/tests/test_msms.py
index 054a63cffa472d01fbef5d5cd20289cd0a409fb6..9041f94fab817441da03ae794fe63d793ad7d208 100755
--- a/modules/bindings/tests/test_msms.py
+++ b/modules/bindings/tests/test_msms.py
@@ -42,7 +42,5 @@ if __name__ == "__main__":
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)
- try:
- unittest.main()
- except Exception, e:
- print e
+ from ost import testutils
+ testutils.RunTests()
diff --git a/modules/config/CMakeLists.txt b/modules/config/CMakeLists.txt
index 617aa51c5b87a2dc03b95d7a92730b097b31d371..1e637d14470c6aa77af76cdd6c58e5ad5561c180 100644
--- a/modules/config/CMakeLists.txt
+++ b/modules/config/CMakeLists.txt
@@ -21,7 +21,6 @@ if (USE_NUMPY)
else()
set(numpy_support 0)
endif()
-
if (PROFILE)
set(profiling_enabled 1)
else()
@@ -62,6 +61,11 @@ if (_DEBIAN_STYLE_LIBEXEC)
else()
set(debian_style_libexec 0)
endif()
+if (ENABLE_INFO)
+ set(info_enabled 1)
+else()
+ set(info_enabled 0)
+endif()
set(config_hh_generator "CMake")
set(CONFIG_HH_FILE "${CMAKE_CURRENT_SOURCE_DIR}/config.hh")
diff --git a/modules/config/config.hh.in b/modules/config/config.hh.in
index a9e33adca707baed39710d3c75f63ca2b210bf0b..c2242500ee2e528294c5beb77a5c650f9adfe288 100644
--- a/modules/config/config.hh.in
+++ b/modules/config/config.hh.in
@@ -33,5 +33,6 @@
#define OST_FFT_USE_THREADS @fftw_use_threads@
#define OST_NUMPY_SUPPORT_ENABLED @numpy_support@
#define OST_DEBIAN_STYLE_LIBEXEC @debian_style_libexec@
+#define OST_INFO_ENABLED @info_enabled@
#endif
diff --git a/modules/conop/doc/cleanup.rst b/modules/conop/doc/cleanup.rst
new file mode 100644
index 0000000000000000000000000000000000000000..35b20e5705b248a995ec61c5e06604c53df0767f
--- /dev/null
+++ b/modules/conop/doc/cleanup.rst
@@ -0,0 +1,8 @@
+:mod:`conop.cleanup <ost.conop.cleanup>` -- Sanitize structures
+================================================================================
+
+.. module:: ost.conop.ceanup
+ :synopsis: Contains functions to sanitize (cleanup) structures by using
+ information from the compound library.
+
+.. autofunction:: ost.conop.cleanup.Cleanup
\ No newline at end of file
diff --git a/modules/conop/doc/conop.rst b/modules/conop/doc/conop.rst
index 8c3f413469872a1d95f9da98e37f4e21ffb24bfc..fb72db2645a92ea70f3db4f686c0f33a35c7e956 100644
--- a/modules/conop/doc/conop.rst
+++ b/modules/conop/doc/conop.rst
@@ -20,3 +20,4 @@ In this module
aminoacid
connectivity
compoundlib
+ cleanup
\ No newline at end of file
diff --git a/modules/conop/pymod/CMakeLists.txt b/modules/conop/pymod/CMakeLists.txt
index 5affa4b457d780b7368b34a097bec832d2c3f36c..c1bf89d0e29cda36f4b4bcb9b0b357449aaa8ad7 100644
--- a/modules/conop/pymod/CMakeLists.txt
+++ b/modules/conop/pymod/CMakeLists.txt
@@ -4,7 +4,10 @@ set(OST_CONOP_PYMOD_SOURCES
export_compound.cc
export_amino_acids.cc
export_conop.cc
+ export_non_standard.cc
export_ring_finder.cc
)
-pymod(NAME conop CPP ${OST_CONOP_PYMOD_SOURCES} PY __init__.py)
\ No newline at end of file
+if (NOT ENABLE_STATIC)
+ pymod(NAME conop CPP ${OST_CONOP_PYMOD_SOURCES} PY __init__.py cleanup.py)
+endif()
diff --git a/modules/conop/pymod/__init__.py b/modules/conop/pymod/__init__.py
index 44aaed354facbf286933d5e2ff19dd89bf7544e1..a534ea808bf883c616c7eb7165af5b71155fdc5b 100644
--- a/modules/conop/pymod/__init__.py
+++ b/modules/conop/pymod/__init__.py
@@ -18,6 +18,17 @@
#------------------------------------------------------------------------------
from _ost_conop import *
+# The 20 standard amino acids in no particular order
+STANDARD_AMINOACIDS=(
+ 'ALA', 'ARG', 'ASN',
+ 'ASP', 'GLN', 'GLU',
+ 'LYS', 'SER', 'CYS',
+ 'MET', 'TRP', 'TYR',
+ 'THR', 'VAL', 'ILE',
+ 'LEU', 'GLY', 'PRO',
+ 'HIS', 'PHE',
+)
+
def ConnectAll(ent):
'''
Uses the current default builder to connect the atoms of the entity, assign
diff --git a/modules/conop/pymod/cleanup.py b/modules/conop/pymod/cleanup.py
new file mode 100644
index 0000000000000000000000000000000000000000..9ecf9c7ef12b8bb4fce889a5fb8062aab2364eda
--- /dev/null
+++ b/modules/conop/pymod/cleanup.py
@@ -0,0 +1,167 @@
+from ost import conop, mol
+
+def Cleanup(entity, strip_water=True, canonicalize=True, remove_ligands=True):
+ """
+ This function returns a cleaned-up (simplified) version of the protein
+ structure. Different parameters affect the behaviour of the function.
+
+ :param strip_water: Whether to remove water from the structure
+ :param canonicalize: Whether to strip off modifications of amino acids and map
+ them back to their parent standard amino acid, e.g. selenium methionine to
+ methionine.For more complex amino acids, where the relation between the
+ modified and the standard parent amino acid is not known, sidechain atoms
+ are removed. D-peptide-linking residues are completely removed as well.
+ :param remove_ligands: Whether to remove ligands from the structure
+
+ :return: a cleaned version of the entity
+ """
+ #setup
+ builder = conop.GetBuilder()
+ if not hasattr(builder, "compound_lib") :
+ raise RuntimeError( "Cannot cleanup structure, since the default builder doesn't use the compound library")
+ compound_lib = builder.compound_lib
+ clean_entity = entity.Copy()
+ ed = clean_entity.EditXCS()
+ #remove water residues
+ if strip_water:
+ _StripWater(clean_entity, ed)
+ #replace modified residues before removing ligands to avoid removing MSE and others
+ if canonicalize:
+ _CanonicalizeResidues(clean_entity, ed, compound_lib)
+ #remove all hetatoms that are not water
+ if remove_ligands:
+ _RemoveLigands(clean_entity, ed)
+ return clean_entity
+
+
+def _StripWater(clean_entity, ed) :
+ """
+ This function removes water residues from the structure
+ """
+ for res in clean_entity.residues:
+ if res.IsValid():
+ if res.chem_class == mol.WATER:
+ ed.DeleteResidue(res.handle)
+ ed.UpdateICS()
+ return
+
+def _RemoveLigands(clean_entity, ed) :
+ """
+ This function removes ligands from the structure
+ """
+ for res in clean_entity.residues:
+ if res.IsValid():
+ #WHEN mmCIF WILL BE USED, CHANGE IsPeptideLinking() TO IsProtein()
+ if not res.IsPeptideLinking() and res.atoms[0].is_hetatom and res.chem_class != mol.WATER:
+ ed.DeleteResidue(res.handle)
+ ed.UpdateICS()
+ return
+
+def _CanonicalizeResidues(clean_entity, ed, compound_lib) :
+ """
+ This function strips off modifications of amino acids and maps
+ them back to their parent standard amino acid, e.g. selenium methionine to
+ methionine.For more complex amino acids, where the relation between the
+ modified and the standard parent amino acid is not known, sidechain atoms
+ are removed. D-peptide-linking residues are completely removed as well.
+ """
+
+ for res in clean_entity.residues:
+ if res.IsValid() and res.IsPeptideLinking() :
+ parent_olc = res.one_letter_code
+ if parent_olc == "X" :
+ _DeleteSidechain(res, ed)
+ for atom in res.atoms:
+ atom.is_hetatom = False
+ else:
+ parent_tlc = conop.OneLetterCodeToResidueName(parent_olc)
+ parent_res = compound_lib.FindCompound(parent_tlc)
+ if not parent_res:
+ _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
+ else:
+ #collect atom's names
+ modif_atom_names = set([atom.name for atom in res.atoms
+ if atom.element != "H" and atom.element != "D" ])
+ #if the res is the first or last take all the atoms from the parent res
+ if res.FindAtom("OXT").IsValid() :
+ parent_atom_names = set([atom.name for atom in parent_res.atom_specs
+ if atom.element != "H" and atom.element != "D" ])
+ else:
+ parent_atom_names = set([atom.name for atom in parent_res.atom_specs
+ if atom.element != "H" and atom.element != "D" and not atom.is_leaving ])
+ additional_parent_atoms = parent_atom_names - modif_atom_names
+ additional_modif_atoms = modif_atom_names - parent_atom_names
+ #WHEN mmCIF WILL BE USED, CHANGE IsPeptideLinking() TO IsProtein(), TO EXCLUDE LIGANDS FROM CANONICALISATION
+ if res.atoms[0].is_hetatom :
+ old_name = res.name
+ ed.RenameResidue(res, parent_tlc)
+ if additional_parent_atoms:
+ if additional_modif_atoms:
+ #replacement
+ _Replacement(res, ed, old_name)
+ else:
+ #deletion
+ _Deletion(res, ed)
+ elif additional_modif_atoms:
+ #addition
+ _Addition(res, ed, additional_modif_atoms)
+ else:
+ #unchanged, later check stereochemistry or H atoms
+ _Unchanged(res, ed)
+ #the res is a peptide but not a ligand (is a protein res)
+ else:
+ if additional_parent_atoms:# if the sidechain is incomplete
+ _DeleteSidechain(res, ed)
+ ed.UpdateICS()
+ return
+
+def _Replacement(res, ed, old_name) :
+ #TEMP ONLY MSE
+ if old_name == "MSE" :
+ for atom in res.atoms:
+ atom.is_hetatom = False
+ sel = res.FindAtom("SE")
+ if sel.IsValid() :
+ ed.InsertAtom( res, "SD", sel.pos, "S", sel.occupancy, sel.b_factor ) #S radius=~1;SE=~1.2
+ ed.DeleteAtom( sel )
+ else:
+ _DeleteSidechain(res, ed)
+ else:
+ _DeleteSidechain(res, ed)
+ return
+
+def _Deletion(res, ed) :
+ _DeleteSidechain(res, ed)
+ for atom in res.atoms :
+ atom.is_hetatom = False
+ return
+
+def _Addition(res, ed, additional_modif_atoms) :
+ for add_atom_name in additional_modif_atoms:
+ add_atom = res.FindAtom( add_atom_name )
+ if add_atom.IsValid() :
+ ed.DeleteAtom( add_atom )
+ for atom in res.atoms:
+ atom.is_hetatom = False
+ return
+
+def _Unchanged(res, ed) :
+ if res.chem_class == mol.D_PEPTIDE_LINKING:
+ ed.DeleteResidue(res)
+ else:
+ _DeleteSidechain(res, ed)
+ for atom in res.atoms :
+ atom.is_hetatom = False
+ return
+
+def _DeleteSidechain(res, ed) :
+ for atom in res.atoms:
+ if not atom.name in ['CA','CB','C','N','O']:
+ ed.DeleteAtom(atom)
+ return
+
+#visible functions
+__all__ = [Cleanup]
diff --git a/modules/conop/pymod/export_builder.cc b/modules/conop/pymod/export_builder.cc
index 4bd468f36b23180c726f661f34a89227ee7168c0..1897983f90b7c4065316633db738732c0ba4b93f 100644
--- a/modules/conop/pymod/export_builder.cc
+++ b/modules/conop/pymod/export_builder.cc
@@ -36,6 +36,8 @@ void export_Builder() {
.add_property("dialect", &Builder::GetDialect, &Builder::SetDialect)
.add_property("strict_hydrogens", &Builder::GetStrictHydrogenMode,
&Builder::SetStrictHydrogenMode)
+ .add_property("bond_feasibility_check", &Builder::GetBondFeasibilityCheck,
+ &Builder::SetBondFeasibilityCheck)
.def("GetDialect", &Builder::GetDialect)
.def("SetDialect", &Builder::SetDialect)
.def("CompleteAtoms", &Builder::CompleteAtoms)
@@ -48,6 +50,8 @@ void export_Builder() {
.def("AssignTorsionsToResidue", &Builder::AssignTorsionsToResidue)
.def("FillAtomProps", &Builder::FillAtomProps)
.def("IsResidueComplete", &Builder::IsResidueComplete)
+ .def("SetBondFeasibilityFlag", &Builder::SetBondFeasibilityCheck)
+ .def("GetBondFeasibilityFlag", &Builder::GetBondFeasibilityCheck)
;
class_<HeuristicBuilder, bases<Builder> >("HeuristicBuilder", init<>())
@@ -56,5 +60,6 @@ void export_Builder() {
init<const CompoundLibPtr&>())
.add_property("compound_lib", &RuleBasedBuilder::GetCompoundLib)
.def("GetUnknownAtoms", &RuleBasedBuilder::GetUnknownAtoms)
+
;
}
diff --git a/modules/conop/pymod/export_compound.cc b/modules/conop/pymod/export_compound.cc
index a2599acf43b004562cd20efd198456a9a577b10a..0b7e0dde8d24422a0758d91019aebf0d1252701b 100644
--- a/modules/conop/pymod/export_compound.cc
+++ b/modules/conop/pymod/export_compound.cc
@@ -57,11 +57,17 @@ char get_chemclass(CompoundPtr compound)
return char(compound->GetChemClass());
}
+
void set_chemclass(CompoundPtr compound, char cc)
{
compound->SetChemClass(ChemClass(cc));
}
+char get_chemtype(CompoundPtr compound)
+{
+ return char(compound->GetChemType());
+}
+
CompoundPtr find_compound(CompoundLibPtr comp_lib,
const String& tlc, const String& dialect)
{
@@ -92,6 +98,7 @@ void export_Compound() {
.def("IsPeptideLinking", &Compound::IsPeptideLinking)
.add_property("chem_class", &get_chemclass,
&set_chemclass)
+ .add_property("chem_type", &get_chemtype)
.add_property("formula",make_function(&Compound::GetFormula,
return_value_policy<copy_const_reference>()),
&Compound::SetFormula)
diff --git a/modules/conop/pymod/export_non_standard.cc b/modules/conop/pymod/export_non_standard.cc
new file mode 100644
index 0000000000000000000000000000000000000000..025d2819a100584c85f3b088ce5320fdf02d0762
--- /dev/null
+++ b/modules/conop/pymod/export_non_standard.cc
@@ -0,0 +1,50 @@
+//------------------------------------------------------------------------------
+// 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
+//------------------------------------------------------------------------------
+#include <boost/python.hpp>
+#include <ost/mol/mol.hh>
+#include <ost/conop/nonstandard.hh>
+
+using namespace boost::python;
+
+using namespace ost::conop;
+using namespace ost::mol;
+
+object copy_conserved_handle(ResidueHandle src_res, ResidueHandle dst_res,
+ XCSEditor edi) {
+ bool has_cbeta = false;
+ bool ret = CopyConserved(src_res, dst_res, edi, has_cbeta);
+ return make_tuple(ret, has_cbeta);
+}
+
+object copy_non_conserved_handle(ResidueHandle src_res, ResidueHandle dst_res,
+ XCSEditor edi) {
+ bool has_cbeta = false;
+ bool ret = CopyNonConserved(src_res, dst_res, edi, has_cbeta);
+ return make_tuple(ret, has_cbeta);
+}
+
+
+
+void export_NonStandard()
+{
+ def("CopyNonConserved",©_non_conserved_handle);
+ def("CopyConserved", copy_conserved_handle);
+ def("CopyResidue", &CopyResidue);
+ }
+
diff --git a/modules/conop/pymod/wrap_conop.cc b/modules/conop/pymod/wrap_conop.cc
index 2aba86654fb077bc42751b173a5185f22bb18ffc..6573bf41a7e6c8fcb471cbf25a79be77b1b03dfa 100644
--- a/modules/conop/pymod/wrap_conop.cc
+++ b/modules/conop/pymod/wrap_conop.cc
@@ -25,6 +25,8 @@ void export_Sanitizer();
void export_Conop();
void export_RingFinder();
void export_AminoAcids();
+void export_NonStandard();
+
BOOST_PYTHON_MODULE(_ost_conop)
{
export_Builder();
@@ -32,4 +34,5 @@ BOOST_PYTHON_MODULE(_ost_conop)
export_Compound();
export_RingFinder();
export_AminoAcids();
+ export_NonStandard();
}
diff --git a/modules/conop/src/CMakeLists.txt b/modules/conop/src/CMakeLists.txt
index 127bd15ea7757eaaa50abeda7c7e07d3f295f3f0..344f5e00755d3ba733f1d6a877840037c8da802b 100644
--- a/modules/conop/src/CMakeLists.txt
+++ b/modules/conop/src/CMakeLists.txt
@@ -7,6 +7,7 @@ amino_acids.hh
compound.hh
compound_lib.hh
module_config.hh
+nonstandard.hh
rule_based_builder.hh
ring_finder.hh
)
@@ -18,12 +19,13 @@ conop.cc
heuristic_builder.cc
compound.cc
compound_lib.cc
+nonstandard.cc
rule_based_builder.cc
ring_finder.cc
)
module(NAME conop SOURCES ${OST_CONOP_SOURCES}
- HEADERS ${OST_CONOP_HEADERS} DEPENDS_ON ost_mol ost_geom ost_db)
+ HEADERS ${OST_CONOP_HEADERS} DEPENDS_ON ost_mol ost_mol_alg ost_geom ost_db)
executable(NAME chemdict_tool SOURCES chemdict_tool.cc DEPENDS_ON ost_io STATIC)
diff --git a/modules/conop/src/builder.hh b/modules/conop/src/builder.hh
index f912aba702cd075768da77c1c837f558877f3fda..4b915681a51d2d47c6d36fe449424f5b189de772 100644
--- a/modules/conop/src/builder.hh
+++ b/modules/conop/src/builder.hh
@@ -54,7 +54,7 @@ typedef enum {
class DLLEXPORT_OST_CONOP Builder {
public:
- Builder(): dialect_(PDB_DIALECT), strict_(false) { }
+ Builder(): dialect_(PDB_DIALECT), strict_(false), bond_feasibility_check_(true) { }
virtual ~Builder();
/// \brief add any missing atoms to the residue based on its key,
@@ -143,9 +143,17 @@ public:
/// |brief Connect \p atom with all atoms for whith IsBondFeasible() and
/// AreResiduesConsecutive() returns true
void DistanceBasedConnect(mol::AtomHandle atom);
+
+ /// \brief Set bond feasibility check flag
+ void SetBondFeasibilityCheck(bool b_feas_flag) { bond_feasibility_check_ = b_feas_flag; }
+
+ /// \brief Get bond feasibility check flag
+ bool GetBondFeasibilityCheck() const { return bond_feasibility_check_; }
+
private:
Dialect dialect_;
bool strict_;
+ bool bond_feasibility_check_;
};
diff --git a/modules/conop/src/compound.hh b/modules/conop/src/compound.hh
index d3f47bd973166a8bdc169729eef1be8db61a9d50..e33a7e38cfb840ebc5e5e050fbd7da55073e2c68 100644
--- a/modules/conop/src/compound.hh
+++ b/modules/conop/src/compound.hh
@@ -25,6 +25,7 @@
#include <ost/conop/module_config.hh>
#include <ost/mol/chem_class.hh>
+#include <ost/mol/chem_type.hh>
namespace ost { namespace conop {
@@ -120,7 +121,7 @@ public:
} Dialect;
Compound(const String& id)
- : olc_('?'), tlc_(id), chem_class_(), dialect_(Compound::PDB) {
+ : olc_('?'), tlc_(id), chem_class_(), chem_type_(), dialect_(Compound::PDB){
}
/// \brief three-letter code that is unique for every compound
@@ -166,6 +167,18 @@ public:
return chem_class_;
}
+ void SetChemType(mol::ChemType chem_type) {
+ chem_type_=chem_type;
+ }
+
+ /// \brief PDB ligand classification from component dictionary
+ ///
+ /// The PDB classifies all compounds into 7 categories. This classification
+ /// is extracted from the PDB component dictionary (field: pdbx_type)
+ mol::ChemType GetChemType() const {
+ return chem_type_;
+ }
+
bool IsPeptideLinking() const {
return chem_class_.IsPeptideLinking();
}
@@ -221,6 +234,7 @@ private:
AtomSpecList atom_specs_;
BondSpecList bond_specs_;
mol::ChemClass chem_class_;
+ mol::ChemType chem_type_;
Dialect dialect_;
Date creation_date_;
Date mod_date_;
diff --git a/modules/conop/src/compound_lib.cc b/modules/conop/src/compound_lib.cc
index c16c8505a8ca06f703d2d3c4cbf5263d0764c610..c05e60fb6d2ce72343e6ab44d637526c16639707 100644
--- a/modules/conop/src/compound_lib.cc
+++ b/modules/conop/src/compound_lib.cc
@@ -41,6 +41,7 @@ const char* CREATE_CMD[]={
" olc VARCHAR(1) NOT NULL, "
" dialect VARCHAR(1) NOT NULL, "
" chem_class VARCHAR(1), "
+" chem_type VARCHAR(1), "
" formula VARCHAR(64) NOT NULL, "
" pdb_initial TIMESTAMP, "
" pdb_modified TIMESTAMP "
@@ -79,8 +80,8 @@ const char* CREATE_CMD[]={
const char* INSERT_COMPOUND_STATEMENT="INSERT INTO chem_compounds "
-" (tlc, olc, dialect, chem_class, formula, pdb_initial, pdb_modified) "
-" VALUES (?, ?, ?, ?, ?, DATE(?), DATE(?))";
+" (tlc, olc, dialect, chem_class, chem_type, formula, pdb_initial, pdb_modified) "
+" VALUES (?, ?, ?, ?, ?, ?, DATE(?), DATE(?))";
const char* INSERT_ATOM_STATEMENT="INSERT INTO atoms "
" (compound_id, name, alt_name, element, is_aromatic, stereo_conf, "
@@ -106,11 +107,13 @@ void CompoundLib::AddCompound(const CompoundPtr& compound)
compound->GetID().length(), NULL);
char olc=compound->GetOneLetterCode();
sqlite3_bind_text(stmt, 2, &olc, 1, NULL);
- char chem_type=compound->GetChemClass();
+ char chem_class=compound->GetChemClass();
+ char chem_type=compound->GetChemType();
char dialect=compound->GetDialect();
sqlite3_bind_text(stmt, 3, &dialect, 1, NULL);
- sqlite3_bind_text(stmt, 4, &chem_type, 1, NULL);
- sqlite3_bind_text(stmt, 5, compound->GetFormula().c_str(),
+ sqlite3_bind_text(stmt, 4, &chem_class, 1, NULL);
+ sqlite3_bind_text(stmt, 5, &chem_type, 1, NULL);
+ sqlite3_bind_text(stmt, 6, compound->GetFormula().c_str(),
compound->GetFormula().length(), NULL);
std::stringstream ss;
ss << compound->GetCreationDate().year << "-"
@@ -121,9 +124,9 @@ void CompoundLib::AddCompound(const CompoundPtr& compound)
ss << compound->GetModificationDate().year << "-"
<< compound->GetModificationDate().month << "-"
<< compound->GetModificationDate().day;
- sqlite3_bind_text(stmt, 6, date.c_str(), date.length(), NULL);
+ sqlite3_bind_text(stmt, 7, date.c_str(), date.length(), NULL);
date=ss.str();
- sqlite3_bind_text(stmt, 7, date.c_str(), date.length(), NULL);
+ sqlite3_bind_text(stmt, 8, date.c_str(), date.length(), NULL);
} else {
LOG_ERROR(sqlite3_errmsg(conn_));
sqlite3_finalize(stmt);
@@ -242,11 +245,18 @@ CompoundLibPtr CompoundLib::Load(const String& database, bool readonly)
int flags=readonly ? SQLITE_OPEN_READONLY : SQLITE_OPEN_READWRITE;
CompoundLibPtr lib(new CompoundLib);
int retval=sqlite3_open_v2(database.c_str(), &lib->conn_, flags, NULL);
- if (SQLITE_OK==retval) {
- return lib;
+ if (SQLITE_OK!=retval) {
+ LOG_ERROR(sqlite3_errmsg(lib->conn_));
+ return CompoundLibPtr();
}
- LOG_ERROR(sqlite3_errmsg(lib->conn_));
- return CompoundLibPtr();
+ // check if column chem_type exists in database
+ String aq="SELECT chem_type FROM chem_compounds LIMIT 1";
+ sqlite3_stmt* stmt;
+ retval=sqlite3_prepare_v2(lib->conn_, aq.c_str(),
+ static_cast<int>(aq.length()),
+ &stmt, NULL);
+ lib->chem_type_available_ = retval==SQLITE_OK;
+ return lib;
}
void CompoundLib::LoadAtomsFromDB(CompoundPtr comp, int pk) {
@@ -308,9 +318,12 @@ CompoundPtr CompoundLib::FindCompound(const String& id,
if (i!=compound_cache_.end()) {
return i->second;
}
- String query="SELECT id, tlc, olc, chem_class, dialect, formula "
- " FROM chem_compounds"
- " WHERE tlc='"+id+"' AND dialect='"+String(1, char(dialect))+"'";
+ String query="SELECT id, tlc, olc, chem_class, dialect, formula";
+ if(chem_type_available_) {
+ query+=", chem_type";
+ }
+ query+=" FROM chem_compounds"
+ " WHERE tlc='"+id+"' AND dialect='"+String(1, char(dialect))+"'";
sqlite3_stmt* stmt;
int retval=sqlite3_prepare_v2(conn_, query.c_str(),
static_cast<int>(query.length()),
@@ -330,6 +343,9 @@ CompoundPtr CompoundLib::FindCompound(const String& id,
compound->SetDialect(Compound::Dialect(sqlite3_column_text(stmt, 4)[0]));
const char* f=reinterpret_cast<const char*>(sqlite3_column_text(stmt, 5));
compound->SetFormula(f);
+ if(chem_type_available_) {
+ compound->SetChemType(mol::ChemType(sqlite3_column_text(stmt, 6)[0]));
+ }
// Load atoms and bonds
this->LoadAtomsFromDB(compound, pk);
this->LoadBondsFromDB(compound, pk);
@@ -348,7 +364,7 @@ CompoundPtr CompoundLib::FindCompound(const String& id,
}
CompoundLib::CompoundLib()
- : conn_(NULL) {
+ : conn_(NULL), chem_type_available_(false) {
}
CompoundLib::~CompoundLib() {
diff --git a/modules/conop/src/compound_lib.hh b/modules/conop/src/compound_lib.hh
index 0db0f763768cdc2870a7289c942d5c4233c999df..a552c5aee7754aea6a6759911389a4931c3ec3d0 100644
--- a/modules/conop/src/compound_lib.hh
+++ b/modules/conop/src/compound_lib.hh
@@ -52,6 +52,7 @@ private:
private:
CompoundMap compound_cache_;
sqlite3* conn_;
+ bool chem_type_available_; // weather pdbx_type is available in db
};
}}
diff --git a/modules/conop/src/heuristic_builder.cc b/modules/conop/src/heuristic_builder.cc
index 89b8ad8e1720754b0941e8b1a7d8977e252c14fc..458370078ea9171766bee2013506a170d0ac869d 100644
--- a/modules/conop/src/heuristic_builder.cc
+++ b/modules/conop/src/heuristic_builder.cc
@@ -209,19 +209,36 @@ void HeuristicBuilder::ConnectivityFromAtomNames(const mol::ResidueHandle& res,
<< it2->GetName() << ") in connectivity table of "
<< res.GetKey() << "... ");
int conn=centry.Check(it1->GetName(),it2->GetName());
- if (conn==1 && this->IsBondFeasible(*it1, *it2)) {
- LOG_TRACE( "found");
- editor.Connect(*it1,*it2);
- } else if(conn==2 && this->IsBondFeasible(*it2, *it1)) {
- LOG_TRACE( "found (reversed)");
- editor.Connect(*it2,*it1);
+ if (conn==1) {
+ if (this->GetBondFeasibilityCheck()==false) {
+ LOG_TRACE( "found");
+ editor.Connect(*it1,*it2);
+ } else {
+ if (this->IsBondFeasible(*it1, *it2)) {
+ LOG_TRACE( "found");
+ editor.Connect(*it1,*it2);
+ } else {
+ LOG_TRACE( "not found");
+ }
+ }
+ } else if (conn==2) {
+ if (this->GetBondFeasibilityCheck()==false) {
+ LOG_TRACE( "found (reversed)");
+ editor.Connect(*it2,*it1);
+ } else {
+ if(this->IsBondFeasible(*it2, *it1)) {
+ LOG_TRACE( "found (reversed)");
+ editor.Connect(*it2,*it1);
+ }
+ }
} else {
- LOG_TRACE( "not found");
+ LOG_TRACE( "not found");
}
}
} else {
unknown_atoms.push_back(*it1);
- }
+ LOG_TRACE( "atom not found, pushing it to unknown atoms");
+ }
}
}
diff --git a/modules/conop/src/nonstandard.cc b/modules/conop/src/nonstandard.cc
new file mode 100644
index 0000000000000000000000000000000000000000..5effd8d9014ca886d63bb50f5457cc487fa782f0
--- /dev/null
+++ b/modules/conop/src/nonstandard.cc
@@ -0,0 +1,265 @@
+//------------------------------------------------------------------------------
+// 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
+//------------------------------------------------------------------------------
+
+/*
+ Author: Marco Biasini, Juergen Haas
+ */
+
+#include <ost/log.hh>
+#include <ost/dyn_cast.hh>
+#include <ost/conop/conop.hh>
+#include <ost/mol/mol.hh>
+#include <ost/mol/alg/construct_cbeta.hh>
+#include <ost/conop/rule_based_builder.hh>
+#include <ost/conop/compound_lib.hh>
+#include "nonstandard.hh"
+using namespace ost::mol;
+using namespace ost;
+using namespace ost::conop;
+
+namespace ost { namespace conop {
+
+namespace {
+
+bool CheckBackboneAtoms(ResidueHandle res)
+{
+ String atom_names[]={"N", "CA", "C", "O"};
+ std::vector<String> missing;
+ for (int i =0; i<4; ++i) {
+ if (!res.FindAtom(atom_names[i])) {
+ missing.push_back(atom_names[i]);
+ }
+ }
+ if (!missing.empty()) {
+ std::stringstream ss;
+ ss << "residue " << res.GetQualifiedName() << " is missing atoms ";
+ for (std::vector<String>::const_iterator
+ i=missing.begin(), e=missing.end(); i!=e; ++i) {
+ if (i!=missing.begin()) {
+ ss << ", ";
+ }
+ ss << *i;
+ }
+ LOG_WARNING(ss.str());
+ return false;
+ }
+ return true;
+}
+
+bool CheckCalphaAtom(ResidueHandle res)
+{
+ String atom_names[]={"N", "CA", "C", "O"};
+ std::vector<String> missing;
+ for (int i =0; i<4; ++i) {
+ if (!res.FindAtom(atom_names[i])) {
+ missing.push_back(atom_names[i]);
+ }
+ }
+ if (!res.FindAtom("CA")) {
+ LOG_WARNING("residue " << res.GetQualifiedName() << " is missing CA atom");
+ return false;
+ }
+ return true;
+}
+
+}
+
+bool CopyResidue(ResidueHandle src_res, ResidueHandle dst_res, XCSEditor& edi)
+{
+ bool has_cbeta = false;
+ bool ret;
+ if (src_res.GetName()==dst_res.GetName()) {
+ ret = CopyConserved(src_res, dst_res, edi, has_cbeta);
+ } else {
+ ret = CopyNonConserved(src_res, dst_res, edi, has_cbeta);
+ }
+ // insert Cbeta, unless dst residue is glycine.
+ if (!has_cbeta && dst_res.GetName()!="GLY") {
+ geom::Vec3 cbeta_pos=mol::alg::CBetaPosition(dst_res);
+ edi.InsertAtom(dst_res, "CB", cbeta_pos, "C");
+ }
+ return ret;
+}
+
+bool CopyConserved(ResidueHandle src_res, ResidueHandle dst_res, XCSEditor& edi,
+ bool& has_cbeta)
+{
+ // check if the residue name of dst and src are the same. In the easy
+ // case, the two residue names match and we just copy over all atoms.
+ // If they don't match, we are dealing with modified residues.
+
+ //~ return copy_conserved(src_res, dst_res, edi, has_cbeta);
+
+ if (dst_res.GetName()==src_res.GetName()) {
+ return CopyIdentical(src_res, dst_res, edi, has_cbeta);
+ } else if (src_res.GetName()=="MSE") {
+ return CopyMSE(src_res, dst_res, edi, has_cbeta);
+ } else {
+ return CopyModified(src_res, dst_res, edi, has_cbeta);
+ }
+}
+
+bool CopyIdentical(ResidueHandle src_res, ResidueHandle dst_res, XCSEditor& edi,
+ bool& has_cbeta)
+{
+ //~ return copy_identical();
+ AtomHandleList atoms=src_res.GetAtomList();
+ for (AtomHandleList::const_iterator
+ a=atoms.begin(), e=atoms.end(); a!=e; ++a) {
+ if (a->GetName()=="CB") {
+ has_cbeta=true;
+ }
+ if (a->GetElement()=="D" || a->GetElement()=="H") {
+ continue;
+ }
+ edi.InsertAtom(dst_res, a->GetName(), a->GetPos(), a->GetElement(),
+ a->GetOccupancy(), a->GetBFactor());
+ }
+ return true;
+}
+
+
+bool CopyMSE(ResidueHandle src_res, ResidueHandle dst_res, XCSEditor& edi,
+ bool& has_cbeta)
+{
+ // selenium methionine is easy. We copy all atoms and substitute the SE
+ // with SD
+ AtomHandleList atoms=src_res.GetAtomList();
+ for (AtomHandleList::const_iterator
+ a=atoms.begin(), e=atoms.end(); a!=e; ++a) {
+ if (a->GetName()=="CB") {
+ has_cbeta=true;
+ }
+ if (a->GetElement()=="D" || a->GetElement()=="H") {
+ continue;
+ }
+ if (a->GetName()=="SE") {
+ edi.InsertAtom(dst_res, "SD", a->GetPos(), "S",
+ a->GetOccupancy(), a->GetBFactor());
+ } else {
+ edi.InsertAtom(dst_res, a->GetName(), a->GetPos(), a->GetElement(),
+ a->GetOccupancy(), a->GetBFactor());
+ }
+ }
+ return true;
+}
+
+bool CopyModified(ResidueHandle src_res, ResidueHandle dst_res,
+ XCSEditor& edi, bool& has_cbeta)
+{
+ // FIXME: for now this functions ignores chirality changes of sidechain
+ // chiral atoms. To detect those changes, we would need to store the
+ // chirality of those centers in the compound library.
+
+ // For now, this function just handles cases where the src_res contains
+ // additional atoms, but the dst_res doesn't contain any atoms the src_res
+ // doesn't have. If these two requirements are not met, we fall back to
+ // CopyNonConserved.
+
+ // first let's get our hands on the component library
+ conop::BuilderP builder=conop::Conopology::Instance().GetBuilder("DEFAULT");
+ conop::RuleBasedBuilderPtr rbb=dyn_cast<conop::RuleBasedBuilder>(builder);
+ conop::CompoundLibPtr comp_lib=rbb->GetCompoundLib();
+
+ CompoundPtr src_compound=comp_lib->FindCompound(src_res.GetName(),
+ Compound::PDB);
+ if (!src_compound) {
+ // OK, that's bad. Let's copy the backbone and be done with it!
+ return CopyNonConserved(src_res, dst_res, edi, has_cbeta);
+ }
+ // since dst_res is one of the 20 amino acids, we don't have to check for
+ // existence of the compound. We know it is there!
+ CompoundPtr dst_compound=comp_lib->FindCompound(dst_res.GetName(),
+ Compound::PDB);
+ std::set<String> dst_atoms;
+ std::set<String> src_atoms;
+ // to compare the atoms of dst_res with those of src_res, let's create two
+ // sets containing all heavy atoms.
+ for (AtomSpecList::const_iterator i=dst_compound->GetAtomSpecs().begin(),
+ e=dst_compound->GetAtomSpecs().end(); i!=e; ++i) {
+ if (i->element=="H" || i->element=="D") {
+ continue;
+ }
+ dst_atoms.insert(i->name);
+ }
+ for (AtomSpecList::const_iterator i=src_compound->GetAtomSpecs().begin(),
+ e=src_compound->GetAtomSpecs().end(); i!=e; ++i) {
+ if (i->element=="H" || i->element=="D") {
+ continue;
+ }
+ src_atoms.insert(i->name);
+ }
+ for (std::set<String>::const_iterator i=dst_atoms.begin(),
+ e=dst_atoms.end(); i!=e; ++i) {
+ if (src_atoms.find(*i)==src_atoms.end()) {
+ return CopyNonConserved(src_res, dst_res, edi, has_cbeta);
+ }
+ }
+ // Muahaha, all is good. Let's copy the atoms. Muahaha
+ AtomHandleList atoms=src_res.GetAtomList();
+ for (AtomHandleList::const_iterator
+ a=atoms.begin(), e=atoms.end(); a!=e; ++a) {
+ if (a->GetName()=="CB") {
+ if (dst_res.GetName()=="GLY") {
+ continue;
+ }
+ has_cbeta=true;
+ }
+ if (a->GetElement()=="D" || a->GetElement()=="H") {
+ continue;
+ }
+ if (dst_atoms.find(a->GetName())==dst_atoms.end()) {
+ continue;
+ }
+ edi.InsertAtom(dst_res, a->GetName(), a->GetPos(), a->GetElement(),
+ a->GetOccupancy(), a->GetBFactor());
+ }
+ return true;
+}
+
+
+bool CopyNonConserved(ResidueHandle src_res, ResidueHandle dst_res,
+ XCSEditor& edi, bool& has_cbeta)
+{
+ AtomHandleList atoms=src_res.GetAtomList();
+ for (AtomHandleList::const_iterator
+ a=atoms.begin(), e=atoms.end(); a!=e; ++a) {
+ String name=a->GetName();
+ if (name=="CA" || name=="N" || name=="C" || name=="O" || name=="CB") {
+ if (name=="CB") {
+ if (dst_res.GetName()=="GLY") {
+ continue;
+ }
+ has_cbeta=true;
+ }
+ if (a->GetElement()=="D" || a->GetElement()=="H") {
+ continue;
+ }
+ edi.InsertAtom(dst_res, a->GetName(), a->GetPos(), a->GetElement(),
+ a->GetOccupancy(), a->GetBFactor());
+ }
+ }
+ return false;
+}
+
+
+
+
+
+}}
diff --git a/modules/conop/src/nonstandard.hh b/modules/conop/src/nonstandard.hh
new file mode 100644
index 0000000000000000000000000000000000000000..f8ad1cfa33d07b8d4c51db0b9019de340a882163
--- /dev/null
+++ b/modules/conop/src/nonstandard.hh
@@ -0,0 +1,97 @@
+//------------------------------------------------------------------------------
+// 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_CONOP_NONSTANDARD_HH
+#define OST_CONOP_NONSTANDARD_HH
+/*
+ Author: Marco Biasini, Juergen Haas
+ */
+#include "module_config.hh"
+
+
+
+
+namespace ost { namespace conop {
+
+
+/// \brief copies all atom of src_res to dst_res
+/// \param has_cbeta will be set to true if the src_res has a cbeta and the
+/// dst_residue is not a glycine, it will be inserted if in the dst should
+/// be one and in src it was not present
+
+
+bool DLLEXPORT_OST_CONOP CopyResidue(ost::mol::ResidueHandle src_res,
+ ost::mol::ResidueHandle dst_res,
+ ost::mol::XCSEditor& edi);
+
+/// \brief copies all atom of src_res to dst_res
+/// \param has_cbeta will be set to true if the src_res has a cbeta and the
+/// dst_residue is not a glycine
+
+
+bool DLLEXPORT_OST_CONOP CopyIdentical(ost::mol::ResidueHandle src_res,
+ ost::mol::ResidueHandle dst_res,
+ ost::mol::XCSEditor& edi,
+ bool& has_cbeta);
+
+/// \brief copies atoms of src_res to dst_res
+///
+/// src_res and dst_res are thought to be conserved, e.g. the parent standard
+/// amino acid of both residues is the same. This includes cases where e.g. the
+/// src_rs is and MSE and the dst_res is a MET. This function automatically
+/// tries to do the right thing an keep as many atoms as possible from src_res
+
+
+
+bool DLLEXPORT_OST_CONOP CopyConserved(ost::mol::ResidueHandle src_res,
+ ost::mol::ResidueHandle dst_res,
+ ost::mol::XCSEditor& edi,
+ bool& has_cbeta);
+
+/// \brief construct dst_res in case src_res and dst_res are not conserved.
+///
+/// This essentially copies the backbone of src_res to dst_res. The CB atom is
+/// only copied if dst_res is not equal to glycine.
+
+
+bool DLLEXPORT_OST_CONOP CopyNonConserved(ost::mol::ResidueHandle src_res,
+ ost::mol::ResidueHandle dst_res,
+ ost::mol::XCSEditor& edi,
+ bool& has_cbeta);
+
+/// \brief construct dst_res from src_res when src_res is an MSE
+
+bool DLLEXPORT_OST_CONOP CopyMSE(ost::mol::ResidueHandle src_res,
+ ost::mol::ResidueHandle dst_res,
+ ost::mol::XCSEditor& edi,
+ bool& has_cbeta);
+
+/// \brief construct a dst_res with only atoms matching the standard aminoacid
+/// from src_res when src_res is an is modified
+
+bool DLLEXPORT_OST_CONOP CopyModified(ost::mol::ResidueHandle src_res,
+ ost::mol::ResidueHandle dst_res,
+ ost::mol::XCSEditor& edi,
+ bool& has_cbeta);
+
+
+
+}}
+
+#endif
diff --git a/modules/conop/src/rule_based_builder.cc b/modules/conop/src/rule_based_builder.cc
index 57c8f515407f89bbcebd8255075b919de2695e6f..33d33c667faebb47593eebe53f28285c448b1956 100644
--- a/modules/conop/src/rule_based_builder.cc
+++ b/modules/conop/src/rule_based_builder.cc
@@ -121,6 +121,7 @@ void RuleBasedBuilder::FillResidueProps(mol::ResidueHandle residue)
if (!last_compound_)
return;
residue.SetChemClass(last_compound_->GetChemClass());
+ residue.SetChemType(last_compound_->GetChemType());
residue.SetOneLetterCode(last_compound_->GetOneLetterCode());
};
@@ -172,6 +173,7 @@ void RuleBasedBuilder::ReorderAtoms(mol::ResidueHandle residue,
LOG_WARNING("residue " << residue << " doesn't look like a standard "
<< residue.GetKey() << " (" << compound->GetFormula() << ")");
residue.SetChemClass(mol::ChemClass(mol::ChemClass::UNKNOWN));
+ residue.SetChemType(mol::ChemType(mol::ChemType::UNKNOWN));
residue.SetOneLetterCode('?');
}
}
@@ -235,12 +237,20 @@ void RuleBasedBuilder::ConnectAtomsOfResidue(mol::ResidueHandle rh)
const BondSpec& bond=*j;
mol::AtomHandle a1=this->LocateAtom(atoms, bond.atom_one);
mol::AtomHandle a2=this->LocateAtom(atoms, bond.atom_two);
- if (a1.IsValid() && a2.IsValid() && this->IsBondFeasible(a1, a2)) {
- if (this->GetStrictHydrogenMode() &&
- (a1.GetElement()=="H" || a2.GetElement()=="D")) {
- continue;
+ if (a1.IsValid() && a2.IsValid()) {
+ if (this->GetBondFeasibilityCheck()==false) {
+ if (this->GetStrictHydrogenMode() && (a1.GetElement()=="H" || a2.GetElement()=="D")) {
+ continue;
+ }
+ e.Connect(a1, a2, bond.order);
+ } else {
+ if (IsBondFeasible(a1, a2)) {
+ if (this->GetStrictHydrogenMode() && (a1.GetElement()=="H" || a2.GetElement()=="D")) {
+ continue;
+ }
+ e.Connect(a1, a2, bond.order);
+ }
}
- e.Connect(a1, a2, bond.order);
}
}
for (mol::AtomHandleList::iterator i=atoms.begin(), e=atoms.end(); i!=e; ++i) {
diff --git a/modules/conop/src/rule_based_builder.hh b/modules/conop/src/rule_based_builder.hh
index 9ecc45c101cbbb2c6777ff7fb985bb2e9e921db1..71a6fd03453ba9c418a6e39d8c0e011161f13be6 100644
--- a/modules/conop/src/rule_based_builder.hh
+++ b/modules/conop/src/rule_based_builder.hh
@@ -109,7 +109,7 @@ public:
/// by ignoring it or by inserting a dummy atom.
virtual void OnMissingAtom(const mol::ResidueHandle& residue,
const String& atom_name) { }
-
+
/// \brief Fill in missing information based on atom name.
virtual void FillAtomProps(mol::AtomHandle atom, const AtomSpec& spec);
@@ -123,6 +123,7 @@ public:
virtual bool IsResidueComplete(const mol::ResidueHandle& residue);
CompoundLibPtr GetCompoundLib() const { return compound_lib_; }
+
private:
CompoundLibPtr compound_lib_;
CompoundPtr last_compound_;
@@ -139,7 +140,6 @@ private:
void AssignBackBoneTorsionsToResidue(mol::ResidueHandle residue);
-
};
typedef boost::shared_ptr<RuleBasedBuilder> RuleBasedBuilderPtr;
diff --git a/modules/conop/tests/CMakeLists.txt b/modules/conop/tests/CMakeLists.txt
index aa06791bf0be4d64640499010893d9db179f3e33..6a832115b5933b66241c9dec5ce23c21dd532c48 100644
--- a/modules/conop/tests/CMakeLists.txt
+++ b/modules/conop/tests/CMakeLists.txt
@@ -4,6 +4,8 @@ set(OST_CONOP_UNIT_TESTS
tests.cc
test_builder.cc
test_compound.py
+ test_cleanup.py
+ test_nonstandard.py
)
ost_unittest(MODULE conop
diff --git a/modules/conop/tests/sample_noligands.pdb b/modules/conop/tests/sample_noligands.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..7fd199276d45124bbe2b2bc6ddf7d47b780d9401
--- /dev/null
+++ b/modules/conop/tests/sample_noligands.pdb
@@ -0,0 +1,65 @@
+HETATM 1 N MSE A 1 16.152 35.832 19.337 1.00 68.79 N
+ANISOU 1 N MSE A 1 9680 7396 9061 1038 -716 -25 N
+HETATM 2 CA MSE A 1 16.961 36.379 20.419 1.00 66.57 C
+ANISOU 2 CA MSE A 1 9387 7212 8694 1121 -806 40 C
+HETATM 3 C MSE A 1 18.345 36.796 19.931 1.00 62.52 C
+ANISOU 3 C MSE A 1 8685 6846 8225 1266 -870 -107 C
+HETATM 4 O MSE A 1 19.030 36.049 19.227 1.00 60.36 O
+ANISOU 4 O MSE A 1 8358 6511 8064 1396 -922 -219 O
+HETATM 5 CB MSE A 1 17.100 35.372 21.563 1.00 69.52 C
+ANISOU 5 CB MSE A 1 9961 7405 9049 1204 -927 192 C
+HETATM 6 CG MSE A 1 17.608 35.983 22.861 1.00 69.50 C
+ANISOU 6 CG MSE A 1 9977 7515 8914 1239 -1006 292 C
+HETATM 7 SE MSE A 1 16.174 36.321 24.145 0.70149.62 SE
+ANISOU 7 SE MSE A 1 20306 17658 18883 1013 -917 492 SE
+HETATM 8 CE MSE A 1 16.439 38.231 24.424 1.00101.32 C
+ANISOU 8 CE MSE A 1 13992 11855 12651 950 -853 413 C
+ATOM 9 N GLY A 2 21.960 55.913 14.093 1.00 32.26 N
+ANISOU 9 N GLY A 2 3786 4717 3755 -417 -110 -697 N
+ATOM 10 CA GLY A 2 21.067 57.037 14.316 1.00 33.47 C
+ANISOU 10 CA GLY A 2 4071 4728 3919 -478 -95 -611 C
+ATOM 11 C GLY A 2 20.632 57.066 15.769 1.00 28.81 C
+ANISOU 11 C GLY A 2 3536 4062 3349 -382 -126 -599 C
+ATOM 12 O GLY A 2 19.474 57.360 16.089 1.00 26.62 O
+ANISOU 12 O GLY A 2 3358 3653 3104 -343 -120 -528 O
+HETATM 694 N MLY A 3 26.382 48.690 2.460 1.00 30.43 N
+ANISOU 694 N MLY A 3 2388 5919 3254 -646 317 -1852 N
+HETATM 695 CA MLY A 3 27.776 48.333 2.142 1.00 32.62 C
+ANISOU 695 CA MLY A 3 2438 6444 3514 -645 358 -2093 C
+HETATM 696 CB MLY A 3 28.523 49.535 1.556 1.00 34.25 C
+ANISOU 696 CB MLY A 3 2578 6874 3563 -918 442 -2107 C
+HETATM 697 CG MLY A 3 28.053 50.058 0.208 1.00 51.47 C
+ANISOU 697 CG MLY A 3 4819 9152 5586 -1157 527 -2046 C
+HETATM 698 CD MLY A 3 29.170 50.911 -0.420 1.00 65.96 C
+ANISOU 698 CD MLY A 3 6527 11268 7265 -1416 622 -2140 C
+HETATM 699 CE MLY A 3 28.648 51.881 -1.478 1.00 78.91 C
+ANISOU 699 CE MLY A 3 8300 12955 8728 -1697 684 -1985 C
+HETATM 700 NZ MLY A 3 27.996 53.093 -0.885 1.00 83.04 N
+ANISOU 700 NZ MLY A 3 9040 13267 9244 -1780 633 -1724 N
+HETATM 701 CH1 MLY A 3 27.490 53.898 -2.008 1.00 82.17 C
+ANISOU 701 CH1 MLY A 3 9059 13197 8964 -2028 679 -1578 C
+HETATM 702 CH2 MLY A 3 29.059 53.885 -0.248 1.00 83.95 C
+ANISOU 702 CH2 MLY A 3 9084 13473 9342 -1885 652 -1769 C
+HETATM 703 C MLY A 3 28.551 47.875 3.386 1.00 35.38 C
+ANISOU 703 C MLY A 3 2698 6760 3986 -436 275 -2175 C
+HETATM 704 O MLY A 3 29.262 46.867 3.369 1.00 36.09 O
+ANISOU 704 O MLY A 3 2632 6928 4151 -274 255 -2373 O
+HETATM 24 N DHA A 4 26.289 27.329 2.438 1.00 21.02 N
+HETATM 25 CA DHA A 4 26.295 27.688 3.823 1.00 20.17 C
+HETATM 26 CB DHA A 4 27.128 28.481 4.578 1.00 25.40 C
+HETATM 27 C DHA A 4 25.128 27.215 4.536 1.00 14.98 C
+HETATM 28 O DHA A 4 24.918 27.318 5.770 1.00 15.17 O
+ATOM 1454 N CYS A 5 35.381 45.298 39.476 1.00 31.23 N
+ATOM 1455 CA CYS A 5 35.559 43.873 39.703 1.00 26.90 C
+ATOM 1456 C CYS A 5 34.291 43.354 40.319 1.00 28.31 C
+ATOM 1457 OXT CYS A 5 33.569 44.119 40.933 1.00 32.71 O
+ATOM 1458 CB CYS A 5 36.760 43.592 40.596 1.00 27.44 C
+ATOM 1460 H CYS A 5 34.717 45.766 40.024 1.00 0.00 H
+HETATM 1345 N DAL A 6 16.130 53.915 24.417 1.00 8.63 N
+HETATM 1346 CA DAL A 6 16.958 55.083 24.235 1.00 24.17 C
+HETATM 1347 CB DAL A 6 16.321 56.394 24.733 1.00 30.20 C
+HETATM 1348 C DAL A 6 17.335 55.218 22.790 1.00 32.54 C
+HETATM 1349 O DAL A 6 16.693 54.552 21.946 1.00 27.41 O
+HETATM 1350 OXT DAL A 6 18.286 55.960 22.546 1.00 18.81 O
+HETATM 36 O HOH A 19 0.180 48.781 4.764 1.00 23.28 O
+END
diff --git a/modules/conop/tests/sample_nowater.pdb b/modules/conop/tests/sample_nowater.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..0f8c440aa83c10dec2cfffe71cbe524a15d0af15
--- /dev/null
+++ b/modules/conop/tests/sample_nowater.pdb
@@ -0,0 +1,71 @@
+HETATM 1 N MSE A 1 16.152 35.832 19.337 1.00 68.79 N
+ANISOU 1 N MSE A 1 9680 7396 9061 1038 -716 -25 N
+HETATM 2 CA MSE A 1 16.961 36.379 20.419 1.00 66.57 C
+ANISOU 2 CA MSE A 1 9387 7212 8694 1121 -806 40 C
+HETATM 3 C MSE A 1 18.345 36.796 19.931 1.00 62.52 C
+ANISOU 3 C MSE A 1 8685 6846 8225 1266 -870 -107 C
+HETATM 4 O MSE A 1 19.030 36.049 19.227 1.00 60.36 O
+ANISOU 4 O MSE A 1 8358 6511 8064 1396 -922 -219 O
+HETATM 5 CB MSE A 1 17.100 35.372 21.563 1.00 69.52 C
+ANISOU 5 CB MSE A 1 9961 7405 9049 1204 -927 192 C
+HETATM 6 CG MSE A 1 17.608 35.983 22.861 1.00 69.50 C
+ANISOU 6 CG MSE A 1 9977 7515 8914 1239 -1006 292 C
+HETATM 7 SE MSE A 1 16.174 36.321 24.145 0.70149.62 SE
+ANISOU 7 SE MSE A 1 20306 17658 18883 1013 -917 492 SE
+HETATM 8 CE MSE A 1 16.439 38.231 24.424 1.00101.32 C
+ANISOU 8 CE MSE A 1 13992 11855 12651 950 -853 413 C
+ATOM 9 N GLY A 2 21.960 55.913 14.093 1.00 32.26 N
+ANISOU 9 N GLY A 2 3786 4717 3755 -417 -110 -697 N
+ATOM 10 CA GLY A 2 21.067 57.037 14.316 1.00 33.47 C
+ANISOU 10 CA GLY A 2 4071 4728 3919 -478 -95 -611 C
+ATOM 11 C GLY A 2 20.632 57.066 15.769 1.00 28.81 C
+ANISOU 11 C GLY A 2 3536 4062 3349 -382 -126 -599 C
+ATOM 12 O GLY A 2 19.474 57.360 16.089 1.00 26.62 O
+ANISOU 12 O GLY A 2 3358 3653 3104 -343 -120 -528 O
+HETATM 694 N MLY A 3 26.382 48.690 2.460 1.00 30.43 N
+ANISOU 694 N MLY A 3 2388 5919 3254 -646 317 -1852 N
+HETATM 695 CA MLY A 3 27.776 48.333 2.142 1.00 32.62 C
+ANISOU 695 CA MLY A 3 2438 6444 3514 -645 358 -2093 C
+HETATM 696 CB MLY A 3 28.523 49.535 1.556 1.00 34.25 C
+ANISOU 696 CB MLY A 3 2578 6874 3563 -918 442 -2107 C
+HETATM 697 CG MLY A 3 28.053 50.058 0.208 1.00 51.47 C
+ANISOU 697 CG MLY A 3 4819 9152 5586 -1157 527 -2046 C
+HETATM 698 CD MLY A 3 29.170 50.911 -0.420 1.00 65.96 C
+ANISOU 698 CD MLY A 3 6527 11268 7265 -1416 622 -2140 C
+HETATM 699 CE MLY A 3 28.648 51.881 -1.478 1.00 78.91 C
+ANISOU 699 CE MLY A 3 8300 12955 8728 -1697 684 -1985 C
+HETATM 700 NZ MLY A 3 27.996 53.093 -0.885 1.00 83.04 N
+ANISOU 700 NZ MLY A 3 9040 13267 9244 -1780 633 -1724 N
+HETATM 701 CH1 MLY A 3 27.490 53.898 -2.008 1.00 82.17 C
+ANISOU 701 CH1 MLY A 3 9059 13197 8964 -2028 679 -1578 C
+HETATM 702 CH2 MLY A 3 29.059 53.885 -0.248 1.00 83.95 C
+ANISOU 702 CH2 MLY A 3 9084 13473 9342 -1885 652 -1769 C
+HETATM 703 C MLY A 3 28.551 47.875 3.386 1.00 35.38 C
+ANISOU 703 C MLY A 3 2698 6760 3986 -436 275 -2175 C
+HETATM 704 O MLY A 3 29.262 46.867 3.369 1.00 36.09 O
+ANISOU 704 O MLY A 3 2632 6928 4151 -274 255 -2373 O
+HETATM 24 N DHA A 4 26.289 27.329 2.438 1.00 21.02 N
+HETATM 25 CA DHA A 4 26.295 27.688 3.823 1.00 20.17 C
+HETATM 26 CB DHA A 4 27.128 28.481 4.578 1.00 25.40 C
+HETATM 27 C DHA A 4 25.128 27.215 4.536 1.00 14.98 C
+HETATM 28 O DHA A 4 24.918 27.318 5.770 1.00 15.17 O
+ATOM 1454 N CYS A 5 35.381 45.298 39.476 1.00 31.23 N
+ATOM 1455 CA CYS A 5 35.559 43.873 39.703 1.00 26.90 C
+ATOM 1456 C CYS A 5 34.291 43.354 40.319 1.00 28.31 C
+ATOM 1457 OXT CYS A 5 33.569 44.119 40.933 1.00 32.71 O
+ATOM 1458 CB CYS A 5 36.760 43.592 40.596 1.00 27.44 C
+ATOM 1460 H CYS A 5 34.717 45.766 40.024 1.00 0.00 H
+HETATM 1345 N DAL A 6 16.130 53.915 24.417 1.00 8.63 N
+HETATM 1346 CA DAL A 6 16.958 55.083 24.235 1.00 24.17 C
+HETATM 1347 CB DAL A 6 16.321 56.394 24.733 1.00 30.20 C
+HETATM 1348 C DAL A 6 17.335 55.218 22.790 1.00 32.54 C
+HETATM 1349 O DAL A 6 16.693 54.552 21.946 1.00 27.41 O
+HETATM 1350 OXT DAL A 6 18.286 55.960 22.546 1.00 18.81 O
+HETATM 29 C1 GOL A 17 3.793 59.768 8.209 1.00 31.00 C
+HETATM 30 O1 GOL A 17 3.244 58.473 8.337 1.00 27.42 O
+HETATM 31 C2 GOL A 17 4.701 60.020 9.406 1.00 26.81 C
+HETATM 32 O2 GOL A 17 5.573 58.919 9.512 1.00 26.44 O
+HETATM 33 C3 GOL A 17 5.505 61.287 9.156 1.00 24.74 C
+HETATM 34 O3 GOL A 17 6.429 61.468 10.222 1.00 31.06 O
+HETATM 35 CL CL A 18 11.844 59.221 16.755 0.79 32.84 CL
+END
diff --git a/modules/conop/tests/sample_test_cleanup.pdb b/modules/conop/tests/sample_test_cleanup.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..cce7fe04d4fe753d68c9e73620fea8617ce07059
--- /dev/null
+++ b/modules/conop/tests/sample_test_cleanup.pdb
@@ -0,0 +1,72 @@
+HETATM 1 N MSE A 1 16.152 35.832 19.337 1.00 68.79 N
+ANISOU 1 N MSE A 1 9680 7396 9061 1038 -716 -25 N
+HETATM 2 CA MSE A 1 16.961 36.379 20.419 1.00 66.57 C
+ANISOU 2 CA MSE A 1 9387 7212 8694 1121 -806 40 C
+HETATM 3 C MSE A 1 18.345 36.796 19.931 1.00 62.52 C
+ANISOU 3 C MSE A 1 8685 6846 8225 1266 -870 -107 C
+HETATM 4 O MSE A 1 19.030 36.049 19.227 1.00 60.36 O
+ANISOU 4 O MSE A 1 8358 6511 8064 1396 -922 -219 O
+HETATM 5 CB MSE A 1 17.100 35.372 21.563 1.00 69.52 C
+ANISOU 5 CB MSE A 1 9961 7405 9049 1204 -927 192 C
+HETATM 6 CG MSE A 1 17.608 35.983 22.861 1.00 69.50 C
+ANISOU 6 CG MSE A 1 9977 7515 8914 1239 -1006 292 C
+HETATM 7 SE MSE A 1 16.174 36.321 24.145 0.70149.62 SE
+ANISOU 7 SE MSE A 1 20306 17658 18883 1013 -917 492 SE
+HETATM 8 CE MSE A 1 16.439 38.231 24.424 1.00101.32 C
+ANISOU 8 CE MSE A 1 13992 11855 12651 950 -853 413 C
+ATOM 9 N GLY A 2 21.960 55.913 14.093 1.00 32.26 N
+ANISOU 9 N GLY A 2 3786 4717 3755 -417 -110 -697 N
+ATOM 10 CA GLY A 2 21.067 57.037 14.316 1.00 33.47 C
+ANISOU 10 CA GLY A 2 4071 4728 3919 -478 -95 -611 C
+ATOM 11 C GLY A 2 20.632 57.066 15.769 1.00 28.81 C
+ANISOU 11 C GLY A 2 3536 4062 3349 -382 -126 -599 C
+ATOM 12 O GLY A 2 19.474 57.360 16.089 1.00 26.62 O
+ANISOU 12 O GLY A 2 3358 3653 3104 -343 -120 -528 O
+HETATM 694 N MLY A 3 26.382 48.690 2.460 1.00 30.43 N
+ANISOU 694 N MLY A 3 2388 5919 3254 -646 317 -1852 N
+HETATM 695 CA MLY A 3 27.776 48.333 2.142 1.00 32.62 C
+ANISOU 695 CA MLY A 3 2438 6444 3514 -645 358 -2093 C
+HETATM 696 CB MLY A 3 28.523 49.535 1.556 1.00 34.25 C
+ANISOU 696 CB MLY A 3 2578 6874 3563 -918 442 -2107 C
+HETATM 697 CG MLY A 3 28.053 50.058 0.208 1.00 51.47 C
+ANISOU 697 CG MLY A 3 4819 9152 5586 -1157 527 -2046 C
+HETATM 698 CD MLY A 3 29.170 50.911 -0.420 1.00 65.96 C
+ANISOU 698 CD MLY A 3 6527 11268 7265 -1416 622 -2140 C
+HETATM 699 CE MLY A 3 28.648 51.881 -1.478 1.00 78.91 C
+ANISOU 699 CE MLY A 3 8300 12955 8728 -1697 684 -1985 C
+HETATM 700 NZ MLY A 3 27.996 53.093 -0.885 1.00 83.04 N
+ANISOU 700 NZ MLY A 3 9040 13267 9244 -1780 633 -1724 N
+HETATM 701 CH1 MLY A 3 27.490 53.898 -2.008 1.00 82.17 C
+ANISOU 701 CH1 MLY A 3 9059 13197 8964 -2028 679 -1578 C
+HETATM 702 CH2 MLY A 3 29.059 53.885 -0.248 1.00 83.95 C
+ANISOU 702 CH2 MLY A 3 9084 13473 9342 -1885 652 -1769 C
+HETATM 703 C MLY A 3 28.551 47.875 3.386 1.00 35.38 C
+ANISOU 703 C MLY A 3 2698 6760 3986 -436 275 -2175 C
+HETATM 704 O MLY A 3 29.262 46.867 3.369 1.00 36.09 O
+ANISOU 704 O MLY A 3 2632 6928 4151 -274 255 -2373 O
+HETATM 24 N DHA A 4 26.289 27.329 2.438 1.00 21.02 N
+HETATM 25 CA DHA A 4 26.295 27.688 3.823 1.00 20.17 C
+HETATM 26 CB DHA A 4 27.128 28.481 4.578 1.00 25.40 C
+HETATM 27 C DHA A 4 25.128 27.215 4.536 1.00 14.98 C
+HETATM 28 O DHA A 4 24.918 27.318 5.770 1.00 15.17 O
+ATOM 1454 N CYS A 5 35.381 45.298 39.476 1.00 31.23 N
+ATOM 1455 CA CYS A 5 35.559 43.873 39.703 1.00 26.90 C
+ATOM 1456 C CYS A 5 34.291 43.354 40.319 1.00 28.31 C
+ATOM 1457 OXT CYS A 5 33.569 44.119 40.933 1.00 32.71 O
+ATOM 1458 CB CYS A 5 36.760 43.592 40.596 1.00 27.44 C
+ATOM 1460 H CYS A 5 34.717 45.766 40.024 1.00 0.00 H
+HETATM 1345 N DAL A 6 16.130 53.915 24.417 1.00 8.63 N
+HETATM 1346 CA DAL A 6 16.958 55.083 24.235 1.00 24.17 C
+HETATM 1347 CB DAL A 6 16.321 56.394 24.733 1.00 30.20 C
+HETATM 1348 C DAL A 6 17.335 55.218 22.790 1.00 32.54 C
+HETATM 1349 O DAL A 6 16.693 54.552 21.946 1.00 27.41 O
+HETATM 1350 OXT DAL A 6 18.286 55.960 22.546 1.00 18.81 O
+HETATM 29 C1 GOL A 17 3.793 59.768 8.209 1.00 31.00 C
+HETATM 30 O1 GOL A 17 3.244 58.473 8.337 1.00 27.42 O
+HETATM 31 C2 GOL A 17 4.701 60.020 9.406 1.00 26.81 C
+HETATM 32 O2 GOL A 17 5.573 58.919 9.512 1.00 26.44 O
+HETATM 33 C3 GOL A 17 5.505 61.287 9.156 1.00 24.74 C
+HETATM 34 O3 GOL A 17 6.429 61.468 10.222 1.00 31.06 O
+HETATM 35 CL CL A 18 11.844 59.221 16.755 0.79 32.84 CL
+HETATM 36 O HOH A 19 0.180 48.781 4.764 1.00 23.28 O
+END
diff --git a/modules/conop/tests/test_cleanup.py b/modules/conop/tests/test_cleanup.py
new file mode 100644
index 0000000000000000000000000000000000000000..1dc280f4fbaac9867c7f7a1063217bb4527cfbd0
--- /dev/null
+++ b/modules/conop/tests/test_cleanup.py
@@ -0,0 +1,164 @@
+import unittest
+from ost import geom, conop
+from ost.conop import cleanup
+
+class TestCleanUp(unittest.TestCase):
+
+ def setUp(self):
+ self.comp_lib=conop.GetBuilder().compound_lib
+ self.ent = io.LoadPDB("sample_test_cleanup.pdb")
+ self.ent_no_wat = io.LoadPDB("sample_nowater.pdb")
+ self.ent_no_lig = io.LoadPDB("sample_noligands.pdb")
+
+ def testStripWater(self):
+ self.new_ent = cleanup.Cleanup(self.ent, strip_water=True, canonicalize=False, remove_ligands=False)
+ self.assertEqual( self.new_ent.residue_count, self.ent_no_wat.residue_count )
+ self.assertTrue( self.new_ent.residues[0].IsValid() )
+ self.assertEqual( self.new_ent.residues[0].qualified_name, self.ent_no_wat.residues[0].qualified_name)
+ self.assertTrue( self.new_ent.residues[1].IsValid() )
+ self.assertEqual( self.new_ent.residues[1].qualified_name, self.ent_no_wat.residues[1].qualified_name)
+ self.assertTrue( self.new_ent.residues[2].IsValid() )
+ self.assertEqual( self.new_ent.residues[2].qualified_name, self.ent_no_wat.residues[2].qualified_name)
+ self.assertTrue( self.new_ent.residues[3].IsValid() )
+ self.assertEqual( self.new_ent.residues[3].qualified_name, self.ent_no_wat.residues[3].qualified_name)
+ self.assertTrue( self.new_ent.residues[4].IsValid() )
+ self.assertEqual( self.new_ent.residues[4].qualified_name, self.ent_no_wat.residues[4].qualified_name)
+ self.assertTrue( self.new_ent.residues[5].IsValid() )
+ self.assertEqual( self.new_ent.residues[5].qualified_name, self.ent_no_wat.residues[5].qualified_name)
+ self.assertTrue( self.new_ent.residues[6].IsValid() )
+ self.assertEqual( self.new_ent.residues[6].qualified_name, self.ent_no_wat.residues[6].qualified_name)
+ self.assertTrue( self.new_ent.residues[7].IsValid() )
+ self.assertEqual( self.new_ent.residues[7].qualified_name, self.ent_no_wat.residues[7].qualified_name)
+
+ def testCanonicalize(self):
+ self.new_ent = cleanup.Cleanup(self.ent, strip_water=False, canonicalize=True, remove_ligands=False)
+ #standard residue must be the same
+ self.gly = self.ent.residues[1]
+ self.new_gly = self.new_ent.residues[1]
+ self.assertTrue(self.new_gly.IsValid())
+ self.assertTrue(self.new_gly.IsPeptideLinking())
+ self.assertEqual(self.gly.atom_count, self.new_gly.atom_count)
+ #TEMP del sidechain of incomplete residue and OXT if present
+ self.new_cys = self.new_ent.residues[4]
+ self.new_cys_atoms = set([atm.name for atm in self.new_cys.atoms])
+ self.assertEqual( len(self.new_cys_atoms), 4, msg = repr(self.new_cys_atoms))
+ self.assertTrue( "CB" in self.new_cys_atoms)
+ self.assertTrue( "CA" in self.new_cys_atoms)
+ self.assertTrue( "C" in self.new_cys_atoms)
+ self.assertFalse( "OXT" in self.new_cys_atoms)
+ self.assertTrue( "N" in self.new_cys_atoms)
+ #test replacement of atoms
+ self.mse = self.ent.residues[0]
+# self.assertTrue( self.mse.IsValid())
+# self.assertTrue( self.mse.IsPeptideLinking())
+ self.sel = self.mse.FindAtom("SE")
+# self.assertTrue( self.sel.IsValid())
+ self.met = self.new_ent.residues[0]
+ self.assertTrue(self.met.IsValid())
+ self.assertEqual(self.mse.atom_count, self.met.atom_count)
+ self.assertEqual(self.met.name, "MET")
+ self.assertEqual(self.met.one_letter_code, "M")
+ self.assertTrue(self.met.IsPeptideLinking())
+ self.sul = self.met.FindAtom("SD")
+ self.assertTrue(self.sul.IsValid())
+ self.assertTrue(geom.Equal(self.sul.pos,self.sel.pos), msg = "sul:%s sel:%s"%(str(self.sul.pos), str(self.sel.pos)) )
+ self.assertEqual(self.sul.element, "S")
+# self.AssertTrue( sul.mass == conop.Conopology.Instance().GetDefaultAtomMass("S"))
+# self.AssertTrue( sul.radius == conop.Conopology.Instance().GetDefaultAtomRadius("S"))
+ for atm in self.met.atoms:
+ self.assertFalse( atm.is_hetatom)
+ #test addition
+ self.mly = self.ent.residues[2]
+# self.assertTrue( self.mly.IsValid())
+# self.assertTrue( self.mly.IsPeptideLinking())
+ self.new_lys = self.new_ent.residues[2]
+ self.assertTrue(self.new_lys.IsValid())
+ self.assertTrue(self.new_lys.IsPeptideLinking())
+ self.assertEqual(self.new_lys.name, "LYS")
+ self.assertEqual(self.new_lys.one_letter_code, "K")
+ self.new_lys_atoms = set([atm.name for atm in self.new_lys.atoms])
+ self.canon_lys = self.comp_lib.FindCompound("LYS")
+ self.canon_lys_atoms = set([atom.name for atom in self.canon_lys.atom_specs
+ if atom.element != "H" and atom.element != "D" and not atom.is_leaving ])
+ self.assertEqual(self.canon_lys_atoms, self.new_lys_atoms)
+ self.assertFalse(self.canon_lys_atoms - self.new_lys_atoms)
+ self.assertFalse(self.new_lys_atoms - self.canon_lys_atoms) #test the reverse
+ for atm in self.new_lys.atoms:
+ self.assertFalse( atm.is_hetatom)
+ #deletions
+ self.dha = self.ent.residues[3]
+# self.assertTrue( self.dha.IsValid())
+# self.assertTrue( self.dha.IsPeptideLinking())
+ self.new_ser = self.new_ent.residues[3]
+ self.assertTrue(self.new_ser.IsValid())
+ self.assertTrue(self.new_ser.IsPeptideLinking())
+ self.assertEqual(self.new_ser.name, "SER")
+ self.assertEqual(self.new_ser.one_letter_code, "S")
+ self.new_ser_atoms = set([atm.name for atm in self.new_ser.atoms])
+ self.canon_ser = self.comp_lib.FindCompound("SER")
+ self.canon_ser_atoms = set([atom.name for atom in self.canon_ser.atom_specs
+ if atom.element != "H" and atom.element != "D" and not atom.is_leaving ])
+ #TEMP
+ self.assertEqual( len(self.new_ser_atoms), 5)
+ self.assertTrue( "CB" in self.new_ser_atoms)
+ self.assertTrue( "CA" in self.new_ser_atoms)
+ self.assertTrue( "C" in self.new_ser_atoms)
+ self.assertTrue( "O" in self.new_ser_atoms)
+ self.assertTrue( "N" in self.new_ser_atoms)
+ #AFTER TEMP
+ #self.assertEqual( self.canon_ser_atoms, self.new_ser_atoms)
+ #self.assertFalse(self.canon_ser_atoms - self.new_ser_atoms)
+ #self.assertFalse(self.new_ser_atoms - self.canon_ser_atoms) #test the reverse
+ for atm in self.new_ser.atoms:
+ self.assertFalse( atm.is_hetatom)
+ #test deletion of whole residue
+ self.assertEqual(self.ent.residues[5].chem_class, "D_PEPTIDE_LINKING")
+ self.assertNotEqual(self.new_ent.residues[5].name, "DAL")
+ self.assertNotEqual(self.ent.residue_count, self.new_ent.residue_count)
+
+ def testRemoveLigands(self):
+ self.new_ent = cleanup.Cleanup(self.ent, strip_water=False, canonicalize=False, remove_ligands=True)
+ self.assertEqual(self.new_ent.residue_count, self.ent_no_lig.residue_count )
+ #MSE
+ self.assertTrue(self.new_ent.residues[0].IsValid() )
+ self.assertEqual(self.new_ent.residues[0].qualified_name, self.ent_no_lig.residues[0].qualified_name)
+ self.assertTrue(self.new_ent.residues[0].IsPeptideLinking())
+ self.assertTrue(self.new_ent.residues[0].atoms[0].is_hetatom)
+ #GLY
+ self.assertTrue(self.new_ent.residues[1].IsValid() )
+ self.assertEqual(self.new_ent.residues[1].qualified_name, self.ent_no_lig.residues[1].qualified_name)
+ self.assertTrue(self.new_ent.residues[1].IsPeptideLinking())
+ self.assertFalse(self.new_ent.residues[1].atoms[0].is_hetatom)
+ #MLY
+ self.assertTrue(self.new_ent.residues[2].IsValid() )
+ self.assertEqual(self.new_ent.residues[2].qualified_name, self.ent_no_lig.residues[2].qualified_name)
+ self.assertTrue(self.new_ent.residues[2].IsPeptideLinking())
+ self.assertTrue(self.new_ent.residues[2].atoms[0].is_hetatom)
+ #DHA
+ self.assertTrue(self.new_ent.residues[3].IsValid() )
+ self.assertEqual(self.new_ent.residues[3].qualified_name, self.ent_no_lig.residues[3].qualified_name)
+ self.assertTrue(self.new_ent.residues[3].IsPeptideLinking())
+ self.assertTrue(self.new_ent.residues[3].atoms[0].is_hetatom)
+ #CYS
+ self.assertTrue(self.new_ent.residues[4].IsValid() )
+ self.assertEqual(self.new_ent.residues[4].qualified_name, self.ent_no_lig.residues[4].qualified_name)
+ self.assertTrue(self.new_ent.residues[4].IsPeptideLinking())
+ self.assertFalse(self.new_ent.residues[4].atoms[0].is_hetatom)
+ #DAL
+ self.assertTrue(self.new_ent.residues[5].IsValid() )
+ self.assertEqual(self.new_ent.residues[5].qualified_name, self.ent_no_lig.residues[5].qualified_name)
+ self.assertTrue(self.new_ent.residues[5].IsPeptideLinking())
+ self.assertTrue(self.new_ent.residues[5].atoms[0].is_hetatom)
+ #HOH
+ self.assertTrue(self.new_ent.residues[6].IsValid() )
+ self.assertEqual(self.new_ent.residues[6].qualified_name, self.ent_no_lig.residues[6].qualified_name)
+ self.assertFalse(self.new_ent.residues[6].IsPeptideLinking()) # here assertFalse instead of assertTrue
+ self.assertTrue(self.new_ent.residues[6].atoms[0].is_hetatom)
+
+if not hasattr(conop.GetBuilder(), 'compound_lib'):
+ print 'Default builder without compound lib. Ignoring test_cleanup.py tests'
+ sys.exit()
+
+if __name__== '__main__':
+ from ost import testutils
+ testutils.RunTests()
diff --git a/modules/conop/tests/test_compound.py b/modules/conop/tests/test_compound.py
index 2c57bce756e0f26deab7e69467807993e96c51aa..a215a78f7a5dd966c2619346aaabf0f084b7bbd7 100644
--- a/modules/conop/tests/test_compound.py
+++ b/modules/conop/tests/test_compound.py
@@ -26,6 +26,6 @@ if __name__=='__main__':
if not hasattr(builder, 'compound_lib'):
print 'default builder does not use compound library. ignoring unit tests'
else:
- suite = unittest.TestLoader().loadTestsFromTestCase(TestCompound)
- unittest.TextTestRunner().run(suite)
+ from ost import testutils
+ testutils.RunTests()
diff --git a/modules/conop/tests/test_heuristic_builder.cc b/modules/conop/tests/test_heuristic_builder.cc
index 4220f3110ca1af0ecec5acc183dba6d1ad5b5f11..0e3a811ae922d0d8375fe98ab96163765f5766f4 100644
--- a/modules/conop/tests/test_heuristic_builder.cc
+++ b/modules/conop/tests/test_heuristic_builder.cc
@@ -65,6 +65,21 @@ ResidueHandle make_leu(ChainHandle chain)
return res;
}
+ResidueHandle make_defective_leu(ChainHandle chain)
+{
+ XCSEditor e=chain.GetEntity().EditXCS();
+ ResidueHandle res=e.AppendResidue(chain, "LEU");
+
+ e.InsertAtom(res, "N", geom::Vec3(19.003,32.473,60.366));
+ e.InsertAtom(res, "CA", geom::Vec3(18.330,32.402,61.664));
+ e.InsertAtom(res, "C", geom::Vec3(17.884,33.787,62.117));
+ e.InsertAtom(res, "O", geom::Vec3(17.853,34.091,63.308));
+ e.InsertAtom(res, "CB", geom::Vec3(19.269,31.793,102.710));
+ e.InsertAtom(res, "CG", geom::Vec3(19.695,30.340,62.501));
+ e.InsertAtom(res, "CD1", geom::Vec3(20.585,29.897,63.648));
+ e.InsertAtom(res, "CD2", geom::Vec3(18.461,29.459,62.420));
+ return res;
+}
void verify_connectivity_x(const ResidueHandle& res)
{
@@ -154,12 +169,25 @@ BOOST_AUTO_TEST_CASE(name_based_connect)
heuristic_builder.FillAtomProps(*i);
}
+ EntityHandle de=CreateEntity();
+ ChainHandle dc=de.EditXCS().InsertChain("A");
+ ResidueHandle dile=make_defective_leu(dc);
+ HeuristicBuilder dheuristic_builder;
+ dheuristic_builder.SetBondFeasibilityCheck(false);
+ for (AtomHandleIter i=de.AtomsBegin(),x=de.AtomsEnd(); i!=x; ++i) {
+ dheuristic_builder.FillAtomProps(*i);
+ }
+
BOOST_MESSAGE("running distance based checks on arginine");
heuristic_builder.ConnectAtomsOfResidue(arg);
verify_connectivity(arg);
BOOST_MESSAGE("running distance based checks on leu");
heuristic_builder.ConnectAtomsOfResidue(ile);
verify_connectivity(ile);
+
+ BOOST_MESSAGE("running distance based checks on defective leu");
+ dheuristic_builder.ConnectAtomsOfResidue(dile);
+ verify_connectivity(dile);
}
BOOST_AUTO_TEST_CASE(test_assign_torsions){
diff --git a/modules/conop/tests/test_nonstandard.py b/modules/conop/tests/test_nonstandard.py
new file mode 100644
index 0000000000000000000000000000000000000000..170749c6eacd73bc64f4b6826e4df5d80f104512
--- /dev/null
+++ b/modules/conop/tests/test_nonstandard.py
@@ -0,0 +1,127 @@
+import unittest
+from ost import conop
+
+
+class TestNonStandard(unittest.TestCase):
+
+ def test_fastModified(self):
+ # phoshoserine: test if we correctly strip off modifications
+ tpl=io.LoadPDB('testfiles/sep.pdb')
+ new_hdl=mol.CreateEntity();
+ ed=new_hdl.EditXCS()
+ c=ed.InsertChain('A')
+ ed.AppendResidue(c, 'SER')
+
+ err, has_cbeta=conop.CopyConserved(tpl.residues[0], new_hdl.residues[0], ed)
+ self.assertTrue(err)
+ self.assertTrue(has_cbeta)
+ residues=new_hdl.residues
+ self.assertEqual(len(residues), 1)
+ self.assertEqual(len(residues[0].atoms), 6)
+ self.assertTrue(new_hdl.FindAtom("A", mol.ResNum(1), "N").IsValid())
+ self.assertTrue(new_hdl.FindAtom("A", mol.ResNum(1), "CA").IsValid())
+ self.assertTrue(new_hdl.FindAtom("A", mol.ResNum(1), "C").IsValid())
+ self.assertTrue(new_hdl.FindAtom("A", mol.ResNum(1), "O").IsValid())
+ self.assertTrue(new_hdl.FindAtom("A", mol.ResNum(1), "CB").IsValid())
+ self.assertTrue(new_hdl.FindAtom("A", mol.ResNum(1), "OG").IsValid())
+
+
+ def test_CBeta(self):
+ # test if the dst residues contain cbeta, unless they are glycines
+ 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')
+ ed.AppendResidue(c, 'HIS')
+ err, has_cbeta=conop.CopyConserved(tpl.residues[0], new_hdl.residues[0], ed)
+ self.assertTrue(has_cbeta)
+ self.assertTrue(err)
+ err, has_cbeta=conop.CopyConserved(tpl.residues[1], new_hdl.residues[1], ed)
+ self.assertFalse(has_cbeta)
+ self.assertTrue(err)
+ err, has_cbeta=conop.CopyConserved(tpl.residues[2], new_hdl.residues[2], ed)
+ self.assertFalse(has_cbeta)
+ self.assertTrue(err)
+ err, has_cbeta=conop.CopyConserved(tpl.residues[3], new_hdl.residues[3], ed)
+ self.assertTrue(has_cbeta)
+ self.assertTrue(err)
+
+ residues=new_hdl.residues
+ self.assertEqual(len(residues), 4)
+ self.assertTrue(residues[0].FindAtom("CB").IsValid())
+ self.assertFalse(residues[1].FindAtom("CB").IsValid())
+ self.assertFalse(residues[2].FindAtom("CB").IsValid())
+ self.assertTrue(residues[3].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')
+ ed.AppendResidue(c, 'MET')
+ ed.AppendResidue(c, 'GLY')
+ ed.AppendResidue(c, 'GLY')
+ ed.AppendResidue(c, 'HIS')
+ ed.AppendResidue(c, 'HIS')
+ ed.AppendResidue(c, 'GLY')
+ ed.AppendResidue(c, 'HIS')
+ ed.AppendResidue(c, 'MET')
+
+ # MET to MET
+ err =conop.CopyResidue(tpl.residues[0], new_hdl.residues[0], ed)
+ self.assertTrue(err)
+ #GLY to GLY
+ err =conop.CopyResidue(tpl.residues[1], new_hdl.residues[1], ed)
+ self.assertTrue(err)
+ # GLY to GLY
+ err =conop.CopyResidue(tpl.residues[2], new_hdl.residues[2], ed)
+ self.assertTrue(err)
+ #now we copy a HIS to a HIS
+ err =conop.CopyResidue(tpl.residues[3], new_hdl.residues[3], ed)
+ self.assertTrue(err)
+ # copy a GLY to a HIS
+ err, has_cbeta=conop.CopyNonConserved(tpl.residues[1], new_hdl.residues[4], ed)
+ self.assertFalse(has_cbeta)
+ # copy a MET to a GLY
+ err =conop.CopyResidue(tpl.residues[0], new_hdl.residues[5], ed)
+ self.assertFalse(err)
+ # copy a MET to a HIS
+ err =conop.CopyResidue(tpl.residues[0], new_hdl.residues[6], ed)
+ self.assertFalse(err)
+ # copy a GLY to a MET with adding CB
+ err=conop.CopyResidue(tpl.residues[1], new_hdl.residues[7], ed)
+ self.assertFalse(err)
+
+ residues=new_hdl.residues
+ self.assertEqual(len(residues), 8)
+ # MET to MET
+ self.assertTrue(residues[0].FindAtom("CB").IsValid())
+ #GLY to GLY
+ self.assertFalse(residues[1].FindAtom("CB").IsValid())
+ #now we copy a GLY to a GLY
+ self.assertFalse(residues[2].FindAtom("CB").IsValid())
+ #now we copy a HIS to a HIS
+ self.assertTrue(residues[3].FindAtom("CB").IsValid())
+ #now we copy a GLY to a HIS without adding CB
+ self.assertFalse(residues[4].FindAtom("CB").IsValid())
+ #now we copy a MET to a GLY
+ self.assertFalse(residues[5].FindAtom("CB").IsValid())
+ # copy a MET to a HIS
+ self.assertTrue(residues[6].FindAtom("CB").IsValid())
+ # copy a GLY to a MET with adding CB
+ self.assertTrue(residues[7].FindAtom("CB").IsValid())
+
+
+if __name__ == "__main__":
+ builder=conop.GetBuilder()
+ if not hasattr(builder, 'compound_lib'):
+ print 'default builder does not use compound library. ignoring unit tests'
+ else:
+ from ost import testutils
+ testutils.RunTests()
+
+
diff --git a/modules/conop/tests/test_rule_based_builder.cc b/modules/conop/tests/test_rule_based_builder.cc
index 0bc08d4047027a9d7895a6ae6e824b4358155ff0..50e34860a606912aa978fc3429dc1b1f87c2656a 100644
--- a/modules/conop/tests/test_rule_based_builder.cc
+++ b/modules/conop/tests/test_rule_based_builder.cc
@@ -119,6 +119,35 @@ ResidueHandle make_uracil2(ChainHandle chain)
return res;
}
+ResidueHandle make_defective_uracil2(ChainHandle chain)
+{
+ XCSEditor e=chain.GetEntity().EditXCS();
+ ResidueHandle res = e.AppendResidue(chain, "U");
+
+ e.InsertAtom(res, "P", geom::Vec3(16.249, 28.254, 44.759));
+ e.InsertAtom(res, "OP1", geom::Vec3(16.654, 28.055, 46.181));
+ e.InsertAtom(res, "OP2", geom::Vec3(17.115, 27.731, 43.656));
+ e.InsertAtom(res, "O5'", geom::Vec3(14.826, 27.572, 44.574));
+ e.InsertAtom(res, "C5'", geom::Vec3(14.711, 26.206, 44.216));
+ e.InsertAtom(res, "C4'", geom::Vec3(13.279, 25.889, 43.887));
+ e.InsertAtom(res, "O4'", geom::Vec3(12.832, 26.793, 42.838));
+ e.InsertAtom(res, "C3'", geom::Vec3(13.155, 24.434, 43.329));
+ e.InsertAtom(res, "O3'", geom::Vec3(12.269, 23.625, 44.098));
+ e.InsertAtom(res, "C2'", geom::Vec3(12.871, 24.595, 41.875));
+ e.InsertAtom(res, "O2'", geom::Vec3(11.811, 23.752, 41.462));
+ e.InsertAtom(res, "C1'", geom::Vec3(12.424, 26.056, 41.694));
+ e.InsertAtom(res, "N1", geom::Vec3(13.030, 26.692, 40.497));
+ e.InsertAtom(res, "C2", geom::Vec3(12.517, 26.365, 39.228));
+ e.InsertAtom(res, "O2", geom::Vec3(11.579, 25.594, 39.068));
+ e.InsertAtom(res, "N3", geom::Vec3(13.141, 26.987, 38.161));
+ e.InsertAtom(res, "C4", geom::Vec3(14.197, 27.888, 38.210));
+ e.InsertAtom(res, "O4", geom::Vec3(14.627, 28.368, 37.156));
+ e.InsertAtom(res, "C5", geom::Vec3(14.671, 28.189, 39.542));
+ e.InsertAtom(res, "C6", geom::Vec3(14.087, 27.597, 80.612));
+
+ return res;
+}
+
void verify_nucleotide_connectivity(const ResidueHandle& res)
{
BOOST_CHECK(BondExists(res.FindAtom("P"),
@@ -217,16 +246,28 @@ BOOST_AUTO_TEST_CASE(nucleotide_based_connect)
}
RuleBasedBuilder rb_builder = RuleBasedBuilder(compound_lib);
+ RuleBasedBuilder drb_builder = RuleBasedBuilder(compound_lib);
+ drb_builder.SetBondFeasibilityCheck(false);
+
EntityHandle e=CreateEntity();
ChainHandle c=e.EditXCS().InsertChain("A");
ResidueHandle c0=make_cytosine(c);
ResidueHandle u1=make_uracil1(c);
ResidueHandle u2=make_uracil2(c);
+
+ EntityHandle de=CreateEntity();
+ ChainHandle dc=de.EditXCS().InsertChain("A");
+ ResidueHandle du2=make_defective_uracil2(dc);
+
for (AtomHandleIter i=e.AtomsBegin(),x=e.AtomsEnd(); i!=x; ++i) {
rb_builder.FillAtomProps(*i);
}
+ for (AtomHandleIter i=de.AtomsBegin(),x=de.AtomsEnd(); i!=x; ++i) {
+ drb_builder.FillAtomProps(*i);
+ }
+
// running positive test
BOOST_MESSAGE("running distance based checks on cytosine");
rb_builder.ConnectAtomsOfResidue(c0);
@@ -247,6 +288,12 @@ BOOST_AUTO_TEST_CASE(nucleotide_based_connect)
BOOST_MESSAGE("connecting cytosine to second uracil");
rb_builder.ConnectResidueToNext(c0, u2);
verify_nucleotide_nolink(c0, u2);
+
+ // running positive test
+ BOOST_MESSAGE("running distance based checks on defective uracil");
+ drb_builder.ConnectAtomsOfResidue(du2);
+ verify_nucleotide_connectivity(du2);
+
}
BOOST_AUTO_TEST_SUITE_END( )
diff --git a/modules/conop/tests/testfiles/cbeta.pdb b/modules/conop/tests/testfiles/cbeta.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..fcb59f778ba67b568a83c99605d14f3c8cdc96a4
--- /dev/null
+++ b/modules/conop/tests/testfiles/cbeta.pdb
@@ -0,0 +1,27 @@
+ATOM 1 N MET A 55 -11.301 11.863 12.812 1.00 46.35 N
+ATOM 2 CA MET A 55 -10.174 12.241 13.713 1.00 45.84 C
+ATOM 3 C MET A 55 -9.595 11.051 14.465 1.00 44.35 C
+ATOM 4 O MET A 55 -10.219 9.989 14.526 1.00 46.54 O
+ATOM 5 CB MET A 55 -10.591 13.367 14.670 1.00 48.03 C
+ATOM 6 CG MET A 55 -11.911 13.150 15.404 1.00 49.20 C
+ATOM 7 SD MET A 55 -12.173 14.422 16.660 1.00 55.85 S
+ATOM 8 CE MET A 55 -10.955 13.907 17.875 1.00 52.51 C
+ATOM 9 N GLY A 56 -8.383 11.240 14.995 1.00 42.02 N
+ATOM 10 CA GLY A 56 -7.611 10.243 15.755 1.00 39.04 C
+ATOM 11 C GLY A 56 -7.093 9.042 14.960 1.00 35.73 C
+ATOM 12 O GLY A 56 -7.875 8.322 14.336 1.00 35.25 O
+ATOM 18 N GLY A 57 -5.757 8.838 14.934 1.00 32.59 N
+ATOM 19 CA GLY A 57 -5.167 7.704 14.210 1.00 30.22 C
+ATOM 20 C GLY A 57 -5.475 6.389 14.924 1.00 28.03 C
+ATOM 21 O GLY A 57 -5.774 6.389 16.125 1.00 25.91 O
+ATOM 25 N HIS A 58 -5.434 5.288 14.176 1.00 26.73 N
+ATOM 26 CA HIS A 58 -5.705 3.960 14.726 1.00 26.95 C
+ATOM 27 C HIS A 58 -4.622 3.524 15.706 1.00 27.12 C
+ATOM 28 O HIS A 58 -3.426 3.545 15.366 1.00 27.18 O
+ATOM 29 CB HIS A 58 -5.849 2.928 13.607 1.00 26.98 C
+ATOM 30 CG HIS A 58 -7.149 3.014 12.872 1.00 27.32 C
+ATOM 31 ND1 HIS A 58 -8.359 3.179 13.510 1.00 28.47 N
+ATOM 32 CD2 HIS A 58 -7.428 2.948 11.552 1.00 26.86 C
+ATOM 33 CE1 HIS A 58 -9.327 3.211 12.613 1.00 28.81 C
+ATOM 34 NE2 HIS A 58 -8.789 3.073 11.416 1.00 28.59 N
+END
diff --git a/modules/conop/tests/testfiles/sep.pdb b/modules/conop/tests/testfiles/sep.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..f381b42b76b5bac59fc77925b742811410a8f157
--- /dev/null
+++ b/modules/conop/tests/testfiles/sep.pdb
@@ -0,0 +1,10 @@
+HETATM 2554 N SEP A 338 22.112 31.452 4.376 1.00 36.83 N
+HETATM 2555 CA SEP A 338 21.303 32.489 4.986 1.00 35.62 C
+HETATM 2556 CB SEP A 338 20.220 31.868 5.843 1.00 36.98 C
+HETATM 2557 OG SEP A 338 19.529 32.909 6.526 1.00 38.75 O
+HETATM 2558 C SEP A 338 22.121 33.517 5.710 1.00 36.32 C
+HETATM 2559 O SEP A 338 23.245 32.996 6.389 1.00 28.28 O
+HETATM 2560 P SEP A 338 18.280 33.605 5.779 1.00 36.73 P
+HETATM 2561 O1P SEP A 338 17.256 33.885 6.849 1.00 38.47 O
+HETATM 2562 O2P SEP A 338 17.811 32.606 4.750 1.00 39.29 O
+HETATM 2563 O3P SEP A 338 18.956 34.824 5.189 1.00 32.24 O
\ No newline at end of file
diff --git a/modules/db/src/CMakeLists.txt b/modules/db/src/CMakeLists.txt
index 7ccafdebd3bd5c0dbea2e72ebef42f05c066af08..8da34460be841e381308fcff5e6ca7e47cd59115 100644
--- a/modules/db/src/CMakeLists.txt
+++ b/modules/db/src/CMakeLists.txt
@@ -12,7 +12,8 @@ sqlite3.c
module(NAME db SOURCES ${OST_DB_SOURCES} HEADERS ${OST_DB_HEADERS}
DEPENDS_ON ost_base)
+add_definitions(-DSQLITE_OMIT_LOAD_EXTENSION)
if(WIN32)
set_target_properties(ost_db PROPERTIES LINK_FLAGS "/DEF:sqlite3.def")
add_definitions(/DSQLITE_ENABLE_COLUMN_METADATA)
-endif(WIN32)
\ No newline at end of file
+endif(WIN32)
diff --git a/modules/geom/pymod/CMakeLists.txt b/modules/geom/pymod/CMakeLists.txt
index 240dd87a2465360ea53b669be92eb28ea8b2898a..f79aeac4c2f9c8c127e28b0071c0ef502ba0ac38 100644
--- a/modules/geom/pymod/CMakeLists.txt
+++ b/modules/geom/pymod/CMakeLists.txt
@@ -16,4 +16,6 @@ set(OST_GEOM_PYMOD_SOURCES
export_quat.cc
)
-pymod(NAME geom CPP ${OST_GEOM_PYMOD_SOURCES} PY __init__.py)
\ No newline at end of file
+if (NOT ENABLE_STATIC)
+ pymod(NAME geom CPP ${OST_GEOM_PYMOD_SOURCES} PY __init__.py)
+endif()
diff --git a/modules/geom/pymod/export_mat2.cc b/modules/geom/pymod/export_mat2.cc
index fa1e382c9c62b7bc7ef789303d41cc88bcca6316..0338f1ddd482fea1c6c5bf0078b262234119374a 100644
--- a/modules/geom/pymod/export_mat2.cc
+++ b/modules/geom/pymod/export_mat2.cc
@@ -33,6 +33,16 @@ String mat2_repr(const geom::Mat2& m) {
<< m(1,0) << ", " << m(1,1) << ")";
return ss.str();
}
+
+list mat2_data(const geom::Mat2& m)
+{
+ list nrvo;
+ for(size_t k=0;k<4;++k) {
+ nrvo.append(m.Data()[k]);
+ }
+ return nrvo;
+}
+
void export_Mat2()
{
using namespace geom;
@@ -51,8 +61,11 @@ void export_Mat2()
.def(self * self)
.def(self * Vec2())
.def(self / Real())
+ .def(self == self)
+ .def(self != self)
.def(self_ns::str(self))
.def("__getitem__",Mat2_getitem)
.def("__setitem__",Mat2_setitem)
+ .add_property("data",mat2_data)
;
}
diff --git a/modules/geom/pymod/export_mat3.cc b/modules/geom/pymod/export_mat3.cc
index 4d86381a4db04b747f6834f6e56d5b3890c0de3c..1e543b7d912cb9b20f96f54ba8de2bb902dd5249 100644
--- a/modules/geom/pymod/export_mat3.cc
+++ b/modules/geom/pymod/export_mat3.cc
@@ -63,6 +63,14 @@ String mat3_repr(const geom::Mat3& m)
return ss.str();
}
+list mat3_data(const geom::Mat3& m)
+{
+ list nrvo;
+ for(size_t k=0;k<9;++k) {
+ nrvo.append(m.Data()[k]);
+ }
+ return nrvo;
+}
void export_Mat3()
{
@@ -82,12 +90,15 @@ void export_Mat3()
.def(self * self)
.def(self *= self)
.def(self / Real())
+ .def(self == self)
+ .def(self != self)
.def(self_ns::str(self))
.def("__getitem__",Mat3_getitem)
.def("__getitem__",Mat3_getslice)
.def("__setitem__",Mat3_setitem)
.def("__setitem__",Mat3_setslice)
.def("GetCol", &Mat3::GetCol)
- .def("GetRow", &Mat3::GetRow)
+ .def("GetRow", &Mat3::GetRow)
+ .add_property("data",mat3_data)
;
}
diff --git a/modules/geom/pymod/export_mat4.cc b/modules/geom/pymod/export_mat4.cc
index 7a5805dc6c45305fcebc5742428065d9d49f2afe..1745e35b7e64a277eb102497736b343b4089f5d8 100644
--- a/modules/geom/pymod/export_mat4.cc
+++ b/modules/geom/pymod/export_mat4.cc
@@ -85,6 +85,14 @@ String mat4_repr(const geom::Mat4& m) {
return ss.str();
}
+list mat4_data(const geom::Mat4& m)
+{
+ list nrvo;
+ for(size_t k=0;k<16;++k) {
+ nrvo.append(m.Data()[k]);
+ }
+ return nrvo;
+}
void export_Mat4()
{
@@ -104,6 +112,8 @@ void export_Mat4()
.def(self *= self)
.def(self * Vec4())
.def(self / Real())
+ .def(self == self)
+ .def(self != self)
.def(self_ns::str(self))
.def("__repr__", mat4_repr)
.def("__getitem__",Mat4_getitem)
@@ -115,5 +125,6 @@ void export_Mat4()
.def("PasteRotation",&Mat4::PasteRotation)
.def("ExtractTranslation",&Mat4::ExtractTranslation)
.def("PasteTranslation",&Mat4::PasteTranslation)
+ .add_property("data",mat4_data)
;
}
diff --git a/modules/geom/pymod/export_quat.cc b/modules/geom/pymod/export_quat.cc
index 7368ede77f65fa3995899c14ebcaecf41add681a..7e233f69c363e9a5c568545c302f8c0a6df3fa1d 100644
--- a/modules/geom/pymod/export_quat.cc
+++ b/modules/geom/pymod/export_quat.cc
@@ -40,6 +40,7 @@ void export_Quat()
.def(self += self)
.def(self -= self)
.def(self == self)
+ .def(self != self)
.def(-self)
.def(self * Real())
.def(self * Quat())
@@ -58,7 +59,6 @@ void export_Quat()
;
def("Conjugate",&Conjugate);
def("Slerp",&Slerp);
- def("Grassman",&Grassmann);
def("Normalize",normalize);
}
diff --git a/modules/geom/pymod/export_vec2.cc b/modules/geom/pymod/export_vec2.cc
index eec194418d780663aab9ecfe8e09388067c7f28f..161bda9f6d93b2515d59eb941c785adac4df0d71 100644
--- a/modules/geom/pymod/export_vec2.cc
+++ b/modules/geom/pymod/export_vec2.cc
@@ -35,6 +35,15 @@ String vec2_repr(const geom::Vec2& v)
return ss.str();
}
+list vec2_data(const geom::Vec2& v)
+{
+ list nrvo;
+ for(size_t k=0;k<2;++k) {
+ nrvo.append(v.Data()[k]);
+ }
+ return nrvo;
+}
+
void export_Vec2()
{
using namespace geom;
@@ -58,6 +67,8 @@ void export_Vec2()
.def(self / Real())
.def(self + self)
.def(self - self)
+ .def(self == self)
+ .def(self != self)
.def("__repr__", vec2_repr)
.def(self_ns::str(self))
.def("__getitem__",Vec2_getitem)
@@ -66,6 +77,7 @@ void export_Vec2()
.def("GetY", &Vec2::GetY)
.add_property("x", &Vec2::GetX, &Vec2::SetX)
.add_property("y", &Vec2::GetY, &Vec2::SetY)
+ .add_property("data",vec2_data)
;
class_<Vec2List>("Vec2List", init<>())
.def(vector_indexing_suite<Vec2List>())
diff --git a/modules/geom/pymod/export_vec3.cc b/modules/geom/pymod/export_vec3.cc
index 623671de519d14f73d7843115a5d5b18e74c8da8..aab91add33e3a2fa09378c5e1734789199eb2bfb 100644
--- a/modules/geom/pymod/export_vec3.cc
+++ b/modules/geom/pymod/export_vec3.cc
@@ -38,6 +38,15 @@ String vec3_repr(const geom::Vec3& v)
return ss.str();
}
+list vec3_data(const geom::Vec3& v)
+{
+ list nrvo;
+ for(size_t k=0;k<3;++k) {
+ nrvo.append(v.Data()[k]);
+ }
+ return nrvo;
+}
+
void export_Vec3()
{
using namespace geom;
@@ -61,6 +70,8 @@ void export_Vec3()
.def(self + Real())
.def(Real() + self)
.def(self - self)
+ .def(self == self)
+ .def(self != self)
.def(self_ns::str(self))
.def("__getitem__",Vec3_getitem)
.def("__setitem__",Vec3_setitem)
@@ -71,6 +82,7 @@ void export_Vec3()
.add_property("x", &Vec3::GetX, &Vec3::SetX)
.add_property("y", &Vec3::GetY, &Vec3::SetY)
.add_property("z", &Vec3::GetZ, &Vec3::SetZ)
+ .add_property("data",vec3_data)
;
def("Normalize", &NormalizeV3);
@@ -82,5 +94,7 @@ void export_Vec3()
.add_property("center", &Vec3List::GetCenter)
.add_property("inertia", &Vec3List::GetInertia)
.add_property("principal_axes", &Vec3List::GetPrincipalAxes)
+ .def("GetODRLine", &Vec3List::GetODRLine)
+ .def("FitCylinder", &Vec3List::FitCylinder)
;
}
diff --git a/modules/geom/pymod/export_vec4.cc b/modules/geom/pymod/export_vec4.cc
index bb3d80f90cc62205ec40e6fd22a736d05c0b1d20..986fbfa73a8b61b04eb077f75d25026fa0e3dccc 100644
--- a/modules/geom/pymod/export_vec4.cc
+++ b/modules/geom/pymod/export_vec4.cc
@@ -34,6 +34,15 @@ String vec4_repr(const geom::Vec4& v)
return ss.str();
}
+list vec4_data(const geom::Vec4& v)
+{
+ list nrvo;
+ for(size_t k=0;k<4;++k) {
+ nrvo.append(v.Data()[k]);
+ }
+ return nrvo;
+}
+
void export_Vec4()
{
using namespace geom;
@@ -58,9 +67,16 @@ void export_Vec4()
.def(self / Real())
.def(self + self)
.def(self - self)
+ .def(self == self)
+ .def(self != self)
.def(self_ns::str(self))
.def("__getitem__",Vec4_getitem)
.def("__setitem__",Vec4_setitem)
+ .add_property("x", &Vec4::GetX, &Vec4::SetX)
+ .add_property("y", &Vec4::GetY, &Vec4::SetY)
+ .add_property("z", &Vec4::GetZ, &Vec4::SetZ)
+ .add_property("w", &Vec4::GetW, &Vec4::SetW)
+ .add_property("data",vec4_data)
;
}
diff --git a/modules/geom/pymod/export_vecmat2_op.cc b/modules/geom/pymod/export_vecmat2_op.cc
index 4215e25fdf4cbc28f0dfdc09f5820cb1adc5ea91..8f594681fd9a58b2e50595ece974fa63396fddc9 100644
--- a/modules/geom/pymod/export_vecmat2_op.cc
+++ b/modules/geom/pymod/export_vecmat2_op.cc
@@ -33,8 +33,11 @@ Real (*Mat2Det)(const Mat2& m) = &Det;
Mat2 (*Mat2Invert)(const Mat2& m) = &Invert;
Mat2 (*Mat2Transpose)(const Mat2& m) = &Transpose;
Real (*Vec2Angle)(const Vec2& v1, const Vec2& v2) = &Angle;
+Real (*Vec2SignedAngle)(const Vec2& v1, const Vec2& v2) = &SignedAngle;
Vec2 (*Vec2Normalize)(const Vec2& v1) = &Normalize;
Vec2 (*Vec2Rotate)(const Vec2& v1,Real ang) = &Rotate;
+Vec2 (*Vec2Min)(const Vec2&, const Vec2&) = &Min;
+Vec2 (*Vec2Max)(const Vec2&, const Vec2&) = &Max;
void export_VecMat2_op()
{
@@ -51,6 +54,9 @@ void export_VecMat2_op()
def("Invert",Mat2Invert);
def("Transpose",Mat2Transpose);
def("Angle",Vec2Angle);
+ def("SignedAngle",Vec2SignedAngle);
def("Normalize",Vec2Normalize);
def("Rotate",Vec2Rotate);
+ def("Min",Vec2Min);
+ def("Max",Vec2Max);
}
diff --git a/modules/geom/pymod/export_vecmat3_op.cc b/modules/geom/pymod/export_vecmat3_op.cc
index fe4444b75a176651a700c032895d04a926fc2257..b858001faac7bdaf6485c4433e6acb6b0da69cbd 100644
--- a/modules/geom/pymod/export_vecmat3_op.cc
+++ b/modules/geom/pymod/export_vecmat3_op.cc
@@ -36,7 +36,10 @@ Mat3 (*Mat3Invert)(const Mat3& m) = &Inver
Mat3 (*Mat3Transpose)(const Mat3& m) = &Transpose;
Real (*Mat3Comp)(const Mat3& m, unsigned int i, unsigned int j) = &Comp;
Real (*Mat3Minor)(const Mat3& m, unsigned int i, unsigned int j) = &Minor;
-
+Vec3 (*Vec3Min)(const Vec3&, const Vec3&) = &Min;
+Vec3 (*Vec3Max)(const Vec3&, const Vec3&) = &Max;
+Real (*Vec3Distance2WithPBC)(const Vec3&, const Vec3&, const Vec3&) = &Distance2WithPBC;
+Real (*Vec3DistanceWithPBC)(const Vec3&, const Vec3&, const Vec3&) = &DistanceWithPBC;
void export_VecMat3_op()
{
@@ -60,4 +63,12 @@ void export_VecMat3_op()
def("EulerTransformation",EulerTransformation);
def("AxisRotation",AxisRotation);
def("OrthogonalVector",OrthogonalVector);
+ def("Min",Vec3Min);
+ def("Max",Vec3Max);
+ def("Distance2WithPBC",Vec3Distance2WithPBC);
+ def("DistanceWithPBC",Vec3DistanceWithPBC);
+ def("MinDistance",MinDistance);
+ def("MinDistanceWithPBC",MinDistanceWithPBC);
+ def("WrapVec3",WrapVec3);
+ def("WrapVec3List",WrapVec3List);
}
diff --git a/modules/geom/pymod/export_vecmat4_op.cc b/modules/geom/pymod/export_vecmat4_op.cc
index 9d91f48bbf9c3e8f6378e6822fdeeeefcd10fd16..af64cef7476c00ee2c31db423ec40af4d3674aa9 100644
--- a/modules/geom/pymod/export_vecmat4_op.cc
+++ b/modules/geom/pymod/export_vecmat4_op.cc
@@ -36,6 +36,8 @@ Mat4 (*Mat4Transpose)(const Mat4& m) = &Trans
Real (*Mat4Comp)(const Mat4& m, unsigned int i, unsigned int j) = &Comp;
Real (*Mat4Minor)(const Mat4& m, unsigned int i, unsigned int j) = &Minor;
Real (*Vec4Angle)(const Vec4& v1, const Vec4& v2) = &Angle;
+Vec4 (*Vec4Min)(const Vec4&, const Vec4&) = &Min;
+Vec4 (*Vec4Max)(const Vec4&, const Vec4&) = &Max;
void export_VecMat4_op()
@@ -55,4 +57,6 @@ void export_VecMat4_op()
def("Comp",Mat4Comp);
def("Minor",Mat4Minor);
def("Angle",Vec4Angle);
+ def("Min",Vec4Min);
+ def("Max",Vec4Max);
}
diff --git a/modules/geom/pymod/wrap_geom.cc b/modules/geom/pymod/wrap_geom.cc
index 3c61a57c8b911c6b0a063c8bfedc258529a23011..76bb7930057165463a426f60e133f15314b00618 100644
--- a/modules/geom/pymod/wrap_geom.cc
+++ b/modules/geom/pymod/wrap_geom.cc
@@ -36,12 +36,12 @@ extern void export_Composite2_op();
extern void export_Composite3_op();
extern void export_Quat();
-namespace {
+namespace details {
#if (defined(OST_STATIC_PROPERTY_WORKAROUND))
struct Axis_ {
- int X() const { return geom::Axis::X; }
- int Y() const { return geom::Axis::Y; }
- int Z() const { return geom::Axis::Z; }
+ int X() { return geom::Axis::X; }
+ int Y() { return geom::Axis::Y; }
+ int Z() { return geom::Axis::Z; }
};
#else
struct Axis_ {};
@@ -67,17 +67,17 @@ BOOST_PYTHON_MODULE(_ost_geom)
#if (defined(OST_STATIC_PROPERTY_WORKAROUND))
// workaround for a problem with boost python and python 2.6.3/4
- object axis=class_<Axis_>("Axis_")
- .add_property("X", &Axis_::X)
- .add_property("Y", &Axis_::Y)
- .add_property("Z", &Axis_::Z)
+ class_<details::Axis_> axis("Axis_");
+ axis.add_property("X", &details::Axis_::X);
+ axis.add_property("Y", &details::Axis_::Y);
+ axis.add_property("Z", &details::Axis_::Z);
;
scope().attr("Axis")=axis();
#else
- class_<Axis_>("Axis")
- .def_readonly("X",geom::Axis::X)
- .def_readonly("Y",geom::Axis::Y)
- .def_readonly("Z",geom::Axis::Z)
+ class_<details::Axis_>("Axis")
+ .def_readonly("X", geom::Axis::X)
+ .def_readonly("Y", geom::Axis::Y)
+ .def_readonly("Z", geom::Axis::Z)
;
#endif
}
diff --git a/modules/geom/src/composite3.cc b/modules/geom/src/composite3.cc
index 686e843e150c15729acd330cd8bc8d4112249c7f..347629d2c059cd3be0ecdef523ab65363e20adb3 100644
--- a/modules/geom/src/composite3.cc
+++ b/modules/geom/src/composite3.cc
@@ -224,25 +224,12 @@ Vec3 Rotation3::GetRotationAxis() const
}
Real Rotation3::GetRotationAngle() const
{
- return 2.0*acos(q_.GetAngle());
+ //return 2.0*acos(q_.GetAngle());
+ return q_.GetAngle();
}
Mat3 Rotation3::GetRotationMatrix() const
{
- Real ww = q_.GetAngle()*q_.GetAngle();
- Real wx = q_.GetAngle()*q_.GetAxis().GetX();
- Real wy = q_.GetAngle()*q_.GetAxis().GetY();
- Real wz = q_.GetAngle()*q_.GetAxis().GetZ();
- Real xx = q_.GetAxis().GetX()*q_.GetAxis().GetX();
- Real xy = q_.GetAxis().GetX()*q_.GetAxis().GetY();
- Real xz = q_.GetAxis().GetX()*q_.GetAxis().GetZ();
- Real yy = q_.GetAxis().GetY()*q_.GetAxis().GetY();
- Real yz = q_.GetAxis().GetY()*q_.GetAxis().GetZ();
- Real zz = q_.GetAxis().GetZ()*q_.GetAxis().GetZ();
-
-
- return Mat3((ww+xx-yy-zz), 2.0*(-wz+xy), 2.0*(wy+xz),
- 2.0*(wz+xy), (ww-xx+yy-zz), 2.0*(-wx+yz),
- 2.0*(-wy+xz), 2.0*(wx+yz),(ww-xx-yy+zz));
+ return q_.ToRotationMatrix();
}
void Rotation3::SetOrigin(const Vec3& o)
@@ -279,10 +266,7 @@ void Rotation3::SetRotationMatrix(const Mat3& rot)
}
Vec3 Rotation3::Apply(const Vec3& v) const
{
- // We can use Conjugate instead of Invert because q is guaranteed to
- // be unit Quat
- return origin_+(Grassmann(Grassmann(q_,Quat(0,v-origin_)),
- Conjugate(q_))).GetAxis();
+ return origin_+q_.Rotate(v-origin_);
}
bool Rotation3::operator==(const Rotation3& rhs) const
@@ -299,7 +283,8 @@ Quat Rotation3::generate_from_eulers(Real phi, Real theta, Real psi)
}
Quat Rotation3::generate_from_axis_angle(const Vec3& axis, Real angle)
{
- return Quat(cos(angle/2.0),sin(angle/2.0)*Normalize(axis));
+ //return Quat(cos(angle/2.0),sin(angle/2.0)*Normalize(axis));
+ return Quat(angle, axis);
}
/*
diff --git a/modules/geom/src/composite3_op.cc b/modules/geom/src/composite3_op.cc
index 09fb2c72e7430c2fc938534ff4167052485a4b24..87f799d516ab3be540ee287dbb2ceed98fee6d4a 100644
--- a/modules/geom/src/composite3_op.cc
+++ b/modules/geom/src/composite3_op.cc
@@ -178,5 +178,76 @@ bool IsInSphere(const Sphere& s, const Vec3& v){
return Length(s.GetOrigin()-v)<=s.GetRadius();
}
+Line3 Vec3List::FitCylinder(const Vec3 initial_direction, const Vec3 center){
+ //This function fits a cylinder to the positions in Vec3List
+ //It takes as argument an initial guess for the direction and the geometric
+ //center of the atoms. The center is not changed during optimisation as the
+ //best fitting cylinder can be shown to have its axis pass through the geometric center
+ Line3 axis=Line3(center,center+initial_direction), axis_old;
+ Real radius,res_sum_old,res_sum,delta_0=0.01,prec=0.0000001,err,norm,delta;
+ unsigned long n_step=1000, n_res=this->size();
+ Vec3 v,gradient;
+
+ radius=0.0;
+ delta=delta_0;
+ for (Vec3List::const_iterator i=this->begin(),e=this->end(); i!=e; ++i) {
+ radius+=geom::Distance(axis,(*i));
+ }
+ radius/=Real(n_res);
+ res_sum=0.0;
+ for (Vec3List::const_iterator i=this->begin(),e=this->end(); i!=e; ++i) {
+ res_sum+=pow(Distance(axis,(*i))-radius,2.);
+ }
+ unsigned long k=0;
+ err=2.0*prec;
+ while (err>prec and k<n_step) {
+ res_sum_old=res_sum;
+ axis_old=axis;
+ radius=0.0;
+ if (k>50) {
+ delta=delta_0*pow((50./k),2.0);
+ }
+ for (Vec3List::const_iterator i=this->begin(),e=this->end(); i!=e; ++i) {
+ radius+=Distance(axis,(*i));
+ }
+ radius/=Real(n_res);
+ for (int j=0; j!=3; ++j){
+ res_sum=0.0;
+ v=Vec3(0.0,0.0,0.0);
+ v[j]=delta;
+ axis=Line3(axis_old.GetOrigin(),axis_old.GetOrigin()+axis_old.GetDirection()+v);
+ radius=0.0;
+ for (Vec3List::const_iterator i=this->begin(),e=this->end(); i!=e; ++i) {
+ radius+=Distance(axis,(*i));
+ }
+ radius/=Real(n_res);
+ for (Vec3List::const_iterator i=this->begin(),e=this->end(); i!=e; ++i) {
+ res_sum+=pow(Distance(axis,(*i))-radius,2.);
+ }
+ gradient[j]=(res_sum-res_sum_old)/delta;
+ }
+ norm=Dot(gradient,gradient);
+ if (norm>1.) {
+ gradient=Normalize(gradient);
+ }
+ axis=Line3(axis_old.GetOrigin(),axis_old.GetOrigin()+axis_old.GetDirection()-delta*gradient);
+ radius=0.0;
+ for (Vec3List::const_iterator i=this->begin(),e=this->end(); i!=e; ++i) {
+ radius+=Distance(axis,(*i));
+ }
+ radius/=Real(n_res);
+ res_sum=0.0;
+ for (Vec3List::const_iterator i=this->begin(),e=this->end(); i!=e; ++i) {
+ res_sum+=pow(Distance(axis,(*i))-radius,2.);
+ }
+ err=fabs((res_sum-res_sum_old)/float(n_res));
+ k++;
+ }
+ if (err>prec) {
+ std::cout<<"axis fitting did not converge"<<std::endl;
+ }
+ return axis;
+}
+
} // ns
diff --git a/modules/geom/src/quat.cc b/modules/geom/src/quat.cc
index b923a668008fbe908f55bd1a10a584598ea930de..44e39ee2bb71d9c308d07cfb8a43ffa8403e6f8f 100644
--- a/modules/geom/src/quat.cc
+++ b/modules/geom/src/quat.cc
@@ -287,7 +287,8 @@ Vec3 Quat::GetAxis() const
Real Quat::GetAngle() const
{
- Real ww = std::acos(w/Length(Vec3(x,y,z)));
+ //Real ww = std::acos(w/Length(Vec3(x,y,z)));
+ Real ww = 2.0*std::acos(w);
return ww;
}
@@ -454,30 +455,12 @@ Quat Log(const Quat& q)
Vec3 Quat::Rotate(const Vec3& vec) const {
Quat tmp(0.0, vec[0], vec[1], vec[2]);
+ // We use Conjugate instead of Invert here because we assume *this to be normalized
Quat conj=Conjugate(*this);
Quat res=*this*tmp*conj;
return Vec3(res.x, res.y, res.z);
}
-Quat Grassmann(const Quat& lhs, const Quat& rhs)
-{
- return Quat(lhs.GetAngle()*rhs.GetAngle()-
- lhs.GetAxis().x*rhs.GetAxis().x-
- lhs.GetAxis().y*rhs.GetAxis().y-
- lhs.GetAxis().z*rhs.GetAxis().z,
- lhs.GetAngle()*rhs.GetAxis().x+
- lhs.GetAxis().x*rhs.GetAngle()+
- lhs.GetAxis().y*rhs.GetAxis().z-
- lhs.GetAxis().z*rhs.GetAxis().y,
- lhs.GetAngle()*rhs.GetAxis().y-
- lhs.GetAxis().x*rhs.GetAxis().z+
- lhs.GetAxis().y*rhs.GetAngle()+
- lhs.GetAxis().z*rhs.GetAxis().x,
- lhs.GetAngle()*rhs.GetAxis().z+
- lhs.GetAxis().x*rhs.GetAxis().y-
- lhs.GetAxis().y*rhs.GetAxis().x+
- lhs.GetAxis().z*rhs.GetAngle());
-}
std::ostream& operator<<(std::ostream& str, const Quat& q)
{
diff --git a/modules/geom/src/quat.hh b/modules/geom/src/quat.hh
index 4347952c0068515cfaf7e1ce38714611990fe5bc..881f69b5bdd8a8112eefe3ffc642ceed525efe42 100644
--- a/modules/geom/src/quat.hh
+++ b/modules/geom/src/quat.hh
@@ -93,6 +93,7 @@ public:
Quat& operator/=(const Quat& q);
// comparable
bool operator==(const Quat& q) const;
+ bool operator!=(const Quat& q) const { return !this->operator==(q); }
// Apply rotation to vector.
Vec3 Rotate(const Vec3& vec) const;
@@ -115,8 +116,6 @@ Quat DLLEXPORT_OST_GEOM Inv(const Quat& q);
Quat DLLEXPORT_OST_GEOM Exp(const Quat& q);
Quat DLLEXPORT_OST_GEOM Log(const Quat& q);
-Quat DLLEXPORT_OST_GEOM Grassmann(const Quat& lhs, const Quat& rhs);
-
//normalize quaternion
Quat DLLEXPORT_OST_GEOM Normalize(const Quat& q);
diff --git a/modules/geom/src/vec3.cc b/modules/geom/src/vec3.cc
index 84467ced5a4ddf66dd5ae23e1de054c7cb8e175d..ea07f3cca30b46f4aeef0139d7f4a0a0aab9345b 100644
--- a/modules/geom/src/vec3.cc
+++ b/modules/geom/src/vec3.cc
@@ -68,5 +68,18 @@ Vec3 Vec3List::GetCenter() const
return center/=this->size();
}
+Line3 Vec3List::GetODRLine()
+{
+ Vec3 center=this->GetCenter();
+ Vec3 direction=this->GetPrincipalAxes().GetRow(2);
+ return Line3(center,center+direction);
+}
+Plane Vec3List::GetODRPlane()
+{
+ Vec3 origin=this->GetCenter();
+ Vec3 normal=this->GetPrincipalAxes().GetRow(0);
+ return Plane(origin,normal);
+}
+
}
diff --git a/modules/geom/src/vec3.hh b/modules/geom/src/vec3.hh
index db2b8bb7097dc76d0b74c7906a0ea4a63bda5929..ac3458837fc20245ac7d185a56a58cbf69b8eb08 100644
--- a/modules/geom/src/vec3.hh
+++ b/modules/geom/src/vec3.hh
@@ -34,7 +34,8 @@ namespace geom {
// fw decl
class Vec2;
class Vec4;
-
+class Line3;
+class Plane;
/// \brief Three dimensional vector class, using Real precision.
class DLLEXPORT_OST_GEOM Vec3:
@@ -193,6 +194,7 @@ inline std::ostream& operator<<(std::ostream& os, const Vec3& v)
#include <ost/geom/vec2.hh>
#include <ost/geom/vec4.hh>
#include <ost/geom/mat3.hh>
+#include <ost/geom/composite3.hh>
namespace geom {
@@ -216,6 +218,10 @@ public:
Vec3 GetCenter() const;
Mat3 GetPrincipalAxes() const;
+ Line3 GetODRLine();
+ Plane GetODRPlane();
+ Line3 FitCylinder(const Vec3 initial_direction, const Vec3 center);
+
};
diff --git a/modules/geom/src/vecmat2_op.cc b/modules/geom/src/vecmat2_op.cc
index 69f2e8e8ce2200b5d6994498b787291ad8b4a247..ea0a4521376d510ccc9db2a0471fe275bd9833cd 100644
--- a/modules/geom/src/vecmat2_op.cc
+++ b/modules/geom/src/vecmat2_op.cc
@@ -55,11 +55,15 @@ Real Angle(const Vec2& v1, const Vec2& v2)
Real SignedAngle(const Vec2& v1, const Vec2& v2)
{
- Vec3 vc;
- vc=Cross(Vec3(v1),Vec3(v2));
- if(Length(v1)==0.0 || Length(v2)==0.0 || Length(vc)==0.0)
+ if(Length(v1)==0.0 || Length(v2)==0.0){
return 0.0;
- return acos(Dot(v1,v2)/Length(v1)/Length(v2))*vc.z/std::fabs(vc.z);
+ }
+ Vec3 vc=Cross(Vec3(v1),Vec3(v2));
+ Real sign=1.0;
+ if(vc.z!=0.0){
+ sign=vc.z/std::fabs(vc.z);
+ }
+ return acos(Dot(v1,v2)/Length(v1)/Length(v2))*sign;
}
Vec2 Rotate(const Vec2& v,Real ang)
diff --git a/modules/geom/src/vecmat3_op.cc b/modules/geom/src/vecmat3_op.cc
index 7fb8e2feff5aded2ce280c74e8d9f893465c9b77..50b5b612e939d66e6d8119ddced416ff87e52f99 100644
--- a/modules/geom/src/vecmat3_op.cc
+++ b/modules/geom/src/vecmat3_op.cc
@@ -142,16 +142,16 @@ Mat3 EulerTransformation(Real theta, Real phi, Real xi)
}
Vec3 OrthogonalVector(const Vec3& vec) {
- if (vec[0] < vec[1]) {
- if (vec[0] < vec[2])
+ if (std::abs(vec[0]) < std::abs(vec[1])) {
+ if (std::abs(vec[0]) < std::abs(vec[2]))
return Normalize(Cross(vec, Vec3(1, 0, 0)+vec));
else
return Normalize(Cross(vec, Vec3(0, 0, 1)+vec));
} else {
- if (vec[1] < vec[2])
+ if (std::abs(vec[1]) < std::abs(vec[2]))
return Normalize(Cross(vec, Vec3(0, 1, 0)+vec));
else
- return Normalize(Cross(vec, Vec3(0, 0, 2)+vec));
+ return Normalize(Cross(vec, Vec3(0, 0, 1)+vec));
}
}
@@ -192,19 +192,61 @@ Real DihedralAngle(const Vec3& p1, const Vec3& p2, const Vec3& p3,
Dot(r12cross, r23cross));
}
+
Real MinDistance(const Vec3List& l1, const Vec3List& l2)
{
// returns the minimal distance between two sets of points (Vec3List)
if (l1.size()==0 || l2.size()==0){throw std::runtime_error("cannot calculate minimal distance: empty Vec3List");}
- Real min=Distance(*l1.begin(),*l2.begin());
+ Real min=Length2(*l1.begin()-*l2.begin());
Real d;
for (Vec3List::const_iterator p1=l1.begin(),e1=l1.end(); p1!=e1; p1++) {
for (Vec3List::const_iterator p2=l2.begin(),e2=l2.end(); p2!=e2; p2++) {
- d=Distance(*p1,*p2);
+ d=Length2(*p1-*p2);
if (d<min) min=d;
}
}
- return min;
+ return std::sqrt(min);
}
+Real MinDistanceWithPBC(const Vec3List& l1, const Vec3List& l2, Vec3& basis_vec)
+{
+ // returns the minimal distance between two sets of points (Vec3List)
+ // given the periodic boundary condition along x,y,z given in the basis_vec
+ if (l1.size()==0 || l2.size()==0){throw std::runtime_error("cannot calculate minimal distance: empty Vec3List");}
+ Real min=Length2(*l1.begin()-*l2.begin());
+ Real d;
+ Vec3 v;
+ for (int i=0; i<3; i++) {
+ basis_vec[i]=std::fabs(basis_vec[i]);
+ }
+ for (Vec3List::const_iterator p1=l1.begin(),e1=l1.end(); p1!=e1; p1++) {
+ for (Vec3List::const_iterator p2=l2.begin(),e2=l2.end(); p2!=e2; p2++) {
+ d=Distance2WithPBC(*p1, *p2, basis_vec);
+ if (d<min) min=d;
+ }
+ }
+ return std::sqrt(min);
+}
+
+Vec3 WrapVec3(const Vec3& v1,const Vec3& box_center,const Vec3& basis_vec){
+ Vec3 v;
+ Real r;
+ for (int i=0; i<3; i++) {
+ r=(v1[i]-box_center[i])/basis_vec[i];
+ r=(r > 0.0) ? std::floor(r + 0.5) : std::ceil(r - 0.5);
+ v[i]=v1[i]-basis_vec[i]*r;
+ }
+ return v;
+}
+
+Vec3List WrapVec3List(const Vec3List& vl, const Vec3& box_center,const Vec3& basis_vec){
+ Vec3List vl_out;
+ vl_out.reserve(vl_out.size());
+ for (Vec3List::const_iterator v1=vl.begin(),e=vl.end();v1!=e ; v1++) {
+ vl_out.push_back(WrapVec3(*v1,box_center,basis_vec));
+ }
+ return vl_out;
+}
+
+
} // ns
diff --git a/modules/geom/src/vecmat3_op.hh b/modules/geom/src/vecmat3_op.hh
index 373b9561b1338fe3907e5e37809b4d71b501911f..5489ea9e8f1c48f669053fafa45f14220b52384f 100644
--- a/modules/geom/src/vecmat3_op.hh
+++ b/modules/geom/src/vecmat3_op.hh
@@ -194,9 +194,34 @@ inline Real Distance(const Vec3& p1, const Vec3& p2)
return Length(p1-p2);
}
+
+//! return the squared distance between two points with periodic boundaries in x,y,z given in basis_vec
+inline Real Distance2WithPBC(const Vec3& v1, const Vec3& v2, const Vec3& basis_vec){
+ Vec3 v;
+ v=v1-v2;
+ for (int i=0; i<3; i++) {
+ if (std::fabs(v[i])>basis_vec[i]/2.){
+ v[i]=std::fabs(v[i])-basis_vec[i]*int(std::fabs(v[i])/basis_vec[i]+0.5);
+ }
+ }
+ return Length2(v);
+}
+//! return the distance between two points with periodic boundaries in x,y,z given in basis_vec
+inline Real DistanceWithPBC(const Vec3& v1, const Vec3& v2, const Vec3& basis_vec){
+ return sqrt(Distance2WithPBC(v1, v2, basis_vec));
+}
//! returns the minimal distance between the points in two Vec3List
Real MinDistance(const Vec3List& l1, const Vec3List& l2);
+//! returns the minimal distance between the points in two Vec3List
+// with periodic boundaries in x,y,z given in basis_vec
+Real MinDistanceWithPBC(const Vec3List& l1, const Vec3List& l2, Vec3& basis_vec);
+
+//!wraps a vector in a box with periodic boundaries
+Vec3 WrapVec3(const Vec3& v1,const Vec3& box_center,const Vec3& basis_vec);
+//!wraps all the verctors in a Vec3List in a box with periodic boundaries
+Vec3List WrapVec3List(const Vec3List& vl,const Vec3& box_center,const Vec3& basis_vec);
+
} // ns
#endif
diff --git a/modules/geom/tests/CMakeLists.txt b/modules/geom/tests/CMakeLists.txt
index 7a7dace6b3ed006ba13997889693a4b3910949f8..027a167490b6256249a53a4cf1e569a237f3c8af 100644
--- a/modules/geom/tests/CMakeLists.txt
+++ b/modules/geom/tests/CMakeLists.txt
@@ -7,11 +7,12 @@ set(GEOM_UNITTESTS
test_op2.cc
test_op3.cc
test_op4.cc
+ test_quat.cc
test_vec2.cc
test_vec3.cc
test_vec4.cc
tests.cc
- test_repr.py
+ test_geom.py
)
ost_unittest(MODULE geom
diff --git a/modules/geom/tests/test_composite3.cc b/modules/geom/tests/test_composite3.cc
index 6548b53da1d70c45acb5e39b5ecd5e9584a998a8..f5cd5cf6bfbe0f411490361103e9bf0e13b5c0b9 100644
--- a/modules/geom/tests/test_composite3.cc
+++ b/modules/geom/tests/test_composite3.cc
@@ -17,6 +17,7 @@
// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
//------------------------------------------------------------------------------
+#include <cmath>
#include <ost/geom/geom.hh>
#include "helper.hh"
@@ -193,4 +194,14 @@ BOOST_AUTO_TEST_CASE(func_composite3)
}
+BOOST_AUTO_TEST_CASE(rotation3)
+{
+ Vec3 v(1,0,0);
+ Rotation3 r(Vec3(0,1,0), 30.0*M_PI/180.0);
+ Vec3 vrot=r.Apply(v);
+ BOOST_CHECK_CLOSE(Real(cos(30.0*M_PI/180.0)), Real(vrot[0]), Real(1e-5));
+ BOOST_CHECK_SMALL(vrot[1],float(1e-5));
+ BOOST_CHECK_CLOSE(Real(-sin(30.0*M_PI/180.0)), Real(vrot[2]), Real(1e-5));
+}
+
BOOST_AUTO_TEST_SUITE_END()
diff --git a/modules/geom/tests/test_geom.py b/modules/geom/tests/test_geom.py
new file mode 100644
index 0000000000000000000000000000000000000000..f563add91955b88fcc383b714df2f472a1a9b64e
--- /dev/null
+++ b/modules/geom/tests/test_geom.py
@@ -0,0 +1,85 @@
+#------------------------------------------------------------------------------
+# 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
+#------------------------------------------------------------------------------
+
+import unittest
+if __name__== '__main__':
+ import sys
+ sys.path.insert(0,"../../../stage/lib64/openstructure/")
+ sys.path.insert(0,"../../../stage/lib/openstructure/")
+
+import ost
+import ost.geom as geom
+
+class TestGeom(unittest.TestCase):
+ def runTest(self):
+ self.test_repr()
+ self.test_data()
+
+ def test_repr(self):
+ v=geom.Vec2(1,2)
+ v2=eval(repr(v))
+ self.assertTrue(geom.Equal(v, v2))
+
+ v=geom.Vec3(1,2,3)
+ v2=eval(repr(v))
+ self.assertTrue(geom.Equal(v, v2))
+
+ v=geom.Vec4(1,2,3,4)
+ v2=eval(repr(v))
+ self.assertTrue(geom.Equal(v, v2))
+
+ m=geom.Mat2(1,2,3,4)
+ m2=eval(repr(m))
+ self.assertTrue(geom.Equal(m, m2))
+
+ m=geom.Mat3(1,2,3,4,5,6,7,8,9)
+ m2=eval(repr(m))
+ self.assertTrue(geom.Equal(m, m2))
+
+ m=geom.Mat4(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16)
+ m2=eval(repr(m))
+ self.assertTrue(geom.Equal(m, m2))
+
+ def test_data(self):
+ self.assertEqual(geom.Vec2(1,2).data,[1,2])
+ self.assertEqual(geom.Vec3(1,2,3).data,[1,2,3])
+ self.assertEqual(geom.Vec4(1,2,3,4).data,[1,2,3,4])
+ self.assertEqual(geom.Mat2(1,2,
+ 3,4).data,
+ [1,2,
+ 3,4])
+ self.assertEqual(geom.Mat3(1,2,3,
+ 4,5,6,
+ 7,8,9).data,
+ [1,2,3,
+ 4,5,6,
+ 7,8,9])
+ self.assertEqual(geom.Mat4(1,2,3,4,
+ 5,6,7,8,
+ 9,10,11,12,
+ 13,14,15,16).data,
+ [1,2,3,4,
+ 5,6,7,8,
+ 9,10,11,12,
+ 13,14,15,16])
+
+if __name__== '__main__':
+ from ost import testutils
+ testutils.RunTests()
+
diff --git a/modules/geom/tests/test_quat.cc b/modules/geom/tests/test_quat.cc
new file mode 100644
index 0000000000000000000000000000000000000000..ccaf9ab2dd4aa7d4730cfd511dcdd7d0ad9fe811
--- /dev/null
+++ b/modules/geom/tests/test_quat.cc
@@ -0,0 +1,58 @@
+//------------------------------------------------------------------------------
+// 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
+//------------------------------------------------------------------------------
+
+#include <ost/geom/geom.hh>
+
+#include "helper.hh"
+using namespace geom;
+
+#define BOOST_TEST_DYN_LINK
+#include <boost/test/unit_test.hpp>
+
+BOOST_AUTO_TEST_SUITE( geom )
+
+BOOST_AUTO_TEST_CASE(init_quat)
+{
+ // default
+ Quat q1;
+ BOOST_CHECK_CLOSE(Real(q1.w), Real(1.0), Real(1.0e-5));
+ BOOST_CHECK_CLOSE(Real(q1.x), Real(0.0), Real(1.0e-5));
+ BOOST_CHECK_CLOSE(Real(q1.y), Real(0.0), Real(1.0e-5));
+ BOOST_CHECK_CLOSE(Real(q1.z), Real(0.0), Real(1.0e-5));
+
+ Quat q2(2.0,3.0,4.0,5.0);
+ BOOST_CHECK_CLOSE(Real(q2.w), Real(2.0), Real(1.0e-5));
+ BOOST_CHECK_CLOSE(Real(q2.x), Real(3.0), Real(1.0e-5));
+ BOOST_CHECK_CLOSE(Real(q2.y), Real(4.0), Real(1.0e-5));
+ BOOST_CHECK_CLOSE(Real(q2.z), Real(5.0), Real(1.0e-5));
+}
+
+BOOST_AUTO_TEST_CASE(quat_rotate)
+{
+ Vec3 v(1,0,0);
+ Quat q(30.0*M_PI/180.0,Vec3(0,1,0));
+ Vec3 vrot=q.Rotate(v);
+ BOOST_CHECK_CLOSE(Real(cos(30.0*M_PI/180.0)), Real(vrot[0]), Real(1e-5));
+ BOOST_CHECK_SMALL(vrot[1],float(1e-5));
+ BOOST_CHECK_CLOSE(Real(-sin(30.0*M_PI/180.0)), Real(vrot[2]), Real(1e-5));
+}
+
+
+BOOST_AUTO_TEST_SUITE_END()
+
diff --git a/modules/geom/tests/test_repr.py b/modules/geom/tests/test_repr.py
deleted file mode 100644
index e69358f20f783c7f8b731de7f13deb569105a0fa..0000000000000000000000000000000000000000
--- a/modules/geom/tests/test_repr.py
+++ /dev/null
@@ -1,39 +0,0 @@
-import unittest
-from ost import geom
-
-class TestRepr(unittest.TestCase):
- def testReprVec2(self):
- v=geom.Vec2(1,2)
- v2=eval(repr(v))
- assert geom.Equal(v, v2)
-
- def testReprVec3(self):
- v=geom.Vec3(1,2,3)
- v2=eval(repr(v))
- assert geom.Equal(v, v2)
-
- def testReprVec4(self):
- v=geom.Vec4(1,2,3,4)
- v2=eval(repr(v))
- assert geom.Equal(v, v2)
-
- def testReprMat2(self):
- m=geom.Mat2(1,2,3,4)
- m2=eval(repr(m))
- assert geom.Equal(m, m2)
-
- def testReprMat3(self):
- m=geom.Mat3(1,2,3,4,5,6,7,8,9)
- m2=eval(repr(m))
- assert geom.Equal(m, m2)
-
- def testReprMat4(self):
- m=geom.Mat4(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16)
- m2=eval(repr(m))
- assert geom.Equal(m, m2)
-
-if __name__ == "__main__":
- try:
- unittest.main()
- except Exception, e:
- print e
\ No newline at end of file
diff --git a/modules/gfx/pymod/CMakeLists.txt b/modules/gfx/pymod/CMakeLists.txt
index 210cce509623565695582e20969f818e8f2e042d..a3d8b251dda72f07f6e7394ad4fb3d0996fb4bd4 100644
--- a/modules/gfx/pymod/CMakeLists.txt
+++ b/modules/gfx/pymod/CMakeLists.txt
@@ -14,13 +14,14 @@ set(OST_GFX_PYMOD_SOURCES
export_gradient.cc
export_color_ops.cc
export_glwin_base.cc
+ export_exporter.cc
)
if (ENABLE_IMG)
set(OST_GFX_PYMOD_SOURCES ${OST_GFX_PYMOD_SOURCES} export_map.cc)
endif()
-pymod(NAME gfx CPP ${OST_GFX_PYMOD_SOURCES} PY __init__.py)
+pymod(NAME gfx CPP ${OST_GFX_PYMOD_SOURCES} PY __init__.py py_gfx_obj.py)
set(GRADIENT_FILE
gradients.xml
diff --git a/modules/gfx/pymod/__init__.py b/modules/gfx/pymod/__init__.py
index 0cd783f9fa44d36dd8ab1696257b943e1d2732c6..be887c4ab071e3c4f2da12a771e7e1edad6b8b30 100644
--- a/modules/gfx/pymod/__init__.py
+++ b/modules/gfx/pymod/__init__.py
@@ -17,6 +17,7 @@
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
#------------------------------------------------------------------------------
from _ost_gfx import *
+from py_gfx_obj import PyGfxObj
WHITE=Color(1.0,1.0,1.0)
BLACK=Color(0.0,0.0,0.0)
@@ -243,7 +244,7 @@ def _primlist_add_text(self,text,pos,color=None,point_size=None):
if not point_size:
point_size=1.0
self._add_text(text,pos,color,point_size)
-
+
PrimList.AddPoint=_primlist_add_point
PrimList.AddLine=_primlist_add_line
PrimList.AddSphere=_primlist_add_sphere
diff --git a/modules/gfx/pymod/export_exporter.cc b/modules/gfx/pymod/export_exporter.cc
new file mode 100644
index 0000000000000000000000000000000000000000..655fe54f77282e2d6656142addf51e18006d7f7c
--- /dev/null
+++ b/modules/gfx/pymod/export_exporter.cc
@@ -0,0 +1,38 @@
+//------------------------------------------------------------------------------
+// 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
+//------------------------------------------------------------------------------
+#include <boost/python.hpp>
+using namespace boost::python;
+
+#include <ost/gfx/exporter.hh>
+#include <ost/gfx/gost_exporter.hh>
+#include <ost/gfx/collada_exporter.hh>
+
+using namespace ost;
+using namespace ost::gfx;
+
+void export_Exporter()
+{
+ class_<Exporter, boost::noncopyable>("Exporter", no_init);
+
+ class_<GostExporter, bases<Exporter>, boost::noncopyable>("GostExporter", init<const std::string&>())
+ ;
+
+ class_<ColladaExporter, bases<Exporter>, boost::noncopyable>("ColladaExporter", init<const std::string&, optional<float> >())
+ ;
+}
diff --git a/modules/gfx/pymod/export_gfx_obj.cc b/modules/gfx/pymod/export_gfx_obj.cc
index 1d2ed62cd446fa5689230ff4eeda73cb5f7d787a..45093dd9bb8927e213c5af627babd19fe9d8f9ce 100644
--- a/modules/gfx/pymod/export_gfx_obj.cc
+++ b/modules/gfx/pymod/export_gfx_obj.cc
@@ -25,7 +25,6 @@ using namespace ost::gfx;
#include "color_by_def.hh"
-namespace {
// convenience for python
void set_mat_amb2(GfxObjBase* b, float c) {b->SetMatAmb(Color(c,c,c,1.0));}
void set_mat_diff2(GfxObjBase* b, float c) {b->SetMatDiff(Color(c,c,c,1.0));}
@@ -58,7 +57,63 @@ namespace {
LOG_INFO("AALines(bool) is deprecated, use SetAALines(bool) instead");
b->SetAALines(f);
}
-}
+
+ class GfxObjWrap: public GfxObj, public wrapper<GfxObj>
+ {
+ public:
+ GfxObjWrap(const std::string& name):
+ GfxObj(name)
+ {}
+
+ virtual geom::AlignedCuboid GetBoundingBox() const
+ {
+ if(override f = this->get_override("GetBoundingBox")) {
+ return f();
+ } else {
+ return GfxObj::GetBoundingBox();
+ }
+ }
+
+ geom::AlignedCuboid default_GetBoundingBox() const {
+ return GfxObj::GetBoundingBox();
+ }
+
+ virtual void CustomRenderGL(RenderPass pass) {
+ if(override f = this->get_override("_CustomRenderGL")) {
+ f(pass);
+ } else {
+ GfxObj::CustomRenderGL(pass);
+ }
+ }
+
+ void default_CustomRenderGL(RenderPass pass) {
+ GfxObj::CustomRenderGL(pass);
+ }
+
+ virtual void CustomPreRenderGL(bool rebuild) {
+ if(override f = this->get_override("_CustomPreRenderGL")) {
+ f(rebuild);
+ } else {
+ GfxObj::CustomPreRenderGL(rebuild);
+ }
+ }
+
+ void default_CustomPreRenderGL(bool rebuild) {
+ GfxObj::CustomPreRenderGL(rebuild);
+ }
+
+ virtual void InitGL() {
+ if(override f = this->get_override("_InitGL")) {
+ f();
+ } else {
+ GfxObj::InitGL();
+ }
+ }
+
+ void default_InitGL() {
+ GfxObj::InitGL();
+ }
+ };
void export_GfxObj()
{
@@ -102,9 +157,13 @@ void export_GfxObj()
.add_property("opacity",&GfxObjBase::GetOpacity,&GfxObjBase::SetOpacity)
COLOR_BY_DEF()
;
- //register_ptr_to_python<GfxObjBaseP>();
- class_<GfxObj, boost::shared_ptr<GfxObj>, bases<GfxObjBase>, boost::noncopyable>("GfxObj",no_init)
+ enum_<RenderPass>("RenderPass")
+ .value("STANDARD_RENDER_PASS",STANDARD_RENDER_PASS)
+ .value("TRANSPARENT_RENDER_PASS",TRANSPARENT_RENDER_PASS)
+ ;
+
+ class_<GfxObjWrap, boost::shared_ptr<GfxObj>, bases<GfxObjBase>, boost::noncopyable>("GfxObj",init<const std::string&>())
.def("GetTF", &GfxObj::GetTF, return_value_policy<copy_const_reference>())
.def("SetTF", &GfxObj::SetTF)
.def("FlagRebuild",&GfxObj::FlagRebuild)
@@ -116,7 +175,10 @@ void export_GfxObj()
.def("GetAALines",&GfxObj::GetAALines)
.def("GetLineWidth",&GfxObj::GetLineWidth)
.def("GetLineHalo",&GfxObj::GetLineHalo)
- ;
- //register_ptr_to_python<GfxObjP>();
+ .def("GetBoundingBox",&GfxObj::GetBoundingBox, &GfxObjWrap::default_GetBoundingBox)
+ .def("_CustomRenderGL",&GfxObj::CustomRenderGL, &GfxObjWrap::default_CustomRenderGL)
+ .def("_CustomPreRenderGL",&GfxObj::CustomPreRenderGL, &GfxObjWrap::default_CustomPreRenderGL)
+ .def("_InitGL",&GfxObj::InitGL, &GfxObjWrap::default_InitGL)
+ ;
}
diff --git a/modules/gfx/pymod/export_gradient.cc b/modules/gfx/pymod/export_gradient.cc
index e24cc9cee5fec611fc536b8c0ab5a4e95c3712a1..6cb26cee020a295eb56111aa4101d189470eadc3 100644
--- a/modules/gfx/pymod/export_gradient.cc
+++ b/modules/gfx/pymod/export_gradient.cc
@@ -26,7 +26,7 @@ using namespace ost;
using namespace ost::gfx;
namespace {
- Gradient* make_gradient(const dict& d)
+ Gradient* make_gradient_d(const dict& d)
{
std::auto_ptr<Gradient> grad(new Gradient);
list keys = d.keys();
@@ -57,13 +57,42 @@ namespace {
}
return grad.release();
}
+
+ Gradient* make_gradient_l(const list& l)
+ {
+ std::auto_ptr<Gradient> grad(new Gradient);
+ float mf = len(l)<2 ? 0.0 : 1.0/static_cast<float>(len(l)-1);
+ for(int i=0;i<len(l);++i) {
+ float mark = static_cast<float>(i)*mf;
+ Color col;
+ object val = l[i];
+ extract<Color> cex(val);
+ if(cex.check()) {
+ // use gfx.Color
+ col=cex();
+ } else {
+ // try simple sequence
+ if(len(val)!=3) {
+ throw std::runtime_error("expected values of gfx.Color or float triplets");
+ }
+ try {
+ col=gfx::Color(extract<float>(val[0]),extract<float>(val[1]),extract<float>(val[2]));
+ } catch (...) {
+ throw std::runtime_error("expected values of gfx.Color or float triplets");
+ }
+ }
+ grad->SetColorAt(mark,col);
+ }
+ return grad.release();
+ }
}
void export_gradient()
{
class_<Gradient>("Gradient", init<>())
.def(init<const String&>())
- .def("__init__", make_constructor(make_gradient))
+ .def("__init__", make_constructor(make_gradient_d))
+ .def("__init__", make_constructor(make_gradient_l))
.def("SetColorAt", &Gradient::SetColorAt)
.def("GetColorAt", &Gradient::GetColorAt)
.def("GetStops", &Gradient::GetStops)
diff --git a/modules/gfx/pymod/export_primitives.cc b/modules/gfx/pymod/export_primitives.cc
index 91ce753ed91df2006caf3928438d4ed1937032cc..01b328d7288116ab8c6dcd9e7d86c5c3ad97fb07 100644
--- a/modules/gfx/pymod/export_primitives.cc
+++ b/modules/gfx/pymod/export_primitives.cc
@@ -25,8 +25,7 @@ using namespace ost::gfx;
void export_primitives()
{
- class_<Primitive, boost::shared_ptr<Primitive>,
- bases<GfxNode>, boost::noncopyable>("Primitive", no_init)
+ class_<Primitive, bases<GfxNode>, boost::noncopyable>("Primitive", no_init)
.def("HasOutline", &Primitive::HasOutline)
.def("HasFill", &Primitive::HasFill)
.def("SetFill", &Primitive::SetFill)
@@ -40,10 +39,10 @@ void export_primitives()
.def("GetOutlineColor", &Primitive::GetOutlineColor,
return_value_policy<copy_const_reference>())
;
- class_<Cuboid, boost::shared_ptr<Cuboid>, bases<Primitive>,
+ class_<Cuboid, bases<Primitive>,
boost::noncopyable>("Cuboid", init<const String&, const geom::Cuboid>())
;
- class_<Quad, boost::shared_ptr<Quad>, bases<Primitive>,
+ class_<Quad, bases<Primitive>,
boost::noncopyable>("Quad", init<const String&, const geom::Vec3&,
const geom::Vec3&, const geom::Vec3&,
const geom::Vec3&>())
diff --git a/modules/gfx/pymod/export_primlist.cc b/modules/gfx/pymod/export_primlist.cc
index b8326509d8ed7065f120ab4760a541b5766e207b..bb986d7e14c1580555d2bb3b4db2fb497c1c9fcc 100644
--- a/modules/gfx/pymod/export_primlist.cc
+++ b/modules/gfx/pymod/export_primlist.cc
@@ -25,8 +25,90 @@ using namespace boost::python;
using namespace ost;
using namespace ost::gfx;
+#if OST_NUMPY_SUPPORT_ENABLED
+#include <numpy/arrayobject.h>
+#endif
+
+namespace {
+ void add_mesh(PrimList& p, object ova, object ona, object oca, object oia)
+ {
+#if OST_NUMPY_SUPPORT_ENABLED
+ if(!PyArray_Check(ova.ptr())) {
+ throw std::runtime_error("ova is not a numpy array");
+ }
+ PyArrayObject* va=reinterpret_cast<PyArrayObject*>(ova.ptr());
+ if(!PyArray_ISCONTIGUOUS(va)) {
+ throw std::runtime_error("expected vertex array to be contiguous");
+ }
+ if(!PyArray_TYPE(va)==NPY_FLOAT) {
+ throw std::runtime_error("expected vertex array to be of dtype=float32");
+ }
+ size_t v_size=PyArray_SIZE(va);
+ if(v_size%3!=0) {
+ throw std::runtime_error("expected vertex array size to be divisible by 3");
+ }
+ size_t v_count=v_size/3;
+ float* vp=reinterpret_cast<float*>(PyArray_DATA(va));
+ float* np=0;
+ float* cp=0;
+ if(ona!=object()) {
+ if(!PyArray_Check(ona.ptr())) {
+ throw std::runtime_error("ona is not a numpy array");
+ }
+ PyArrayObject* na=reinterpret_cast<PyArrayObject*>(ona.ptr());
+ if(!PyArray_ISCONTIGUOUS(na)) {
+ throw std::runtime_error("expected normal array to be contiguous");
+ }
+ if(!PyArray_TYPE(na)==NPY_FLOAT) {
+ throw std::runtime_error("expected normal array to be of dtype=float32");
+ }
+ if(PyArray_SIZE(na)!=v_size) {
+ throw std::runtime_error("expected normal array size to match vertex array size");
+ }
+ np=reinterpret_cast<float*>(PyArray_DATA(na));
+ }
+ if(oca!=object()) {
+ if(!PyArray_Check(oca.ptr())) {
+ throw std::runtime_error("oca is not a numpy array");
+ }
+ PyArrayObject* ca=reinterpret_cast<PyArrayObject*>(oca.ptr());
+ if(!PyArray_ISCONTIGUOUS(ca)) {
+ throw std::runtime_error("expected color array to be contiguous");
+ }
+ if(!PyArray_TYPE(ca)==NPY_FLOAT) {
+ throw std::runtime_error("expected color array to be of dtype=float32");
+ }
+ if(PyArray_SIZE(ca)!=v_count*4) {
+ throw std::runtime_error("expected color array size to equal vertex-count x 4");
+ }
+ cp=reinterpret_cast<float*>(PyArray_DATA(ca));
+ }
+ if(!PyArray_Check(oia.ptr())) {
+ throw std::runtime_error("oia is not a numpy array");
+ }
+ PyArrayObject* ia=reinterpret_cast<PyArrayObject*>(oia.ptr());
+ if(!PyArray_ISCONTIGUOUS(ia)) {
+ throw std::runtime_error("expected vertex array to be contiguous");
+ }
+ if(!PyArray_TYPE(ia)==NPY_UINT) {
+ throw std::runtime_error("expected vertex array to be of dtype=uint32");
+ }
+ size_t i_size=PyArray_SIZE(ia);
+ unsigned int* ip=reinterpret_cast<unsigned int*>(PyArray_DATA(ia));
+
+ p.AddMesh(vp,np,cp,v_count,ip,i_size/3);
+#else
+ throw std::runtime_error("AddMesh requires compiled-in numpy support");
+#endif
+ }
+}
+
void export_primlist()
{
+#if OST_NUMPY_SUPPORT_ENABLED
+ import_array(); // magic handshake for numpy module
+#endif
+
class_<PrimList, bases<GfxObj>, boost::shared_ptr<PrimList>, boost::noncopyable>("PrimList", init<const String& >())
.def("Clear",&PrimList::Clear)
.def("_add_line",&PrimList::AddLine)
@@ -34,6 +116,7 @@ void export_primlist()
.def("_add_sphere",&PrimList::AddSphere)
.def("_add_cyl",&PrimList::AddCyl)
.def("_add_text",&PrimList::AddText)
+ .def("AddMesh",add_mesh)
.def("SetColor",&PrimList::SetColor)
.def("SetDiameter",&PrimList::SetDiameter)
.def("SetRadius",&PrimList::SetRadius)
diff --git a/modules/gfx/pymod/export_scene.cc b/modules/gfx/pymod/export_scene.cc
index f5692fad5b197d02c94f024add51392e78f72b2b..8b73a3391ec8a0a8ac5f4e41357b17738320d1d2 100644
--- a/modules/gfx/pymod/export_scene.cc
+++ b/modules/gfx/pymod/export_scene.cc
@@ -21,6 +21,7 @@ using namespace boost::python;
#include <ost/gfx/gfx_object.hh>
#include <ost/gfx/scene.hh>
+#include <ost/gfx/exporter.hh>
using namespace ost;
using namespace ost::gfx;
@@ -63,6 +64,7 @@ void export_Scene()
void (Scene::* export1)(const String&, uint, uint, bool) = &Scene::Export;
void (Scene::* export2)(const String&, bool) = &Scene::Export;
+ void (Scene::* export3)(Exporter*) const = &Scene::Export;
void (Scene::*remove1)(const GfxNodeP&) = &Scene::Remove;
void (Scene::*remove2)(const String&) = &Scene::Remove;
void (Scene::*center_on1)(const String&) = &Scene::CenterOn;
@@ -116,6 +118,7 @@ void export_Scene()
.def("SetFogColor",&Scene::SetFogColor)
.def("GetFogColor",&Scene::GetFogColor)
.add_property("fogcol", &Scene::GetFogColor, &Scene::SetFogColor)
+ .add_property("fog_color", &Scene::GetFogColor, &Scene::SetFogColor)
.def("SetFOV",&Scene::SetFOV)
.def("GetFOV",&Scene::GetFOV)
.add_property("fov", &Scene::GetFOV, &Scene::SetFOV)
@@ -159,8 +162,9 @@ void export_Scene()
.def("SetLightProp",set_light_prop1)
.def("SetLightProp",set_light_prop2)
.def("Apply", apply)
- .def("Export",export1, arg("transparent")=true)
- .def("Export",export2, arg("transparent")=true)
+ .def("Export",export1, arg("transparent")=false)
+ .def("Export",export2, arg("transparent")=false)
+ .def("Export",export3)
.def("ExportPov",&Scene::ExportPov,
scene_export_pov_overloads())
.def("PushView",&Scene::PushView)
@@ -169,14 +173,25 @@ void export_Scene()
.def("BlurSnapshot",&Scene::BlurSnapshot)
.def("RemoveAll", &Scene::RemoveAll)
.def("SetShadow",&Scene::SetShadow)
+ .add_property("shadow",&Scene::GetShadow,&Scene::SetShadow)
.def("SetShadowQuality",&Scene::SetShadowQuality)
+ .add_property("shadow_quality",&Scene::GetShadowQuality,&Scene::SetShadowQuality)
.def("SetShadowWeight",&Scene::SetShadowWeight)
+ .add_property("shadow_weight",&Scene::GetShadowWeight,&Scene::SetShadowWeight)
.def("SetDepthDarkening",&Scene::SetDepthDarkening)
.def("SetDepthDarkeningWeight",&Scene::SetDepthDarkeningWeight)
.def("SetAmbientOcclusion",&Scene::SetAmbientOcclusion)
+ .add_property("ambient_occlusion",&Scene::GetAmbientOcclusion,&Scene::SetAmbientOcclusion)
+ .add_property("ao",&Scene::GetAmbientOcclusion,&Scene::SetAmbientOcclusion)
.def("SetAmbientOcclusionWeight",&Scene::SetAmbientOcclusionWeight)
+ .add_property("ambient_occlusion_weight",&Scene::GetAmbientOcclusionWeight,&Scene::SetAmbientOcclusionWeight)
+ .add_property("ao_weight",&Scene::GetAmbientOcclusionWeight,&Scene::SetAmbientOcclusionWeight)
.def("SetAmbientOcclusionMode",&Scene::SetAmbientOcclusionMode)
+ .add_property("ambient_occlusion_mode",&Scene::GetAmbientOcclusionMode,&Scene::SetAmbientOcclusionMode)
+ .add_property("ao_mode",&Scene::GetAmbientOcclusionMode,&Scene::SetAmbientOcclusionMode)
.def("SetAmbientOcclusionQuality",&Scene::SetAmbientOcclusionQuality)
+ .add_property("ambient_occlusion_quality",&Scene::GetAmbientOcclusionQuality,&Scene::SetAmbientOcclusionQuality)
+ .add_property("ao_quality",&Scene::GetAmbientOcclusionQuality,&Scene::SetAmbientOcclusionQuality)
.def("AttachObserver",&Scene::AttachObserver)
.def("StartOffscreenMode",&Scene::StartOffscreenMode)
.def("StopOffscreenMode",&Scene::StopOffscreenMode)
@@ -185,5 +200,7 @@ void export_Scene()
.add_property("root_node", &Scene::GetRootNode)
.def("SetBeaconOff",&Scene::SetBeaconOff)
.def("__getitem__",scene_getitem)
+ .add_property("show_center",&Scene::GetShowCenter, &Scene::SetShowCenter)
+ .add_property("fix_center",&Scene::GetFixCenter, &Scene::SetFixCenter)
;
}
diff --git a/modules/gfx/pymod/py_gfx_obj.py b/modules/gfx/pymod/py_gfx_obj.py
new file mode 100644
index 0000000000000000000000000000000000000000..ac91e9073a47b061ee57145e0d3d7b6b6a51dcc5
--- /dev/null
+++ b/modules/gfx/pymod/py_gfx_obj.py
@@ -0,0 +1,79 @@
+#------------------------------------------------------------------------------
+# 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
+#------------------------------------------------------------------------------
+import traceback
+from _ost_gfx import *
+
+class PyGfxObj(GfxObj):
+ def __init__(self,name):
+ """
+ requires a unique name not yet utilized in the Scene;
+ do not place OpenGL calls in the ctor, use InitGL for
+ that purpose
+ """
+ GfxObj.__init__(self,name)
+ self._valid_flag=False
+
+ def _InitGL(self):
+ try:
+ self.InitGL()
+ self._valid_flag=True
+ except:
+ traceback.print_exc()
+
+ def InitGL(self):
+ """
+ called once for each OpenGL context (usually one time),
+ allows one-time OpenGL initialization to be implemented,
+ such as vbo allocation
+ """
+ pass
+
+
+ def _CustomPreRenderGL(self,rebuild):
+ if not self._valid_flag:
+ return
+ try:
+ self.CustomPreRenderGL(rebuild)
+ except:
+ self._valid_flag=False
+ traceback.print_exc()
+
+ def CustomPreRenderGL(self,rebuild):
+ """
+ called just before CustomRenderGL is called; the flag
+ indicates that a rebuild is required or was requested
+ """
+ pass
+
+
+ def _CustomRenderGL(self,render_pass):
+ if not self._valid_flag:
+ return
+ try:
+ self.CustomRenderGL(render_pass)
+ except:
+ self._valid_flag=False
+ traceback.print_exc()
+
+ def CustomRenderGL(self,render_pass):
+ """
+ called for each scene refresh
+ """
+ pass
+
diff --git a/modules/gfx/pymod/scene_observer_proxy.hh b/modules/gfx/pymod/scene_observer_proxy.hh
index 63209cb200551e0e9f2f8812374b74c1ef70715c..8ba5faa6be1b1b56c004567dbc6efc3a252f2543 100644
--- a/modules/gfx/pymod/scene_observer_proxy.hh
+++ b/modules/gfx/pymod/scene_observer_proxy.hh
@@ -16,7 +16,6 @@
using namespace ost;
using namespace ost::gfx;
-namespace {
class SceneObserverProxy: public SceneObserver {
public:
@@ -75,6 +74,5 @@ private:
PyObject* self;
};
-}
#endif
diff --git a/modules/gfx/pymod/wrap_gfx.cc b/modules/gfx/pymod/wrap_gfx.cc
index 0198d3a0fb27ae5869ff572b9335e6580737b8e9..28229edf12ada259a25443f363d43db51199291d 100644
--- a/modules/gfx/pymod/wrap_gfx.cc
+++ b/modules/gfx/pymod/wrap_gfx.cc
@@ -37,6 +37,8 @@ extern void export_primlist();
extern void export_primitives();
extern void export_color();
extern void export_gradient();
+extern void export_Exporter();
+
#if OST_IMG_ENABLED
extern void export_Map();
#endif
@@ -135,6 +137,8 @@ BOOST_PYTHON_MODULE(_ost_gfx)
;
#endif
+ export_primitives();
+ export_Exporter();
}
diff --git a/modules/gfx/src/CMakeLists.txt b/modules/gfx/src/CMakeLists.txt
index 4f23812fd1120c170b45ff54ace477657314d9f2..9309a6af7ebec7fed643e303a732bf1b0c53b4ab 100644
--- a/modules/gfx/src/CMakeLists.txt
+++ b/modules/gfx/src/CMakeLists.txt
@@ -1,6 +1,7 @@
set(OST_GFX_HEADERS
render_pass.hh
bitmap_io.hh
+collada_exporter.hh
color.hh
entity.hh
entity_fw.hh
@@ -37,6 +38,9 @@ module_config.hh
primitives.hh
povray_fw.hh
povray.hh
+exporter.hh
+exporter_fw.hh
+gost_exporter.hh
)
set(OST_GFX_COLOR_OPS_HEADERS
@@ -89,6 +93,7 @@ endif()
set(OST_GFX_SOURCES
bitmap_io.cc
+collada_exporter.cc
color.cc
primitives.cc
entity.cc
@@ -108,6 +113,7 @@ vertex_array.cc
vertex_array_helper.cc
material.cc
povray.cc
+gost_exporter.cc
texture.cc
color_ops/color_op.cc
color_ops/by_element_color_op.cc
diff --git a/modules/gfx/src/collada_exporter.cc b/modules/gfx/src/collada_exporter.cc
new file mode 100644
index 0000000000000000000000000000000000000000..902334f851fc0df651f58f380e3c3771e8ae1e96
--- /dev/null
+++ b/modules/gfx/src/collada_exporter.cc
@@ -0,0 +1,279 @@
+//------------------------------------------------------------------------------
+// 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
+//------------------------------------------------------------------------------
+
+/*
+ Author: Ansgar Philippsen
+*/
+
+#include <sstream>
+#include <boost/format.hpp>
+
+#include "collada_exporter.hh"
+#include "scene.hh"
+
+namespace ost { namespace gfx {
+
+ColladaExporter::ColladaExporter(const std::string& file, float scale):
+ file_(file),
+ out_(file_.c_str()),
+ scale_(scale),
+ obj_()
+{
+ out_ << "<?xml version=\"1.0\" encoding=\"utf-8\"?>\n";
+ out_ << "<COLLADA version=\"1.4.0\" xmlns=\"http://www.collada.org/2005/11/COLLADASchema\">\n";
+}
+
+ColladaExporter::~ColladaExporter()
+{
+ out_ << "</COLLADA>\n";
+}
+
+void ColladaExporter::SceneStart(const Scene* scene)
+{
+ out_ << " <library_cameras>\n";
+ out_ << " <camera id=\"Camera-Camera\" name=\"Camera-Camera\">\n";
+ out_ << " <optics>\n";
+ out_ << " <technique_common>\n";
+ out_ << " <perspective>\n";
+ out_ << " <yfov>" << scene->GetFOV() << "</yfov>\n";
+ out_ << " <znear>" << scene->GetNear() << "</znear>\n";
+ out_ << " <zfar>" << scene->GetFar() << "</zfar>\n";
+ out_ << " </perspective>\n";
+ out_ << " </technique_common>\n";
+ out_ << " </optics>\n";
+ out_ << " </camera>\n";
+ out_ << " </library_cameras>\n";
+
+ out_ << " <library_geometries>\n" << std::endl;
+}
+
+void ColladaExporter::SceneEnd(const Scene* scene)
+{
+ out_ << " </library_geometries>\n" << std::endl;
+
+ out_ << " <library_visual_scenes>\n";
+ out_ << " <visual_scene id=\"Scene\" name=\"Scene\">\n";
+
+ out_ << " <node id=\"Camera\" name=\"Camera\">\n";
+ out_ << " <instance_camera url=\"#Camera-Camera\"/>\n";
+ out_ << " </node>\n";
+
+ out_ << " <node id=\"Root\" name=\"Root\">\n";
+ out_ << " <matrix>\n";
+ geom::Mat4 tm=scene->GetTransform().GetMatrix();
+ out_ << " " << tm(0,0) << " " << tm(0,1) << " " << tm(0,2) << " " << tm(0,3) << "\n";
+ out_ << " " << tm(1,0) << " " << tm(1,1) << " " << tm(1,2) << " " << tm(1,3) << "\n";
+ out_ << " " << tm(2,0) << " " << tm(2,1) << " " << tm(2,2) << " " << tm(2,3) << "\n";
+ out_ << " " << tm(3,0) << " " << tm(3,1) << " " << tm(3,2) << " " << tm(3,3) << "\n";
+ out_ << " </matrix>\n";
+ for(std::vector<std::string>::const_iterator oit=obj_.begin();oit!=obj_.end();++oit) {
+ out_ << " <node id=\"" << *oit << "\" name=\"" << *oit <<"\">\n";
+ out_ << " <instance_geometry url=\"#" << *oit << "\"/>\n";
+ out_ << " </node>\n";
+ }
+ out_ << " </node>\n";
+ out_ << " </visual_scene>\n";
+ out_ << " </library_visual_scenes>\n";
+
+ out_ << " <scene>\n";
+ out_ << " <instance_visual_scene url=\"#Scene\"/>\n";
+ out_ << " </scene>\n";
+}
+
+void ColladaExporter::NodeStart(const std::string& name, NodeType t)
+{
+ if(name!="Scene") {
+ obj_.push_back(name);
+ out_ << "<geometry id=\"" << name << "\" name=\"" << name << "\">\n";
+ out_ << " <mesh>\n";
+ }
+}
+
+void ColladaExporter::NodeEnd(const std::string& name)
+{
+ if(name!="Scene") {
+ out_ << " </mesh>\n";
+ out_ << "</geometry>\n";
+ }
+}
+
+void ColladaExporter::WriteVertexData(const float* vdata,
+ const float* ndata,
+ const float* cdata,
+ const float* tdata,
+ size_t stride2, size_t count)
+{
+ std::string name=obj_.back();
+ size_t stride=stride2/sizeof(float);
+
+ out_ << " <source id=\"" << name+"-Positions" << "\">\n";
+ out_ << " <float_array count=\"" << count*3 << "\" id=\"" << name+"-Positions-array" << "\">\n";
+ if(vdata) {
+ const float* src=vdata;
+ for(unsigned int i=0;i<count;++i) {
+ out_ << scale_*src[0] << " ";
+ out_ << scale_*src[1] << " ";
+ out_ << scale_*src[2] << " ";
+ src+=stride;
+ }
+ } else {
+ for(unsigned int i=0;i<count;++i) {
+ out_ << "0.0 0.0 0.0 ";
+ }
+ }
+ out_ << " </float_array>\n";
+ out_ << " <technique_common>\n";
+ out_ << " <accessor count=\"" << count << "\" source=\"#" << name + "-Positions-array" << "\" stride=\"3\">\n";
+ out_ << " <param name=\"X\" type=\"float\"/>\n";
+ out_ << " <param name=\"Y\" type=\"float\"/>\n";
+ out_ << " <param name=\"Z\" type=\"float\"/>\n";
+ out_ << " </accessor>\n";
+ out_ << " </technique_common>\n";
+ out_ << " </source>\n";
+
+ // normals, lots of code duplication for now
+ out_ << " <source id=\"" << name+"-Normals" << "\">\n";
+ out_ << " <float_array count=\"" << count*3 << "\" id=\"" << name+"-Normals-array" << "\">\n";
+ if(ndata) {
+ const float* src=ndata;
+ for(unsigned int i=0;i<count;++i) {
+ out_ << src[0] << " ";
+ out_ << src[1] << " ";
+ out_ << src[2] << " ";
+ src+=stride;
+ }
+ } else {
+ for(unsigned int i=0;i<count;++i) {
+ out_ << "0.0 0.0 0.0 ";
+ }
+ }
+ out_ << " </float_array>\n";
+ out_ << " <technique_common>\n";
+ out_ << " <accessor count=\"" << count << "\" source=\"#" << name + "-Normals-array" << "\" stride=\"3\">\n";
+ out_ << " <param name=\"X\" type=\"float\"/>\n";
+ out_ << " <param name=\"Y\" type=\"float\"/>\n";
+ out_ << " <param name=\"Z\" type=\"float\"/>\n";
+ out_ << " </accessor>\n";
+ out_ << " </technique_common>\n";
+ out_ << " </source>\n";
+
+ // colors, again lots of code duplication
+ out_ << " <source id=\"" << name+"-Colors" << "\">\n";
+ //out_ << " <float_array count=\"" << count*4 << "\" id=\"" << name+"-Colors-array" << "\">\n";
+ out_ << " <float_array count=\"" << count*3 << "\" id=\"" << name+"-Colors-array" << "\">\n";
+ if(cdata) {
+ const float* src=cdata;
+ for(unsigned int i=0;i<count;++i) {
+ out_ << src[0] << " ";
+ out_ << src[1] << " ";
+ out_ << src[2] << " ";
+ //out_ << src[3] << " ";
+ src+=stride;
+ }
+ } else {
+ for(unsigned int i=0;i<count;++i) {
+ out_ << "0.0 0.0 0.0 ";
+ }
+ }
+ out_ << " </float_array>\n";
+ out_ << " <technique_common>\n";
+ //out_ << " <accessor count=\"" << count << "\" source=\"#" << name + "-Colors-array" << "\" stride=\"4\">\n";
+ out_ << " <accessor count=\"" << count << "\" source=\"#" << name + "-Colors-array" << "\" stride=\"3\">\n";
+ out_ << " <param name=\"R\" type=\"float\"/>\n";
+ out_ << " <param name=\"G\" type=\"float\"/>\n";
+ out_ << " <param name=\"B\" type=\"float\"/>\n";
+ //out_ << " <param name=\"A\" type=\"float\"/>\n";
+ out_ << " </accessor>\n";
+ out_ << " </technique_common>\n";
+ out_ << " </source>\n";
+
+ out_ << " <vertices id=\"" << name+"-Vertex" << "\">\n";
+ out_ << " <input semantic=\"POSITION\" source =\"#" << name+"-Positions" << "\"/>\n";
+ //out_ << " <input semantic=\"NORMAL\" source =\"#" << name+"-Normals" << "\"/>\n";
+ //out_ << " <input semantic=\"COLOR\" source =\"#" << name+"-Colors" << "\"/>\n";
+ out_ << " </vertices>\n";
+}
+
+void ColladaExporter::WritePointData(const unsigned int* i, size_t count)
+{
+}
+
+void ColladaExporter::WriteLineData(const unsigned int* ij, size_t count)
+{
+}
+
+void ColladaExporter::WriteTriData(const unsigned int* ijk, size_t count)
+{
+ std::string name=obj_.back();
+
+ out_ << " <triangles count=\"" << count << "\">\n";
+ out_ << " <input offset=\"0\" semantic=\"VERTEX\" source =\"#" << name+"-Vertex" << "\"/>\n";
+ out_ << " <input offset=\"1\" semantic=\"NORMAL\" source =\"#" << name+"-Normals" << "\"/>\n";
+ out_ << " <input offset=\"2\" semantic=\"COLOR\" source =\"#" << name+"-Colors" << "\"/>\n";
+ out_ << " <p>\n";
+ for(unsigned int c=0;c<count*3;c+=3) {
+ out_ << ijk[c+0] << " ";
+ out_ << ijk[c+0] << " ";
+ out_ << ijk[c+0] << " ";
+ out_ << ijk[c+1] << " ";
+ out_ << ijk[c+1] << " ";
+ out_ << ijk[c+1] << " ";
+ out_ << ijk[c+2] << " ";
+ out_ << ijk[c+2] << " ";
+ out_ << ijk[c+2] << " ";
+ }
+ out_ << " </p>\n";
+ out_ << " </triangles>\n";
+}
+
+void ColladaExporter::WriteQuadData(const unsigned int* ijkl, size_t count)
+{
+ std::string name=obj_.back();
+
+ out_ << " <triangles count=\"" << count << "\">\n";
+ out_ << " <input offset=\"0\" semantic=\"VERTEX\" source =\"#" << name+"-Vertex" << "\"/>\n";
+ out_ << " <input offset=\"1\" semantic=\"NORMAL\" source =\"#" << name+"-Normals" << "\"/>\n";
+ out_ << " <input offset=\"2\" semantic=\"COLOR\" source =\"#" << name+"-Colors" << "\"/>\n";
+ out_ << " <p>\n";
+ for(unsigned int c=0;c<count*4;c+=4) {
+ out_ << ijkl[c+0] << " ";
+ out_ << ijkl[c+0] << " ";
+ out_ << ijkl[c+0] << " ";
+ out_ << ijkl[c+1] << " ";
+ out_ << ijkl[c+1] << " ";
+ out_ << ijkl[c+1] << " ";
+ out_ << ijkl[c+2] << " ";
+ out_ << ijkl[c+2] << " ";
+ out_ << ijkl[c+2] << " ";
+ //
+ out_ << ijkl[c+0] << " ";
+ out_ << ijkl[c+0] << " ";
+ out_ << ijkl[c+0] << " ";
+ out_ << ijkl[c+2] << " ";
+ out_ << ijkl[c+2] << " ";
+ out_ << ijkl[c+2] << " ";
+ out_ << ijkl[c+3] << " ";
+ out_ << ijkl[c+3] << " ";
+ out_ << ijkl[c+3] << " ";
+ }
+ out_ << " </p>\n";
+ out_ << " </triangles>\n";
+}
+
+}} // ns
diff --git a/modules/gfx/src/collada_exporter.hh b/modules/gfx/src/collada_exporter.hh
new file mode 100644
index 0000000000000000000000000000000000000000..c0192a10097e6cb0d2b48801431a3be2437509d5
--- /dev/null
+++ b/modules/gfx/src/collada_exporter.hh
@@ -0,0 +1,62 @@
+//------------------------------------------------------------------------------
+// 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_GFX_COLLADA_EXPORTER_HH
+#define OST_GFX_COLLADA_EXPORTER_HH
+
+/*
+ Author: Ansgar Philippsen
+*/
+
+#include <string>
+#include <fstream>
+#include <vector>
+
+#include "module_config.hh"
+#include "exporter.hh"
+
+namespace ost { namespace gfx {
+
+class DLLEXPORT_OST_GFX ColladaExporter: public Exporter
+{
+public:
+ ColladaExporter(const std::string& collada_file, float scale=1.0);
+ virtual ~ColladaExporter();
+
+ // exporter interface
+ virtual void SceneStart(const Scene* scene);
+ virtual void SceneEnd(const Scene* scene);
+ virtual void NodeStart(const std::string& name, NodeType t);
+ virtual void NodeEnd(const std::string& name);
+ virtual void WriteVertexData(const float* v, const float* n, const float* c, const float* t,
+ size_t stride, size_t count);
+ virtual void WritePointData(const unsigned int* i, size_t count);
+ virtual void WriteLineData(const unsigned int* ij, size_t count);
+ virtual void WriteTriData(const unsigned int* ijk, size_t count);
+ virtual void WriteQuadData(const unsigned int* ijkl, size_t count);
+
+private:
+ std::string file_;
+ std::ofstream out_;
+ float scale_;
+ std::vector<std::string> obj_;
+};
+
+}} // ns
+
+#endif
diff --git a/modules/gfx/src/color.cc b/modules/gfx/src/color.cc
index f99de522b962df1c1ce030b74c97a551fb0cd492..f40e69c53629e136a661b380424d4e075419ae50 100644
--- a/modules/gfx/src/color.cc
+++ b/modules/gfx/src/color.cc
@@ -81,9 +81,9 @@ geom::Vec3 HSVtoRGB(const geom::Vec3& hsv)
geom::Vec3 RGBtoHSV(const geom::Vec3& rgb)
{
geom::Vec3 hsv;
- double var_R = ( rgb[0] / 255.0 );
- double var_G = ( rgb[1] / 255.0 );
- double var_B = ( rgb[2] / 255.0 );
+ double var_R = ( rgb[0] );
+ double var_G = ( rgb[1] );
+ double var_B = ( rgb[2] );
double var_Min = std::min(std::min( var_R, var_G), var_B );
double var_Max = std::max(std::max( var_R, var_G), var_B );
@@ -107,13 +107,18 @@ geom::Vec3 RGBtoHSV(const geom::Vec3& rgb)
} else if ( var_B == var_Max ){
hsv[0] = ( 2.0 / 3.0 ) + del_G - del_R;
}
- if ( hsv[0] < 0 ){
- hsv[0] += 1;
+ if ( hsv[0] < 0.0 ){
+ hsv[0] += 1.0;
}
- if ( hsv[0] > 1 ){
- hsv[0] -= 1;
+ if ( hsv[0] > 1.0 ){
+ hsv[0] -= 1.0;
}
}
+
+ hsv[0]=hsv[0]*360.0;
+ hsv[1]=hsv[1]*100.0;
+ hsv[2]=hsv[2]*100.0;
+
return hsv;
}
} // anon ns
@@ -126,6 +131,11 @@ geom::Vec3 Color::ToHSV()
Color HSV(double h, double s, double v)
{
+ if(h>1.0 || s>1.0 || v>1.0) {
+ h=h/360.0;
+ s=s/100.0;
+ v=v/100.0;
+ }
geom::Vec3 rgb=HSVtoRGB(geom::Vec3(h,s,v));
return Color(rgb[0],rgb[1],rgb[2]);
}
diff --git a/modules/gfx/src/color.hh b/modules/gfx/src/color.hh
index 1fdee9fa64eb146ee45e8a4882e833dc43ee4b0e..533381dbc07d06880f2f2b3ab00a2b1a3e72c0f3 100644
--- a/modules/gfx/src/color.hh
+++ b/modules/gfx/src/color.hh
@@ -85,6 +85,13 @@ private:
float rgba[4];
};
+/*!
+ \brief HSV color spec
+
+ h: Hue from 0 to 360 (0=red, 120=green, 240=blue)
+ s: Saturation from 0 (no color) to 100 (full color)
+ v: Value from 0 (no light, black) to 100 (full light)
+*/
Color DLLEXPORT_OST_GFX HSV(double h, double s, double v);
DLLEXPORT_OST_GFX std::ostream& operator<<(std::ostream&, const Color& c);
diff --git a/modules/gfx/src/entity.cc b/modules/gfx/src/entity.cc
index b5f0f6b75c4e6d516caa1bcffa28c26fbbe45ac8..dff4bfa1fb8465036438a59ebdf8f72dc2a3277b 100644
--- a/modules/gfx/src/entity.cc
+++ b/modules/gfx/src/entity.cc
@@ -54,6 +54,7 @@
#if OST_SHADER_SUPPORT_ENABLED
#include "shader.hh"
#endif
+#include "exporter.hh"
namespace ost {
@@ -401,6 +402,23 @@ void Entity::CustomRenderPov(PovState& pov)
}
}
+void Entity::Export(Exporter* ex)
+{
+ ex->NodeStart(GetName(),Exporter::OBJ);
+ // in the simplest case, just export va
+ if(rebuild_ || refresh_) {
+ PreRenderGL(true);
+ }
+
+ for (RendererMap::iterator it=renderer_.begin(); it!=renderer_.end(); ++it) {
+ if(it->second->IsEnabled() && it->second->HasDataToRender()){
+ it->second->Export(ex);
+ }
+ }
+
+ ex->NodeEnd(GetName());
+}
+
mol::AtomHandle Entity::PickAtom(const geom::Line3& line, Real line_width)
{
mol::AtomHandle picked_atom;
diff --git a/modules/gfx/src/entity.hh b/modules/gfx/src/entity.hh
index 7e6d595fa27f0e34c7d4e7eff73732f28dbca6a6..7663fe3782fe053df4eb7f0428d6401da26905c9 100644
--- a/modules/gfx/src/entity.hh
+++ b/modules/gfx/src/entity.hh
@@ -324,6 +324,8 @@ public:
void SetSeqHack(bool b);
bool GetSeqHack() const;
+ virtual void Export(Exporter* ex);
+
protected:
virtual void CustomPreRenderGL(bool flag);
diff --git a/modules/gfx/src/exporter.hh b/modules/gfx/src/exporter.hh
new file mode 100644
index 0000000000000000000000000000000000000000..20b0601aee6a110a4c713a687db50d4834c5978c
--- /dev/null
+++ b/modules/gfx/src/exporter.hh
@@ -0,0 +1,56 @@
+//------------------------------------------------------------------------------
+// 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_GFX_EXPORTER_HH
+#define OST_GFX_EXPORTER_HH
+
+#include <ost/gfx/module_config.hh>
+
+namespace ost { namespace gfx {
+
+class Scene;
+
+class DLLEXPORT_OST_GFX Exporter
+{
+public:
+ enum NodeType {
+ ROOT=1,
+ GROUP=2,
+ OBJ=3
+ };
+
+ virtual ~Exporter() {}
+ virtual void SceneStart(const Scene* scene) {}
+ virtual void SceneEnd(const Scene* scene) {}
+
+ virtual void NodeStart(const std::string& name, NodeType t) {}
+ virtual void NodeEnd(const std::string& name) {}
+
+ // this indicates beginning of new data, including a reset of the indices
+ // may occur more than once for a given node
+ virtual void WriteVertexData(const float* v, const float* n, const float* c, const float* t,
+ size_t stride, size_t count) {}
+ virtual void WritePointData(const unsigned int* i, size_t count) {}
+ virtual void WriteLineData(const unsigned int* ij, size_t count) {}
+ virtual void WriteTriData(const unsigned int* ijk, size_t count) {}
+ virtual void WriteQuadData(const unsigned int* ijkl, size_t count) {}
+};
+
+}} // ns
+
+#endif
diff --git a/modules/gfx/src/exporter_fw.hh b/modules/gfx/src/exporter_fw.hh
new file mode 100644
index 0000000000000000000000000000000000000000..499248014e24d9df5374569c7a66d5227a4c8443
--- /dev/null
+++ b/modules/gfx/src/exporter_fw.hh
@@ -0,0 +1,28 @@
+//------------------------------------------------------------------------------
+// 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_GFX_EXPORTER_FW_HH
+#define OST_GFX_EXPORTER_FW_HH
+
+namespace ost { namespace gfx {
+
+ class Exporter;
+
+}} // ns
+
+#endif
diff --git a/modules/gfx/src/gfx_node.cc b/modules/gfx/src/gfx_node.cc
index e7f038a2668e2d4fdd162e00f29e4acd37592881..8d417aeec6660d3ecf3aa689cf68d3e90c781fa7 100644
--- a/modules/gfx/src/gfx_node.cc
+++ b/modules/gfx/src/gfx_node.cc
@@ -18,9 +18,11 @@
//------------------------------------------------------------------------------
#include <boost/bind.hpp>
#include <ost/dyn_cast.hh>
+
#include "gfx_node.hh"
#include "gfx_object.hh"
#include "scene.hh"
+#include "exporter.hh"
namespace ost { namespace gfx {
@@ -101,6 +103,16 @@ void GfxNode::RenderPov(PovState& pov)
}
}
+void GfxNode::Export(Exporter* ex)
+{
+ if(!IsVisible()) return;
+ ex->NodeStart(GetName(),Exporter::GROUP);
+ for(GfxNodeVector::iterator it=node_vector_.begin();it!=node_vector_.end();++it) {
+ (*it)->Export(ex);
+ }
+ ex->NodeEnd(GetName());
+}
+
String GfxNode::GetName() const
{
return name_;
diff --git a/modules/gfx/src/gfx_node.hh b/modules/gfx/src/gfx_node.hh
index b211ca8a9ccb7cda837e109a338ac79d33201301..6cff8388518b96924eec6802dad40e5631cf8c4c 100644
--- a/modules/gfx/src/gfx_node.hh
+++ b/modules/gfx/src/gfx_node.hh
@@ -34,6 +34,7 @@
#include "gfx_object_fw.hh"
#include "gfx_node_visitor.hh"
#include "povray_fw.hh"
+#include "exporter_fw.hh"
namespace ost { namespace gfx {
@@ -56,10 +57,11 @@ class DLLEXPORT_OST_GFX GfxNode: public boost::enable_shared_from_this<GfxNode>
// render all child leaves and nodes
virtual void RenderGL(RenderPass pass);
-
// render all child leaves and nodes into POVray state
virtual void RenderPov(PovState& pov);
+ virtual void Export(Exporter* ex);
+
// visitor interface
virtual void Apply(GfxNodeVisitor& v, GfxNodeVisitor::Stack st);
diff --git a/modules/gfx/src/gfx_object.cc b/modules/gfx/src/gfx_object.cc
index a7f061e402af59d1a442648a6d238bb4cfc31283..1f0486017c6139adc74134f712d72409486744cd 100644
--- a/modules/gfx/src/gfx_object.cc
+++ b/modules/gfx/src/gfx_object.cc
@@ -33,6 +33,7 @@
#include "povray.hh"
#include "impl/mapped_property.hh"
+#include "exporter.hh"
#if OST_IMG_ENABLED
# include <ost/img/alg/stat.hh>
@@ -180,6 +181,9 @@ void GfxObj::RenderGL(RenderPass pass)
}
}
+void GfxObj::InitGL()
+{
+}
void GfxObj::RenderPov(PovState& pov)
{
@@ -195,6 +199,20 @@ void GfxObj::RenderPov(PovState& pov)
}
}
+
+void GfxObj::Export(Exporter* ex)
+{
+ if(IsVisible()) {
+ ex->NodeStart(GetName(),Exporter::OBJ);
+ // in the simplest case, just export va
+ if(rebuild_ || refresh_) {
+ PreRenderGL(true);
+ }
+ va_.Export(ex);
+ ex->NodeEnd(GetName());
+ }
+}
+
void GfxObj::Apply(GfxNodeVisitor& v, GfxNodeVisitor::Stack st)
{
v.VisitObject(this,st);
diff --git a/modules/gfx/src/gfx_object.hh b/modules/gfx/src/gfx_object.hh
index 1865e7662607ae51624f2c0ec1e5898b41ecb21e..d241be75e19f15158d173554f01384b26cdab15f 100644
--- a/modules/gfx/src/gfx_object.hh
+++ b/modules/gfx/src/gfx_object.hh
@@ -40,6 +40,7 @@
#include "gfx_prim.hh"
#include "vertex_array.hh"
#include "input.hh"
+#include "exporter_fw.hh"
namespace ost { namespace gfx {
@@ -56,7 +57,8 @@ public:
virtual void DeepSwap(GfxObj& go);
virtual void RenderGL(RenderPass pass);
virtual void RenderPov(PovState& pov);
- virtual void Apply(GfxNodeVisitor& v,GfxNodeVisitor::Stack st);
+ virtual void Export(Exporter* ex);
+ virtual void Apply(GfxNodeVisitor& v, GfxNodeVisitor::Stack st);
virtual int GetType() const;
//
@@ -118,6 +120,15 @@ public:
*/
virtual void CustomRenderGL(RenderPass pass);
+ // implemented in derived classes to deal with initialization etc
+ // called just before CustomRenderGL is called
+ // the boolean flag indicated that a re-build was requested
+ virtual void CustomPreRenderGL(bool rebuild);
+
+ // implemented in derived classes for first GL initialization
+ // which should be done here, not in the ctor
+ virtual void InitGL();
+
// implemented in derived classes for the actual POVray export
virtual void CustomRenderPov(PovState& pov);
@@ -186,7 +197,6 @@ public:
protected:
void PreRenderGL(bool flag);
- virtual void CustomPreRenderGL(bool flag);
private:
GfxObj(const GfxObj& o);
diff --git a/modules/gfx/src/gost_exporter.cc b/modules/gfx/src/gost_exporter.cc
new file mode 100644
index 0000000000000000000000000000000000000000..79a6e9b28390f1ce2d1890e88d824de48856e358
--- /dev/null
+++ b/modules/gfx/src/gost_exporter.cc
@@ -0,0 +1,277 @@
+//------------------------------------------------------------------------------
+// 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
+//------------------------------------------------------------------------------
+
+/*
+ Author: Ansgar Philippsen
+*/
+
+#include <sstream>
+
+#include "gost_exporter.hh"
+#include "scene.hh"
+
+namespace ost { namespace gfx {
+
+ namespace {
+ enum TYPE {
+ GOST_UNKNOWN=0,
+ GOST_SCENE=1,
+ GOST_START_NODE=2,
+ GOST_END_NODE=3,
+ GOST_DATA=4,
+ GOST_FRAME=5
+ };
+
+ enum NODE_TYPE {
+ GOST_ROOT=1,
+ GOST_GROUP=2,
+ GOST_OBJ=3
+ };
+
+ enum DATA_TYPE {
+ GOST_VDATA=1,
+ GOST_NDATA=2,
+ GOST_CDATA=3,
+ GOST_TDATA=4,
+ GOST_PINDEX=5,
+ GOST_LINDEX=6,
+ GOST_TINDEX=7,
+ GOST_QINDEX=8
+ };
+ }
+
+GostExporter::GostExporter(const std::string& fname):
+ file_(0)
+{
+ file_=fopen(fname.c_str(),"w");
+ if(!file_) {
+ std::ostringstream m;
+ m << "Could not open '" << fname << "' for writing";
+ throw Error(m.str());
+ }
+ char headr[]={'G','O','S','T','1','0'};
+ fwrite(headr,sizeof(char),6,file_);
+}
+
+GostExporter::~GostExporter()
+{
+ fclose(file_);
+ file_=0;
+}
+
+void GostExporter::SceneStart(const Scene* scene)
+{
+ int type=GOST_SCENE;
+ int subtype=0;
+ size_t size=0;
+
+ fwrite(&type,sizeof(int),1,file_);
+ fwrite(&subtype,sizeof(int),1,file_);
+ fwrite(&size,sizeof(size_t),1,file_);
+}
+
+void GostExporter::SceneEnd(const Scene* scene)
+{}
+
+void GostExporter::NodeStart(const std::string& name, NodeType t)
+{
+ int type=GOST_START_NODE;
+ int subtype=0;
+ if(t==Exporter::ROOT) subtype=GOST_ROOT;
+ else if(t==Exporter::GROUP) subtype=GOST_GROUP;
+ else if(t==Exporter::OBJ) subtype=GOST_OBJ;
+ size_t size=name.size();
+
+ fwrite(&type,sizeof(int),1,file_);
+ fwrite(&subtype,sizeof(int),1,file_);
+ fwrite(&size,sizeof(size_t),1,file_);
+ fwrite(name.c_str(),sizeof(char), size,file_);
+}
+
+void GostExporter::NodeEnd(const std::string& name)
+{
+ int type=GOST_END_NODE;
+ int subtype=0;
+ size_t size=0;
+
+ fwrite(&type,sizeof(int),1,file_);
+ fwrite(&subtype,sizeof(int),1,file_);
+ fwrite(&size,sizeof(size_t),1,file_);
+}
+
+void GostExporter::WriteVertexData(const float* vdata, const float* ndata,
+ const float* cdata, const float* tdata,
+ size_t stride2, size_t count)
+{
+ std::vector<float> buffer(count*4);
+ int type=GOST_DATA;
+ int subtype=0;
+ size_t size=0;
+ size_t stride=stride2/sizeof(float);
+
+ if(vdata) {
+ // positions
+ subtype=GOST_VDATA;
+ size=sizeof(float)*3*count+sizeof(size_t);
+ float* dest=&buffer[0];
+ const float* src=vdata;
+ for(size_t i=0;i<count;++i) {
+ dest[0]=src[0];
+ dest[1]=src[1];
+ dest[2]=src[2];
+ src+=stride;
+ dest+=3;
+ }
+ fwrite(&type,sizeof(int),1,file_);
+ fwrite(&subtype,sizeof(int),1,file_);
+ fwrite(&size,sizeof(size_t),1,file_);
+ //
+ fwrite(&count,sizeof(size_t),1,file_);
+ fwrite(&buffer[0],sizeof(float),3*count,file_);
+ }
+
+ if(ndata) {
+ // normals
+ subtype=GOST_NDATA;
+ size=sizeof(float)*count*3+sizeof(size_t);
+ float* dest=&buffer[0];
+ const float* src=ndata;
+ for(size_t i=0;i<count;++i) {
+ dest[0]=src[0];
+ dest[1]=src[1];
+ dest[2]=src[2];
+ src+=stride;
+ dest+=3;
+ }
+ fwrite(&type,sizeof(int),1,file_);
+ fwrite(&subtype,sizeof(int),1,file_);
+ fwrite(&size,sizeof(size_t),1,file_);
+ //
+ fwrite(&count,sizeof(size_t),1,file_);
+ fwrite(&buffer[0],sizeof(float),3*count,file_);
+ }
+
+ if(cdata) {
+ // colors
+ subtype=GOST_CDATA;
+ size=sizeof(float)*count*4+sizeof(size_t);
+ float* dest=&buffer[0];
+ const float* src=cdata;
+ for(size_t i=0;i<count;++i) {
+ dest[0]=src[0];
+ dest[1]=src[1];
+ dest[2]=src[2];
+ dest[3]=src[3];
+ src+=stride;
+ dest+=4;
+ }
+ fwrite(&type,sizeof(int),1,file_);
+ fwrite(&subtype,sizeof(int),1,file_);
+ fwrite(&size,sizeof(size_t),1,file_);
+ //
+ fwrite(&count,sizeof(size_t),1,file_);
+ fwrite(&buffer[0],sizeof(float),4*count,file_);
+ }
+
+ if(tdata) {
+ // texture coordinates
+ subtype=GOST_TDATA;
+ size=sizeof(float)*count*2+sizeof(size_t);
+ float* dest=&buffer[0];
+ const float* src=tdata;
+ for(size_t i=0;i<count;++i) {
+ dest[0]=src[0];
+ dest[1]=src[1];
+ src+=stride;
+ dest+=2;
+ }
+ fwrite(&type,sizeof(int),1,file_);
+ fwrite(&subtype,sizeof(int),1,file_);
+ fwrite(&size,sizeof(size_t),1,file_);
+ //
+ fwrite(&count,sizeof(size_t),1,file_);
+ fwrite(&buffer[0],sizeof(float),2*count,file_);
+ }
+}
+
+void GostExporter::WritePointData(const unsigned int* i, size_t count)
+{
+ int type=GOST_DATA;
+ int subtype=GOST_PINDEX;
+ size_t size=sizeof(unsigned int)*count+sizeof(size_t);
+ fwrite(&type,sizeof(int),1,file_);
+ fwrite(&subtype,sizeof(int),1,file_);
+ fwrite(&size,sizeof(size_t),1,file_);
+ //
+ fwrite(&count,sizeof(size_t),1,file_);
+ fwrite(i,sizeof(unsigned int),count,file_);
+}
+
+void GostExporter::WriteLineData(const unsigned int* ij, size_t count)
+{
+ int type=GOST_DATA;
+ int subtype=GOST_LINDEX;
+ size_t size=sizeof(unsigned int)*2*count+sizeof(size_t);
+ fwrite(&type,sizeof(int),1,file_);
+ fwrite(&subtype,sizeof(int),1,file_);
+ fwrite(&size,sizeof(size_t),1,file_);
+ //
+ fwrite(&count,sizeof(size_t),1,file_);
+ fwrite(ij,sizeof(unsigned int),2*count,file_);
+}
+
+void GostExporter::WriteTriData(const unsigned int* ijk, size_t count)
+{
+ int type=GOST_DATA;
+ int subtype=GOST_TINDEX;
+ size_t size=sizeof(unsigned int)*3*count+sizeof(size_t);
+ fwrite(&type,sizeof(int),1,file_);
+ fwrite(&subtype,sizeof(int),1,file_);
+ fwrite(&size,sizeof(size_t),1,file_);
+ //
+ fwrite(&count,sizeof(size_t),1,file_);
+ fwrite(ijk,sizeof(unsigned int),3*count,file_);
+}
+
+void GostExporter::WriteQuadData(const unsigned int* ijkl, size_t count)
+{
+ int type=GOST_DATA;
+ int subtype=GOST_QINDEX;
+ size_t size=sizeof(unsigned int)*4*count+sizeof(size_t);
+ fwrite(&type,sizeof(int),1,file_);
+ fwrite(&subtype,sizeof(int),1,file_);
+ fwrite(&size,sizeof(size_t),1,file_);
+ //
+ fwrite(&count,sizeof(size_t),1,file_);
+ fwrite(ijkl,sizeof(unsigned int),4*count,file_);
+}
+
+void GostExporter::SetFrame(size_t frame)
+{
+ int type=GOST_FRAME;
+ int subtype=0;
+ size_t size=sizeof(size_t);
+ fwrite(&type,sizeof(int),1,file_);
+ fwrite(&subtype,sizeof(int),1,file_);
+ fwrite(&size,sizeof(size_t),1,file_);
+ //
+ fwrite(&frame,sizeof(size_t),1,file_);
+}
+
+}} // ns
diff --git a/modules/gfx/src/gost_exporter.hh b/modules/gfx/src/gost_exporter.hh
new file mode 100644
index 0000000000000000000000000000000000000000..03f47680eeabba9fe36236ff057b5e13f4385c9c
--- /dev/null
+++ b/modules/gfx/src/gost_exporter.hh
@@ -0,0 +1,54 @@
+//------------------------------------------------------------------------------
+// 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_GFX_GOST_EXPORTER_HH
+#define OST_GFX_GOST_EXPORTER_HH
+
+#include <cstdio>
+
+#include "exporter.hh"
+
+namespace ost { namespace gfx {
+
+class DLLEXPORT_OST_GFX GostExporter: public Exporter
+{
+public:
+ GostExporter(const std::string& fname);
+ virtual ~GostExporter();
+
+ // exporter interface
+ virtual void SceneStart(const Scene* scene);
+ virtual void SceneEnd(const Scene* scene);
+ virtual void NodeStart(const std::string& name, NodeType t);
+ virtual void NodeEnd(const std::string& name);
+ virtual void WriteVertexData(const float* v, const float* n, const float* c, const float* t,
+ size_t stride, size_t count);
+ virtual void WritePointData(const unsigned int* i, size_t count);
+ virtual void WriteLineData(const unsigned int* ij, size_t count);
+ virtual void WriteTriData(const unsigned int* ijk, size_t count);
+ virtual void WriteQuadData(const unsigned int* ijkl, size_t count);
+
+ // gost interface
+ void SetFrame(size_t f);
+private:
+ FILE* file_;
+};
+
+}} // ns
+
+#endif
diff --git a/modules/gfx/src/impl/backbone_trace.cc b/modules/gfx/src/impl/backbone_trace.cc
index 01bbfb26514dd4118f84c982b0bf93a01a6abf82..ad9e8c961b0cedea3073cdd8183fc636662b5397 100644
--- a/modules/gfx/src/impl/backbone_trace.cc
+++ b/modules/gfx/src/impl/backbone_trace.cc
@@ -84,11 +84,15 @@ public:
// determine atom to add to list
mol::AtomHandle ca = res.GetCentralAtom();
if (ca) {
+ float rad=1.0;
+ if(ca.HasProp("trace_rad")) {
+ rad=ca.GetFloatProp("trace_rad");
+ }
NodeEntry entry={ca, GfxObj::Ele2Color(ca.GetElement()),
GfxObj::Ele2Color(ca.GetElement()),
geom::Vec3(), // this will be set by the gfx trace obj
res.GetCentralNormal(),
- 1.0,
+ rad,
geom::Vec3(),geom::Vec3(),geom::Vec3(), // for later use in NA rendering
false,id_counter_++};
list_.push_back(entry);
@@ -164,7 +168,13 @@ void BackboneTrace::OnUpdatedPositions()
for(NodeEntryListList::iterator nitnit=node_list_list_.begin();nitnit!=node_list_list_.end();++nitnit) {
NodeEntryList& nlist=*nitnit;
for(NodeEntryList::iterator nit=nlist.begin();nit!=nlist.end();++nit) {
- nit->normal=nit->atom.GetResidue().GetCentralNormal();
+ mol::AtomHandle ca=nit->atom;
+ nit->normal=ca.GetResidue().GetCentralNormal();
+ if(ca.HasProp("trace_rad")) {
+ nit->rad=ca.GetFloatProp("trace_rad");
+ } else {
+ nit->rad=1.0;
+ }
}
PrepList(nlist);
}
diff --git a/modules/gfx/src/impl/entity_renderer.cc b/modules/gfx/src/impl/entity_renderer.cc
index 3464d1292297e3161e3aaed4a1130974b7763fb1..fb22e24a375988bdcb36bf8b9b1b9b0e34695fef 100644
--- a/modules/gfx/src/impl/entity_renderer.cc
+++ b/modules/gfx/src/impl/entity_renderer.cc
@@ -156,6 +156,11 @@ void EntityRenderer::RenderPov(PovState& pov, const std::string& name)
va_.RenderPov(pov,name);
}
+void EntityRenderer::Export(Exporter* ex)
+{
+ va_.Export(ex);
+}
+
bool EntityRenderer::HasSelection() const
{
return (sel_.IsValid() && sel_.GetAtomCount()>0);
diff --git a/modules/gfx/src/impl/entity_renderer.hh b/modules/gfx/src/impl/entity_renderer.hh
index ceed73fa4d8d2f41a739c949a6e978ae29b18fbc..14c0332c3b5a15d0d0f101b19aad3e9363d03047 100644
--- a/modules/gfx/src/impl/entity_renderer.hh
+++ b/modules/gfx/src/impl/entity_renderer.hh
@@ -39,8 +39,9 @@
#include <ost/gfx/module_config.hh>
#include <ost/gfx/render_pass.hh>
#include <ost/gfx/vertex_array.hh>
+#include <ost/gfx/exporter_fw.hh>
+
#include <ost/gfx/render_options/render_options.hh>
-#include <ost/gfx/impl/mapped_property.hh>
#include <ost/gfx/color_ops/color_op.hh>
#include <ost/gfx/color_ops/by_element_color_op.hh>
@@ -51,7 +52,9 @@
#if OST_IMG_ENABLED
#include <ost/gfx/color_ops/map_handle_color_op.hh>
#endif //OST_IMG_ENABLED
-#include <ost/gfx/impl/entity_renderer_fw.hh>
+
+#include "mapped_property.hh"
+#include "entity_renderer_fw.hh"
namespace ost { namespace gfx { namespace impl {
@@ -123,6 +126,9 @@ public:
///\brief povray rendering call
virtual void RenderPov(PovState& pov, const std::string& name);
+ ///\brief scene exporter interface
+ virtual void Export(Exporter* ex);
+
virtual bool CanSetOptions(RenderOptionsPtr& render_options)=0;
virtual void SetOptions(RenderOptionsPtr& render_options)=0;
diff --git a/modules/gfx/src/prim_list.cc b/modules/gfx/src/prim_list.cc
index 6113aecfb45e02867496f1c6129a92d9da8db2a1..a9debc0edd67dfa55d9a4057fb9ad0b77bdf4d2f 100644
--- a/modules/gfx/src/prim_list.cc
+++ b/modules/gfx/src/prim_list.cc
@@ -38,7 +38,8 @@ PrimList::PrimList(const String& name):
texts_(),
sphere_detail_(4),
arc_detail_(4),
- simple_va_()
+ simple_va_(),
+ vas_()
{}
void PrimList::Clear()
@@ -48,13 +49,14 @@ void PrimList::Clear()
spheres_.clear();
cyls_.clear();
texts_.clear();
+ vas_.clear();
Scene::Instance().RequestRedraw();
this->FlagRebuild();
}
geom::AlignedCuboid PrimList::GetBoundingBox() const
{
- if(points_.empty() && lines_.empty() && spheres_.empty() && cyls_.empty()) {
+ if(points_.empty() && lines_.empty() && spheres_.empty() && cyls_.empty() && texts_.empty() && vas_.empty()) {
return geom::AlignedCuboid(geom::Vec3(-1,-1,-1),geom::Vec3(1,1,1));
}
geom::Vec3 minc(std::numeric_limits<float>::max(),
@@ -101,6 +103,11 @@ void PrimList::ProcessLimits(geom::Vec3& minc, geom::Vec3& maxc,
minc=geom::Min(minc,tpos);
maxc=geom::Max(maxc,tpos);
}
+ for(std::vector<IndexedVertexArray>::const_iterator it=vas_.begin();it!=vas_.end();++it) {
+ geom::AlignedCuboid bb=it->GetBoundingBox();
+ minc=geom::Min(minc,bb.GetMin());
+ maxc=geom::Max(maxc,bb.GetMax());
+ }
minc-=1.0;
maxc+=1.0;
}
@@ -152,12 +159,15 @@ void PrimList::CustomRenderGL(RenderPass pass)
va_.RenderGL();
simple_va_.RenderGL();
render_text();
+ for(std::vector<IndexedVertexArray>::iterator it=vas_.begin();it!=vas_.end();++it) {
+ it->RenderGL();
+ }
}
}
void PrimList::CustomRenderPov(PovState& pov)
{
- if(points_.empty() && lines_.empty()) return;
+ if(points_.empty() && lines_.empty() && spheres_.empty() && cyls_.empty()) return;
pov.write_merge_or_union(GetName());
for(SpherePrimList::const_iterator it=points_.begin();it!=points_.end();++it) {
@@ -262,6 +272,42 @@ void PrimList::SetColor(const Color& c)
FlagRebuild();
}
+void PrimList::AddMesh(float* v, float* n, float* c, size_t nv, unsigned int* i, size_t ni)
+{
+ static float dummy_normal[]={0.0,0.0,1.0};
+ static float dummy_color[]={1.0,1.0,1.0,1.0};
+ vas_.push_back(IndexedVertexArray());
+ IndexedVertexArray& va=vas_.back();
+ va.SetLighting(true);
+ va.SetTwoSided(true);
+ va.SetColorMaterial(true);
+ va.SetCullFace(false);
+ float* vv=v;
+ float* nn=n;
+ if(!n) {
+ nn=dummy_normal;
+ va.SetLighting(false);
+ }
+ float* cc=c;
+ if(!c) {
+ cc=dummy_color;
+ }
+ for(size_t k=0;k<nv;++k) {
+ va.Add(geom::Vec3(vv[0],vv[1],vv[2]),
+ geom::Vec3(nn[0],nn[1],nn[2]),
+ Color(cc[0],cc[1],cc[2],cc[3]));
+ vv+=3;
+ if(n) nn+=3;
+ if(c) cc+=4;
+ }
+ unsigned int* ii=i;
+ for(size_t k=0;k<ni;++k) {
+ va.AddTri(ii[0],ii[1],ii[2]);
+ ii+=3;
+ }
+ Scene::Instance().RequestRedraw();
+ FlagRebuild();
+}
////////////////////////////////
// private methods
diff --git a/modules/gfx/src/prim_list.hh b/modules/gfx/src/prim_list.hh
index 4e8a4c297ea044eda07d2cc199a4988b3d7e4e23..395e53e2ad22ce359b37281caead22cad1a423e9 100644
--- a/modules/gfx/src/prim_list.hh
+++ b/modules/gfx/src/prim_list.hh
@@ -139,6 +139,24 @@ class DLLEXPORT_OST_GFX PrimList: public GfxObj
// TODO: add point and line pixel width
+ /*!
+ \brief add triangle mesh
+
+ v : pointer to nv*3 floats for the positions (mandatory)
+ n : pointer to nv*3 floats for the normals (may be NULL)
+ c : pointer to nv*4 floats for the colors (may be NULL)
+ nv: number of vertices, normals, and colors
+ i : pointer to ni*3 vertex indices
+ ni: number of index triplets
+
+ Python interface, using numpy arrays:
+
+ AddMesh(vertex_array, normal_array, color_array, index_array)
+
+ where normal_array and color_array may be None
+ */
+ void AddMesh(float* v, float* n, float* c, size_t nv, unsigned int* i, size_t ni);
+
protected:
virtual void CustomPreRenderGL(bool flag);
@@ -152,6 +170,8 @@ class DLLEXPORT_OST_GFX PrimList: public GfxObj
unsigned int arc_detail_;
IndexedVertexArray simple_va_;
+
+ std::vector<IndexedVertexArray> vas_;
void prep_simple_va();
void prep_va();
diff --git a/modules/gfx/src/scene.cc b/modules/gfx/src/scene.cc
index 7b7ddce245d1d46502519157a1c65608e1fd4c35..1bd5e460742f0a774bd7e7d46eba5974b4804dd7 100644
--- a/modules/gfx/src/scene.cc
+++ b/modules/gfx/src/scene.cc
@@ -42,6 +42,7 @@
#include "gl_helper.hh"
#include <ost/config.hh>
+
#include "scene.hh"
#include "input.hh"
#include "gfx_node.hh"
@@ -49,6 +50,7 @@
#include "gfx_test_object.hh"
#include "bitmap_io.hh"
#include "entity.hh"
+#include "exporter.hh"
#include "povray.hh"
#include "offscreen_buffer.hh"
@@ -107,7 +109,8 @@ Scene::Scene():
light_amb_(0.1,0.1,0.1),
light_diff_(0.9,0.9,0.9),
light_spec_(0.5,0.5,0.5),
- axis_flag_(false),
+ cor_flag_(false),
+ fix_cor_flag_(true),
fog_flag_(true),
fog_color_(0.0,0.0,0.0,0.0),
auto_autoslab_(true),
@@ -194,6 +197,15 @@ void Scene::SetShadowQuality(int q)
#endif
}
+int Scene::GetShadowQuality() const
+{
+#if OST_SHADER_SUPPORT_ENABLED
+ return impl::SceneFX::Instance().shadow_quality;
+#else
+ return 0;
+#endif
+}
+
void Scene::SetShadowWeight(float w)
{
#if OST_SHADER_SUPPORT_ENABLED
@@ -202,6 +214,15 @@ void Scene::SetShadowWeight(float w)
#endif
}
+float Scene::GetShadowWeight() const
+{
+#if OST_SHADER_SUPPORT_ENABLED
+ return impl::SceneFX::Instance().shadow_weight;
+#else
+ return 0.0;
+#endif
+}
+
void Scene::SetDepthDarkening(bool f)
{
#if OST_SHADER_SUPPORT_ENABLED
@@ -247,6 +268,15 @@ void Scene::SetAmbientOcclusionWeight(float f)
#endif
}
+float Scene::GetAmbientOcclusionWeight() const
+{
+#if OST_SHADER_SUPPORT_ENABLED
+ return impl::SceneFX::Instance().amb_occl_factor;
+#else
+ return 1.0;
+#endif
+}
+
void Scene::SetAmbientOcclusionMode(uint m)
{
#if OST_SHADER_SUPPORT_ENABLED
@@ -256,6 +286,15 @@ void Scene::SetAmbientOcclusionMode(uint m)
#endif
}
+uint Scene::GetAmbientOcclusionMode() const
+{
+#if OST_SHADER_SUPPORT_ENABLED
+ return impl::SceneFX::Instance().amb_occl_mode;
+#else
+ return 0;
+#endif
+}
+
void Scene::SetAmbientOcclusionQuality(uint m)
{
#if OST_SHADER_SUPPORT_ENABLED
@@ -265,6 +304,15 @@ void Scene::SetAmbientOcclusionQuality(uint m)
#endif
}
+uint Scene::GetAmbientOcclusionQuality() const
+{
+#if OST_SHADER_SUPPORT_ENABLED
+ return impl::SceneFX::Instance().amb_occl_quality;
+#else
+ return 0;
+#endif
+}
+
void Scene::SetShadingMode(const std::string& smode)
{
#if OST_SHADER_SUPPORT_ENABLED
@@ -309,12 +357,18 @@ void Scene::SetBeaconOff()
namespace {
-void set_light_dir(Vec3 ld)
-{
- GLfloat l_pos[]={0.0, 0.0, 0.0, 0.0};
- l_pos[0]=-ld[0]; l_pos[1]=-ld[1]; l_pos[2]=-ld[2];
- glLightfv(GL_LIGHT0, GL_POSITION, l_pos);
-}
+ void set_light_dir(Vec3 ld)
+ {
+ GLfloat l_pos[]={0.0, 0.0, 0.0, 0.0};
+ l_pos[0]=-ld[0]; l_pos[1]=-ld[1]; l_pos[2]=-ld[2];
+ glLightfv(GL_LIGHT0, GL_POSITION, l_pos);
+ }
+
+ struct GfxObjInitGL: public GfxNodeVisitor {
+ virtual void VisitObject(GfxObj* o, const Stack& st) {
+ o->InitGL();
+ }
+ };
}
@@ -458,6 +512,10 @@ void Scene::InitGL(bool full)
glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_WRAP_T, GL_CLAMP);
glTexEnvf(GL_TEXTURE_ENV,GL_TEXTURE_ENV_MODE, GL_REPLACE);
+ LOG_DEBUG("Scene: calling gl init for all objects");
+ GfxObjInitGL initgl;
+ this->Apply(initgl);
+
LOG_DEBUG("Scene: gl init done");
gl_init_=true;
@@ -776,9 +834,13 @@ void Scene::Add(const GfxNodeP& n, bool redraw)
LOG_DEBUG("Scene: graphical object added @" << n.get() << std::endl);
- if(root_node_->GetChildCount()==0) {
- GfxObjP go = boost::dynamic_pointer_cast<GfxObj>(n);
- if(go) {
+ GfxObjP go = boost::dynamic_pointer_cast<GfxObj>(n);
+
+ if(go) {
+ if(gl_init_) {
+ go->InitGL();
+ }
+ if(root_node_->GetChildCount()==0) {
SetCenter(go->GetCenter());
}
do_autoslab_=true;
@@ -957,10 +1019,18 @@ void Scene::OnInput(const InputEvent& e)
gluUnProject(wx+2.0,wy+2.0,wz,mm,pm,vp,&ox,&oy,&oz);
Vec2 fxy = Vec2(ox,oy);
- if(e.GetCommand()==INPUT_COMMAND_TRANSX) {
- transform_.ApplyXAxisTranslation(e.GetDelta()*fxy[0]);
+ if(fix_cor_flag_) {
+ if(e.GetCommand()==INPUT_COMMAND_TRANSX) {
+ transform_.SetCenter(transform_.GetCenter()+Transpose(transform_.GetRot())*Vec3(-fxy[0]*e.GetDelta(),0.0,0.0));
+ } else {
+ transform_.SetCenter(transform_.GetCenter()+Transpose(transform_.GetRot())*Vec3(0.0,-fxy[1]*e.GetDelta(),0.0));
+ }
} else {
- transform_.ApplyYAxisTranslation(e.GetDelta()*fxy[1]);
+ if(e.GetCommand()==INPUT_COMMAND_TRANSX) {
+ transform_.ApplyXAxisTranslation(e.GetDelta()*fxy[0]);
+ } else {
+ transform_.ApplyYAxisTranslation(e.GetDelta()*fxy[1]);
+ }
}
} else if(e.GetCommand()==INPUT_COMMAND_TRANSZ) {
float currz=transform_.GetTrans()[2];
@@ -1576,6 +1646,13 @@ void Scene::ExportPov(const std::string& fname, const std::string& wdir)
pov.write_postamble();
}
+void Scene::Export(Exporter* ex) const
+{
+ ex->SceneStart(this);
+ root_node_->Export(ex);
+ ex->SceneEnd(this);
+}
+
void Scene::ResetProjection()
{
LOG_TRACE("Scene: projection matrix " << fov_ << " " << znear_ << " " << zfar_);
@@ -1743,6 +1820,12 @@ void Scene::SetTestMode(bool f)
}
}
+void Scene::SetShowCenter(bool f)
+{
+ cor_flag_=f;
+ RequestRedraw();
+}
+
void Scene::prep_glyphs()
{
glGenTextures(1,&glyph_tex_id_);
@@ -1803,6 +1886,32 @@ void Scene::render_scene()
impl::SceneFX::Instance().Preprocess();
#endif
+ if(cor_flag_) {
+ geom::Vec3 cen=transform_.GetCenter();
+ glPushAttrib(GL_ENABLE_BIT | GL_LIGHTING_BIT | GL_LINE_BIT | GL_CURRENT_BIT);
+#if OST_SHADER_SUPPORT_ENABLED
+ Shader::Instance().PushProgram();
+ Shader::Instance().Activate("");
+#endif
+ glLineWidth(1.5);
+ glDisable(GL_LIGHTING);
+ glDisable(GL_COLOR_MATERIAL);
+
+ glBegin(GL_LINES);
+ glColor3f(0.5,0.5,0.5);
+ glVertex3f(cen[0]-1.0,cen[1],cen[2]);
+ glVertex3f(cen[0]+1.0,cen[1],cen[2]);
+ glVertex3f(cen[0],cen[1]-1.0,cen[2]);
+ glVertex3f(cen[0],cen[1]+1.0,cen[2]);
+ glVertex3f(cen[0],cen[1],cen[2]-1.0);
+ glVertex3f(cen[0],cen[1],cen[2]+1.0);
+ glEnd();
+ glPopAttrib();
+#if OST_SHADER_SUPPORT_ENABLED
+ Shader::Instance().PopProgram();
+#endif
+ }
+
root_node_->RenderGL(STANDARD_RENDER_PASS);
glEnable(GL_BLEND);
glBlendFunc(GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA);
@@ -1865,7 +1974,7 @@ void Scene::stereo_projection(int view)
glFrustum(left,right,bot,top,zn,zf);
Real dist = -transform_.GetTrans()[2]+stereo_distance_;
glTranslated(0.0,0.0,-dist);
- glRotated(180.0/M_PI*atan(0.1*ff/iod),0.0,1.0,0.0);
+ glRotated(-180.0/M_PI*atan(0.1*ff/iod),0.0,1.0,0.0);
glTranslated(0.0,0.0,dist);
} else {
// correct off-axis frustims
@@ -1874,10 +1983,12 @@ void Scene::stereo_projection(int view)
// correction of near clipping plane to avoid extreme drifting
// of left and right view
+#if 0
if(iod*zn/fo<2.0) {
zn=2.0*fo/iod;
zf=std::max(zn+Real(0.2),zf);
}
+#endif
Real sd = -ff*0.5*iod*zn/fo;
left+=sd;
@@ -1895,6 +2006,9 @@ void Scene::stereo_projection(int view)
void Scene::render_stereo()
{
+ glPushAttrib(GL_ALL_ATTRIB_BITS);
+ glPushClientAttrib(GL_ALL_ATTRIB_BITS);
+
int old_stereo_eye=stereo_eye_;
stereo_eye_=-1;
stereo_projection(-1);
@@ -1912,6 +2026,7 @@ void Scene::render_stereo()
stereo_eye_=1;
stereo_projection(1);
render_scene();
+
glEnable(GL_TEXTURE_2D);
#if OST_SHADER_SUPPORT_ENABLED
if(OST_GL_VERSION_2_0) {
@@ -1928,7 +2043,6 @@ void Scene::render_stereo()
Shader::Instance().Activate("");
#endif
- glPushAttrib(GL_ALL_ATTRIB_BITS);
glDisable(GL_DEPTH_TEST);
glDisable(GL_LIGHTING);
glDisable(GL_COLOR_MATERIAL);
@@ -1949,7 +2063,7 @@ void Scene::render_stereo()
glLoadIdentity();
if(stereo_mode_==2) {
- // draw interlace lines in stencil buffer
+ // draw interlaced lines in stencil buffer
glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT);
glLineWidth(1.0);
glEnable(GL_STENCIL_TEST);
@@ -2014,10 +2128,14 @@ void Scene::render_stereo()
glEnd();
// restore settings
+ glCopyTexImage2D(GL_TEXTURE_2D, 0, GL_RGBA, 0, 0, 0, 0, 0);
+ glBindTexture(GL_TEXTURE_2D, 0);
+ glDisable(GL_TEXTURE_2D);
glMatrixMode(GL_PROJECTION);
glPopMatrix();
glMatrixMode(GL_MODELVIEW);
glPopMatrix();
+ glPopClientAttrib();
glPopAttrib();
#if OST_SHADER_SUPPORT_ENABLED
Shader::Instance().PopProgram();
diff --git a/modules/gfx/src/scene.hh b/modules/gfx/src/scene.hh
index 932f7e5a7a0cf8f11a14b2c60f41f759184d8149..a5868d0606581bff66c84b32b5d53f071bc44751 100644
--- a/modules/gfx/src/scene.hh
+++ b/modules/gfx/src/scene.hh
@@ -42,6 +42,7 @@
#include "scene_observer.hh"
#include "gfx_prim.hh"
#include "povray_fw.hh"
+#include "exporter_fw.hh"
namespace ost { namespace gfx {
@@ -95,27 +96,25 @@ class DLLEXPORT_OST_GFX Scene {
/// \brief turn fog on or off
void SetFog(bool f);
-
/// \brief check fog status
bool GetFog() const;
-
/// \brief set the fog color
void SetFogColor(const Color& c);
-
/// \brief get the fog color
Color GetFogColor() const;
/// \brief turn shadow mapping on and off
void SetShadow(bool f);
-
/// \brief get shadow mapping status
bool GetShadow() const;
-
/// \brief shadow quality from 0 (low) to 3 (high), default=1
void SetShadowQuality(int q);
-
+ /// \brief get shadow quality
+ int GetShadowQuality() const;
/// \brief multiplier for shadow strength
void SetShadowWeight(float w);
+ /// \brief get shadow strength
+ float GetShadowWeight() const;
/// experimental feature
void SetDepthDarkening(bool f);
@@ -129,9 +128,15 @@ class DLLEXPORT_OST_GFX Scene {
/// experimental feature
void SetAmbientOcclusionWeight(float f);
/// experimental feature
+ float GetAmbientOcclusionWeight() const;
+ /// experimental feature
void SetAmbientOcclusionMode(uint m);
/// experimental feature
+ uint GetAmbientOcclusionMode() const;
+ /// experimental feature
void SetAmbientOcclusionQuality(uint q);
+ /// experimental feature
+ uint GetAmbientOcclusionQuality() const;
/// \brief select shading mode
/// one of fallback, basic, default, hf, toon1, toon2
@@ -256,6 +261,10 @@ class DLLEXPORT_OST_GFX Scene {
/// \brief export scene into povray files named fname.pov and fname.inc
void ExportPov(const std::string& fname, const std::string& wdir=".");
+
+ /// \rbrief export scene via exporter
+ void Export(Exporter* ex) const;
+
//@}
/// \brief entry point for gui events (internal use)
void OnInput(const InputEvent& e);
@@ -409,6 +418,17 @@ class DLLEXPORT_OST_GFX Scene {
/// \brief stops offline rendering in interactive mode
void StopOffscreenMode();
+ /// \brief show center of rotation of true
+ void SetShowCenter(bool f);
+
+ bool GetShowCenter() const {return cor_flag_;}
+
+ /// \brief if true fix center of rotation upon input induced shift
+ void SetFixCenter(bool f) {fix_cor_flag_=f;}
+
+ /// \brief return flag
+ bool GetFixCenter() const {return fix_cor_flag_;}
+
/// experimental feature
void SetBlur(uint n);
/// experimental feature
@@ -472,7 +492,8 @@ private:
Color light_diff_;
Color light_spec_;
- bool axis_flag_;
+ bool cor_flag_;
+ bool fix_cor_flag_;
bool fog_flag_;
Color fog_color_;
bool auto_autoslab_;
diff --git a/modules/gfx/src/vertex_array.cc b/modules/gfx/src/vertex_array.cc
index c1c53d57fa29110368a7b1a5a2da28fb2c7c5612..b9c45e5a7ce54f274b2b1e0b029f100fd81772ec 100644
--- a/modules/gfx/src/vertex_array.cc
+++ b/modules/gfx/src/vertex_array.cc
@@ -30,6 +30,7 @@
#include "scene.hh"
#include "vertex_array_helper.hh"
#include "povray.hh"
+#include "exporter.hh"
#if OST_SHADER_SUPPORT_ENABLED
#include "shader.hh"
@@ -108,7 +109,7 @@ unsigned int IndexedVertexArray::GetFormat()
void IndexedVertexArray::Cleanup()
{
if(initialized_) {
- glDeleteTextures(1,&tex_id_);
+ //glDeleteTextures(1,&tex_id_);
glDeleteLists(outline_mat_dlist_,1);
#if OST_SHADER_SUPPORT_ENABLED
glDeleteBuffers(7,buffer_id_);
@@ -431,6 +432,12 @@ void IndexedVertexArray::RenderGL()
glPushAttrib(GL_ALL_ATTRIB_BITS);
glPushClientAttrib(GL_CLIENT_VERTEX_ARRAY_BIT);
+
+ if(use_tex_) {
+ glEnable(GL_TEXTURE_2D);
+ } else {
+ glDisable(GL_TEXTURE_2D);
+ }
if(outline_mode_>0) {
LOG_TRACE("outline rendering");
@@ -654,6 +661,14 @@ void IndexedVertexArray::RenderPov(PovState& pov, const std::string& name)
pov.inc() << "}\n";
}
+void IndexedVertexArray::Export(Exporter* ex) const
+{
+ ex->WriteVertexData(entry_list_[0].v,entry_list_[0].n, entry_list_[0].c, entry_list_[0].t, sizeof(Entry), entry_list_.size());
+ ex->WriteLineData(&line_index_list_[0],line_index_list_.size()/2);
+ ex->WriteTriData(&tri_index_list_[0],tri_index_list_.size()/3);
+ ex->WriteQuadData(&quad_index_list_[0],quad_index_list_.size()/4);
+}
+
void IndexedVertexArray::Clear()
{
dirty_=true;
@@ -685,7 +700,7 @@ void IndexedVertexArray::Reset()
outline_exp_factor_=0.1;
outline_exp_color_=Color(0,0,0);
draw_normals_=false;
- use_tex_=true;
+ use_tex_=false;
}
void IndexedVertexArray::FlagRefresh()
diff --git a/modules/gfx/src/vertex_array.hh b/modules/gfx/src/vertex_array.hh
index 3d24320e7900985df54c352135b35e173e488d5c..ee63c939aae475959cfa12963b730f7326392df6 100644
--- a/modules/gfx/src/vertex_array.hh
+++ b/modules/gfx/src/vertex_array.hh
@@ -39,6 +39,7 @@
#include "material.hh"
#include "gfx_prim.hh"
#include "povray_fw.hh"
+#include "exporter_fw.hh"
namespace ost { namespace gfx {
@@ -162,6 +163,8 @@ class DLLEXPORT_OST_GFX IndexedVertexArray {
// POVray export
void RenderPov(PovState& pov, const std::string& name);
+ void Export(Exporter* ex) const;
+
// only removes the drawing elements
void Clear();
// removes all elements and resets internal state to default
diff --git a/modules/gfx/tests/test_gfx.py b/modules/gfx/tests/test_gfx.py
index b6911eee12fc2a5401a11d1284dc14d1eb7e3f17..ffca3b507ebbc6dfc8fe3d50c1701af75d0f0574 100644
--- a/modules/gfx/tests/test_gfx.py
+++ b/modules/gfx/tests/test_gfx.py
@@ -1,3 +1,22 @@
+#------------------------------------------------------------------------------
+# 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
+#------------------------------------------------------------------------------
+
import unittest
if __name__== '__main__':
import sys
@@ -9,15 +28,44 @@ import ost.mol as mol
import ost.gfx as gfx
import ost.geom as geom
+if ost.WITH_NUMPY:
+ has_numpy=True
+ try:
+ import numpy
+ except ImportError, e:
+ has_numpy=False
+else:
+ has_numpy=False
+
def col_delta(c1,c2):
return geom.Distance(geom.Vec3(c1[0],c1[1],c1[2]),geom.Vec3(c2[0],c2[1],c2[2]))
+class MyGfxObj(gfx.GfxObj):
+ def __init__(self,name):
+ gfx.GfxObj.__init__(self,name)
+ self.rendered=False
+
+ def CustomRenderGL(self,render_pass):
+ self.rendered=True
+
class TestGfx(unittest.TestCase):
def runTest(self):
self.test_gradient()
self.test_color()
self.test_primlist()
self.test_entity_reset()
+ self.test_custom_gfx_obj()
+ self.test_gfxobj_conv()
+
+ def test_gfxobj_conv(self):
+ e=mol.CreateEntity()
+ gfx.Scene().Add(gfx.Entity("foo2",e))
+ gfx.Scene()["foo2"].SetColor(gfx.YELLOW)
+
+ def test_custom_gfx_obj(self):
+ myobj=MyGfxObj("foo")
+ gfx.Scene().Add(myobj)
+ #self.assertTrue(myobj.rendered)
def test_entity_reset(self):
eh=mol.CreateEntity()
@@ -32,7 +80,8 @@ class TestGfx(unittest.TestCase):
def test_gradient(self):
gs=[gfx.Gradient(),
- gfx.Gradient({0.0: [1,0,0], 1.0: gfx.Color(0,1,0)})]
+ gfx.Gradient({0.0: [1,0,0], 1.0: gfx.Color(0,1,0)}),
+ gfx.Gradient([[1,0,0], gfx.Color(0,1,0)])]
gs[0].SetColorAt(0.0,gfx.Color(1.0,0.0,0.0))
gs[0].SetColorAt(1.0,gfx.Color(0.0,1.0,0.0))
for g in gs:
@@ -71,7 +120,18 @@ class TestGfx(unittest.TestCase):
pl.AddCyl(geom.Vec3(0,0,0),geom.Vec3(1,2,3),radius1=0.5,radius2=0.1,color1=gfx.BLUE,color2=gfx.GREEN)
pl.AddText("foo",[0,2,3])
pl.AddText("bar",[-2,0,0],color=gfx.WHITE,point_size=8)
+ if has_numpy:
+ pl.AddMesh(numpy.zeros((5,3),dtype=numpy.float32),
+ numpy.zeros((5,3),dtype=numpy.float32),
+ numpy.zeros((5,4),dtype=numpy.float32),
+ numpy.zeros((2,3),dtype=numpy.uint32))
+ pl.AddMesh(numpy.zeros((7,3),dtype=numpy.float32),
+ None,
+ None,
+ numpy.zeros((4,3),dtype=numpy.uint32))
+
if __name__== '__main__':
- unittest.main()
+ from ost import testutils
+ testutils.RunTests()
diff --git a/modules/gfx/tests/test_gost_export.py b/modules/gfx/tests/test_gost_export.py
new file mode 100644
index 0000000000000000000000000000000000000000..efb56861b18f52fae0b92d25e62477b06901fdfe
--- /dev/null
+++ b/modules/gfx/tests/test_gost_export.py
@@ -0,0 +1,22 @@
+import desost_util as util
+
+e=io.LoadPDB("../../../examples/demos/data/sdh.pdb")
+
+s=util.CreateSurf(e.Select("chain=A"),density=4)
+
+scene.Add(gfx.Entity("trace",gfx.TUBE,e.Select("chain=A")))
+scene["trace"].tube_options.arc_detail=8
+scene["trace"].tube_options.spline_detail=8
+scene["trace"].tube_options.tube_radius=1.0
+grad=gfx.Gradient()
+grad.SetColorAt(0.0,gfx.RED)
+grad.SetColorAt(0.5,gfx.GREEN)
+grad.SetColorAt(1.0,gfx.BLUE)
+scene["trace"].ColorBy("rnum",grad)
+
+scene.Add(gfx.Surface("surf",s))
+scene["surf"].ColorBy("rnum",grad)
+
+if not gui_mode:
+ ge = gfx.GostExporter("test.gost")
+ scene.Export(ge)
diff --git a/modules/gfx/tests/test_gost_import.py b/modules/gfx/tests/test_gost_import.py
new file mode 100644
index 0000000000000000000000000000000000000000..deebd2d31d805c7c0cc190d5ad273262dc7728bf
--- /dev/null
+++ b/modules/gfx/tests/test_gost_import.py
@@ -0,0 +1,15 @@
+import struct
+
+with open("test.gost","rb") as gf:
+
+ header = gf.read(6)
+ if str(header[0:4]) != "GOST":
+ raise RuntimeError("file format mismatch")
+ raw = gf.read(16)
+
+ while raw:
+ (type, subtype,size) = struct.unpack("iiL",raw)
+ 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/export_data_viewer.cc b/modules/gui/pymod/export_data_viewer.cc
index 993f272a8bbf28417568c1118e1b847acb040665..6efdef65e1a980d4a77b4b79111a0e77bd38babf 100644
--- a/modules/gui/pymod/export_data_viewer.cc
+++ b/modules/gui/pymod/export_data_viewer.cc
@@ -67,12 +67,12 @@ void export_data_viewer()
.def("SetData",&DataViewer::SetData)
.def("SetName",&DataViewer::SetName)
.def("GetOverlayManager",&DataViewer::GetOverlayManager)
- .def("GetNormalizer",&DataViewer::GetNormalizer,
- return_value_policy<return_by_value>())
+ .def("GetNormalizer",&DataViewer::GetNormalizer,return_value_policy<return_by_value>())
.def("Renormalize",&DataViewer::Renormalize)
.def("AddOverlay",&DataViewer::AddOverlay,o_AddOverlay())
.def("ClearOverlays",&DataViewer::ClearOverlays)
.def("GetSelection",&DataViewer::GetSelection)
+ .def("SetSelection",&DataViewer::SetSelection)
.def("UpdateView",&DataViewer::UpdateView)
.def("Recenter",&DataViewer::Recenter)
.def("AddDockWidget",add_dock1)
@@ -80,6 +80,24 @@ void export_data_viewer()
.def("SetSlab", &DataViewer::SetSlab)
.def("GetSlab", &DataViewer::GetSlab)
.add_property("slab", &DataViewer::GetSlab, &DataViewer::SetSlab)
+ .def("SetZoomScale", &DataViewer::SetZoomScale)
+ .def("GetZoomScale", &DataViewer::GetZoomScale)
+ .add_property("zoomscale", &DataViewer::GetZoomScale, &DataViewer::SetZoomScale)
+ .def("SetViewerMin", &DataViewer::SetViewerMin)
+ .def("GetViewerMin", &DataViewer::GetViewerMin)
+ .add_property("viewer_min", &DataViewer::GetViewerMin, &DataViewer::SetViewerMin)
+ .def("SetViewerMax", &DataViewer::SetViewerMax)
+ .def("GetViewerMax", &DataViewer::GetViewerMax)
+ .add_property("viewer_max", &DataViewer::GetViewerMax, &DataViewer::SetViewerMax)
+ .def("SetGamma", &DataViewer::SetGamma)
+ .def("GetGamma", &DataViewer::GetGamma)
+ .add_property("gamma", &DataViewer::GetGamma, &DataViewer::SetGamma)
+ .def("SetInvert", &DataViewer::SetInvert)
+ .def("GetInvert", &DataViewer::GetInvert)
+ .add_property("invert", &DataViewer::GetInvert, &DataViewer::SetInvert)
+ .def("SetOffset", &DataViewer::SetOffset)
+ .def("GetOffset", &DataViewer::GetOffset)
+ .add_property("offset", &DataViewer::GetOffset, &DataViewer::SetOffset)
.def("AddDockWidget",add_dock3)
.def("AddDockWidget",add_dock4)
.def("RemoveDockWidget",&DataViewer::RemoveDockWidget)
diff --git a/modules/gui/pymod/export_tool.cc b/modules/gui/pymod/export_tool.cc
index fbcf9375b7ba02a8c23599cd3650a7571f39672a..c5165570e5cf113da1392e422488dbf9acb5feb7 100644
--- a/modules/gui/pymod/export_tool.cc
+++ b/modules/gui/pymod/export_tool.cc
@@ -32,7 +32,6 @@ using namespace boost::python;
using namespace ost::gui;
using namespace ost;
-namespace {
struct WrappedTool : public Tool
{
@@ -81,7 +80,6 @@ struct WrappedTool : public Tool
};
-namespace {
void tm_add_tool(ToolManager& tm, QPtr<WrappedTool> tool)
{
@@ -127,13 +125,10 @@ object get_delta_wrapper(MouseEvent& me)
return qpoint_to_bp_object(delta);
}
-}
-
ToolOption* (ToolOptions::*get_option_a)(const String&,
const String&) const=&ToolOptions::GetOption;
ToolOption* (ToolOptions::*get_option_b)(const String&) const=&ToolOptions::GetOption;
-}
void export_Tool()
{
diff --git a/modules/gui/pymod/scene/loaders.xml b/modules/gui/pymod/scene/loaders.xml
index 90021f812619a5d9cfd78745ff439b0fc9db0819..6c0378641a0dd8c22bd0872058f1d523f72bdd1f 100644
--- a/modules/gui/pymod/scene/loaders.xml
+++ b/modules/gui/pymod/scene/loaders.xml
@@ -1,8 +1,11 @@
<!DOCTYPE EMDataInfo>
<EMDataInfo>
<GenericLoaders>
+ <GenericLoader ExtName="cif" Name="pdb.org (mmCIF)"
+ Url="http://www.pdb.org/pdb/files/${ID}.cif.gz" Default="1"
+ FileType="cif.gz"/>
<GenericLoader ExtName="pdbredo" Name="pdbredo" Url="http://www.cmbi.ru.nl/pdb_redo/ak/${ID}/${ID}_besttls.pdb" />
- <GenericLoader ExtName="" Name="pdb.org" Url="http://www.pdb.org/pdb/files/${ID}.pdb" Default="1" />
+ <GenericLoader ExtName="" Name="pdb.org" FileType="pdb.gz" Url="http://www.pdb.org/pdb/files/${ID}.pdb.gz"/>
<GenericLoader ExtName="emdb" Name="emdb" Url="ftp://emdb.rutgers.edu/structures/EMD-${ID}/map/emd_${ID}.map.gz" FileType="map.gz" Img="1"/>
</GenericLoaders>
</EMDataInfo>
diff --git a/modules/gui/pymod/traj.py b/modules/gui/pymod/traj.py
index 6df252b35e7db3501fd374b74cbb765d5049b28b..1fcb1c77959528cdda00f05140f89902d4c86863 100644
--- a/modules/gui/pymod/traj.py
+++ b/modules/gui/pymod/traj.py
@@ -21,12 +21,13 @@ from PyQt4.QtGui import *
from ost import *
class TrajWidget(QWidget):
- def __init__(self, traj=None, render_mode=gfx.SIMPLE, parent=None):
+ def __init__(self, traj=None, render_mode=gfx.SIMPLE, sel='', parent=None):
QWidget.__init__(self, parent, Qt.Tool)
self.render_mode=render_mode
vb=QVBoxLayout()
hb=QHBoxLayout()
hb2=QHBoxLayout()
+ self.selection=sel
self.callback=None
self._slider=QSlider(self)
self._slider.setOrientation(Qt.Horizontal)
@@ -116,7 +117,8 @@ class TrajWidget(QWidget):
self._traj=traj
if self._traj:
ev=traj.GetEntity()
- self.gfx_entity=gfx.Entity("mol",self.render_mode, ev)
+ self.gfx_entity=gfx.Entity("mol",self.render_mode,
+ ev.Select(self.selection))
gfx.Scene().Add(self.gfx_entity)
gfx.Scene().CenterOn(self.gfx_entity)
# enable the blur effect
diff --git a/modules/gui/src/CMakeLists.txt b/modules/gui/src/CMakeLists.txt
index c8dc99f72669ed86d28e8cdd768b59ff18b3ad63..50c89edb8b7ee2ee3f3ff059e2fc2128ce72ba11 100644
--- a/modules/gui/src/CMakeLists.txt
+++ b/modules/gui/src/CMakeLists.txt
@@ -441,7 +441,8 @@ endif()
set(QT_USE_QTOPENGL 1)
set(QT_USE_QTNETWORK 1)
include(${QT_USE_FILE})
-qt4_wrap_cpp(OST_GUI_MOCS "${HEADERS_TO_BE_MOCCED}")
+qt4_wrap_cpp(OST_GUI_MOCS "${HEADERS_TO_BE_MOCCED}"
+ OPTIONS -DBOOST_TT_HAS_OPERATOR_HPP_INCLUDED)
module(NAME gui SOURCES ${OST_GUI_MOCS} ${OST_GUI_SOURCES}
HEADERS ${OST_GUI_TOOLS_HEADERS} IN_DIR tools
${OST_GUI_SEQUENCE_VIEWER_HEADERS} IN_DIR sequence_viewer
@@ -463,7 +464,8 @@ endif()
include_directories(${PYTHON_INCLUDE_PATH})
qt4_add_resources(OST_QT_RESOURCE dngr.qrc)
-qt4_wrap_cpp(OST_GOSTY_MOC "gosty.hh")
+qt4_wrap_cpp(OST_GOSTY_MOC "gosty.hh"
+ OPTIONS -DBOOST_TT_HAS_OPERATOR_HPP_INCLUDED)
# if someone has ANY idea why windows already has the boost program options
# symbols defined, please talk to Marco and Juergen. You will be rewarded with
# dogfood for a lifetime!
diff --git a/modules/gui/src/data_viewer/data_viewer.cc b/modules/gui/src/data_viewer/data_viewer.cc
index 14e15380a5c3dbc2e271b8dec3d99cdefb59bea1..2bc7d368f8ce6b178a01d9580de9d7d383edddd2 100644
--- a/modules/gui/src/data_viewer/data_viewer.cc
+++ b/modules/gui/src/data_viewer/data_viewer.cc
@@ -118,6 +118,12 @@ Extent DataViewer::GetSelection() const
return panel_->GetSelection();
}
+void DataViewer::SetSelection(const Extent& selection)
+{
+ assert(panel_);
+ panel_->SetSelection(selection);
+}
+
void DataViewer::SetName(const String& name)
{
setWindowTitle(QString::fromStdString(name));
@@ -128,6 +134,66 @@ int DataViewer::GetSlab() const
return panel_->GetSlab();
}
+void DataViewer::SetZoomScale(Real zoomscale)
+{
+ panel_->SetZoomScale(zoomscale);
+}
+
+Real DataViewer::GetZoomScale() const
+{
+ return panel_->GetZoomScale();
+}
+
+void DataViewer::SetViewerMin(Real min)
+{
+ panel_->SetViewerMin(min);
+}
+
+Real DataViewer::GetViewerMin() const
+{
+ return panel_->GetViewerMin();
+}
+
+void DataViewer::SetViewerMax(Real max)
+{
+ panel_->SetViewerMax(max);
+}
+
+Real DataViewer::GetViewerMax() const
+{
+ return panel_->GetViewerMax();
+}
+
+void DataViewer::SetGamma(Real gamma)
+{
+ panel_->SetGamma(gamma);
+}
+
+Real DataViewer::GetGamma() const
+{
+ return panel_->GetGamma();
+}
+
+void DataViewer::SetInvert(bool invert)
+{
+ panel_->SetInvert(invert);
+}
+
+bool DataViewer::GetInvert() const
+{
+ return panel_->GetInvert();
+}
+
+void DataViewer::SetOffset(const geom::Vec2& offset)
+{
+ panel_->SetOffset(offset);
+}
+
+geom::Vec2 DataViewer::GetOffset() const
+{
+ return panel_->GetOffset();
+}
+
int DataViewer::AddOverlay(const OverlayPtr& ov, bool make_active)
{
int retval= ov_manager_->AddOverlay(ov,make_active);
diff --git a/modules/gui/src/data_viewer/data_viewer.hh b/modules/gui/src/data_viewer/data_viewer.hh
index 3fd08f9775ea06762342272e6ce41d5f40737856..e9e417f6b0c6a0076ab728ae8dd60b0dacabf71d 100644
--- a/modules/gui/src/data_viewer/data_viewer.hh
+++ b/modules/gui/src/data_viewer/data_viewer.hh
@@ -80,6 +80,9 @@ public:
//! return currently active selection
Extent GetSelection() const;
+ //! set currently active selection
+ void SetSelection(const Extent& selection);
+
//! set the name, displayed as the window title
void SetName(const String& name);
@@ -101,9 +104,41 @@ public:
//! event filter for DataViewerPanel
virtual bool eventFilter(QObject * object, QEvent *event);
- void SetSlab(int slab);
+ //! set z slab
+ void SetSlab(int slab);
+ //! get z slab
int GetSlab() const;
+ //! set zoom scale (range: 1e-8 to 1e8)
+ void SetZoomScale(Real zoomscale);
+ //! get zoom scale (range: 1e-8 to 1e8)
+ Real GetZoomScale() const;
+
+ //! set minimum level of the viewer (e.g. the value that will be displayed as black)
+ void SetViewerMin(Real min);
+ //! get minimum level of the viewer (e.g. the value that will be displayed as black)
+ Real GetViewerMin() const;
+
+ //! set maximum level of the viewer (e.g. the value that will be displayed as white)
+ void SetViewerMax(Real max);
+ //! get maximum level of the viewer (e.g. the value that will be displayed as white)
+ Real GetViewerMax() const;
+
+ //! set viewer gamma
+ void SetGamma(Real gamma);
+ //! get viewer gamma
+ Real GetGamma() const;
+
+ //! set invert flag
+ void SetInvert(bool invert);
+ //! get invert flag
+ bool GetInvert() const;
+
+ //! set image offset
+ void SetOffset(const geom::Vec2& offset);
+ //! get image offset
+ geom::Vec2 GetOffset() const;
+
signals:
void released();
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 ec113e525419d81359650d68106d9a868ec9d7e6..eb53154eef140a11ab9d215ab5a5137ce0127821 100644
--- a/modules/gui/src/data_viewer/data_viewer_panel_base.cc
+++ b/modules/gui/src/data_viewer/data_viewer_panel_base.cc
@@ -46,7 +46,7 @@ namespace ost { namespace img { namespace gui {
DataViewerPanelBase::DataViewerPanelBase(const Data& data,QWidget* parent):
QWidget(parent),
DataObserver(data),
- popupmenu_(new QMenu),
+ popupmenu_(new QMenu(this)),
data_min_(0.0),
data_max_(0.0),
data_min_pos_(),
@@ -643,6 +643,18 @@ Extent DataViewerPanelBase::GetSelection() const
return selection_;
}
+void DataViewerPanelBase::SetSelection(const Extent& selection)
+{
+ selection_=selection;
+ update_rubberband_from_selection_();
+ if(selection==Extent()){
+ rubberband_->hide();
+ }else{
+ rubberband_->show();
+ }
+ UpdateView(false);
+}
+
Real DataViewerPanelBase::GetZoomScale() const
{
return zoom_scale_;
@@ -782,7 +794,7 @@ void DataViewerPanelBase::extract_ri()
void DataViewerPanelBase::zoom(int d)
{
- // maximal zoom = 2^8, therefore zoom_level_ goes from 8 to 8 and delta from -16 to 16
+ // maximal zoom = 2^8, therefore zoom_level_ goes from -8 to 8 and delta from -16 to 16
int old_zoom_level=zoom_level_;
int dl=std::max(d,-16);
dl=std::min(dl,16);
@@ -927,6 +939,53 @@ void DataViewerPanelBase::SetInvert(bool invert)
UpdateView(true);
}
+Real DataViewerPanelBase::GetGamma() const
+{
+ return normalizer_->GetGamma();
+}
+
+void DataViewerPanelBase::SetGamma(Real gamma)
+{
+ UpdateNormalizer(normalizer_->GetMinimum(),
+ normalizer_->GetMaximum(),
+ gamma,normalizer_->GetInvert());
+ UpdateView(true);
+}
+
+Real DataViewerPanelBase::GetViewerMin() const
+{
+ return normalizer_->GetMinimum();
+}
+
+void DataViewerPanelBase::SetViewerMin(Real min)
+{
+ UpdateNormalizer(min,normalizer_->GetMaximum(),normalizer_->GetGamma(),normalizer_->GetInvert());
+ UpdateView(true);
+}
+
+Real DataViewerPanelBase::GetViewerMax() const
+{
+ return normalizer_->GetMaximum();
+}
+
+void DataViewerPanelBase::SetViewerMax(Real max)
+{
+ UpdateNormalizer(normalizer_->GetMinimum(),max,normalizer_->GetGamma(),normalizer_->GetInvert());
+ UpdateView(true);
+}
+
+geom::Vec2 DataViewerPanelBase::GetOffset() const
+{
+ return geom::Vec2(offset_x_,offset_y_);
+}
+
+void DataViewerPanelBase::SetOffset(const geom::Vec2& offset)
+{
+ offset_x_=offset[0];
+ offset_y_=offset[1];
+ UpdateView(true);
+}
+
void DataViewerPanelBase::SetAntialiasing(bool f)
{
antialiasing_=f;
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 60999a9003355073ef1810d7067c0a7f635a0847..4c4b59bb5df8bb4df9853d6f10dd42d577e78ed0 100644
--- a/modules/gui/src/data_viewer/data_viewer_panel_base.hh
+++ b/modules/gui/src/data_viewer/data_viewer_panel_base.hh
@@ -101,6 +101,9 @@ public:
*/
Extent GetSelection() const;
+ //! set currently active selection
+ void SetSelection(const Extent& extent);
+
//! convert window coordinates to image point
Point WinToPoint(int mx, int my) const;
Point WinToPoint(const QPoint& p) const;
@@ -174,6 +177,12 @@ public:
Real GetDataMax() const;
bool GetInvert() const;
void SetInvert(bool invert);
+ Real GetGamma() const;
+ void SetGamma(Real gamma);
+ void SetViewerMin(Real min);
+ Real GetViewerMin() const;
+ void SetViewerMax(Real max);
+ Real GetViewerMax() const;
void UpdateNormalizer(Real min, Real max, Real gamma, bool invert);
int GetSlab();
void SetSlab(int slab);
@@ -181,6 +190,10 @@ public:
int GetSelectionMode();
void SetAntialiasing(bool f);
bool GetAntialiasing() const;
+ geom::Vec2 GetOffset() const;
+ void SetOffset(const geom::Vec2& offset);
+
+
signals:
void clicked(const geom::Vec3& mousepos);
diff --git a/modules/gui/src/data_viewer/info_panel.cc b/modules/gui/src/data_viewer/info_panel.cc
index 34f1790aa10636f60aa6fda2a8897de3dc044175..f90d45b17feb18b469fb205e4ad36f684f395932 100644
--- a/modules/gui/src/data_viewer/info_panel.cc
+++ b/modules/gui/src/data_viewer/info_panel.cc
@@ -46,18 +46,18 @@ InfoPanelLabel::InfoPanelLabel(const QString& t, QWidget* parent):
InfoPanel::InfoPanel(QWidget* parent):
QWidget(parent),
- image_extent_(new InfoPanelLabel),
- image_size_(new InfoPanelLabel),
- image_sampling_(new InfoPanelLabel),
- image_type_(new InfoPanelLabel),
- mouse_xy_(new InfoPanelLabel),
- mouse_val_(new InfoPanelLabel),
- click_xy_(new InfoPanelLabel),
- click_val_(new InfoPanelLabel),
- selection_xy_(new InfoPanelLabel),
- size_xy_(new InfoPanelLabel),
- distance_(new InfoPanelLabel),
- popupmenu_(new QMenu),
+ image_extent_(new InfoPanelLabel("",this)),
+ image_size_(new InfoPanelLabel("",this)),
+ image_sampling_(new InfoPanelLabel("",this)),
+ image_type_(new InfoPanelLabel("",this)),
+ mouse_xy_(new InfoPanelLabel("",this)),
+ mouse_val_(new InfoPanelLabel("",this)),
+ click_xy_(new InfoPanelLabel("",this)),
+ click_val_(new InfoPanelLabel("",this)),
+ selection_xy_(new InfoPanelLabel("",this)),
+ size_xy_(new InfoPanelLabel("",this)),
+ distance_(new InfoPanelLabel("",this)),
+ popupmenu_(new QMenu(this)),
amp_pha_(false),
click_(geom::Vec2())
{
diff --git a/modules/gui/src/data_viewer/mask_overlay.cc b/modules/gui/src/data_viewer/mask_overlay.cc
index 6b52851831d44995a70eb3f6beffe518bada2447..c0c0e6560344c59f75cb95031a1a372086aba0ad 100644
--- a/modules/gui/src/data_viewer/mask_overlay.cc
+++ b/modules/gui/src/data_viewer/mask_overlay.cc
@@ -57,43 +57,46 @@ MaskOverlay::MaskOverlay(const MaskPtr& m):
void MaskOverlay::OnDraw(QPainter& pnt, DataViewerPanel* dvp, bool is_active)
{
+ QPainter::RenderHints render_hints=pnt.renderHints();
+ pnt.setRenderHints(render_hints | QPainter::Antialiasing);
for (int i=0;i<static_cast<int>(polygons_.size());++i){
if(is_active){
if(i==active_){
- pnt.setPen(QPen(QColor(255,255,0),2));
+ pnt.setPen(QPen(QColor(255,255,0),1));
pnt.setBrush(QColor(255,255,0,30));
}else{
- pnt.setPen(QPen(QColor(255,0,0),2));
+ pnt.setPen(QPen(QColor(255,0,0),1));
pnt.setBrush(QColor(255,0,0,30));
}
}else{
- pnt.setPen(QPen(QColor(100,100,100),2));
+ pnt.setPen(QPen(QColor(100,100,100),1));
pnt.setBrush(QColor(100,100,100,30));
}
geom::Polygon2 pol=polygons_[i];
QPolygon qpol;
for(int j=0;j<static_cast<int>(pol.GetNodeCount());++j){
qpol << dvp->FracPointToWinCenter(pol.GetNode(j)+shift_);
- pnt.drawEllipse(qpol.back(),3,3);
+ pnt.drawEllipse(qpol.back(),4,4);
}
pnt.drawPolygon(qpol);
}
if(add_mode_) {
if(is_active){
- pnt.setPen(QPen(QColor(255,0,255),3));
+ pnt.setPen(QPen(QColor(255,0,255),1));
pnt.setBrush(QColor(255,0,255,30));
}else{
- pnt.setPen(QPen(QColor(100,100,100),2));
+ pnt.setPen(QPen(QColor(100,100,100),1));
pnt.setBrush(QColor(100,100,100,30));
}
QPolygon qpol;
for(int j=0;j<static_cast<int>(new_poly_.GetNodeCount());++j){
qpol << dvp->FracPointToWinCenter(new_poly_.GetNode(j)+shift_);
- pnt.drawEllipse(qpol.back(),3,3);
+ pnt.drawEllipse(qpol.back(),4,4);
}
pnt.drawPolygon(qpol);
}
+ pnt.setRenderHints(render_hints);
}
bool MaskOverlay::OnMouseEvent(QMouseEvent* e, DataViewerPanel* dvp,
@@ -118,7 +121,7 @@ bool MaskOverlay::OnMouseEvent(QMouseEvent* e, DataViewerPanel* dvp,
if(active_>=0){
geom::Polygon2 pol=polygons_[active_];
for(unsigned int j=0;j<pol.GetNodeCount();++j){
- if(Length(mousepos-(pol.GetNode(j)+shift_))<3){
+ if(Length(mousepos-(pol.GetNode(j)+shift_))<4){
active_node_=j;
return true;
}
@@ -128,7 +131,7 @@ bool MaskOverlay::OnMouseEvent(QMouseEvent* e, DataViewerPanel* dvp,
if(i!=active_){
geom::Polygon2 pol=polygons_[i];
for(unsigned int j=0;j<pol.GetNodeCount();++j){
- if(Length(mousepos-pol.GetNode(j))<3){
+ if(Length(mousepos-(pol.GetNode(j)+shift_))<4){
active_=i;
active_node_=j;
return true;
@@ -142,7 +145,7 @@ bool MaskOverlay::OnMouseEvent(QMouseEvent* e, DataViewerPanel* dvp,
}
}
if(e->buttons() & Qt::LeftButton && active_>=0 && active_node_>=0 && ! (e->modifiers() & Qt::ShiftModifier)){
- polygons_[active_].SetNode(active_node_,mousepos);
+ polygons_[active_].SetNode(active_node_,mousepos-shift_);
}
return false;
}
diff --git a/modules/gui/src/data_viewer/overlay_manager_gui.cc b/modules/gui/src/data_viewer/overlay_manager_gui.cc
index 74d24415c5bc1431389b8437becad5e4db400782..ba9d884cbd88b0f603c670a93dcfb995eb168177 100644
--- a/modules/gui/src/data_viewer/overlay_manager_gui.cc
+++ b/modules/gui/src/data_viewer/overlay_manager_gui.cc
@@ -135,6 +135,7 @@ void OverlayManagerGUI::OnAddOverlay(OverlayManager* m, int id)
OverlayPtr ov = m->RetrieveOverlay(id);
connect(ov.get(),SIGNAL(InfoTextChanged(const QString&)),this,SLOT(SetInfoText(const QString&)));
OverlayEntry oe;
+ oe.row=0.0;
oe.a=new OverlayCustomActCheckBox(id,m);
connect(oe.a,SIGNAL(toggled(bool)),oe.a,SLOT(OnToggle(bool)));
active_group_->addButton(oe.a);
diff --git a/modules/gui/src/gosty.cc b/modules/gui/src/gosty.cc
index 3ea2bdda6e64bb18677c0cb86ac08fb303bddf95..49750b9dca33c65e927d52dad461d5973b96fc80 100644
--- a/modules/gui/src/gosty.cc
+++ b/modules/gui/src/gosty.cc
@@ -205,7 +205,6 @@ int main(int argc, char** argv)
QCoreApplication::setOrganizationName("OpenStructure");
QCoreApplication::setOrganizationDomain("openstructure.org");
QCoreApplication::setApplicationName(QString(argv[2]));
- app.setLibraryPaths(QStringList());
if (int rv=setup_resources(app)<0) {
return rv;
}
diff --git a/modules/gui/src/loader_manager.cc b/modules/gui/src/loader_manager.cc
index 3febfd7ad3ade3945477ad06ab834648433017e2..bfe2853dc926669bdf33ddbee80bb360925c46f0 100644
--- a/modules/gui/src/loader_manager.cc
+++ b/modules/gui/src/loader_manager.cc
@@ -30,12 +30,13 @@
namespace ost { namespace gui {
-LoaderManager::LoaderManager()
+LoaderManager::LoaderManager():
+ site_loaders_(),
+ site_actions_(new QActionGroup(GostyApp::Instance()->GetPerspective()->GetMenuBar())),
+ default_site_()
+
{
- QMenuBar* menu_bar = GostyApp::Instance()->GetPerspective()->GetMenuBar();
- site_actions_=new QActionGroup(menu_bar);
site_actions_->setExclusive(true);
- site_menu_=new QMenu();
}
void LoaderManager::AddRemoteSiteLoader(const QString& ident, RemoteSiteLoader* site_loader)
@@ -48,7 +49,6 @@ void LoaderManager::AddRemoteSiteLoader(const QString& ident, RemoteSiteLoader*
if(site_actions_->checkedAction()==NULL){
action->setChecked(true);
}
- site_menu_->addAction(action);
}
void LoaderManager::RemoveRemoteSiteLoader(const QString& ident)
@@ -65,7 +65,6 @@ void LoaderManager::RemoveRemoteSiteLoader(const QString& ident)
}
if(action){
site_actions_->removeAction(action);
- site_menu_->removeAction(action);
}
}
@@ -95,10 +94,6 @@ std::vector<String> LoaderManager::GetSiteLoaderIdents()
return sites;
}
-QMenu* LoaderManager::GetSiteMenu(){
- return site_menu_;
-}
-
RemoteSiteLoader* LoaderManager::GetDefaultRemoteSiteLoader()
{
return GetRemoteSiteLoader(GetDefaultRemoteSiteIdent());
diff --git a/modules/gui/src/loader_manager.hh b/modules/gui/src/loader_manager.hh
index fb6dfe8e8aef97705f382ac3776150159a08bed7..f969b289c45282d13e5f8541f31f0f96e66157e2 100644
--- a/modules/gui/src/loader_manager.hh
+++ b/modules/gui/src/loader_manager.hh
@@ -31,11 +31,6 @@ namespace ost { namespace gui {
class DLLEXPORT_OST_GUI LoaderManager {
- QMap<QString,RemoteSiteLoader*> site_loaders_;
- QActionGroup* site_actions_;
- QMenu* site_menu_;
- QString default_site_;
-
public:
LoaderManager();
virtual ~LoaderManager();
@@ -48,6 +43,13 @@ public:
QString GetDefaultRemoteSiteIdent();
void SetDefaultRemoteSiteIdent(const QString& ident);
QMenu* GetSiteMenu();
+
+private:
+ QMap<QString,RemoteSiteLoader*> site_loaders_;
+ QActionGroup* site_actions_;
+ QString default_site_;
+
+
};
typedef boost::shared_ptr<LoaderManager> LoaderManagerPtr;
diff --git a/modules/gui/src/main.cc b/modules/gui/src/main.cc
index 61d6b05d8227dd1d1f36be1578c514607fa62a24..f3b1c6f6e76f005ab2701a976980bd5af5cfb3a9 100644
--- a/modules/gui/src/main.cc
+++ b/modules/gui/src/main.cc
@@ -93,7 +93,9 @@ void GostyMainWindow::OnQuit()
//SetFullScreen(false);
GostyApp::Instance()->OnQuit();
deleteLater();
- QApplication::exit(0);
+ // exit has to be called on the instance not the class,
+ // otherwise the aboutToQuit singal doesn't get emitted
+ QApplication::instance()->exit(0);
}
void GostyMainWindow::closeEvent(QCloseEvent * event)
diff --git a/modules/gui/src/messages/log_reader.cc b/modules/gui/src/messages/log_reader.cc
index 3562df102ffb13a9a72bae29183d56732830849f..33ad612ba2e73ce8245c481c5e2701e17aaec82c 100644
--- a/modules/gui/src/messages/log_reader.cc
+++ b/modules/gui/src/messages/log_reader.cc
@@ -72,8 +72,6 @@ QMessageBox::Icon LogReader::GetIconForSeverity(int severity){
}
LogReader::~LogReader() {
- ost::Logger& logger = ost::Logger::Instance();
- logger.PopSink();
}
}
diff --git a/modules/gui/src/messages/message_widget.cc b/modules/gui/src/messages/message_widget.cc
index 983a4ec169ee450f4b88ef2a0821c1fa90420582..038840ae1482d064608385c2e62225c8b7f19b88 100644
--- a/modules/gui/src/messages/message_widget.cc
+++ b/modules/gui/src/messages/message_widget.cc
@@ -61,6 +61,7 @@ MessageWidget::MessageWidget(QWidget* parent) :
view_->setDragEnabled(true);
view_->setContextMenuPolicy(Qt::CustomContextMenu);
view_->setFrameShape(QFrame::NoFrame);
+ view_->setVerticalScrollMode(QAbstractItemView::ScrollPerPixel);
layout->addWidget(view_);
connect(view_, SIGNAL(customContextMenuRequested(const QPoint&)), this,
diff --git a/modules/gui/src/panels/panel_bar.cc b/modules/gui/src/panels/panel_bar.cc
index 706c0294176bcec6e5b4a287964d77bc69bda47e..81312afb1016eff513857e790ec64bcadce9962f 100644
--- a/modules/gui/src/panels/panel_bar.cc
+++ b/modules/gui/src/panels/panel_bar.cc
@@ -35,17 +35,17 @@ namespace ost {
namespace gui {
PanelBar::PanelBar(QWidget* parent) :
- Widget(NULL, parent)
+ Widget(NULL, parent),
+ layout_(new QStackedLayout(this)),
+ view_modes_( new QActionGroup(this)),
+ view_mode_menu_(new QMenu("View Mode",this)),
+ current_view_mode_(NULL),
+ widget_states_(),
+ drop_box_(new DropBox), // DropBox having no parent is done on purpose (otherwise it will not hide properly)
+ show_action_(new QAction(this))
{
- widget_states_ = QList<WidgetState> ();
-
- view_modes_ = new QActionGroup(this);
- view_mode_menu_ = new QMenu("View Mode");
connect(view_mode_menu_,SIGNAL(triggered(QAction*)),this,SLOT(ChangeViewMode(QAction*)));
- current_view_mode_ = NULL;
-
- layout_ = new QStackedLayout(this);
layout_->setMargin(0);
layout_->setSpacing(0);
this->setLayout(layout_);
@@ -53,16 +53,18 @@ PanelBar::PanelBar(QWidget* parent) :
this->setVisible(false);
- show_action_ = new QAction(this);
show_action_->setText("Show");
show_action_->setCheckable(true);
show_action_->setChecked(false);
show_action_->setEnabled(false);
connect(show_action_, SIGNAL(triggered(bool)), this,
- SLOT(ShowActionTrigger()));
+ SLOT(ShowActionTrigger()));
this->addAction(show_action_);
+}
- drop_box_ = new DropBox();
+PanelBar::~PanelBar()
+{
+ delete drop_box_; // manually destroy drop_box_ widget, as it has no parent.
}
void PanelBar::AddWidget(Widget* widget, bool is_hidden)
diff --git a/modules/gui/src/panels/panel_bar.hh b/modules/gui/src/panels/panel_bar.hh
index 7c81cbd0be81cd5c4ca11d6e801f1d2ad4787036..463641357c99248957c51e7ed8394c870eef8bf1 100644
--- a/modules/gui/src/panels/panel_bar.hh
+++ b/modules/gui/src/panels/panel_bar.hh
@@ -54,6 +54,7 @@ class DLLEXPORT_OST_GUI PanelBar : public Widget {
Q_OBJECT
public:
PanelBar(QWidget* parent);
+ virtual ~PanelBar();
virtual bool Save(const QString& prefix);
virtual bool Restore(const QString& prefix);
diff --git a/modules/gui/src/panels/panel_manager.cc b/modules/gui/src/panels/panel_manager.cc
index 0bf0b7f0b848a47b6b15f124c451c135113decd3..1c30ad993cd90d7ab7265f071e9f6469489cc12b 100644
--- a/modules/gui/src/panels/panel_manager.cc
+++ b/modules/gui/src/panels/panel_manager.cc
@@ -50,7 +50,7 @@ PanelManager::PanelManager(QWidget* widget):
right_panel_splitter_(new ThinSplitter(Qt::Horizontal, this)),
left_panel_splitter_(new ThinSplitter(Qt::Horizontal, this)),
bottom_panel_splitter_(new ThinSplitter(Qt::Vertical, this)),
- pool_(new WidgetPool())
+ pool_(new WidgetPool(this))
{
PanelBar* bottom_bar = new BottomBar(this);
diff --git a/modules/gui/src/python_shell/python_interpreter_worker.cc b/modules/gui/src/python_shell/python_interpreter_worker.cc
index b89859142642c21d4fc6f624b9727aa27d35dc81..47dbcfc9e27282c6ec3b3f0e06203fb87b87b0b8 100644
--- a/modules/gui/src/python_shell/python_interpreter_worker.cc
+++ b/modules/gui/src/python_shell/python_interpreter_worker.cc
@@ -51,6 +51,12 @@ PythonInterpreterWorker::PythonInterpreterWorker():
main_namespace_["sys"].attr("stdout") = output_redirector_;
}
+PythonInterpreterWorker::~PythonInterpreterWorker()
+{
+ // we have to manually run the exit functions because we cannot use Py_Finalize due to some problems in boost python
+ run_command_(std::pair<unsigned int, QString>(0,"import atexit\natexit._run_exitfuncs()\n"));
+}
+
void PythonInterpreterWorker::Wake()
{
if (awake_) return;
diff --git a/modules/gui/src/python_shell/python_interpreter_worker.hh b/modules/gui/src/python_shell/python_interpreter_worker.hh
index 7d38dd544b040c86a19106751bf4813fe165dd1f..ed80f6fe78b308f1269a5a723bffe46883fbe35b 100644
--- a/modules/gui/src/python_shell/python_interpreter_worker.hh
+++ b/modules/gui/src/python_shell/python_interpreter_worker.hh
@@ -3,8 +3,11 @@
#include <csignal>
#include <utility>
-#include <boost/python.hpp>
-#include <boost/shared_ptr.hpp>
+// workaround for QTBUG-22829: https://bugreports.qt-project.org/browse/QTBUG-22829
+#ifndef Q_MOC_RUN
+ #include <boost/python.hpp>
+ #include <boost/shared_ptr.hpp>
+#endif
#include "output_redirector.hh"
#include <QObject>
#include <QQueue>
@@ -17,6 +20,7 @@ class PythonInterpreterWorker: public QObject
Q_OBJECT
public:
PythonInterpreterWorker();
+ ~PythonInterpreterWorker();
unsigned int AddCommand(const QString& command);
signals:
diff --git a/modules/img/alg/pymod/CMakeLists.txt b/modules/img/alg/pymod/CMakeLists.txt
index c257040e5f976609bd7c0c13469690c2260b758e..be68daec5e5a2446bd3a6548ae34b59cc4884332 100644
--- a/modules/img/alg/pymod/CMakeLists.txt
+++ b/modules/img/alg/pymod/CMakeLists.txt
@@ -6,5 +6,7 @@ export_transcendentals.cc
export_polar.cc
)
-pymod(NAME img_alg OUTPUT_DIR ost/img/alg CPP ${OST_IMG_ALG_PYMOD_SOURCES}
- PY __init__.py)
+if (NOT ENABLE_STATIC)
+ pymod(NAME img_alg OUTPUT_DIR ost/img/alg CPP ${OST_IMG_ALG_PYMOD_SOURCES}
+ PY __init__.py)
+endif()
diff --git a/modules/img/alg/src/CMakeLists.txt b/modules/img/alg/src/CMakeLists.txt
index 11fba15d4e3ffc675692c8ad0d73bb3c1738a5b7..a49b80125f11de0531412e7fd2929577669aa647 100644
--- a/modules/img/alg/src/CMakeLists.txt
+++ b/modules/img/alg/src/CMakeLists.txt
@@ -75,6 +75,7 @@ power_spectrum.hh
randomize.hh
smooth_mask_image.hh
stat.hh
+stat_accumulator.hh
stat_min_max.hh
threshold.hh
transcendentals.hh
@@ -93,7 +94,9 @@ line_average.hh
rscrosscorr.hh
)
+if(ENABLE_INFO)
include(${QT_USE_FILE})
+endif()
module(NAME img_alg SOURCES "${OST_IMG_ALG_SOURCES}"
HEADERS "${OST_IMG_ALG_HEADERS}"
HEADER_OUTPUT_DIR ost/img/alg
diff --git a/modules/img/alg/src/fft.cc b/modules/img/alg/src/fft.cc
index 84ac57b19bed1eda916653ca4a44b355c908892f..49fc3f6260ffdb986a3cb6f91a7da890516b2405 100644
--- a/modules/img/alg/src/fft.cc
+++ b/modules/img/alg/src/fft.cc
@@ -25,8 +25,12 @@
#include <boost/shared_ptr.hpp>
#include <fftw3.h>
+#if OST_INFO_ENABLED
#include <QThread>
-
+#define IDEAL_NUMBER_OF_THREADS() QThread::idealThreadCount()
+#else
+#define IDEAL_NUMBER_OF_THREADS() 1
+#endif
#include <ost/message.hh>
#include <ost/img/value_util.hh>
#include <ost/img/image_state/image_state_def.hh>
@@ -130,7 +134,7 @@ reinterpret_cast<OST_FFTW_fftw_complex*>(out_state->Data().GetData());
for(size_t i=0;i<block_count;i++) {
std::copy(&in_ptr[i*src_size],&in_ptr[(i+1)*src_size],&fftw_in[i*2*dst_size]);
}
- OST_FFTW_fftw_plan_with_nthreads(std::max<int>(1,QThread::idealThreadCount()));
+ OST_FFTW_fftw_plan_with_nthreads(std::max<int>(1,IDEAL_NUMBER_OF_THREADS()));
OST_FFTW_fftw_plan plan = OST_FFTW_fftw_plan_dft_r2c(rank,n,
fftw_in,fftw_out,
FFTW_ESTIMATE);
@@ -213,7 +217,7 @@ ImageStateBasePtr FFTFnc::VisitState<Complex,HalfFrequencyDomain>(const ComplexH
Real* fftw_out = reinterpret_cast<Real*>(out_ptr);
assert(sizeof(OST_FFTW_fftw_complex)==sizeof(Complex));
- OST_FFTW_fftw_plan_with_nthreads(std::max<int>(1,QThread::idealThreadCount()));
+ OST_FFTW_fftw_plan_with_nthreads(std::max<int>(1,IDEAL_NUMBER_OF_THREADS()));
OST_FFTW_fftw_complex* fftw_in =
reinterpret_cast<OST_FFTW_fftw_complex*>(out_ptr);
@@ -259,7 +263,7 @@ ImageStateBasePtr FFTFnc::VisitState<Complex,SpatialDomain>(const ComplexSpatial
reinterpret_cast<OST_FFTW_fftw_complex*>(out_state->Data().GetData());
// in place transform
- OST_FFTW_fftw_plan_with_nthreads(std::max<int>(1,QThread::idealThreadCount()));
+ OST_FFTW_fftw_plan_with_nthreads(std::max<int>(1,IDEAL_NUMBER_OF_THREADS()));
OST_FFTW_fftw_plan plan = OST_FFTW_fftw_plan_dft(rank,n,
fftw_out, fftw_out,
dir,
@@ -297,7 +301,7 @@ ImageStateBasePtr FFTFnc::VisitState<Complex,FrequencyDomain>(const ComplexFrequ
reinterpret_cast<OST_FFTW_fftw_complex*>(out_state->Data().GetData());
// in place transform
- OST_FFTW_fftw_plan_with_nthreads(std::max<int>(1,QThread::idealThreadCount()));
+ OST_FFTW_fftw_plan_with_nthreads(std::max<int>(1,IDEAL_NUMBER_OF_THREADS()));
OST_FFTW_fftw_plan plan = OST_FFTW_fftw_plan_dft(rank,n,
fftw_out, fftw_out,
dir,
diff --git a/modules/img/alg/src/stat.cc b/modules/img/alg/src/stat.cc
index 2a9427abbaea05fdc290d0642ed6918ea6b455dd..01053ab7e28bbccdfaf0a7c4839633246d675995 100644
--- a/modules/img/alg/src/stat.cc
+++ b/modules/img/alg/src/stat.cc
@@ -30,6 +30,7 @@
#include <ost/img/value_util.hh>
#include "stat.hh"
+#include "stat_accumulator.hh"
namespace ost { namespace img { namespace alg {
@@ -58,14 +59,12 @@ void StatBase::VisitState(const ImageStateImpl<T,D>& isi)
return;
}
- Real sum2=0.0;
Vec3 sumcenter(0.0,0.0,0.0);
- Real current_n=1.0;
- Real m2=0.0,m3=0.0,m4=0.0;
ValIndex minindex(std::numeric_limits<Real>::max(),Point(0,0,0));
ValIndex maxindex(-std::numeric_limits<Real>::max(),Point(0,0,0));
min_ = std::numeric_limits<Real>::max();
max_ = -std::numeric_limits<Real>::max();
+ StatAccumulator<> acc;
int wi=isi.GetSize()[0];
int he=isi.GetSize()[1];
@@ -74,23 +73,11 @@ void StatBase::VisitState(const ImageStateImpl<T,D>& isi)
for(int j=0;j<he;++j) {
for(int k=0;k<de;++k) {
Real val=Val2Val<T,Real>(isi.Value(Index(i,j,k)));
- Real delta = val - mean_;
- Real delta_n = delta / current_n;
- Real delta_n2 = delta_n * delta_n;
- Real term = delta * delta_n * (current_n-1);
-
- mean_ += delta_n;
- m4 += term * delta_n2 * (current_n*current_n - 3*current_n + 3) + 6 * delta_n2 * m2 - 4 * delta_n * m3;
- m3 += term * delta_n * (current_n - 2) - 3 * delta_n * m2;
- m2 += term;
-
ValIndex vi(val,Point(i,j,k));
minindex=std::min<ValIndex>(vi,minindex);
maxindex=std::max<ValIndex>(vi,maxindex);
sumcenter+=Vec3(i,j,k)*val;
- sum_+=val;
- sum2+=val*val;
- current_n+=1;
+ acc(val);
}
}
}
@@ -98,16 +85,13 @@ void StatBase::VisitState(const ImageStateImpl<T,D>& isi)
max_=maxindex.first;
minpos_=minindex.second+isi.GetExtent().GetStart();
maxpos_=maxindex.second+isi.GetExtent().GetStart();
- var_=m2/n;
- std_dev_=sqrt(var_);
- rms_=sqrt(sum2/n);
- if(m2<1e20){
- skewness_=0.0;
- kurtosis_= 0.0;
- }else{
- skewness_=m3/sqrt(m2*m2*m2);
- kurtosis_= (n*m4) / (m2*m2) - 3.0;
- }
+ var_=acc.GetVariance();
+ std_dev_=acc.GetStandardDeviation();
+ rms_=acc.GetRootMeanSquare();
+ skewness_=acc.GetSkewness();
+ kurtosis_= acc.GetKurtosis();
+ sum_=acc.GetSum();
+ mean_=acc.GetMean();
if(sum_!=0.0){
center_of_mass_=sumcenter/sum_+isi.GetExtent().GetStart().ToVec3();
}else{
@@ -135,49 +119,32 @@ void StatBase::VisitFunction(const Function& fnc)
return;
}
- Real sum2=0.0;
Vec3 sumcenter(0.0,0.0,0.0);
- Real current_n=1.0;
- Real m2=0.0,m3=0.0,m4=0.0;
ValIndex minindex(std::numeric_limits<Real>::max(),Point(0,0,0));
ValIndex maxindex(-std::numeric_limits<Real>::max(),Point(0,0,0));
min_ = std::numeric_limits<Real>::max();
max_ = -std::numeric_limits<Real>::max();
+ StatAccumulator<> acc;
for(ExtentIterator it(fnc.GetExtent());!it.AtEnd(); ++it) {
Real val=fnc.GetReal(it);
- Real delta = val - mean_;
- Real delta_n = delta / current_n;
- Real delta_n2 = delta_n * delta_n;
- Real term = delta * delta_n * (current_n-1);
-
- mean_ += delta_n;
- m4 += term * delta_n2 * (current_n*current_n - 3*current_n + 3) + 6 * delta_n2 * m2 - 4 * delta_n * m3;
- m3 += term * delta_n * (current_n - 2) - 3 * delta_n * m2;
- m2 += term;
-
ValIndex vi(val,it);
minindex=std::min<ValIndex>(vi,minindex);
maxindex=std::max<ValIndex>(vi,maxindex);
sumcenter+=Point(it).ToVec3()*val;
- sum_+=val;
- sum2+=val*val;
- current_n+=1;
+ acc(val);
}
min_=minindex.first;
max_=maxindex.first;
minpos_=minindex.second;
- maxpos_=maxindex.second;
- var_=m2/n;
- std_dev_=sqrt(var_);
- rms_=sqrt(sum2/n);
- if(m2<1e20){
- skewness_=0.0;
- kurtosis_= 0.0;
- }else{
- skewness_=m3/sqrt(m2*m2*m2);
- kurtosis_= (n*m4) / (m2*m2) - 3.0;
- }
+ maxpos_=maxindex.second;
+ var_=acc.GetVariance();
+ std_dev_=acc.GetStandardDeviation();
+ rms_=acc.GetRootMeanSquare();
+ skewness_=acc.GetSkewness();
+ kurtosis_= acc.GetKurtosis();
+ sum_=acc.GetSum();
+ mean_=acc.GetMean();
if(sum_!=0.0){
center_of_mass_=sumcenter/sum_;
}else{
diff --git a/modules/img/alg/src/stat_accumulator.hh b/modules/img/alg/src/stat_accumulator.hh
new file mode 100644
index 0000000000000000000000000000000000000000..3483890b0ced8c3f5e71382f3273fcdcafc68ef0
--- /dev/null
+++ b/modules/img/alg/src/stat_accumulator.hh
@@ -0,0 +1,202 @@
+//------------------------------------------------------------------------------
+// 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_STAT_ACCUMULATOR_HH
+#define OST_STAT_ACCUMULATOR_HH
+
+#include <ost/base.hh>
+#include <ost/img/alg/module_config.hh>
+
+namespace ost { namespace img { namespace alg {
+
+template<unsigned int MAX_MOMENT=4>
+class DLLEXPORT_IMG_ALG StatAccumulator
+{
+public:
+ StatAccumulator():
+ mean_(0.0),
+ sum_(0.0),
+ sum2_(0.0),
+ m2_(0.0),
+ m3_(0.0),
+ m4_(0.0),
+ n_(1)
+ {}
+
+ void operator()(Real val)
+ {
+ Real delta,delta_n,delta_n2,term;
+ if(MAX_MOMENT>0){
+ delta = val - mean_;
+ delta_n = delta / n_;
+ }
+ if(MAX_MOMENT>3){
+ delta_n2 = delta_n * delta_n;
+ }
+ if(MAX_MOMENT>1){
+ term = delta * delta_n * (n_-1);
+ }
+ if(MAX_MOMENT>3){
+ m4_ += term * delta_n2 * (n_*n_ - 3*n_ + 3) + 6 * delta_n2 * m2_ - 4 * delta_n * m3_;
+ }
+ if(MAX_MOMENT>2){
+ m3_ += term * delta_n * (n_ - 2) - 3 * delta_n * m2_;
+ }
+ if(MAX_MOMENT>1){
+ m2_ += term;
+ }
+ if(MAX_MOMENT>0){
+ mean_ += delta_n;
+ }
+ n_+=1;
+ sum_+=val;
+ sum2_+=val*val;
+ }
+
+ StatAccumulator operator+(const StatAccumulator& acc2) const
+ {
+ StatAccumulator acc(acc2);
+ acc+=*this;
+ return acc;
+ }
+
+ StatAccumulator& operator+=(const StatAccumulator& acc)
+ {
+ if(acc.n_==1){
+ return *this;
+ }
+ if(n_==1){
+ mean_=acc.mean_;
+ sum_=acc.sum_;
+ sum2_=acc.sum2_;
+ m2_=acc.m2_;
+ m3_=acc.m3_;
+ m4_=acc.m4_;
+ n_=acc.n_;
+ return *this;
+ }
+ Real delta,delta_n,delta_n2,na,nanb;
+ Real nb=acc.n_-1;
+ if(MAX_MOMENT>0){
+ na=n_-1;
+ delta = acc.mean_ - mean_;
+ delta_n = delta / (na+nb);
+ }
+ if(MAX_MOMENT>1){
+ nanb=na*nb;
+ }
+ if(MAX_MOMENT>2){
+ delta_n2 = delta_n * delta_n;
+ }
+ if(MAX_MOMENT>3){
+ m4_+=acc.m4_+delta*delta_n*delta_n2*nanb*(na*na-nanb+nb*nb)+6.0*delta_n2*(na*na*acc.m2_+nb*nb*m2_)+4.0*delta_n*(na*acc.m3_-nb*m3_);
+ }
+ if(MAX_MOMENT>2){
+ m3_+=acc.m3_+delta*delta_n2*nanb*(na-nb)+3.0*delta_n*(na*acc.m2_-nb*m2_);
+ }
+ if(MAX_MOMENT>1){
+ m2_ += acc.m2_+delta*delta_n*nanb;
+ }
+ if(MAX_MOMENT>0){
+ mean_ += nb*delta_n;
+ }
+ sum_+=acc.sum_;
+ sum2_+=acc.sum2_;
+ n_+=nb;
+ return *this;
+ }
+
+ Real GetNumSamples() const
+ {
+ return n_-1.0;
+ }
+
+ Real GetMean() const
+ {
+ if(MAX_MOMENT<1){
+ throw Error("Mean was not calculated.");
+ }
+ return mean_;
+ }
+
+ Real GetSum() const
+ {
+ return sum_;
+ }
+
+ Real GetVariance() const
+ {
+ if(MAX_MOMENT<2){
+ throw Error("Variance was not calculated.");
+ }
+ if(n_==1.0){
+ return 0.0;
+ }
+ return m2_/(n_-1);
+ }
+
+ Real GetStandardDeviation() const
+ {
+ return sqrt(GetVariance());
+ }
+
+ Real GetRootMeanSquare() const
+ {
+ if(n_==1.0){
+ return 0.0;
+ }
+ return sqrt(sum2_/(n_-1));
+ }
+
+ Real GetSkewness() const
+ {
+ if(MAX_MOMENT<3){
+ throw Error("Skewness was not calculated.");
+ }
+ if(m2_<1e-20){
+ return 0.0;
+ }else{
+ return m3_/sqrt(m2_*m2_*m2_);
+ }
+ }
+
+ Real GetKurtosis() const
+ {
+ if(MAX_MOMENT<4){
+ throw Error("Kurtosis was not calculated.");
+ }
+ if(m2_<1e-20){
+ return 0.0;
+ }else{
+ return ((n_-1)*m4_) / (m2_*m2_);
+ }
+ }
+
+private:
+ Real mean_;
+ Real sum_;
+ Real sum2_;
+ Real m2_;
+ Real m3_;
+ Real m4_;
+ Real n_;
+};
+
+}}} //ns
+#endif // OST_STAT_ACCUMULATOR_HH
diff --git a/modules/img/alg/tests/CMakeLists.txt b/modules/img/alg/tests/CMakeLists.txt
index cdbd8b459c114e0765bb53280f144043be34a8cc..cea46dcb979d4f6a73e515b81bf26858876f2468 100644
--- a/modules/img/alg/tests/CMakeLists.txt
+++ b/modules/img/alg/tests/CMakeLists.txt
@@ -14,6 +14,7 @@ test_power_spectrum.cc
test_shift.cc
test_stat.cc
test_transform.cc
+test_normalizer.cc
tests.cc
)
diff --git a/modules/img/alg/tests/test_normalizer.cc b/modules/img/alg/tests/test_normalizer.cc
new file mode 100644
index 0000000000000000000000000000000000000000..e072626dbc562e70703ae226606c4c9e0d1f6c9d
--- /dev/null
+++ b/modules/img/alg/tests/test_normalizer.cc
@@ -0,0 +1,76 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2003-2010 by the IPLT authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+/*
+ Author: Andreas Schenk
+*/
+
+#include <iostream>
+
+#include "tests.hh"
+
+#include <ost/img/image.hh>
+#include <ost/img/alg/normalizer_factory.hh>
+#include <ost/img/alg/stat.hh>
+
+
+
+namespace {
+
+using namespace ost::img;
+using namespace ost::img::alg;
+
+void test()
+{
+ boost::test_tools::close_at_tolerance<Real> close_test(::boost::test_tools::percent_tolerance(0.001));
+ ost::img::ImageHandle testimage=ost::img::CreateImage(ost::img::Extent(ost::img::Point(0,0),ost::img::Point(3,3)));
+ int counter=0;
+ for (ost::img::ExtentIterator i(testimage.GetExtent()); !i.AtEnd(); ++i, ++counter) {
+ testimage.SetReal(i, counter);
+ }
+ ost::img::alg::Normalizer norm=ost::img::alg::CreateLinearRangeNormalizer(testimage,0.0,65535.0);
+ ost::img::ImageHandle scaled_image=testimage.Apply(norm);
+ scaled_image+=0.01; //if all values are > 0.0 we can use close_at_tolerance
+ bool failed=false;
+ ost::img::ExtentIterator eit(testimage.GetExtent());
+ for(;!eit.AtEnd();++eit) {
+ if( ! close_test(scaled_image.GetReal(eit),testimage.GetReal(eit)/15.0*65535.0+0.01)){
+ failed=true;
+ break;
+ }
+ }
+ if(failed){
+ BOOST_ERROR("Normalizer failed at point "
+ << ost::img::Point(eit)<< ". Should be "
+ << testimage.GetReal(eit)/15.0*65535.0+0.01 << ", but "
+ << scaled_image.GetReal(eit) << " found.");
+ }
+}
+
+} // ns
+
+test_suite* CreateNormalizerTest()
+{
+ test_suite* ts=BOOST_TEST_SUITE("img alg Normalizer Test");
+
+ ts->add(BOOST_TEST_CASE(&test));
+
+ return ts;
+}
diff --git a/modules/img/alg/tests/test_stat.cc b/modules/img/alg/tests/test_stat.cc
index 3f5e6d2ed6a3a1114f59458361021b7f9a0ccdad..b736c6bd93d30aebbcc2eb05616e70c4d0d19f7e 100644
--- a/modules/img/alg/tests/test_stat.cc
+++ b/modules/img/alg/tests/test_stat.cc
@@ -29,6 +29,7 @@
#include <ost/img/image.hh>
#include <ost/img/alg/stat.hh>
+#include <ost/img/alg/stat_accumulator.hh>
namespace test_stat {
@@ -51,7 +52,40 @@ void test() {
im.Apply(stat);
BOOST_CHECK_CLOSE(stat.GetMean(),Real(5.0),Real(0.0001));
BOOST_CHECK_CLOSE(stat.GetStandardDeviation(),Real(2.58198889747),Real(0.0001));
-
+ BOOST_CHECK_CLOSE(stat.GetSkewness()+Real(0.5),Real(0.5),Real(0.0001));
+ BOOST_CHECK_CLOSE(stat.GetKurtosis(),Real(1.77),Real(0.0001));
+
+ // check for rounding errors
+ im+=10000.0;
+ im.Apply(stat);
+ BOOST_CHECK_CLOSE(stat.GetMean(),Real(10005.0),Real(0.0001));
+ BOOST_CHECK_CLOSE(stat.GetStandardDeviation(),Real(2.58198889747),Real(0.01));
+ BOOST_CHECK_CLOSE(stat.GetSkewness()+Real(0.5),Real(0.5),Real(0.01));
+ BOOST_CHECK_CLOSE(stat.GetKurtosis(),Real(1.77),Real(0.01));
+
+
+ StatAccumulator<> acc;
+ for(int u=0;u<3;++u) {
+ for(int v=0;v<3;++v) {
+ acc(val[u][v]);
+ }
+ }
+ BOOST_CHECK_CLOSE(acc.GetMean(),Real(5.0),Real(0.0001));
+ BOOST_CHECK_CLOSE(acc.GetStandardDeviation(),Real(2.58198889747),Real(0.0001));
+ BOOST_CHECK_CLOSE(acc.GetSkewness()+Real(0.5),Real(0.5),Real(0.0001));
+ BOOST_CHECK_CLOSE(acc.GetKurtosis(),Real(1.77),Real(0.0001));
+
+ StatAccumulator<> acc1,acc2,acc3;
+ for(int u=0;u<3;++u) {
+ acc1(val[u][0]);
+ acc2(val[u][1]);
+ acc3(val[u][2]);
+ }
+ StatAccumulator<> acc_c=acc1+acc2+acc3;
+ BOOST_CHECK_CLOSE(acc_c.GetMean(),Real(5.0),Real(0.0001));
+ BOOST_CHECK_CLOSE(acc_c.GetStandardDeviation(),Real(2.58198889747),Real(0.0001));
+ BOOST_CHECK_CLOSE(acc_c.GetSkewness()+Real(0.5),Real(0.5),Real(0.0001));
+ BOOST_CHECK_CLOSE(acc_c.GetKurtosis(),Real(1.77),Real(0.0001));
}
} // namespace
diff --git a/modules/img/alg/tests/tests.cc b/modules/img/alg/tests/tests.cc
index 0a4ae6cecd7020190c0e6415ae0938ba0061a481..d3db88c2f29c5c3bbb19517e4d0800f9488f4ea3 100644
--- a/modules/img/alg/tests/tests.cc
+++ b/modules/img/alg/tests/tests.cc
@@ -41,6 +41,7 @@ extern test_suite* CreateClearTest();
extern test_suite* CreateFFTTest();
extern test_suite* CreateNegateTest();
extern test_suite* CreateConjugateTest();
+extern test_suite* CreateNormalizerTest();
bool init_ost_img_alg_unit_tests() {
try {
@@ -54,6 +55,7 @@ bool init_ost_img_alg_unit_tests() {
framework::master_test_suite().add(CreateClearTest());
framework::master_test_suite().add(CreateNegateTest());
framework::master_test_suite().add(CreateFFTTest());
+ framework::master_test_suite().add(CreateNormalizerTest());
} catch(std::exception& e) {
return false;
}
diff --git a/modules/img/base/pymod/CMakeLists.txt b/modules/img/base/pymod/CMakeLists.txt
index aecb5eeb9386d66c5495af54ec897e3189dd4763..de787d14064aa27fb4f0117e9f9bf3bdac06c596 100644
--- a/modules/img/base/pymod/CMakeLists.txt
+++ b/modules/img/base/pymod/CMakeLists.txt
@@ -16,5 +16,7 @@ export_map.cc
wrap_img.cc
)
-pymod(NAME img OUTPUT_DIR ost/img
- CPP ${OST_IMG_PYMOD_SOURCES} PY __init__.py)
+if (NOT ENABLE_STATIC)
+ pymod(NAME img OUTPUT_DIR ost/img
+ CPP ${OST_IMG_PYMOD_SOURCES} PY __init__.py)
+endif()
diff --git a/modules/img/base/pymod/export_mask.cc b/modules/img/base/pymod/export_mask.cc
index 3a5faacf883ec2845ba48f06f4021d8bb23d14ba..40f42e9b0f00e1ca5ac20021e8e544e72bc9fd7f 100644
--- a/modules/img/base/pymod/export_mask.cc
+++ b/modules/img/base/pymod/export_mask.cc
@@ -26,7 +26,10 @@
using namespace boost::python;
#include <ost/img/mask.hh>
+#include <ost/config.hh>
+#if(OST_INFO_ENABLED)
#include <ost/img/mask_info_convert.hh>
+#endif
namespace ost { namespace img {
@@ -101,7 +104,10 @@ void export_Mask()
def("Mask",mask2);
def("Mask",mask3);
def("Mask",mask4);
+
+#if(OST_INFO_ENABLED)
def("InfoToMask",InfoToMask);
def("MaskToInfo",MaskToInfo);
-
+#endif
+
}
diff --git a/modules/img/base/src/CMakeLists.txt b/modules/img/base/src/CMakeLists.txt
index d218ac2ad4f265d7dfd8098313b93b46d71f8a60..ff5191865fc22a3364106ba0980174417946742b 100644
--- a/modules/img/base/src/CMakeLists.txt
+++ b/modules/img/base/src/CMakeLists.txt
@@ -29,7 +29,6 @@ extent_mask.cc
spherical_mask.cc
mask_op.cc
circle_mask.cc
-mask_info_convert.cc
image_list.cc
physical_units.cc
progress.cc
@@ -86,13 +85,17 @@ spherical_mask.hh
mask_op.hh
mask.hh
circle_mask.hh
-mask_info_convert.hh
image_list.hh
physical_units.hh
progress.hh
map.hh
)
+if (ENABLE_INFO)
+ list(APPEND OST_IMG_SOURCES mask_info_convert.cc)
+ list(APPEND OST_IMG_HEADERS mask_info_convert.hh)
+ set(INFO_DEPS ost_info)
+endif()
foreach(fname ${OST_IMG_IMAGE_STATE_SOURCES})
set(OST_IMG_SOURCES ${OST_IMG_SOURCES} image_state/${fname})
@@ -106,4 +109,4 @@ module(NAME img SOURCES "${OST_IMG_SOURCES}"
HEADERS ${OST_IMG_RASTER_IMAGE_HEADERS} IN_DIR raster_image
${OST_IMG_IMAGE_STATE_HEADERS} IN_DIR image_state
${OST_IMG_HEADERS}
- DEPENDS_ON ost_geom ost_base ost_info)
+ DEPENDS_ON ost_geom ost_base ${INFO_DEPS})
diff --git a/modules/img/base/tests/test_image.cc b/modules/img/base/tests/test_image.cc
index e04eba193893e5fb730065a25e2a29d159e143ef..160b7e044da1711751b03c677e498a6519460b4d 100644
--- a/modules/img/base/tests/test_image.cc
+++ b/modules/img/base/tests/test_image.cc
@@ -97,17 +97,17 @@ void test_Cctor_Assignement()
ih1.ApplyIP(alg::Randomize());
ImageHandle ih2(ih1);
- BOOST_REQUIRE(ih1==ih2);
+ BOOST_CHECK(ih1==ih2);
for(ExtentIterator it(ih1.GetExtent());!it.AtEnd(); ++it) {
- BOOST_REQUIRE(ih1.GetReal(it)==ih2.GetReal(it));
+ BOOST_CHECK(ih1.GetReal(it)==ih2.GetReal(it));
}
ImageHandle ih3=CreateImage(Size(10));
ih3.ApplyIP(alg::Randomize());
ih3=ih1;
- BOOST_REQUIRE(ih1==ih3);
+ BOOST_CHECK(ih1==ih3);
for(ExtentIterator it(ih1.GetExtent());!it.AtEnd(); ++it) {
- BOOST_REQUIRE(ih1.GetReal(it)==ih3.GetReal(it));
+ BOOST_CHECK(ih1.GetReal(it)==ih3.GetReal(it));
}
}
@@ -176,14 +176,14 @@ void test_Observer()
{
ImageHandle ih = CreateImage();
- BOOST_REQUIRE(ih.obs_);
+ BOOST_CHECK(ih.obs_);
BOOST_CHECK(ih.obs_.get()->GetListSize()==0);
to1 = new MyObserver(ih);
- BOOST_REQUIRE(ih.obs_.get()->GetListSize()==1);
+ BOOST_CHECK(ih.obs_.get()->GetListSize()==1);
to2 = new MyObserver(ih);
- BOOST_REQUIRE(ih.obs_.get()->GetListSize()==2);
+ BOOST_CHECK(ih.obs_.get()->GetListSize()==2);
BOOST_CHECK(to1->update_count==0);
BOOST_CHECK(to1->release_count==0);
@@ -197,7 +197,7 @@ void test_Observer()
delete to2;
- BOOST_REQUIRE(ih.obs_.get()->GetListSize()==1);
+ BOOST_CHECK(ih.obs_.get()->GetListSize()==1);
ImageHandle ih2 = ih;
@@ -241,7 +241,7 @@ void test_Interpolation()
+( dx )*(one-dy)*( dz )*ih3d.GetReal(Point(1,0,1))
+(one-dx)*( dy )*( dz )*ih3d.GetReal(Point(0,1,1))
+( dx )*( dy )*( dz )*ih3d.GetReal(Point(1,1,1));
- BOOST_REQUIRE(check_close(val3,ih3d.GetIntpolReal(Vec3(dx,dy,dz)),1.0e-8));
+ BOOST_CHECK(check_close(val3,ih3d.GetIntpolReal(Vec3(dx,dy,dz)),1.0e-8));
ImageHandle ih2d=CreateImage(Extent(Point(0,0),Point(1,1)));
@@ -254,7 +254,7 @@ void test_Interpolation()
+(one-dx)*( dy )*ih2d.GetReal(Point(0,1))
+( dx )*( dy )*ih2d.GetReal(Point(1,1));
- BOOST_REQUIRE(check_close(val2,ih2d.GetIntpolReal(Vec2(dx,dy)),1.0e-10));
+ BOOST_CHECK(check_close(val2,ih2d.GetIntpolReal(Vec2(dx,dy)),1.0e-10));
ImageHandle ih1d=CreateImage(Extent(Point(0),Point(1)));
ih3d.SetReal(Point(0,0,0), Real(0.000));
@@ -262,7 +262,7 @@ void test_Interpolation()
Real val1= (one-dx)*ih1d.GetReal(Point(0,0))
+( dx )*ih1d.GetReal(Point(1,0));
- BOOST_REQUIRE(check_close(val1,ih1d.GetIntpolReal(dx),1.0e-15));
+ BOOST_CHECK(check_close(val1,ih1d.GetIntpolReal(dx),1.0e-15));
}
@@ -273,50 +273,56 @@ void test_ScalarOps()
ih2+=1.0;
for(ExtentIterator it(ih2.GetExtent()); !it.AtEnd(); ++it) {
- BOOST_REQUIRE(ih2.GetReal(it) == ih1.GetReal(it) + 1.0);
+ BOOST_CHECK(ih2.GetReal(it) == ih1.GetReal(it) + 1.0);
}
ih2 = ih1.Copy();
ih2-=2.5;
for(ExtentIterator it(ih2.GetExtent()); !it.AtEnd(); ++it) {
- BOOST_REQUIRE(ih2.GetReal(it) == ih1.GetReal(it) - 2.5);
+ BOOST_CHECK(ih2.GetReal(it) == ih1.GetReal(it) - 2.5);
}
ih2 = ih1.Copy();
ih2*=0.9;
for(ExtentIterator it(ih2.GetExtent()); !it.AtEnd(); ++it) {
- BOOST_REQUIRE(std::abs(ih2.GetReal(it) - ih1.GetReal(it) * 0.9)<1e-10);
+ BOOST_CHECK(std::abs(ih2.GetReal(it) - ih1.GetReal(it) * 0.9)<1e-10);
}
ih2 = ih1.Copy();
ih2/=2.1;
for(ExtentIterator it(ih2.GetExtent()); !it.AtEnd(); ++it) {
- BOOST_REQUIRE(std::abs(ih2.GetReal(it) - ih1.GetReal(it) / 2.1)<1e-10);
+ BOOST_CHECK(std::abs(ih2.GetReal(it) - ih1.GetReal(it) / 2.1)<1e-10);
}
}
void test_ImageOps()
{
- alg::Randomize rnd;
Extent ex1(Point(-3,-2),Point(2,2));
ImageHandle h1=CreateImage(ex1);
- h1.ApplyIP(rnd);
+ Real count=1.0;
+ for(ExtentIterator it(ex1); !it.AtEnd(); ++it) {
+ h1.SetReal(it,count);
+ count+=1.0;
+ }
Extent ex2(Point(-1,-2),Point(3,4));
ImageHandle h2=CreateImage(ex2, COMPLEX);
- h2.ApplyIP(rnd);
+ for(ExtentIterator it(ex2); !it.AtEnd(); ++it) {
+ h2.SetReal(it,count);
+ count+=1.0;
+ }
// addition
ImageHandle h3=h1+h2;
for(ExtentIterator it(Extent(Point(-4,-3),Point(4,5))); !it.AtEnd(); ++it) {
if(ex1.Contains(it) && ex2.Contains(it)) {
- BOOST_REQUIRE(check_close(std::fabs(h3.GetReal(it)-(h1.GetReal(it)+h2.GetReal(it))),Real(0.0),1e-6));
+ BOOST_CHECK_SMALL(h3.GetReal(it)-(h1.GetReal(it)+h2.GetReal(it)),Real(1e-6));
} else if (ex1.Contains(it)) {
- BOOST_REQUIRE(h3.GetReal(it)==h1.GetReal(it));
+ BOOST_CHECK(h3.GetReal(it)==h1.GetReal(it));
} else {
- BOOST_REQUIRE(h3.GetReal(it)==0.0);
+ BOOST_CHECK(h3.GetReal(it)==0.0);
}
}
@@ -324,28 +330,36 @@ void test_ImageOps()
h3=h1-h2;
for(ExtentIterator it(Extent(Point(-2,-1),Point(1,2))); !it.AtEnd(); ++it) {
if(ex1.Contains(it) && ex2.Contains(it)) {
- BOOST_REQUIRE(check_close(std::fabs(h3.GetReal(it)-(h1.GetReal(it)-h2.GetReal(it))),Real(0.0),1e-6));
+ BOOST_CHECK_SMALL(h3.GetReal(it)-(h1.GetReal(it)-h2.GetReal(it)),Real(1e-6));
} else if (ex1.Contains(it)) {
- BOOST_REQUIRE(h3.GetReal(it)==h1.GetReal(it));
+ BOOST_CHECK(h3.GetReal(it)==h1.GetReal(it));
} else {
- BOOST_REQUIRE(h3.GetReal(it)==0.0);
+ BOOST_CHECK(h3.GetReal(it)==0.0);
}
}
// half frequency tests
h1=CreateImage(Size(4,5),COMPLEX,HALF_FREQUENCY);
h2=CreateImage(Size(4,5),COMPLEX,HALF_FREQUENCY);
- h1.ApplyIP(rnd);
- h2.ApplyIP(rnd);
+ for(ExtentIterator it(h1.GetExtent()); !it.AtEnd(); ++it) {
+ Complex c(count,count+2);
+ h1.SetComplex(it,c);
+ count+=1.0;
+ }
+ for(ExtentIterator it(h2.GetExtent()); !it.AtEnd(); ++it) {
+ Complex c(count,count+2);
+ h2.SetComplex(it,c);
+ count+=1.0;
+ }
h3=h1+h2;
for(ExtentIterator it(h1.GetExtent());!it.AtEnd();++it) {
- BOOST_REQUIRE(std::abs(h1.GetComplex(it)+h2.GetComplex(it)-h3.GetComplex(it))<1e-10);
+ BOOST_CHECK_SMALL(std::abs(h1.GetComplex(it)+h2.GetComplex(it)-h3.GetComplex(it)),Real(1e-10));
}
h3=h1-h2;
for(ExtentIterator it(Extent(Point(-1,0),Point(2,2)));!it.AtEnd();++it) {
- BOOST_REQUIRE(std::abs(h1.GetComplex(it)-h2.GetComplex(it)-h3.GetComplex(it))<1e-10);
+ BOOST_CHECK_SMALL(std::abs(h1.GetComplex(it)-h2.GetComplex(it)-h3.GetComplex(it)),Real(1e-10));
}
}
@@ -408,7 +422,7 @@ void test_DataAlgorithms()
TestOPAlg op_alg;
ImageHandle ih1=CreateImage(Size(1));
- BOOST_REQUIRE(ih1.GetReal(Point(0))==0.0);
+ BOOST_CHECK(ih1.GetReal(Point(0))==0.0);
// in-place alg applied in-place
ih1.ApplyIP(ip_alg);
@@ -442,28 +456,36 @@ void test_Mult()
{
ImageHandle im1=CreateImage(Extent(Point(-2,-1,-3),Point(1,2,1)),REAL);
ImageHandle im2=CreateImage(Extent(Point(-1,-2,-1),Point(2,1,3)),COMPLEX);
- im1.ApplyIP(alg::Randomize());
- im2.ApplyIP(alg::Randomize());
+ Real count=0;
+ for(ExtentIterator it(im1.GetExtent()); !it.AtEnd(); ++it) {
+ im1.SetReal(it,count);
+ count+=1.0;
+ }
+ for(ExtentIterator it(im2.GetExtent()); !it.AtEnd(); ++it) {
+ Complex c(count,count+2);
+ im2.SetComplex(it,c);
+ count+=1.0;
+ }
ImageHandle im12=im1*im2;
- BOOST_REQUIRE(im12.GetExtent()==im1.GetExtent());
+ BOOST_CHECK(im12.GetExtent()==im1.GetExtent());
for(ExtentIterator it(im12.GetExtent());!it.AtEnd();++it) {
- if(im2.GetExtent().Contains(it)) {
- BOOST_REQUIRE(check_close(im12.GetReal(it),im1.GetReal(it)*im2.GetReal(it),1e-10));
+ if(im1.GetExtent().Contains(it) && im2.GetExtent().Contains(it)) {
+ BOOST_CHECK_CLOSE(im12.GetReal(it),im1.GetReal(it)*im2.GetReal(it),Real(1e-10));
} else {
- //BOOST_REQUIRE(im12.GetReal(it)==0.0);
+ //BOOST_CHECK(im21.GetReal(it)==0.0);
}
}
ImageHandle im21=im2*im1;
- BOOST_REQUIRE(im21.GetExtent()==im2.GetExtent());
+ BOOST_CHECK(im21.GetExtent()==im2.GetExtent());
for(ExtentIterator it(im21.GetExtent());!it.AtEnd();++it) {
if(im1.GetExtent().Contains(it) && im2.GetExtent().Contains(it)) {
- BOOST_REQUIRE(std::abs(im21.GetComplex(it)-im2.GetComplex(it)*im1.GetComplex(it))<1e-10);
+ BOOST_CHECK_SMALL(std::abs(im21.GetComplex(it)-im2.GetComplex(it)*im1.GetComplex(it)),Real(1e-10));
} else {
- //BOOST_REQUIRE(im21.GetReal(it)==0.0);
+ //BOOST_CHECK(im21.GetReal(it)==0.0);
}
}
}
@@ -476,46 +498,48 @@ void test_AddSub()
im2.ApplyIP(alg::Randomize());
ImageHandle im12=im1+im2;
- BOOST_REQUIRE(im12.GetExtent()==im1.GetExtent());
+ BOOST_CHECK(im12.GetExtent()==im1.GetExtent());
for(ExtentIterator it(im12.GetExtent());!it.AtEnd();++it) {
if(im2.GetExtent().Contains(it)) {
- BOOST_REQUIRE(check_close(im12.GetReal(it),im1.GetReal(it)+im2.GetReal(it),1e-10));
+ BOOST_CHECK_CLOSE(im12.GetReal(it),im1.GetReal(it)+im2.GetReal(it),Real(1e-10));
} else {
- BOOST_REQUIRE(im12.GetReal(it)==im1.GetReal(it));
+ BOOST_CHECK(im12.GetReal(it)==im1.GetReal(it));
}
}
im12=im1-im2;
- BOOST_REQUIRE(im12.GetExtent()==im1.GetExtent());
+ BOOST_CHECK(im12.GetExtent()==im1.GetExtent());
for(ExtentIterator it(im12.GetExtent());!it.AtEnd();++it) {
if(im2.GetExtent().Contains(it)) {
- BOOST_REQUIRE(check_close(im12.GetReal(it),im1.GetReal(it)-im2.GetReal(it),1e-10));
+ BOOST_CHECK_CLOSE(im12.GetReal(it),im1.GetReal(it)-im2.GetReal(it),Real(1e-10));
} else {
- BOOST_REQUIRE(im12.GetReal(it)==im1.GetReal(it));
+ BOOST_CHECK(im12.GetReal(it)==im1.GetReal(it));
}
}
ImageHandle im21=im2+im1;
- BOOST_REQUIRE(im21.GetExtent()==im2.GetExtent());
+ BOOST_CHECK(im21.GetExtent()==im2.GetExtent());
for(ExtentIterator it(im21.GetExtent());!it.AtEnd();++it) {
if(im2.GetExtent().Contains(it)) {
- BOOST_REQUIRE(im21.GetComplex(it)==im1.GetComplex(it)+im2.GetComplex(it));
+ BOOST_CHECK_CLOSE(real(im21.GetComplex(it)),real(im1.GetComplex(it)+im2.GetComplex(it)),Real(1e-10));
+ BOOST_CHECK_CLOSE(imag(im21.GetComplex(it)),imag(im1.GetComplex(it)+im2.GetComplex(it)),Real(1e-10));
} else {
- BOOST_REQUIRE(im21.GetReal(it)==im2.GetReal(it));
+ BOOST_CHECK_CLOSE(im21.GetReal(it),im2.GetReal(it),Real(1e-10));
}
}
im21=im2-im1;
- BOOST_REQUIRE(im21.GetExtent()==im2.GetExtent());
+ BOOST_CHECK(im21.GetExtent()==im2.GetExtent());
for(ExtentIterator it(im21.GetExtent());!it.AtEnd();++it) {
if(im2.GetExtent().Contains(it)) {
- BOOST_REQUIRE(im21.GetComplex(it)==im2.GetComplex(it)-im1.GetComplex(it));
+ BOOST_CHECK_CLOSE(real(im21.GetComplex(it)),real(im2.GetComplex(it)-im1.GetComplex(it)),Real(1e-10));
+ BOOST_CHECK_CLOSE(imag(im21.GetComplex(it)),imag(im2.GetComplex(it)-im1.GetComplex(it)),Real(1e-10));
} else {
- BOOST_REQUIRE(im21.GetReal(it)==im2.GetReal(it));
+ BOOST_CHECK_CLOSE(im21.GetReal(it),im2.GetReal(it),Real(1e-10));
}
}
}
@@ -532,8 +556,8 @@ void test_Copy()
ImageHandle i3=i1.Copy(false);
BOOST_CHECK(i3.GetSpatialOrigin()==Point(7,3,-2));
for(ExtentIterator it(i1.GetExtent());!it.AtEnd();++it) {
- BOOST_REQUIRE(i1.GetReal(it)==i2.GetReal(it));
- BOOST_REQUIRE(i3.GetReal(it)==0.0);
+ BOOST_CHECK(i1.GetReal(it)==i2.GetReal(it));
+ BOOST_CHECK(i3.GetReal(it)==0.0);
}
// complex half frequency
i1=CreateImage(Size(6,7),COMPLEX,HALF_FREQUENCY);
@@ -554,7 +578,7 @@ void test_Extract()
BOOST_CHECK(i2.GetDomain()==SPATIAL);
BOOST_CHECK(i2.GetExtent()==Extent(Point(2,3),Point(7,8)));
for(ExtentIterator it(i2.GetExtent());!it.AtEnd();++it) {
- BOOST_REQUIRE(i2.GetReal(it)==i1.GetReal(it));
+ BOOST_CHECK(i2.GetReal(it)==i1.GetReal(it));
}
i1=CreateImage(Size(13,20),COMPLEX,FREQUENCY);
@@ -565,7 +589,7 @@ void test_Extract()
BOOST_CHECK(i2.GetDomain()==SPATIAL);
BOOST_CHECK(i2.GetExtent()==Extent(Point(2,3),Point(7,8)));
for(ExtentIterator it(i2.GetExtent());!it.AtEnd();++it) {
- BOOST_REQUIRE(i2.GetComplex(it)==i1.GetComplex(it));
+ BOOST_CHECK(i2.GetComplex(it)==i1.GetComplex(it));
}
i1=CreateImage(Size(13,30),COMPLEX,HALF_FREQUENCY);
@@ -576,7 +600,7 @@ void test_Extract()
BOOST_CHECK(i2.GetDomain()==SPATIAL);
BOOST_CHECK(i2.GetExtent()==Extent(Point(-2,-3),Point(7,8)));
for(ExtentIterator it(i2.GetExtent());!it.AtEnd();++it) {
- BOOST_REQUIRE(i2.GetComplex(it)==i1.GetComplex(it));
+ BOOST_CHECK(i2.GetComplex(it)==i1.GetComplex(it));
}
}
@@ -592,9 +616,9 @@ void test_Paste()
for(ExtentIterator it(i3.GetExtent());!it.AtEnd();++it) {
if(i2.GetExtent().Contains(it)) {
- BOOST_REQUIRE(i3.GetReal(it)==i2.GetReal(it));
+ BOOST_CHECK(i3.GetReal(it)==i2.GetReal(it));
} else {
- BOOST_REQUIRE(i3.GetReal(it)==i1.GetReal(it));
+ BOOST_CHECK(i3.GetReal(it)==i1.GetReal(it));
}
}
}
diff --git a/modules/index.rst b/modules/index.rst
index afc2142cfb81f0b06d9c83755207b29523132d7a..89bb6d3614d7c91c7fb9050a1fc9f9ab73deecc3 100644
--- a/modules/index.rst
+++ b/modules/index.rst
@@ -93,6 +93,9 @@ Varia
**Datasets:** :doc:`tabular data <table>`
+**File Formats:** :doc:`supported file formats <io/formats>`
+
+
Extending OpenStructure
--------------------------------------------------------------------------------
@@ -102,4 +105,4 @@ Extending OpenStructure
-
\ No newline at end of file
+
diff --git a/modules/info/CMakeLists.txt b/modules/info/CMakeLists.txt
index 9214aaa382e2e266e1d41dc1aeab37a69d4001ca..23eb6ec6733d11d5a081328ae04865a0240f66b2 100644
--- a/modules/info/CMakeLists.txt
+++ b/modules/info/CMakeLists.txt
@@ -1,2 +1,4 @@
-add_subdirectory(src)
-add_subdirectory(pymod)
+if (ENABLE_INFO)
+ add_subdirectory(src)
+ add_subdirectory(pymod)
+endif()
\ No newline at end of file
diff --git a/modules/info/pymod/wrap_info.cc b/modules/info/pymod/wrap_info.cc
index 223dbe1a9cfd8bd79ada7978aa6cf6a94e1b6225..4af9741d63430f0964b415d83410641ab9d54762 100644
--- a/modules/info/pymod/wrap_info.cc
+++ b/modules/info/pymod/wrap_info.cc
@@ -34,8 +34,6 @@ using namespace boost::python;
using namespace ost;
using namespace ost::info;
-namespace {
-
InfoHandle (*CreateInfoPtr1)()=CreateInfo;
InfoHandle (*CreateInfoPtr2)(const String&)=CreateInfo;
@@ -94,7 +92,7 @@ void info_handle_apply2b(InfoHandle* h, InfoConstVisitor& v, bool b)
h->Apply(v,b);
}
-void info_handle_remove1(InfoHandle* h, InfoPath& path )
+void info_handle_remove1(InfoHandle* h, const String& path )
{
h->Remove(path);
}
@@ -103,7 +101,7 @@ void info_handle_remove2(InfoHandle* h, InfoGroup& group )
{
h->Remove(group);
}
-void info_handle_remove3(InfoHandle* h, InfoPath& path, bool use_defaults )
+void info_handle_remove3(InfoHandle* h, const String& path, bool use_defaults )
{
h->Remove(path,use_defaults);
}
@@ -154,7 +152,6 @@ InfoItem (InfoGroup::*create_item_b)(const String&, int)=&InfoGroup::CreateItem;
InfoItem (InfoGroup::*create_item_c)(const String&, bool)=&InfoGroup::CreateItem;
InfoItem (InfoGroup::*create_item_d)(const String&, Real)=&InfoGroup::CreateItem;
-}
BOOST_PYTHON_MEMBER_FUNCTION_OVERLOADS(getgroup_overloads, GetGroup, 1, 2)
BOOST_PYTHON_MEMBER_FUNCTION_OVERLOADS(retrievegroup_overloads, RetrieveGroup, 1, 2)
diff --git a/modules/io/doc/formats.rst b/modules/io/doc/formats.rst
index 3912141d21a5a59de7aeb94306e7e014890c1069..fc6fee4cb8e12e0b2ed01731d0a213be18270b76 100644
--- a/modules/io/doc/formats.rst
+++ b/modules/io/doc/formats.rst
@@ -71,3 +71,116 @@ Promod
*Format Name*
promod
+
+
+Image File Formats
+--------------------------------------------------------------------------------
+
+DAT
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+*Recognized File Extensions*
+ dat, img
+
+*Format Name*
+ Simple binary format for square images
+
+DF3
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+*Recognized File Extensions*
+ df3
+
+*Format Name*
+ PovRay Density file format
+
+DM3
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+*Recognized File Extensions*
+ dm3
+
+*Format Name*
+ Format used by Gatan Inc.'s Digital Micrograph software
+
+DX
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+*Recognized File Extensions*
+ dx
+
+*Format Name*
+ Format used by the OpenDX software package
+
+IPL
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+*Recognized File Extensions*
+ ipl
+
+*Format Name*
+ Ditabis Micron Image Plate Scanner Format
+
+JPK
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+*Recognized File Extensions*
+ jpk
+
+*Format Name*
+ Format used by JPK Instruments AG's software (Customized Tiff format)
+
+MRC
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+*Recognized File Extensions*
+ map, ccp4, mrc
+
+*Format Name*
+ Format used by the MRC software package
+
+NanoScope
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+*Recognized File Extensions*
+ mod
+
+*Format Name*
+ Format used by software from Veeco
+
+PNG
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+*Recognized File Extensions*
+ png
+
+*Format Name*
+ Portable Network Graphic image format
+
+Situs
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+*Recognized File Extensions*
+ situs, sit
+
+*Format Name*
+ Format used by the Situs software package
+
+SPI
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+*Recognized File Extensions*
+ spi
+
+*Format Name*
+ Format used by the Spider software package
+
+TIFF
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+*Recognized File Extensions*
+ tif, tiff
+
+*Format Name*
+ Tagged Image File Format
+
diff --git a/modules/io/doc/io.rst b/modules/io/doc/io.rst
index 4746f452cf6e72287c54e2e05012fd775d7be3d3..41759d1987ef149bd53ed942fc21814b22ba43c0 100644
--- a/modules/io/doc/io.rst
+++ b/modules/io/doc/io.rst
@@ -5,6 +5,7 @@
:hidden:
formats
+ mmcif
profile
.. module:: ost.io
diff --git a/modules/io/doc/mmcif.rst b/modules/io/doc/mmcif.rst
new file mode 100644
index 0000000000000000000000000000000000000000..7e1c330a4dc4f0efd72e8eb424ef43539c4d4352
--- /dev/null
+++ b/modules/io/doc/mmcif.rst
@@ -0,0 +1,776 @@
+mmCIF File Format
+--------------------------------------------------------------------------------
+
+The mmCIF file format is an alternate container for structural entities, also
+provided by the PDB. Here we describe how to load those files and how to deal
+with information provided above the common PDB format (:class:`MMCifInfo`,
+:class:`MMCifInfoCitation`, :class:`MMCifInfoTransOperation`,
+:class:`MMCifInfoBioUnit`, :class:`MMCifInfoStructDetails`).
+
+
+Loading mmCIF Files
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. autofunction:: ost.io.LoadMMCIF
+
+
+Categories Available
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The following categories of a mmCIF file are considered by the reader:
+
+* ``atom_site``: Used to build the :class:`entity <ost.mol.EntityHandle>`
+* ``entity``: Involved in setting ChainTypes
+* ``entity_poly``: Involved in setting ChainTypes
+* ``citation``: Goes into :class:`MMCifInfoCitation`
+* ``citation_author``: Goes into :class:`MMCifInfoCitation`
+* ``exptl``: Goes into :class:`MMCifInfo` as :attr:`method <MMCifInfo.method>`.
+* ``refine``: Goes into :class:`MMCifInfo` as
+ :attr:`resolution <MMCifInfo.resolution>`.
+* ``pdbx_struct_assembly``: Used for :class:`MMCifInfoBioUnit`.
+* ``pdbx_struct_assembly_gen``: Used for :class:`MMCifInfoBioUnit`.
+* ``pdbx_struct_oper_list``: Used for :class:`MMCifInfoBioUnit`.
+* ``struct``: Details about a structure, stored in
+ :class:`MMCifInfoStructDetails`.
+* ``struct_conf``: Stores secondary structure information (practically helices)
+ in the :class:`entity <ost.mol.EntityHandle>`
+* ``struct_sheet_range``: Stores secondary structure information for sheets in
+ the :class:`entity <ost.mol.EntityHandle>`
+* ``pdbx_database_PDB_obs_spr``: Verbose information on obsoleted/ superseded
+ entries, stored in :class:`MMCifInfoObsolete`.
+* ``struct_ref`` stored in :class:`MMCifInfoStructRef`
+* ``struct_ref_seq`` stored in :class:`MMCifInfoStructRefSeq`
+* ``struct_ref_seq_dif`` stored in :class:`MMCifInfoStructRefDif`
+
+Info Classes
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Information from mmCIF files which goes beyond structural data, is kept in a
+special container, the :class:`MMCifInfo` class. Here is a detailed description
+of the annotation available.
+
+.. class:: MMCifInfo
+
+ This is the container for all bits of non-molecular data pulled from a mmCIF
+ file.
+
+ .. attribute:: citations
+
+ Stores a list of citations (:class:`MMCifInfoCitation`).
+
+ Also available as :meth:`GetCitations`.
+
+ .. attribute:: biounits
+
+ Stores a list of biounits (:class:`MMCifInfoBioUnit`).
+
+ Also available as :meth:`GetBioUnits`.
+
+ .. attribute:: method
+
+ Stores the experimental method used to create the structure.
+
+ Also available as :meth:`GetMethod`. May also be modified by
+ :meth:`SetMethod`.
+
+ .. attribute:: resolution
+
+ Stores the resolution of the crystal structure.
+
+ Also available as :meth:`GetResolution`. May also be modified by
+ :meth:`SetResolution`.
+
+ .. attribute:: operations
+
+ Stores the operations needed to transform a crystal structure into a
+ bio unit.
+
+ Also available as :meth:`GetOperations`. May also be modified by
+ :meth:`AddOperation`.
+
+ .. attribute:: struct_details
+
+ Stores details about the structure in a :class:`MMCifInfoStructDetails`
+ object.
+
+ Also available as :meth:`GetStructDetails`. May also be modified by
+ :meth:`SetStructDetails`.
+
+ .. attribute:: struct_refs
+
+ Lists all links to external databases in the mmCIF file.
+ .. method:: AddCitation(citation)
+
+ Add a citation to the citation list of an info object.
+
+ :param citation: Citation to be added.
+ :type citation: :class:`MMCifInfoCitation`
+
+ .. method:: AddAuthorsToCitation(id, authors)
+
+ Adds a list of authors to a specific citation.
+
+ :param id: identifier of the citation
+ :type id: :class:`str`
+ :param authors: List of authors.
+ :type authors: :class:`~ost.StringList`
+
+ .. method:: GetCitations()
+
+ See :attr:`citations`
+
+ .. method:: AddBioUnit(biounit)
+
+ Add a bio unit to the bio unit list of an info object.
+
+ :param biounit: Bio unit to be added.
+ :type biounit: :class:`MMCifInfoBioUnit`
+
+ .. method:: GetBioUnits()
+
+ See :attr:`biounits`
+
+ .. method:: SetMethod(method)
+
+ See :attr:`method`
+
+ .. method:: GetMethod()
+
+ See :attr:`method`
+
+ .. method:: SetResolution(resolution)
+
+ See :attr:`resolution`
+
+ .. method:: GetResolution()
+
+ See :attr:`resolution`
+
+ .. method:: AddOperation(operation)
+
+ See :attr:`operations`
+
+ .. method:: GetOperations()
+
+ See :attr:`operations`
+
+ .. method:: SetStructDetails(details)
+
+ See :attr:`struct_details`
+
+ .. method:: GetStructDetails()
+
+.. class:: MMCifInfoCitation
+
+ This stores citation information from an input file.
+
+ .. attribute:: id
+
+ Stores an internal identifier for a citation. If not provided, resembles an
+ empty string.
+
+ Also available as :meth:`GetID`. May also be modified by :meth:`SetID`.
+
+ .. attribute:: cas
+
+ Stores a Chemical Abstract Service identifier, if available. If not
+ provided, resembles an empty string.
+
+ Also available as :meth:`GetCAS`. May also be modified by :meth:`SetCas`.
+
+ .. attribute:: isbn
+
+ Stores the ISBN code, presumably for cited books. If not
+ provided, resembles an empty string.
+
+ Also available as :meth:`GetISBN`. May also be modified by :meth:`SetISBN`.
+
+ .. attribute:: published_in
+
+ Stores the book or journal title of a publication. Should take the full
+ title, no abbreviations. If not provided, resembles an empty string.
+
+ Also available as :meth:`GetPublishedIn`. May also be modified by
+ :meth:`SetPublishedIn`.
+
+ .. attribute:: volume
+
+ Supposed to store volume information for journals. Since the volume number
+ is not always a simple integer, it is stored as a string. If not provided,
+ resembles an empty string.
+
+ Also available as :meth:`GetVolume`. May also be modified by
+ :meth:`SetVolume`.
+
+ .. attribute:: page_first
+
+ Stores the first page of a publication. Since the page numbers are not
+ always a simple integers, they are stored as strings. If not provided,
+ resembles empty strings.
+
+ Also available as :meth:`GetPageFirst`. May also be modified by
+ :meth:`SetPageFirst`.
+
+ .. attribute:: page_last
+
+ Stores the last page of a publication. Since the page numbers are not
+ always a simple integers, they are stored as strings. If not provided,
+ resembles empty strings.
+
+ Also available as :meth:`GetPageLast`. May also be modified by
+ :meth:`SetPageLast`.
+
+ .. attribute:: doi
+
+ Stores the Document Object Identifier as used by doi.org for a cited
+ document. If not provided, resembles a empty strings.
+
+ Also available as :meth:`GetDOI`. May also be modified by :meth:`SetDOI`.
+
+ .. attribute:: pubmed
+
+ Stores the PubMed accession number. If not provided, is set to 0.
+
+ Also available as :meth:`GetPubMed`. May also be modified by
+ :meth:`SetPubmed`.
+
+ .. attribute:: year
+
+ Stores the publication year. If not provided, is set to 0.
+
+ Also available as :meth:`GetYear`. May also be modified by :meth:`SetYear`.
+
+ .. attribute:: title
+
+ Stores a title. If not provided, is set to an empty string.
+
+ Also available as :meth:`GetTitle`. May also be modified by
+ :meth:`SetTitle`.
+
+ .. attribute:: authors
+
+ Stores a :class:`~ost.StringList` of authors.
+
+ Also available as :meth:`GetAuthorList`. May also be modified by
+ :meth:`SetAuthorList`.
+
+ .. method:: GetCAS()
+
+ See :attr:`cas`
+
+ .. method:: SetCAS(cas)
+
+ See :attr:`cas`
+
+ .. method:: GetISBN()
+
+ See :attr:`isbn`
+
+ .. method:: SetISBN(isbn)
+
+ See :attr:`isbn`
+
+ .. method:: GetPublishedIn()
+
+ See :attr:`published_in`
+
+ .. method:: SetPublishedIn(title)
+
+ See :attr:`published_in`
+
+ .. method:: GetVolume()
+
+ See :attr:`volume`
+
+ .. method:: SetVolume(volume)
+
+ See :attr:`volume`
+
+ .. method:: GetPageFirst()
+
+ See :attr:`page_first`
+
+ .. method:: SetPageFirst(first)
+
+ See :attr:`page_first`
+
+ .. method:: GetPageLast()
+
+ See :attr:`page_last`
+
+ .. method:: SetPageLast(last)
+
+ See :attr:`page_last`
+
+ .. method:: GetDOI()
+
+ See :attr:`doi`
+
+ .. method:: SetDOI(doi)
+
+ See :attr:`doi`
+
+ .. method:: GetPubMed()
+
+ See :attr:`pubmed`
+
+ .. method:: SetPubMed(no)
+
+ See :attr:`pubmed`
+
+ .. method:: GetYear()
+
+ See :attr:`year`
+
+ .. method:: SetYear(year)
+
+ See :attr:`year`
+
+ .. method:: GetTitle()
+
+ See :attr:`title`
+
+ .. method:: SetTitle(title)
+
+ See :attr:`title`
+
+ .. method:: GetAuthorList()
+
+ See :attr:`authors`
+
+ .. method:: SetAuthorList(list)
+
+ See :attr:`authors`
+
+
+.. class:: MMCifInfoTransOperation
+
+ This stores operations needed to transform an
+ :class:`entity <ost.mol.EntityHandle>` into a bio unit.
+
+ .. attribute:: id
+
+ A unique identifier. If not provided, resembles an empty string.
+
+ Also available as :meth:`GetID`. May also be modified by
+ :meth:`SetID`.
+
+ .. attribute:: type
+
+ Describes the operation. If not provided, resembles an empty string.
+
+ Also available as :meth:`GetType`. May also be modified by
+ :meth:`SetType`.
+
+ .. attribute:: translation
+
+ The translational vector. Also available as :meth:`GetVector`. May also be
+
+ modified by :meth:`SetVector`.
+
+ .. attribute:: rotation
+
+ The rotational matrix. Also available as :meth:`GetMatrix`. May also be
+
+ modified by :meth:`SetMatrix`.
+
+ .. method:: GetID()
+
+ See :attr:`id`
+
+ .. method:: SetID(id)
+
+ See :attr:`id`
+
+ .. method:: GetType()
+
+ See :attr:`type`
+
+ .. method:: SetType(type)
+
+ See :attr:`type`
+
+ .. method:: GetVector()
+
+ See :attr:`translation`
+
+ .. method:: SetVector(x, y, z)
+
+ See :attr:`translation`
+
+ .. method:: GetMatrix()
+
+ See :attr:`rotation`
+
+ .. method:: SetMatrix(i00,i01, i02, i10,i11, i12, i20,i21, i22)
+
+ See :attr:`rotation`
+
+.. class:: MMCifInfoBioUnit
+
+ This stores information how a structure is to be assembled to form the
+ bio unit.
+
+ .. attribute:: details
+
+ Special aspects of the biological assembly. If not provided, resembles an
+ empty string.
+
+ Also available as :meth:`GetDetails`. May also be modified by
+ :meth:`SetDetails`.
+
+ .. attribute:: chains
+
+ Chains involved in this bio unit. If not provided, resembles an empty list.
+
+ Also available as :meth:`GetChainList`. May also be modified by
+ :meth:`AddChain`.
+
+ .. attribute:: operations
+
+ Translations and rotations needed to create the bio unit. Filled with
+ objects of class :class:`MMCifInfoTransOperation`.
+
+ Also available as :meth:`GetOperations`. May be modified by
+ :meth:`AddOperations`
+
+ .. method:: GetDetails()
+
+ See :attr:`details`
+
+ .. method:: SetDetails(details)
+
+ See :attr:`details`
+
+ .. method:: GetChainList()
+
+ See :attr:`chains`
+
+ .. method:: AddChain(chain name)
+
+ See :attr:`chains`
+
+ .. method:: GetOperations()
+
+ See :attr:`operations`
+
+ .. method:: AddOperations(list of operations)
+
+ See :attr:`operations`
+
+.. function:: PDBize(asu, seqres=None, min_polymer_size=10)
+
+ Returns the biological assembly (bio unit) for an entity. The new entity
+ created is well suited to be saved as a PDB file. Therefore the function
+ tries to meet the requirements of single-character chain names. The
+ following measures are taken.
+
+ - All ligands are put into one chain (_)
+ - Water is put into one chain (-)
+ - Each polymer gets its own chain, named A-Z 0-9 a-z.
+ - The description of non-polymer chains will be put into a generic string
+ property called description on the residue level.
+ - ligands which resemble a polymer but have less than min_polymer_size
+ residues are assigned the same numeric residue number. The residues are
+ distinguished by insertion code.
+
+ Since this function is at the moment mainly used to create biounits from
+ mmCIF files to be saved as PDBs, the function assumes that the
+ :ref:`ChainType` properties are set correctly. :func:`ost.conop.ConnectAll`
+ is used to derive connectivity.
+
+ :param asu: Asymmetric unit to work on. Should be created from a mmCIF
+ file.
+ :type asu: :class:`~ost.mol.EntityHandle>`
+ :param seqres: If set to a valid sequence list, the length of the seqres
+ records will be used to determine if a certain chain has the minimally
+ required length.
+ :type seqres: :class:'~ost.seq.SequenceList'
+ :param min_polymer_size: The minimal number of residues a polymer needs to
+ get its own chain. Everything below that number will be sorted into the
+ ligand chain.
+ :type min_polymer_size: int
+
+.. class:: MMCifInfoStructDetails
+
+ Holds details about the structure.
+
+ .. attribute:: entry_id
+
+ Identifier for a curtain data block. If not provided, resembles an empty
+ string.
+
+ Also available as :meth:`GetEntryID`. May also be modified by
+ :meth:`SetEntryID`.
+
+ .. attribute:: title
+
+ Set a title for the structure.
+
+ Also available as :meth:`GetTitle`. May also be modified by
+ :meth:`SetTitle`.
+
+ .. attribute:: casp_flag
+
+ Tells whether this structure was target in some competition.
+
+ Also available as :meth:`GetCASPFlag`. May also be modified by
+ :meth:`SetCASPFlag`.
+
+ .. attribute:: descriptor
+
+ Descriptor for an NDB structure or the unstructured content of a PDB COMPND
+ record.
+
+ Also available as :meth:`GetDescriptor`. May also be modified by
+ :meth:`SetDescriptor`.
+
+ .. attribute:: mass
+
+ Molecular mass of a molecule.
+
+ Also available as :meth:`GetMass`. May also be modified by
+ :meth:`SetMass`.
+
+ .. attribute:: mass_method
+
+ Method used to determine the molecular weight.
+
+ Also available as :meth:`GetMassMethod`. May also be modified by
+ :meth:`SetMassMethod`.
+
+ .. attribute:: model_details
+
+ Details about how the structure was determined.
+
+ Also available as :meth:`GetModelDetails`. May also be modified by
+ :meth:`SetModelDetails`.
+
+ .. attribute:: model_type_details
+
+ Details about how the type of the structure.
+
+ Also available as :meth:`GetModelTypeDetails`. May also be modified by
+ :meth:`SetModelTypeDetails`.
+
+ .. method:: GetEntryID()
+
+ See :attr:`entry_id`
+
+ .. method:: SetEntryID(id)
+
+ See :attr:`entry_id`
+
+ .. method:: GetTitle()
+
+ See :attr:`title`
+
+ .. method:: SetTitle(title)
+
+ See :attr:`title`
+
+ .. method:: GetCASPFlag()
+
+ See :attr:`casp_flag`
+
+ .. method:: SetCASPFlag(flag)
+
+ See :attr:`casp_flag`
+
+ .. method:: GetDescriptor()
+
+ See :attr:`descriptor`
+
+ .. method:: SetDescriptor(descriptor)
+
+ See :attr:`descriptor`
+
+ .. method:: GetMass()
+
+ See :attr:`mass`
+
+ .. method:: SetMass(mass)
+
+ See :attr:`mass`
+
+ .. method:: GetMassMethod()
+
+ See :attr:`mass_method`
+
+ .. method:: SetMassMethod(method)
+
+ See :attr:`mass_method`
+
+ .. method:: GetModelDetails()
+
+ See :attr:`model_details`
+
+ .. method:: SetModelDetails(details)
+
+ See :attr:`model_details`
+
+ .. method:: GetModelTypeDetails()
+
+ See :attr:`model_type_details`
+
+ .. method:: SetModelTypeDetails(details)
+
+ See :attr:`model_type_details`
+
+.. class:: MMCifInfoObsolete
+
+ Holds details on obsolete/ superseded structures.
+
+ .. attribute:: date
+
+ When was the entry replaced?
+
+ Also available as :meth:`GetDate`. May also be modified by
+ :meth:`SetDate`.
+
+ .. attribute:: id
+
+ Type of change. Either *Obsolete* or *Supersede*. Returns a string starting
+ upper case. Has to be set via ``OBSLTE`` or ``SPRSDE``.
+
+ Also available as :meth:`GetID`. May also be modified by
+ :meth:`SetID`.
+
+ .. attribute:: pdb_id
+
+ ID of the replacing entry.
+
+ Also available as :meth:`GetPDBID`. May also be modified by
+ :meth:`SetPDBID`.
+
+ .. attribute:: replace_pdb_id
+
+ ID of the replaced entry.
+
+ Also available as :meth:`GetReplacedPDBID`. May also be modified by
+ :meth:`SetReplacedPDBID`.
+
+ .. method:: GetDate()
+
+ See :attr:`date`
+
+ .. method:: SetDate(date)
+
+ See :attr:`date`
+
+ .. method:: GetID()
+
+ See :attr:`id`
+
+ .. method:: SetID(id)
+
+ See :attr:`id`
+
+ .. method:: GetPDBID()
+
+ See :attr:`pdb_id`
+
+ .. method:: SetPDBID(flag)
+
+ See :attr:`pdb_id`
+
+ .. method:: GetReplacedPDBID()
+
+ See :attr:`replace_pdb_id`
+
+ .. method:: SetReplacedPDBID(descriptor)
+
+ See :attr:`replace_pdb_id`
+
+.. class:: MMCifINfoStructRef
+
+ Holds the information of the struct_ref category. The category describes the
+ link of polymers in the mmCIF file to sequences stored in external databases
+ such as uniprot. The related categories ``struct_ref_seq`` and
+ ``struct_ref_seq_dif`` also list differences between the sequences of the
+ deposited structure and the sequences in the database. A promintent example of
+ such differences include point mutations and/or expression tags.
+
+ .. attribute:: db_name
+
+
+ Name of the external database, for example UNP for uniprot.
+
+ :type: :class:`str`
+
+
+ .. attribute:: db_id
+
+ Name of the reference sequence in the database pointed to by :attr:`db_name`.
+
+ :type: :class:`str`
+
+ .. attribute:: db_access
+
+ Alternative accession code for the sequence in the database pointed to by
+ :attr:`db_name`.
+
+ :type: :class:`str`
+
+ .. method:: GetAlignedSeq(name)
+
+ Returns the aligned sequence for the given name, None if the sequence does
+ not exist.
+
+ .. attribute:: aligned_seqs
+
+ List of aligned sequences (all entries of the struct_ref_seq category
+ mapping to this struct_ref).
+
+.. class:: MMCifInfoStructRefSeq
+
+ An aligned range of residues between a sequence in a reference database and the
+ deposited sequence.
+
+ .. attribute:: align_id
+
+ Uniquely identifies every struct_ref_seq item in the mmCIF file.
+ :type: :class:`str`
+
+ .. attribute:: seq_begin
+ seq_end
+ The starting point (1-based) and end point of the aligned range in the
+ deposited sequence, respectively.
+
+ :type: :class:`int`
+
+ .. attribute:: db_begin
+ db_end
+ The starting point (1-based) and end point of the aligned range in the
+ database sequence, respectively.
+
+ :type: :class:`int`
+
+ .. attribute:: difs
+
+ List of differences between the deposited sequence and the sequence in the
+ database.
+
+ .. attribute:: chain_name
+
+ Chain name of the polymer in the mmCIF file.
+
+.. class:: MMCifInfoStructRefSeqDif
+
+ A particular difference between the deposited sequence and the sequence in
+ the database.
+
+ .. attribute:: rnum
+
+ The residue number (1-based) of the residue in the deposited sequence
+
+ :type: :class:`int`
+
+ .. attribute:: details
+
+ A textual description of the difference, e.g. point mutation,
+ expressiontag, purification artifact.
+
+ :type: :class:`str`
+.. LocalWords: cas isbn pubmed asu seqres conop ConnectAll casp COMPND OBSLTE
+.. LocalWords: SPRSDE pdb func
diff --git a/modules/io/pymod/CMakeLists.txt b/modules/io/pymod/CMakeLists.txt
index 902089f7f0d3e28b219993f01c79852ac37135c2..007569fff38887504ed15d21231b2b5d4464b346 100644
--- a/modules/io/pymod/CMakeLists.txt
+++ b/modules/io/pymod/CMakeLists.txt
@@ -1,6 +1,7 @@
set(OST_IO_PYMOD_SOURCES
wrap_io.cc
export_pdb_io.cc
+ export_mmcif_io.cc
)
if (ENABLE_IMG)
@@ -13,10 +14,11 @@ set(OST_IO_PYMOD_MODULES
repository.py
)
-
-pymod(NAME io CPP ${OST_IO_PYMOD_SOURCES} PY ${OST_IO_PYMOD_MODULES})
-if (STATIC_LIBRARIES)
- message("adding zlib libraries")
- target_link_libraries(_io ${ZLIB_LIBRARIES})
+if (NOT ENABLE_STATIC)
+ pymod(NAME io CPP ${OST_IO_PYMOD_SOURCES} PY ${OST_IO_PYMOD_MODULES})
+ if (STATIC_LIBRARIES)
+ message("adding zlib libraries")
+ target_link_libraries(_ost_io ${ZLIB_LIBRARIES})
+ endif()
endif()
diff --git a/modules/io/pymod/__init__.py b/modules/io/pymod/__init__.py
index 74047dec07c568e5514e3dfcde4a7df9ec9c02a9..95ea418b344a21910a925f463151d34af4a8eb22 100644
--- a/modules/io/pymod/__init__.py
+++ b/modules/io/pymod/__init__.py
@@ -19,7 +19,7 @@
import os, tempfile, ftplib, httplib
from _ost_io import *
-from ost import mol, conop
+from ost import mol, geom, conop
profiles=None
@@ -86,9 +86,9 @@ def LoadPDB(filename, restrict_chains="", no_hetatms=None,
fault_tolerant=None, load_multi=False, quack_mode=None,
join_spread_atom_records=None, calpha_only=None,
profile='DEFAULT', remote=False, dialect=None,
- strict_hydrogens=None, seqres=False):
+ strict_hydrogens=None, seqres=False, bond_feasibility_check=None):
"""
- Load PDB file from disk and returns one or more entities. Several options
+ Load PDB file from disk and return one or more entities. Several options
allow to customize the exact behaviour of the PDB import. For more information
on these options, see :doc:`profile`.
@@ -147,6 +147,7 @@ def LoadPDB(filename, restrict_chains="", no_hetatms=None,
prof.quack_mode=_override(prof.quack_mode, quack_mode)
prof.strict_hydrogens=_override(prof.strict_hydrogens, strict_hydrogens)
prof.fault_tolerant=_override(prof.fault_tolerant, fault_tolerant)
+ prof.bond_feasibility_check=_override(prof.bond_feasibility_check, bond_feasibility_check)
prof.join_spread_atom_records=_override(prof.join_spread_atom_records,
join_spread_atom_records)
@@ -164,6 +165,7 @@ def LoadPDB(filename, restrict_chains="", no_hetatms=None,
elif prof.dialect=='CHARMM':
builder.dialect=conop.CHARMM_DIALECT
builder.strict_hydrogens=prof.strict_hydrogens
+ builder.bond_feasibility_check=prof.bond_feasibility_check
reader=PDBReader(filename, prof)
reader.read_seqres=seqres
try:
@@ -175,7 +177,7 @@ def LoadPDB(filename, restrict_chains="", no_hetatms=None,
conop_inst.ConnectAll(builder, ent, 0)
ent_list.append(ent)
if len(ent_list)==0:
- raise IOError("File doesn't contain any entities")
+ raise IOError("File '%s' doesn't contain any entities" % filename)
return ent_list
else:
ent=mol.CreateEntity()
@@ -183,7 +185,7 @@ def LoadPDB(filename, restrict_chains="", no_hetatms=None,
reader.Import(ent, restrict_chains)
conop_inst.ConnectAll(builder, ent, 0)
else:
- raise IOError("File doesn't contain any entities")
+ raise IOError("File '%s' doesn't contain any entities" % filename)
if seqres:
return ent, reader.seqres
return ent
@@ -192,10 +194,12 @@ def LoadPDB(filename, restrict_chains="", no_hetatms=None,
def SavePDB(models, filename, dialect=None, pqr=False, profile='DEFAULT'):
"""
- Save entity or list of entities to disk. If a list of entities is supplied the
- PDB file will be saved as a multi PDB file. Each of the entities is wrapped
- into a MODEL/ENDMDL pair.
-
+ Save entity or list of entities to disk. If a list of entities is supplied
+ the PDB file will be saved as a multi PDB file. Each of the entities is
+ wrapped into a MODEL/ENDMDL pair.
+
+ If the atom number exceeds 99999, '*****' is used.
+
:param models: The entity or list of entities (handles or views) to be saved
:param filename: The filename
:type filename: string
@@ -264,6 +268,190 @@ def LoadCHARMMTraj(crd, dcd_file=None, profile='CHARMM',
raise ValueError("No DCD filename given")
return LoadCHARMMTraj_(crd, dcd_file, stride, lazy_load)
+def LoadMMCIF(filename, restrict_chains="", fault_tolerant=None, calpha_only=None, profile='DEFAULT', remote=False, strict_hydrogens=None, seqres=False, info=False):
+ """
+ Load MMCIF file from disk and return one or more entities. Several options
+ allow to customize the exact behaviour of the MMCIF import. For more
+ information on these options, see :doc:`profile`.
+
+ Residues are flagged as ligand if they are mentioned in a HET record.
+
+ :param restrict_chains: If not an empty string, only chains listed in the
+ string will be imported.
+
+ :param fault_tolerant: Enable/disable fault-tolerant import. If set, overrides
+ the value of :attr:`IOProfile.fault_tolerant`.
+
+ :param remote: If set to true, the method tries to load the pdb from the
+ remote pdb repository www.pdb.org. The filename is then interpreted as the
+ pdb id.
+
+ :rtype: :class:`~ost.mol.EntityHandle`.
+
+ :param strict_hydrogens: If set, overrides the value of
+ :attr:`IOProfile.strict_hydrogens`.
+
+ :param seqres: Whether to read SEQRES records. If set to true, the loaded
+ entity and seqres entry will be returned as second item.
+
+ :param info: Whether to return an info container with the other output.
+ Returns a :class:`MMCifInfo` object as last item.
+
+ :raises: :exc:`~ost.io.IOException` if the import fails due to an erroneous
+ or inexistent file
+ """
+ def _override(val1, val2):
+ if val2!=None:
+ return val2
+ else:
+ return val1
+ if isinstance(profile, str):
+ prof = profiles[profile].Copy()
+ else:
+ prof = profile.Copy()
+
+ prof.calpha_only=_override(prof.calpha_only, calpha_only)
+ prof.strict_hydrogens=_override(prof.strict_hydrogens, strict_hydrogens)
+ prof.fault_tolerant=_override(prof.fault_tolerant, fault_tolerant)
+
+ if remote:
+ output_dir = tempfile.gettempdir()
+ if __GetModelFromPDB(filename, output_dir):
+ filename = os.path.join(output_dir, 'pdb%s.ent.gz' % filename)
+ else:
+ raise IOError('Can not load PDB %s from www.pdb.org'%filename)
+
+ conop_inst = conop.Conopology.Instance()
+ builder = conop_inst.GetBuilder("DEFAULT")
+
+ builder.strict_hydrogens = prof.strict_hydrogens
+
+ try:
+ ent = mol.CreateEntity()
+ reader = MMCifReader(filename, ent, prof)
+ reader.read_seqres = seqres
+ #if reader.HasNext():
+ reader.Parse()
+ conop_inst.ConnectAll(builder, ent, 0)
+ #else:
+ # raise IOError("File doesn't contain any entities")
+ if seqres and info:
+ return ent, reader.seqres, reader.info
+ if seqres:
+ return ent, reader.seqres
+ if info:
+ return ent, reader.info
+ return ent
+ except:
+ raise
+
+# this function uses a dirty trick: should be a member of MMCifInfoBioUnit
+# which is totally C++, but we want the method in Python... so we define it
+# here (__init__) and add it as a member to the class. With this, the first
+# arguement is the usual 'self'.
+# documentation for this function was moved to mmcif.rst,
+# MMCifInfoBioUnit.PDBize, since this function is not included in SPHINX.
+def _PDBize(biounit, asu, seqres=None, min_polymer_size=10):
+ def _CopyAtoms(src_res, dst_res, edi, trans=geom.Mat4()):
+ for atom in src_res.atoms:
+ tmp_pos = geom.Vec4(atom.pos)
+ new_atom=edi.InsertAtom(dst_res, atom.name, geom.Vec3(trans*tmp_pos),
+ element=atom.element,
+ occupancy=atom.occupancy,
+ b_factor=atom.b_factor,
+ is_hetatm=atom.is_hetatom)
+
+ chain_names='ABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789abcdefghijklmnopqrstuvwxyz'
+ # create list of operations
+ # for cartesian products, operations are stored in a list, multiplied with
+ # the next list of operations and re-stored... until all lists of operations
+ # are multiplied in an all-against-all manner.
+ operations = biounit.GetOperations()
+ trans_matrices = list()
+ if len(operations) > 0:
+ for op in operations[0]:
+ rot = geom.Mat4()
+ rot.PasteRotation(op.rotation)
+ trans = geom.Mat4()
+ trans.PasteTranslation(op.translation)
+ tr = geom.Mat4()
+ tr = trans * rot
+ trans_matrices.append(tr)
+ for op_n in range(1, len(operations)):
+ tmp_ops = list()
+ for o in operations[op_n]:
+ rot = geom.Mat4()
+ rot.PasteRotation(o.rotation)
+ trans = geom.Mat4()
+ trans.PasteTranslation(o.translation)
+ tr = geom.Mat4()
+ tr = trans * rot
+ for t_o in trans_matrices:
+ tp = t_o * tr
+ tmp_ops.append(tp)
+ trans_matrices = tmp_ops
+ # select chains into a view as basis for each transformation
+ assu = asu.Select('cname=' + ','.join(biounit.GetChainList()))
+ # use each transformation on the view, store as entity and transform, PDBize
+ # the result while adding everything to one large entity
+ pdb_bu = mol.CreateEntity()
+ edi = pdb_bu.EditXCS(mol.BUFFERED_EDIT)
+ cur_chain_name = 0
+ water_chain = mol.ChainHandle()
+ ligand_chain = mol.ChainHandle()
+ for tr in trans_matrices:
+ # do a PDBize, add each new entity to the end product
+ for chain in assu.chains:
+ residue_count = len(chain.residues)
+ if seqres:
+ seqres_chain = seqres.FindSequence(chain.name)
+ if seqres_chain.IsValid():
+ residue_count = len(seqres_chain)
+ if chain.is_polymer and residue_count >= min_polymer_size:
+ if len(chain_names) == cur_chain_name:
+ raise RuntimeError('Running out of chain names')
+ new_chain = edi.InsertChain(chain_names[cur_chain_name])
+ cur_chain_name += 1
+ edi.SetChainDescription(new_chain, chain.description)
+ edi.SetChainType(new_chain, chain.type)
+ new_chain.SetStringProp('original_name', chain.name)
+ for res in chain.residues:
+ new_res = edi.AppendResidue(new_chain, res.name, res.number)
+ _CopyAtoms(res, new_res, edi, tr)
+ elif chain.type == mol.CHAINTYPE_WATER:
+ if not water_chain.IsValid():
+ # water gets '-' as name
+ water_chain = edi.InsertChain('-')
+ edi.SetChainDescription(water_chain, chain.description)
+ edi.SetChainType(water_chain, chain.type)
+ for res in chain.residues:
+ new_res = edi.AppendResidue(water_chain, res.name)
+ new_res.SetStringProp('type', mol.StringFromChainType(chain.type))
+ new_res.SetStringProp('description', chain.description)
+ _CopyAtoms(res, new_res, edi, tr)
+ else:
+ if not ligand_chain.IsValid():
+ # all ligands, put in one chain, are named '_'
+ ligand_chain = edi.InsertChain('_')
+ last_rnum = 0
+ else:
+ last_rnum = ligand_chain.residues[-1].number.num
+ residues=chain.residues
+ ins_code='\0'
+ if len(residues)>1:
+ ins_code='A'
+ for res in chain.residues:
+ new_res = edi.AppendResidue(ligand_chain, res.name,
+ mol.ResNum(last_rnum+1, ins_code))
+ new_res.SetStringProp('description', chain.description)
+ new_res.SetStringProp('type', mol.StringFromChainType(chain.type))
+ ins_code = chr(ord(ins_code)+1)
+ _CopyAtoms(res, new_res, edi, tr)
+ conop.ConnectAll(pdb_bu)
+ return pdb_bu
+
+MMCifInfoBioUnit.PDBize = _PDBize
+
## \example fft_li.py
#
# This scripts loads one or more images and shows their Fourier Transforms on
diff --git a/modules/io/pymod/export_map_io.cc b/modules/io/pymod/export_map_io.cc
index beb7601bc63916a64e52e74035c853ebbb778662..afe494d1997b4d1720fe49592b35c36e51976980 100644
--- a/modules/io/pymod/export_map_io.cc
+++ b/modules/io/pymod/export_map_io.cc
@@ -27,6 +27,7 @@
#include <ost/io/img/map_io_dat_handler.hh>
#include <ost/io/img/map_io_jpk_handler.hh>
#include <ost/io/img/map_io_nanoscope_handler.hh>
+#include <ost/io/img/map_io_ipl_handler.hh>
#include <ost/io/img/image_format.hh>
#include <ost/io/img/load_map.hh>
@@ -79,18 +80,17 @@ void export_map_io()
.export_values()
;
- enum_<Subformat>("Format")
+ enum_<Subformat>("Subformat")
.value("MRC_NEW_FORMAT", MRC_NEW_FORMAT)
.value("MRC_OLD_FORMAT", MRC_OLD_FORMAT)
.value("MRC_AUTO_FORMAT", MRC_AUTO_FORMAT)
.export_values()
;
+
class_<ImageFormatBase>("ImageFormatBase",no_init)
.def("GetMaximum", &ImageFormatBase::GetMaximum)
- .def("SetMaximum", &ImageFormatBase::GetMaximum)
.def("GetMinimum", &ImageFormatBase::GetMinimum)
- .def("SetMinimum", &ImageFormatBase::GetMinimum)
;
class_<DX, bases<ImageFormatBase> >("DX", init<bool>(arg("normalize_on_save") = false))
@@ -154,6 +154,13 @@ void export_map_io()
.def("GetBitDepth", &DAT::GetBitDepth)
;
+ class_<IPL, bases<ImageFormatBase> >("IPL", init<bool,Format>((arg("normalize_on_save") = true,arg("format")=OST_DEFAULT_FORMAT)))
+ .def("SetNormalizeOnSave", &IPL::SetNormalizeOnSave)
+ .def("GetNormalizeOnSave", &IPL::GetNormalizeOnSave)
+ .def("SetBitDepth", &IPL::SetBitDepth)
+ .def("GetBitDepth", &IPL::GetBitDepth)
+ ;
+
class_<JPK, bases<TIF> >("JPK", init<boost::logic::tribool,Format,bool,bool,int>
((arg("normalize_on_save") = boost::logic::tribool(boost::logic::indeterminate),arg("format")=OST_DEFAULT_FORMAT,arg("signed")=false,arg("phasecolor")=false,arg("subimage") = -1)))
;
diff --git a/modules/io/pymod/export_mmcif_io.cc b/modules/io/pymod/export_mmcif_io.cc
new file mode 100644
index 0000000000000000000000000000000000000000..70e6b46590148293e396cd5dc28b9766fdda3ce5
--- /dev/null
+++ b/modules/io/pymod/export_mmcif_io.cc
@@ -0,0 +1,296 @@
+//------------------------------------------------------------------------------
+// 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
+//------------------------------------------------------------------------------
+#include <boost/python.hpp>
+#include <boost/shared_ptr.hpp>
+#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
+using namespace boost::python;
+
+#include <ost/io/mol/io_profile.hh>
+#include <ost/io/mol/mmcif_reader.hh>
+#include <ost/io/mol/mmcif_info.hh>
+using namespace ost;
+using namespace ost::io;
+using namespace ost::mol;
+
+void export_mmcif_io()
+{
+ class_<MMCifReader, boost::noncopyable>("MMCifReader", init<const String&, EntityHandle&, const IOProfile&>())
+ .def("Parse", &MMCifReader::Parse)
+ .def("SetRestrictChains", &MMCifReader::SetRestrictChains)
+ .def("SetReadCanonicalSeqRes", &MMCifReader::SetReadCanonicalSeqRes)
+ .def("GetSeqRes", &MMCifReader::GetSeqRes)
+ .def("GetInfo", make_function(&MMCifReader::GetInfo,
+ return_value_policy<copy_const_reference>()))
+ .add_property("restrict_chains",
+ make_function(&MMCifReader::GetRestrictChains,
+ return_value_policy<copy_const_reference>()),
+ &MMCifReader::SetRestrictChains)
+ .add_property("seqres", &MMCifReader::GetSeqRes)
+ .add_property("read_seqres", &MMCifReader::GetReadSeqRes,
+ &MMCifReader::SetReadSeqRes)
+ .add_property("info", make_function(&MMCifReader::GetInfo,
+ return_value_policy<copy_const_reference>()))
+ ;
+
+ class_<MMCifInfoCitation>("MMCifInfoCitation", init<>())
+ .def("SetID", &MMCifInfoCitation::SetID)
+ .def("GetID", &MMCifInfoCitation::GetID)
+ .def("SetCAS", &MMCifInfoCitation::SetCAS)
+ .def("GetCAS", &MMCifInfoCitation::GetCAS)
+ .def("SetISBN", &MMCifInfoCitation::SetISBN)
+ .def("GetISBN", &MMCifInfoCitation::GetISBN)
+ .def("SetPublishedIn", &MMCifInfoCitation::SetPublishedIn)
+ .def("GetPublishedIn", &MMCifInfoCitation::GetPublishedIn)
+ .def("SetVolume", &MMCifInfoCitation::SetVolume)
+ .def("GetVolume", &MMCifInfoCitation::GetVolume)
+ .def("SetPageFirst", &MMCifInfoCitation::SetPageFirst)
+ .def("GetPageFirst", &MMCifInfoCitation::GetPageFirst)
+ .def("SetPageLast", &MMCifInfoCitation::SetPageLast)
+ .def("GetPageLast", &MMCifInfoCitation::GetPageLast)
+ .def("SetDOI", &MMCifInfoCitation::SetDOI)
+ .def("GetDOI", &MMCifInfoCitation::GetDOI)
+ .def("SetPubMed", &MMCifInfoCitation::SetPubMed)
+ .def("GetPubMed", &MMCifInfoCitation::GetPubMed)
+ .def("SetYear", &MMCifInfoCitation::SetYear)
+ .def("GetYear", &MMCifInfoCitation::GetYear)
+ .def("SetTitle", &MMCifInfoCitation::SetTitle)
+ .def("GetTitle", &MMCifInfoCitation::GetTitle)
+ .def("SetAuthorList", &MMCifInfoCitation::SetAuthorList)
+ .def("GetAuthorList", make_function(&MMCifInfoCitation::GetAuthorList,
+ return_value_policy<copy_const_reference>()))
+ .add_property("id", &MMCifInfoCitation::GetID, &MMCifInfoCitation::SetID)
+ .add_property("cas", &MMCifInfoCitation::GetCAS, &MMCifInfoCitation::SetCAS)
+ .add_property("isbn", &MMCifInfoCitation::GetISBN,
+ &MMCifInfoCitation::SetISBN)
+ .add_property("published_in", &MMCifInfoCitation::GetPublishedIn,
+ &MMCifInfoCitation::SetPublishedIn)
+ .add_property("volume", &MMCifInfoCitation::GetVolume,
+ &MMCifInfoCitation::SetVolume)
+ .add_property("page_first", &MMCifInfoCitation::GetPageFirst,
+ &MMCifInfoCitation::SetPageFirst)
+ .add_property("page_last", &MMCifInfoCitation::GetPageLast,
+ &MMCifInfoCitation::SetPageLast)
+ .add_property("doi", &MMCifInfoCitation::GetDOI, &MMCifInfoCitation::SetDOI)
+ .add_property("pubmed", &MMCifInfoCitation::GetPubMed,
+ &MMCifInfoCitation::SetPubMed)
+ .add_property("year", &MMCifInfoCitation::GetYear,
+ &MMCifInfoCitation::SetYear)
+ .add_property("title", &MMCifInfoCitation::GetTitle,
+ &MMCifInfoCitation::SetTitle)
+ .add_property("authors", make_function(&MMCifInfoCitation::GetAuthorList,
+ return_value_policy<copy_const_reference>()),
+ &MMCifInfoCitation::SetAuthorList)
+ ;
+
+ typedef std::vector<MMCifInfoCitation> MMCifInfoCitationList;
+ class_<std::vector<MMCifInfoCitation> >("MMCifInfoCitationList", init<>())
+ .def(vector_indexing_suite<std::vector<MMCifInfoCitation> >())
+ ;
+
+
+ class_<MMCifInfoTransOp, MMCifInfoTransOpPtr>("MMCifInfoTransOp", init<>())
+ .def("SetID", &MMCifInfoTransOp::SetID)
+ .def("GetID", &MMCifInfoTransOp::GetID)
+ .def("SetType", &MMCifInfoTransOp::SetType)
+ .def("GetType", &MMCifInfoTransOp::GetType)
+ .def("SetVector", &MMCifInfoTransOp::SetVector)
+ .def("GetVector", &MMCifInfoTransOp::GetVector)
+ .def("SetMatrix", &MMCifInfoTransOp::SetMatrix)
+ .def("GetMatrix", &MMCifInfoTransOp::GetMatrix)
+ .add_property("id", &MMCifInfoTransOp::GetID,
+ &MMCifInfoTransOp::SetID)
+ .add_property("type", &MMCifInfoTransOp::GetType,
+ &MMCifInfoTransOp::SetType)
+ .add_property("translation", &MMCifInfoTransOp::GetVector,
+ &MMCifInfoTransOp::SetVector)
+ .add_property("rotation", &MMCifInfoTransOp::GetMatrix,
+ &MMCifInfoTransOp::SetMatrix)
+ ;
+
+ typedef std::vector<MMCifInfoTransOp> MMCifInfoTransOpList;
+ class_<std::vector<MMCifInfoTransOp> >("MMCifInfoTransOpList", init<>())
+ .def(vector_indexing_suite<std::vector<MMCifInfoTransOp> >())
+ ;
+
+ typedef std::vector<MMCifInfoTransOpPtr> MMCifInfoTransOpPtrList;
+ class_<std::vector<MMCifInfoTransOpPtr> >("MMCifInfoTransOpPtrList", init<>())
+ .def(vector_indexing_suite<std::vector<MMCifInfoTransOpPtr>, true >())
+ ;
+
+ typedef std::vector<MMCifInfoTransOpPtrList > MMCifInfoTransOpPtrListList;
+ class_<std::vector<MMCifInfoTransOpPtrList > >("MMCifInfoTransOpPtrListList",
+ init<>())
+ .def(vector_indexing_suite<std::vector<MMCifInfoTransOpPtrList >, true >())
+ ;
+ class_<MMCifInfoStructRef, MMCifInfoStructRefPtr>("MMCifInfoStructRef", no_init)
+ .add_property("id", make_function(&MMCifInfoStructRef::GetID,
+ return_value_policy<copy_const_reference>()))
+ .add_property("db_name", make_function(&MMCifInfoStructRef::GetDBName,
+ return_value_policy<copy_const_reference>()))
+ .add_property("db_id", make_function(&MMCifInfoStructRef::GetDBID,
+ return_value_policy<copy_const_reference>()))
+ .add_property("entity_id", make_function(&MMCifInfoStructRef::GetEntityID,
+ return_value_policy<copy_const_reference>()))
+ .add_property("db_access", make_function(&MMCifInfoStructRef::GetDBAccess,
+ return_value_policy<copy_const_reference>()))
+ .def("GetAlignedSeq", &MMCifInfoStructRef::GetAlignedSeq, arg("align_id"))
+ .def("GetAlignedSeqs", &MMCifInfoStructRef::GetAlignedSeqs)
+ .add_property("aligned_seqs", &MMCifInfoStructRef::GetAlignedSeqs)
+ ;
+ class_<MMCifInfoStructRefSeq, MMCifInfoStructRefSeqPtr>("MMCifInfoStructRefSeq", no_init)
+ .add_property("align_id", make_function(&MMCifInfoStructRefSeq::GetID,
+ return_value_policy<copy_const_reference>()))
+ .add_property("chain_name", make_function(&MMCifInfoStructRefSeq::GetChainName,
+ return_value_policy<copy_const_reference>()))
+ .add_property("seq_begin", &MMCifInfoStructRefSeq::GetSeqBegin)
+ .add_property("seq_end", &MMCifInfoStructRefSeq::GetSeqEnd)
+ .add_property("db_begin", &MMCifInfoStructRefSeq::GetDBBegin)
+ .add_property("db_end", &MMCifInfoStructRefSeq::GetDBEnd)
+ .add_property("difs", make_function(&MMCifInfoStructRefSeq::GetDifs,
+ return_value_policy<copy_const_reference>()))
+ ;
+ class_<MMCifInfoStructRefSeqDif,
+ MMCifInfoStructRefSeqDifPtr>("MMCifInfoStructRefSeqDif", no_init)
+ .add_property("details", make_function(&MMCifInfoStructRefSeqDif::GetDetails,
+ return_value_policy<copy_const_reference>()))
+ .add_property("seq_rnum", &MMCifInfoStructRefSeqDif::GetSeqRNum)
+ .add_property("db_rnum", &MMCifInfoStructRefSeqDif::GetDBRNum)
+ ;
+ class_<MMCifInfoBioUnit>("MMCifInfoBioUnit", init<>())
+ .def("SetDetails", &MMCifInfoBioUnit::SetDetails)
+ .def("GetDetails", &MMCifInfoBioUnit::GetDetails)
+ .def("AddChain", &MMCifInfoBioUnit::AddChain)
+ .def("GetChainList", make_function(&MMCifInfoBioUnit::GetChainList,
+ return_value_policy<copy_const_reference>()))
+ .def("AddOperations", &MMCifInfoBioUnit::AddOperations)
+ .def("GetOperations", make_function(&MMCifInfoBioUnit::GetOperations,
+ return_value_policy<copy_const_reference>()))
+ .add_property("details", &MMCifInfoBioUnit::GetDetails,
+ &MMCifInfoBioUnit::SetDetails)
+ .add_property("chains", make_function(&MMCifInfoBioUnit::GetChainList,
+ return_value_policy<copy_const_reference>()))
+ .add_property("operations", make_function(&MMCifInfoBioUnit::GetOperations,
+ return_value_policy<copy_const_reference>()))
+ ;
+
+ class_<MMCifInfoStructRefs>("MMCifInfoStructRefs", init<>())
+ .def(vector_indexing_suite<MMCifInfoStructRefs, true>())
+ ;
+ class_<MMCifInfoStructRefSeqs>("MMCifInfoStructRefSeqs", init<>())
+ .def(vector_indexing_suite<MMCifInfoStructRefSeqs, true>())
+ ;
+ class_<MMCifInfoStructRefSeqDifs>("MMCifInfoStructRefSeqDifs", init<>())
+ .def(vector_indexing_suite<MMCifInfoStructRefSeqDifs, true>())
+ ;
+ typedef std::vector<MMCifInfoBioUnit> MMCifInfoBioUnitList;
+ class_<std::vector<MMCifInfoBioUnit> >("MMCifInfoBioUnitList", init<>())
+ .def(vector_indexing_suite<std::vector<MMCifInfoBioUnit> >())
+ ;
+
+ class_<MMCifInfoStructDetails>("MMCifInfoStructDetails", init<>())
+ .def("SetEntryID", &MMCifInfoStructDetails::SetEntryID)
+ .def("GetEntryID", &MMCifInfoStructDetails::GetEntryID)
+ .def("SetTitle", &MMCifInfoStructDetails::SetTitle)
+ .def("GetTitle", &MMCifInfoStructDetails::GetTitle)
+ .def("SetCASPFlag", &MMCifInfoStructDetails::SetCASPFlag)
+ .def("GetCASPFlag", &MMCifInfoStructDetails::GetCASPFlag)
+ .def("SetDescriptor", &MMCifInfoStructDetails::SetDescriptor)
+ .def("GetDescriptor", &MMCifInfoStructDetails::GetDescriptor)
+ .def("SetMass", &MMCifInfoStructDetails::SetMass)
+ .def("GetMass", &MMCifInfoStructDetails::GetMass)
+ .def("SetMassMethod", &MMCifInfoStructDetails::SetMassMethod)
+ .def("GetMassMethod", &MMCifInfoStructDetails::GetMassMethod)
+ .def("SetModelDetails", &MMCifInfoStructDetails::SetModelDetails)
+ .def("GetModelDetails", &MMCifInfoStructDetails::GetModelDetails)
+ .def("SetModelTypeDetails", &MMCifInfoStructDetails::SetModelTypeDetails)
+ .def("GetModelTypeDetails", &MMCifInfoStructDetails::GetModelTypeDetails)
+ .add_property("entry_id", &MMCifInfoStructDetails::GetEntryID,
+ &MMCifInfoStructDetails::SetEntryID)
+ .add_property("title", &MMCifInfoStructDetails::GetTitle,
+ &MMCifInfoStructDetails::SetTitle)
+ .add_property("casp_flag", &MMCifInfoStructDetails::GetCASPFlag,
+ &MMCifInfoStructDetails::SetCASPFlag)
+ .add_property("descriptor", &MMCifInfoStructDetails::GetDescriptor,
+ &MMCifInfoStructDetails::SetDescriptor)
+ .add_property("mass", &MMCifInfoStructDetails::GetMass,
+ &MMCifInfoStructDetails::SetMass)
+ .add_property("mass_method", &MMCifInfoStructDetails::GetMassMethod,
+ &MMCifInfoStructDetails::SetMassMethod)
+ .add_property("model_details", &MMCifInfoStructDetails::GetModelDetails,
+ &MMCifInfoStructDetails::SetModelDetails)
+ .add_property("model_type_details",
+ &MMCifInfoStructDetails::GetModelTypeDetails,
+ &MMCifInfoStructDetails::SetModelTypeDetails)
+ ;
+
+ class_<MMCifInfoObsolete>("MMCifInfoObsolete", init<>())
+ .def("SetDate", &MMCifInfoObsolete::SetDate)
+ .def("GetDate", &MMCifInfoObsolete::GetDate)
+ .def("SetID", &MMCifInfoObsolete::SetID)
+ .def("GetID", &MMCifInfoObsolete::GetID)
+ .def("SetPDBID", &MMCifInfoObsolete::SetPDBID)
+ .def("GetPDBID", &MMCifInfoObsolete::GetPDBID)
+ .def("SetReplacedPDBID", &MMCifInfoObsolete::SetReplacedPDBID)
+ .def("GetReplacedPDBID", &MMCifInfoObsolete::GetReplacedPDBID)
+ .add_property("date", &MMCifInfoObsolete::GetDate,
+ &MMCifInfoObsolete::SetDate)
+ .add_property("id", &MMCifInfoObsolete::GetID,
+ &MMCifInfoObsolete::SetID)
+ .add_property("pdb_id", &MMCifInfoObsolete::GetPDBID,
+ &MMCifInfoObsolete::SetPDBID)
+ .add_property("replace_pdb_id", &MMCifInfoObsolete::GetReplacedPDBID,
+ &MMCifInfoObsolete::SetReplacedPDBID)
+ ;
+
+ class_<MMCifInfo>("MMCifInfo", init<>())
+ .def("AddCitation", &MMCifInfo::AddCitation)
+ .def("GetCitations", make_function(&MMCifInfo::GetCitations,
+ return_value_policy<copy_const_reference>()))
+ .def("AddBioUnit", &MMCifInfo::AddBioUnit)
+ .def("GetBioUnits", make_function(&MMCifInfo::GetBioUnits,
+ return_value_policy<copy_const_reference>()))
+ .def("SetMethod", &MMCifInfo::SetMethod)
+ .def("GetMethod", &MMCifInfo::GetMethod)
+ .def("SetResolution", &MMCifInfo::SetResolution)
+ .def("GetResolution", &MMCifInfo::GetResolution)
+ .def("AddAuthorsToCitation", &MMCifInfo::AddAuthorsToCitation)
+ .def("AddOperation", &MMCifInfo::AddOperation)
+ .def("GetOperations", make_function(&MMCifInfo::GetOperations,
+ return_value_policy<copy_const_reference>()))
+ .def("SetStructDetails", &MMCifInfo::SetStructDetails)
+ .def("GetStructDetails", &MMCifInfo::GetStructDetails)
+ .def("SetObsoleteInfo", &MMCifInfo::SetObsoleteInfo)
+ .def("GetObsoleteInfo", &MMCifInfo::GetObsoleteInfo)
+ .add_property("citations", make_function(&MMCifInfo::GetCitations,
+ return_value_policy<copy_const_reference>()))
+ .add_property("biounits", make_function(&MMCifInfo::GetBioUnits,
+ return_value_policy<copy_const_reference>()))
+ .add_property("method", &MMCifInfo::GetMethod, &MMCifInfo::SetMethod)
+ .add_property("resolution", &MMCifInfo::GetResolution,
+ &MMCifInfo::SetResolution)
+ .add_property("operations", make_function(&MMCifInfo::GetOperations,
+ return_value_policy<copy_const_reference>()))
+ .add_property("struct_details", &MMCifInfo::GetStructDetails,
+ &MMCifInfo::SetStructDetails)
+ .add_property("struct_refs", make_function(&MMCifInfo::GetStructRefs,
+ return_value_policy<copy_const_reference>()))
+ .add_property("obsolete", &MMCifInfo::GetObsoleteInfo,
+ &MMCifInfo::SetObsoleteInfo)
+ ;
+}
diff --git a/modules/io/pymod/export_pdb_io.cc b/modules/io/pymod/export_pdb_io.cc
index e431239e2e7d591d508f05d01464be380f468b49..c5abad5d434ddbdf1285c854cf4a427a8d0f34b9 100644
--- a/modules/io/pymod/export_pdb_io.cc
+++ b/modules/io/pymod/export_pdb_io.cc
@@ -36,13 +36,14 @@ void (PDBWriter::*write_b)(const mol::EntityView&)=&PDBWriter::Write;
void export_pdb_io()
{
class_<IOProfile>("IOProfile",
- init<String,bool,bool,bool,bool,bool,bool>((arg("dialect")="PDB",
- arg("strict_hydrogens")=false,
- arg("quack_mode")=false,
- arg("fault_tolerant")=false,
- arg("join_spread_atom_records")=false,
- arg("no_hetatms")=false,
- arg("calpha_only")=false)))
+ init<String,bool,bool,bool,bool,bool,bool,bool>((arg("dialect")="PDB",
+ arg("strict_hydrogens")=false,
+ arg("quack_mode")=false,
+ arg("fault_tolerant")=false,
+ arg("join_spread_atom_records")=false,
+ arg("no_hetatms")=false,
+ arg("calpha_only")=false,
+ arg("bond_feasibility_check")=true)))
.def_readwrite("dialect", &IOProfile::dialect)
.def_readwrite("fault_tolerant", &IOProfile::fault_tolerant)
.def_readwrite("quack_mode", &IOProfile::quack_mode)
@@ -50,6 +51,7 @@ void export_pdb_io()
.def_readwrite("no_hetatms", &IOProfile::no_hetatms)
.def_readwrite("calpha_only", &IOProfile::calpha_only)
.def_readwrite("join_spread_atom_records", &IOProfile::join_spread_atom_records)
+ .def_readwrite("bond_feasibility_check", &IOProfile::bond_feasibility_check)
.def("Copy", &IOProfile::Copy)
.def(self_ns::str(self))
;
diff --git a/modules/io/pymod/wrap_io.cc b/modules/io/pymod/wrap_io.cc
index af5087cd2272c823232aabba9fadd50a0bb6278c..bc10f6f6a32fc6c9e6c3031e5abd94031f367d2e 100644
--- a/modules/io/pymod/wrap_io.cc
+++ b/modules/io/pymod/wrap_io.cc
@@ -72,6 +72,7 @@ BOOST_PYTHON_FUNCTION_OVERLOADS(save_charmm_trj_ov,
}
void export_pdb_io();
+void export_mmcif_io();
#if OST_IMG_ENABLED
void export_map_io();
#endif
@@ -112,12 +113,14 @@ BOOST_PYTHON_MODULE(_ost_io)
def("LoadCRD", &LoadCRD);
def("LoadCHARMMTraj_", &LoadCHARMMTraj, (arg("ent"), arg("trj_filename"),
arg("stride")=1, arg("lazy_load")=false));
- def("SaveCHARMMTraj",SaveCHARMMTraj,save_charmm_trj_ov());
-
def("LoadMAE", &LoadMAE);
export_pdb_io();
+ export_mmcif_io();
#if OST_IMG_ENABLED
export_map_io();
#endif
+ def("SaveCHARMMTraj", &SaveCHARMMTraj,
+ (arg("traj"), arg("pdb_filename"), arg("dcd_filename"), arg("stride")=1,
+ arg("profile")=IOProfile()));
}
diff --git a/modules/io/src/CMakeLists.txt b/modules/io/src/CMakeLists.txt
index 08b65a7a2f2f8509834db7dfcb97a0fdd35d0646..c2a465686698258543707f91b5097e7d5f98ff11 100644
--- a/modules/io/src/CMakeLists.txt
+++ b/modules/io/src/CMakeLists.txt
@@ -13,6 +13,7 @@ io_utils.hh
io_exception.hh
convert.hh
converting_streams.hh
+
formatted_line.hh
)
diff --git a/modules/io/src/img/CMakeLists.txt b/modules/io/src/img/CMakeLists.txt
index 8fa9a30ffd45564867fef83e5b17ef7bee0250b0..d17f46e8ec5e043b1a74c67ee900e5e01271ccd7 100644
--- a/modules/io/src/img/CMakeLists.txt
+++ b/modules/io/src/img/CMakeLists.txt
@@ -7,6 +7,7 @@ map_io_mrc_handler.cc
map_io_dm3_handler.cc
map_io_tiff_handler.cc
map_io_dat_handler.cc
+map_io_ipl_handler.cc
map_io_jpk_handler.cc
map_io_nanoscope_handler.cc
map_io_png_handler.cc
@@ -28,6 +29,7 @@ map_io_situs_handler.hh
map_io_handler.hh
map_io_mrc_handler.hh
map_io_dat_handler.hh
+map_io_ipl_handler.hh
map_io_jpk_handler.hh
map_io_nanoscope_handler.hh
map_io_png_handler.hh
diff --git a/modules/io/src/img/map_io_dx_handler.cc b/modules/io/src/img/map_io_dx_handler.cc
index 70303c97a08da2e8565cc3241ad5e7d9e27d8af8..4509d327d51187961802658a214d69c8b8bdf245 100644
--- a/modules/io/src/img/map_io_dx_handler.cc
+++ b/modules/io/src/img/map_io_dx_handler.cc
@@ -24,6 +24,9 @@
#include <sstream>
#include <ost/log.hh>
+#include <ost/string_ref.hh>
+#include <boost/iostreams/filter/gzip.hpp>
+#include <boost/iostreams/filtering_stream.hpp>
#include <boost/filesystem/fstream.hpp>
#include <boost/filesystem/convenience.hpp>
#include <boost/lexical_cast.hpp>
@@ -43,6 +46,23 @@ namespace ost { namespace io {
using boost::format;
+namespace {
+
+bool IEquals(const StringRef& a, const StringRef& b)
+{
+ if (a.size()!=b.size()) {
+ return false;
+ }
+ for (size_t i=0; i<a.size(); ++i) {
+ if (toupper(a[i])!=b[i]) {
+ return false;
+ }
+ }
+ return true;
+}
+
+}
+
String DX::FORMAT_STRING="defined_dx";
DX::DX (bool normalize_on_save):
@@ -68,8 +88,12 @@ void MapIODxHandler::Import(img::MapHandle& mh, const bf::path& loc,const ImageF
{
throw IOException("could not open "+loc.string());
}
-
- this->Import(mh,infile,form);
+ boost::iostreams::filtering_stream<boost::iostreams::input> in;
+ if (boost::iequals(".gz", boost::filesystem::extension(loc))) {
+ in.push(boost::iostreams::gzip_decompressor());
+ }
+ in.push(infile);
+ this->Import(mh,in,form);
infile.close();
}
@@ -91,6 +115,9 @@ void MapIODxHandler::Import(img::MapHandle& mh, std::istream& infile, const Imag
img::MapHandle mh2;
std::vector<String> tokens;
while (std::getline(infile,line)) {
+ if (line.empty()) {
+ continue;
+ }
// read gridpoints line
if (boost::iequals(line.substr(0,35), "object 1 class gridpositions counts")) {
boost::split(tokens, line, boost::is_any_of(" "), boost::token_compress_on);
@@ -183,14 +210,14 @@ void MapIODxHandler::Import(img::MapHandle& mh, std::istream& infile, const Imag
Real value=0;
for(int i=0; i<num_gridpoints; i+=3) {
std::getline(infile,line);
- boost::split(tokens, line, boost::is_any_of(" "), boost::token_compress_on);
- for (size_t j=0; j<tokens.size()-1; j++) { // three values per line
- try {
- value=boost::lexical_cast<Real>(boost::trim_copy(tokens[j]));
- } catch(boost::bad_lexical_cast&) {
- format fmer = format("Bad value line: Can't convert grid point value '%s' to Real constant.") % line;
- throw IOException(fmer.str());
- }
+ StringRef curr_line(line.c_str(), line.size());
+ std::vector<StringRef> fields=curr_line.split(' ');
+ for (size_t j=0; j<fields.size(); j++) {
+ std::pair<bool, float> result=fields[j].trim().to_float();
+ if (!result.first) {
+ throw IOException((format("Bad value line: Can't convert grid point value '%s' to Real constant.") % line).str());
+ }
+ value=result.second;
mh2.SetReal(img::Point(((i+j)/(v_size*w_size))%u_size,((i+j)/w_size)%v_size, (i+j)%w_size), value);
}
}
@@ -266,10 +293,10 @@ bool MapIODxHandler::MatchType(const ImageFormatBase& formatstruct)
}
bool MapIODxHandler::MatchSuffix(const String& loc)
{
- if(detail::FilenameEndsWith(loc,".dx") ) {
- return true;
- }
- return false;
+ if(detail::FilenameEndsWith(loc,".dx") || detail::FilenameEndsWith(loc,".dx.gz")) {
+ return true;
+ }
+ return false;
}
}} // ns
diff --git a/modules/io/src/img/map_io_ipl_handler.cc b/modules/io/src/img/map_io_ipl_handler.cc
new file mode 100644
index 0000000000000000000000000000000000000000..dd1fb2981a1f8c95f407331086508253a425f450
--- /dev/null
+++ b/modules/io/src/img/map_io_ipl_handler.cc
@@ -0,0 +1,416 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2003-2010 by the IPLT authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software FounIPLion; 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 FounIPLion, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110String::npos301 USA
+//------------------------------------------------------------------------------
+#include <cassert>
+#include <ctime>
+#include <iomanip>
+#include <cstring>
+
+#include <boost/shared_array.hpp>
+#include <boost/filesystem/operations.hpp>
+#include <boost/filesystem/fstream.hpp>
+#include <ost/stdint.hh>
+#include <ost/units.hh>
+#include <ost/log.hh>
+#include <ost/img/image.hh>
+#include <ost/img/alg/normalizer_factory.hh>
+#include <ost/img/progress.hh>
+#include <ost/io/io_exception.hh>
+#include <ost/io/convert.hh>
+#include <ost/io/converting_streams.hh>
+#include <ost/img/alg/discrete_shrink.hh>
+
+#include "map_io_ipl_handler.hh"
+
+namespace ost { namespace io {
+
+String IPL::FORMAT_STRING = "defined_ipl";
+
+IPL::IPL(bool normalize_on_save, Format bit_depth):
+ ImageFormatBase(FORMAT_STRING),
+ normalize_on_save_(normalize_on_save),
+ bit_depth_(OST_DEFAULT_FORMAT)
+{
+ this->SetBitDepth(bit_depth);
+}
+
+Format IPL::GetBitDepth() const
+{
+ return bit_depth_;
+}
+
+void IPL::SetBitDepth (Format bitdepth)
+{
+ if( ! (bitdepth==OST_BIT16_FORMAT || bitdepth==OST_BIT32_FORMAT || bitdepth==OST_DEFAULT_FORMAT))
+ {
+ throw IOException("Unsupported bit depth for IPL file format.");
+ }
+
+ bit_depth_ = bitdepth;
+}
+
+bool IPL::GetNormalizeOnSave() const
+{
+ return normalize_on_save_;
+}
+
+void IPL::SetNormalizeOnSave(bool normalize_on_save)
+{
+ normalize_on_save_ = normalize_on_save;
+}
+
+Real IPL::GetMaximum() const
+{
+ switch(bit_depth_){
+ case OST_BIT32_FORMAT:
+ return 4294967295.0;
+ default:
+ return 65535.0;
+ }
+}
+
+Real IPL::GetMinimum() const
+{
+ return 0.0;
+}
+
+bool MapIOIPLHandler::MatchContent(unsigned char* header)
+{
+ String magic_token("DITABIS micron Data File");
+ if(magic_token.compare(0,magic_token.size(),reinterpret_cast<char*>(header),magic_token.size())==0)
+ {
+ return true;
+ }
+ return false;
+}
+
+namespace detail{
+
+class IPLHeader{
+public:
+ IPLHeader():
+ date(),
+ header_length(2048),
+ size_x(),
+ size_y(),
+ bit_depth(),
+ resolution_x(),
+ resolution_y(),
+ magnification(1),
+ thumb_nail_zoom(10),
+ channel("PMT LOWSENS"),
+ params("dummy.set"),
+ format("2 2 2 2 Standard.fmt"),
+ laser(30),
+ gain(20000),
+ offset_correction(true),
+ offset(0),
+ comment()
+ {}
+ IPLHeader(const img::ConstImageHandle& im,Format bit_depth):
+ date(),
+ header_length(2048),
+ size_x(im.GetSize()[0]),
+ size_y(im.GetSize()[1]),
+ bit_depth(bit_depth==OST_BIT32_FORMAT ? 4: 2),
+ resolution_x(im.GetSpatialSampling()[0]),
+ resolution_y(im.GetSpatialSampling()[1]),
+ magnification(1),
+ thumb_nail_zoom(10),
+ channel("PMT LOWSENS"),
+ params("dummy.set"),
+ format("2 2 2 2 Standard.fmt"),
+ laser(30),
+ gain(20000),
+ offset_correction(true),
+ offset(0),
+ comment()
+ {}
+ String date;
+ int header_length;
+ int size_x;
+ int size_y;
+ int bit_depth;
+ Real resolution_x;
+ Real resolution_y;
+ int magnification;
+ int thumb_nail_zoom;
+ String channel;
+ String params;
+ String format;
+ int laser;
+ int gain;
+ bool offset_correction;
+ int offset;
+ String comment;
+};
+
+std::ostream& operator<< (std::ostream& out, const IPLHeader& h )
+{
+ uint start_pos = out.tellp();
+ out << "DITABIS micron Data File\r\n";
+ time_t rawtime=time(NULL);
+ char * timestr = asctime(localtime(&rawtime));
+ timestr[strlen(timestr)-1] = '\0';
+ out << "CREATED = "<< timestr <<" \r\n";
+ out << "HEADER = "<< h.header_length <<" \r\n";
+ // x and y get swapped here (follows the behaviour of the original conversion software)
+ out << "YPIXEL = "<< h.size_x <<" \r\n";
+ out << "XPIXEL = "<< h.size_y <<" \r\n";
+ out << "BYTE PER PIXEL = "<< h.bit_depth <<" \r\n";
+ // x and y get swapped here (follows the behaviour of the original conversion software)
+ out << "XRESOLUTION = "<< std::setprecision(0)<< h.resolution_y/Units::nm <<" (" << std::setprecision(2)<< h.resolution_y/Units::nm<<") \r\n";
+ out << "YRESOLUTION = "<< std::setprecision(0)<< h.resolution_x/Units::nm <<" (" << std::setprecision(2)<< h.resolution_x/Units::nm<<") \r\n";
+ out << "MAGNIFICATION = "<< h.magnification <<" \r\n";
+ out << "THUMB-NAIL-ZOOM = "<< h.thumb_nail_zoom <<" \r\n";
+ out << "CHANNEL = "<< h.channel <<" \r\n";
+ out << "PARAMS = "<< h.params <<" \r\n";
+ out << "FORMAT = "<< h.format <<" \r\n";
+ out << "LASER = "<< h.laser <<" \r\n";
+ out << "GAIN = "<< h.gain <<" \r\n";
+ if(h.offset_correction){
+ out << "OFFSET CORRECTION = YES \r\n";
+ }else{
+ out << "OFFSET CORRECTION = NO \r\n";
+ }
+ out << "OFFSET = "<< h.offset <<" \r\n";
+ out << "COMMENT = Created by OpenStructure \r\n";
+ out << " \r\n";
+ uint fillsize=h.header_length-out.tellp()+start_pos;
+ char empty[fillsize];
+ std::fill_n(empty,fillsize,0);
+ out.write(empty,fillsize);
+ return out;
+}
+
+std::istream& operator>> (std::istream& in, IPLHeader& h)
+{
+ String line;
+ uint start_pos = in.tellg();
+ do{
+ std::getline(in,line);
+ if(line.find("DITABIS micron Data File")!=String::npos){
+ //ignore
+ }else if(line.find("CREATED")!=String::npos){
+ h.date=line.substr(line.find("=")+2);
+ }else if(line.find("HEADER")!=String::npos){
+ std::istringstream ( line.substr(line.find("=")+2) ) >> h.header_length;
+ // x and y get swapped here (follows the behaviour of the original conversion software)
+ }else if(line.find("XPIXEL")!=String::npos){
+ std::istringstream ( line.substr(line.find("=")+2) ) >> h.size_y;
+ }else if(line.find("YPIXEL")!=String::npos){
+ std::istringstream ( line.substr(line.find("=")+2) ) >> h.size_x;
+ }else if(line.find("BYTE PER PIXEL")!=String::npos){
+ std::istringstream ( line.substr(line.find("=")+2) ) >> h.bit_depth;
+ // x and y get swapped here (follows the behaviour of the original conversion software)
+ }else if(line.find("XRESOLUTION")!=String::npos){
+ std::istringstream ( line.substr(line.find("(")+1) ) >> h.resolution_y;
+ h.resolution_y*=Units::nm;
+ }else if(line.find("YRESOLUTION")!=String::npos){
+ std::istringstream ( line.substr(line.find("(")+1) ) >> h.resolution_x;
+ h.resolution_x*=Units::nm;
+ }else if(line.find("MAGNIFICATION")!=String::npos){
+ std::istringstream ( line.substr(line.find("=")+2) ) >> h.magnification;
+ }else if(line.find("THUMB-NAIL-ZOOM")!=String::npos){
+ std::istringstream ( line.substr(line.find("=")+2) ) >> h.thumb_nail_zoom;
+ }else if(line.find("CHANNEL")!=String::npos){
+ h.channel=line.substr(line.find("=")+2);
+ }else if(line.find("PARAMS")!=String::npos){
+ h.params=line.substr(line.find("=")+2);
+ }else if(line.find("FORMAT")!=String::npos){
+ h.format=line.substr(line.find("=")+2);
+ }else if(line.find("LASER")!=String::npos){
+ std::istringstream ( line.substr(line.find("=")+2) ) >> h.laser;
+ }else if(line.find("GAIN")!=String::npos){
+ std::istringstream ( line.substr(line.find("=")+2) ) >> h.gain;
+ }else if(line.find("OFFSET CORRECTION")!=String::npos){
+ if(line.substr(line.find("=")+2).find("YES")!=String::npos){
+ h.offset_correction=true;
+ }else{
+ h.offset_correction=false;
+ }
+ }else if(line.find("OFFSET")!=String::npos){
+ std::istringstream ( line.substr(line.find("=")+2) ) >> h.offset;
+ }else if(line.find("COMMENT")!=String::npos){
+ h.comment=line.substr(line.find("=")+2);
+ }else if(line.find(" ")!=String::npos){
+ //ignore
+ }else{
+ LOG_ERROR("IPL import: unknown header line: " << line);
+ }
+ }while(in.peek()!=0);
+ uint fillsize=h.header_length-in.tellg()+start_pos;
+ char empty[h.header_length];
+ std::fill_n(empty,fillsize,0);
+ in.read(empty,fillsize);
+ return in;
+}
+
+}//ns
+
+bool MapIOIPLHandler::MatchType(const ImageFormatBase& type)
+{
+ if(type.GetFormatString()==IPL::FORMAT_STRING) {
+ return true;
+ }
+ return false;
+}
+
+bool MapIOIPLHandler::MatchSuffix(const String& loc)
+{
+ if(detail::FilenameEndsWith(loc,".IPL") || detail::FilenameEndsWith(loc,".ipl") ) {
+ return true;
+ }
+ return false;
+}
+
+void MapIOIPLHandler::Import(img::MapHandle& sh, const boost::filesystem::path& loc,const ImageFormatBase& formatstruct )
+{
+ boost::filesystem::ifstream infile(loc, std::ios::binary);
+ if(!infile) {
+ throw IOException("could not open "+loc.string());
+ }
+ this->Import(sh,infile,formatstruct);
+ infile.close();
+}
+
+template <typename DATATYPE>
+void real_filler(img::image_state::RealSpatialImageState& isi, std::istream& file)
+{
+ BinaryIStream<OST_LITTLE_ENDIAN> file_bin(file);
+ img::Size size = isi.GetSize();
+ char this_dummy; //create dummy variable to give to img::Progress as this
+ img::Progress::Instance().Register(&this_dummy,size[1],100);
+ for(unsigned int row=0;row<size[1];row++) {
+ for(unsigned int column=0;column<size[0];column++) {
+ DATATYPE value;
+ file_bin >> value;
+ isi.Value(img::Point(column,row))=static_cast<Real>(value);
+ }
+ img::Progress::Instance().AdvanceProgress(&this_dummy);
+ }
+ img::Progress::Instance().DeRegister(&this_dummy);
+}
+
+template <typename DATATYPE>
+void real_dumper( const img::ConstImageHandle& sh, std::ostream& file, const IPL& formatIPL, int shrinksize)
+{
+ img::image_state::RealSpatialImageState *isi=dynamic_cast<img::image_state::RealSpatialImageState*>(sh.ImageStatePtr().get());
+ if(! isi){
+ throw(IOException("IPL export: dynamic cast failed in real dumper."));
+ }
+ BinaryOStream<OST_LITTLE_ENDIAN> file_bin(file);
+ img::alg::Normalizer norm = img::alg::CreateNoOpNormalizer();
+ if (formatIPL.GetNormalizeOnSave() == true) {
+ norm = img::alg::CreateLinearRangeNormalizer(sh,formatIPL.GetMinimum(),formatIPL.GetMaximum());
+ }
+ img::Size size = isi->GetSize();
+ img::ImageHandle thumbnail=sh.Apply(img::alg::DiscreteShrink(img::Size(shrinksize,shrinksize,1)));
+ img::image_state::RealSpatialImageState *thumb_isi=dynamic_cast<img::image_state::RealSpatialImageState*>(thumbnail.ImageStatePtr().get());
+ if(! thumb_isi){
+ throw(IOException("IPL export: dynamic cast failed in real dumper."));
+ }
+
+ char this_dummy; //create dummy variable to give to img::Progress as this
+ img::Progress::Instance().Register(&this_dummy,size[1]+1,100);
+ for(unsigned int row=0;row<size[1];row++) {
+ for(unsigned int column=0;column<size[0];column++)
+ {
+ file_bin << static_cast<DATATYPE>(norm.Convert(isi->Value(ost::img::Point(column,row,0))));
+ }
+ img::Progress::Instance().AdvanceProgress(&this_dummy);
+ }
+ img::Progress::Instance().AdvanceProgress(&this_dummy);
+ img::Size thumb_size = thumb_isi->GetSize();
+ for(unsigned int row=0;row<thumb_size[1];row++) {
+ for(unsigned int column=0;column<thumb_size[0];column++)
+ {
+ file_bin << static_cast<DATATYPE>(norm.Convert(thumb_isi->Value(ost::img::Point(column,row,0))));
+ }
+ img::Progress::Instance().AdvanceProgress(&this_dummy);
+ }
+ img::Progress::Instance().DeRegister(&this_dummy);
+}
+
+
+void MapIOIPLHandler::Import(img::MapHandle& sh, std::istream& file, const ImageFormatBase& formatstruct)
+{
+
+ IPL form;
+ IPL& formatIPL = form;
+ if (formatstruct.GetFormatString()==IPL::FORMAT_STRING) {
+ formatIPL = formatstruct.As<IPL>();
+ } else {
+ assert (formatstruct.GetFormatString()==UndefinedImageFormat::FORMAT_STRING);
+ }
+
+ detail::IPLHeader header;
+ file >> header;
+
+ sh.Reset(img::Extent(img::Point(0,0),img::Size(header.size_x,header.size_y)), img::REAL, img::SPATIAL);
+ sh.SetSpatialSampling(geom::Vec3(header.resolution_x,header.resolution_y,1.0));
+ img::image_state::RealSpatialImageState * isi;
+ if(! (isi=dynamic_cast<img::image_state::RealSpatialImageState*>(sh.ImageStatePtr().get()))) {
+ throw IOException("internal error in IPL io: expected RealSpatialImageState");
+ }
+
+ if(header.bit_depth==4){
+ real_filler<uint32_t>(*isi,file);
+ }else{
+ real_filler<uint16_t>(*isi,file);
+ }
+}
+
+void MapIOIPLHandler::Export(const img::MapHandle& mh2,
+ const boost::filesystem::path& loc,const ImageFormatBase& formatstruct) const
+{
+ boost::filesystem::ofstream outfile(loc, std::ios::binary);
+ if(!outfile)
+ {
+ throw IOException("could not open "+loc.string());
+ }
+ this->Export(mh2,outfile,formatstruct);
+ outfile.close();
+}
+
+void MapIOIPLHandler::Export(const img::MapHandle& sh, std::ostream& file,const ImageFormatBase& formatstruct) const
+{
+
+ IPL form;
+ IPL& formatIPL = form;
+ if (formatstruct.GetFormatString()==IPL::FORMAT_STRING) {
+ formatIPL = formatstruct.As<IPL>();
+ } else {
+ assert (formatstruct.GetFormatString()==UndefinedImageFormat::FORMAT_STRING);
+ }
+ if (sh.GetSize()[2]!=1 || sh.GetDomain()!=img::SPATIAL || sh.GetType()!=img::REAL) {
+ throw IOException("IPL IO: IPL format only supports spatial 2D images.");
+ }
+ detail::IPLHeader header(sh,formatIPL.GetBitDepth());
+ file << header;
+ if(header.bit_depth==4){
+ real_dumper<uint32_t>(sh,file,formatIPL,header.thumb_nail_zoom);
+ }else{
+ real_dumper<uint16_t>(sh,file,formatIPL,header.thumb_nail_zoom);
+ }
+}
+
+}} // namespaces
+
+
diff --git a/modules/io/src/img/map_io_ipl_handler.hh b/modules/io/src/img/map_io_ipl_handler.hh
new file mode 100644
index 0000000000000000000000000000000000000000..3e76ac9895c0689defe002d0399359e03f3e09aa
--- /dev/null
+++ b/modules/io/src/img/map_io_ipl_handler.hh
@@ -0,0 +1,78 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2003-2010 by the IPLT authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+#ifndef OST_IO_MAP_IO_IPL_HANDLER_HH
+#define OST_IO_MAP_IO_IPL_HANDLER_HH
+
+
+/*
+Andreas Schenk
+*/
+
+#include "map_io_handler.hh"
+
+namespace ost { namespace io {
+
+class DLLEXPORT_OST_IO IPL: public ImageFormatBase
+{
+
+ public:
+
+ IPL(bool normalize_on_save = true, Format bit_depth = OST_DEFAULT_FORMAT);
+
+ Format GetBitDepth() const;
+ void SetBitDepth ( Format bitdepth);
+
+
+ bool GetNormalizeOnSave() const;
+ void SetNormalizeOnSave(bool normalize_on_save=true);
+ Real GetMaximum() const;
+ Real GetMinimum() const;
+ static String FORMAT_STRING;
+
+ private:
+ bool normalize_on_save_;
+ Format bit_depth_;
+
+};
+
+class DLLEXPORT_OST_IO MapIOIPLHandler: public MapIOHandler
+{
+ public:
+ /// \brief Map IO handler to read/write Ipl map files
+ ///
+ /// This map IO handler reads and writes Ipl formatted map files.
+ virtual void Import(img::MapHandle& sh, const boost::filesystem::path& loc,const ImageFormatBase& formatstruct );
+ virtual void Import(img::MapHandle& sh, std::istream& loc, const ImageFormatBase& formatstruct);
+ virtual void Export(const img::MapHandle& sh, const boost::filesystem::path& loc, const ImageFormatBase& formatstruct) const;
+ virtual void Export(const img::MapHandle& sh, std::ostream& loc,const ImageFormatBase& formatstruct) const;
+ static bool MatchContent(unsigned char* header);
+ static bool MatchType(const ImageFormatBase& type);
+ static bool MatchSuffix(const String& loc);
+ static bool ProvidesImport() { return true; }
+ static bool ProvidesExport() { return true; }
+ static String GetFormatName() { return String("IPL"); }
+ static String GetFormatDescription() {return String("Ditabis Micron Image Plate Scanner Format");}
+};
+
+typedef MapIOHandlerFactory<MapIOIPLHandler> MapIOIPLHandlerFactory;
+
+}} // ns
+
+#endif
diff --git a/modules/io/src/img/map_io_mrc_handler.cc b/modules/io/src/img/map_io_mrc_handler.cc
index abdf2807b7a35f05ee25d53f09e099ed408da04e..bdde9d1e1701bb7180874db98d9bf9f7f8dc47a1 100644
--- a/modules/io/src/img/map_io_mrc_handler.cc
+++ b/modules/io/src/img/map_io_mrc_handler.cc
@@ -628,16 +628,17 @@ void complex_filler(img::image_state::ComplexHalfFrequencyImageState& isi,
p[mapc]=-sc;
// complex conjugate
fhandle >> real >> imag;
- isi.Value(p)=Complex(Real(real),-Real(imag));
+ isi.Value(p)=Complex(Real(real),Real(imag));
LOG_DEBUG(" " << p << " " << isi.Value(p));
}
+ fhandle >> real >> imag;
if(sr==header.nr) {
// why set point (py,header.ny/2,pz)?
// isi.Value(Point(py,header.ny/2,pz))=scale*Complex(Real(real),Real(imag));
// LOG_DEBUG("+" << Point(py,header.ny/2,pz) << " <- " << Point(sx,cy,sz) << " " << " " << isi.Value(Point(py,header.ny/2,pz)));
p[mapc]=p[header.mapr];
p[mapr]=header.nr/2;
- isi.Value(p)=Complex(Real(real),Real(imag));
+ isi.Value(p)=Complex(Real(real),-Real(imag));
LOG_DEBUG("+" << p << " " << isi.Value(p));
}
Progress::Instance().AdvanceProgress(&this_dummy);
@@ -649,11 +650,12 @@ void complex_filler(img::image_state::ComplexHalfFrequencyImageState& isi,
for(;sc<header.nc-1;++sc) {
p[mapc]=sc;
fhandle >> real >> imag;
- isi.Value(p)=Complex(Real(real),Real(imag));
+ isi.Value(p)=Complex(Real(real),-Real(imag));
LOG_DEBUG(" " << p << " " << isi.Value(p));
}
+ fhandle >> real >> imag;
p[mapc]=sc;
- isi.Value(p)=Complex(Real(real),-Real(imag));
+ isi.Value(p)=Complex(Real(real),Real(imag));
LOG_DEBUG(" " << p << " " << isi.Value(p));
Progress::Instance().AdvanceProgress(&this_dummy);
}
@@ -740,7 +742,7 @@ void complex_dumper(BinaryOStream<CONVERSIONTYPE>& f,
pnt[mapr]=header.nr/2-sr;
for(int sc=0;sc<header.nc-1;++sc) {
pnt[mapc]=-sc;
- Complex val = conj(norm.Convert(isc->Value(pnt)));
+ Complex val = norm.Convert(isc->Value(pnt));
f << static_cast<B>(val.real()) << static_cast<B>(val.imag());
LOG_DEBUG(" " << pnt << " " << val);
}
@@ -754,12 +756,12 @@ void complex_dumper(BinaryOStream<CONVERSIONTYPE>& f,
for(;sc<header.nc-1;++sc) {
pnt[mapc]=sc;
Complex val =norm.Convert(isc->Value(pnt));
- f << static_cast<B>(val.real()) << static_cast<B>(val.imag());
+ f << static_cast<B>(val.real()) << static_cast<B>(-val.imag());
LOG_DEBUG(" " << pnt << " " << val);
}
pnt[mapc]=sc;
Complex val = norm.Convert(conj(isc->Value(pnt)));
- f << static_cast<B>(val.real()) << static_cast<B>(val.imag());
+ f << static_cast<B>(val.real()) << static_cast<B>(-val.imag());
LOG_DEBUG(" " << pnt << " " << val);
Progress::Instance().AdvanceProgress(&this_dummy);
}
@@ -780,7 +782,7 @@ void import_helper(img::MapHandle& image, std::istream& in,const MRC& formatmrc)
}
if(header.mode==3 || header.mode==4) {
// always assume half-complex mode
- image.Reset(img::Size((header.nx-1)*2,header.ny,header.nz),img::COMPLEX,img::HALF_FREQUENCY);
+ image.Reset(img::Size(header.nx,header.ny,header.nz),img::COMPLEX,img::HALF_FREQUENCY);
if(img::image_state::ComplexHalfFrequencyImageState *cs=dynamic_cast<img::image_state::ComplexHalfFrequencyImageState*>(image.ImageStatePtr().get())) {
if (header.mode==3) {
detail::complex_filler<ushort,CONVERSIONTYPE>(*cs,f,header);
diff --git a/modules/io/src/img/map_io_spi_handler.cc b/modules/io/src/img/map_io_spi_handler.cc
index d22897f4ee3976555418d3fdd8c0f49f49a14aa7..6f5e1798b4674ed037884719036eeeda30323f6e 100644
--- a/modules/io/src/img/map_io_spi_handler.cc
+++ b/modules/io/src/img/map_io_spi_handler.cc
@@ -198,9 +198,6 @@ void prep_header(spider_header& header, const img::Size& size, const geom::Vec3&
header.fNcol = ncol;
header.fLenbyt = ncol*4.0; // record length in bytesS
header.fLabrec = ceil(1024.0 / header.fLenbyt); // nr label records in file header
- if (fmod(1024,header.fLenbyt) != 0.0) {
- header.fLabrec += 1.0;
- }
header.fLabbyt = header.fLabrec * header.fLenbyt;
header.fIangle = 0.0; // flag indicating that tilt angles have been filled
header.fScale = spatial_sampling; // scale
@@ -389,6 +386,10 @@ void real_filler(std::istream& in, const spider_header& header, img::ImageHandle
template <typename B >
void real_dumper(std::ostream& f, const spider_header& header, const img::ImageHandle& mh,const img::alg::Normalizer& norm, bool swap_flag)
{
+ int padding = header.fLabbyt-f.tellp();
+ char* buffer=new char[padding];
+ f.write(buffer,padding);
+ delete[] buffer;
int slice_size=static_cast<int>(header.fNcol) * static_cast<int>(header.fNrow);
boost::scoped_array<B> rawp(new B[slice_size]);
diff --git a/modules/io/src/img/map_io_tiff_handler.cc b/modules/io/src/img/map_io_tiff_handler.cc
index 2ca26e838f363f9de88e4b435a895003aafb8a93..0f418bc896c6f0563a5a3a0d38d1e5aecfe6495e 100644
--- a/modules/io/src/img/map_io_tiff_handler.cc
+++ b/modules/io/src/img/map_io_tiff_handler.cc
@@ -299,19 +299,19 @@ void MapIOTiffHandler::do_export(const img::MapHandle& image,TIFF* tfile,TIF& fo
img::image_state::ComplexSpatialImageState *isc = NULL;
img::image_state::WordSpatialImageState *isw = NULL;
- boost::function<void (TIFF *,img::image_state::RealSpatialImageState*,uint32_t,uint32_t,uint32_t,uint32_t,const img::NormalizerPtr& )> fsr;
- boost::function<void (TIFF *,img::image_state::ComplexSpatialImageState*,uint32_t,uint32_t,uint32_t,uint32_t,const img::NormalizerPtr&)> fsc;
- boost::function<void (TIFF *,img::image_state::WordSpatialImageState*,uint32_t,uint32_t,uint32_t,uint32_t,const img::NormalizerPtr&)> fsw;
+ boost::function<void (TIFF *,img::image_state::RealSpatialImageState*,UINTNN_T,UINTNN_T,UINTNN_T,UINTNN_T,const img::NormalizerPtr& )> fsr;
+ boost::function<void (TIFF *,img::image_state::ComplexSpatialImageState*,UINTNN_T,UINTNN_T,UINTNN_T,UINTNN_T,const img::NormalizerPtr&)> fsc;
+ boost::function<void (TIFF *,img::image_state::WordSpatialImageState*,UINTNN_T,UINTNN_T,UINTNN_T,UINTNN_T,const img::NormalizerPtr&)> fsw;
- uint32_t width=image.GetSize().GetWidth();
- uint32_t height=image.GetSize().GetHeight();
+ UINTNN_T width=image.GetSize().GetWidth();
+ UINTNN_T height=image.GetSize().GetHeight();
uint16 spp=1;
uint16 fmt =0;
uint16 bpp =0 ;
img::Point ori=image.GetSpatialOrigin();
geom::Vec3 sampling=image.GetPixelSampling();
float xreso=sampling[0]/Units::cm,yreso=sampling[1]/Units::cm;
- float xpos=xreso*ori[0],ypos=yreso*ori[1];
+ float xpos=std::max<Real>(0.0,xreso*ori[0]),ypos=std::max<Real>(0.0,yreso*ori[1]); //tiff file format only allows positivie origins, negative origins are lost here
TIFFSetField(tfile,TIFFTAG_IMAGEWIDTH,width);
TIFFSetField(tfile,TIFFTAG_IMAGELENGTH,height);
TIFFSetField(tfile,TIFFTAG_SAMPLESPERPIXEL,spp);
@@ -342,7 +342,7 @@ void MapIOTiffHandler::do_export(const img::MapHandle& image,TIFF* tfile,TIF& fo
case OST_BIT32_FORMAT:
fmt=SAMPLEFORMAT_INT;
bpp=32;
- fsr=detail::do_tiff_write<Real,int32_t,img::image_state::RealSpatialImageState>;
+ fsr=detail::do_tiff_write<Real,INTNN_T,img::image_state::RealSpatialImageState>;
break;
case OST_FLOAT_FORMAT:
fmt=SAMPLEFORMAT_IEEEFP;
@@ -375,7 +375,7 @@ void MapIOTiffHandler::do_export(const img::MapHandle& image,TIFF* tfile,TIF& fo
case OST_BIT32_FORMAT:
fmt=SAMPLEFORMAT_UINT;
bpp=32;
- fsr=detail::do_tiff_write<Real,uint32_t,img::image_state::RealSpatialImageState>;
+ fsr=detail::do_tiff_write<Real,UINTNN_T,img::image_state::RealSpatialImageState>;
break;
case OST_FLOAT_FORMAT:
fmt=SAMPLEFORMAT_IEEEFP;
@@ -410,7 +410,7 @@ void MapIOTiffHandler::do_export(const img::MapHandle& image,TIFF* tfile,TIF& fo
case OST_BIT32_FORMAT:
fmt=SAMPLEFORMAT_COMPLEXINT;
bpp=64;
- fsc=detail::do_tiff_write<Complex,std::complex<int32_t>,img::image_state::ComplexSpatialImageState>;
+ fsc=detail::do_tiff_write<Complex,std::complex<INTNN_T>,img::image_state::ComplexSpatialImageState>;
break;
case OST_FLOAT_FORMAT:
fmt=SAMPLEFORMAT_COMPLEXIEEEFP;
@@ -436,7 +436,7 @@ void MapIOTiffHandler::do_export(const img::MapHandle& image,TIFF* tfile,TIF& fo
}
TIFFSetField(tfile,TIFFTAG_BITSPERSAMPLE,bpp);
- uint32_t rowsperstrip=std::max<int>(1,8192/(width*bpp/8)); //ca. 8 kb per strip (adobe tiff specs recomendation)
+ UINTNN_T rowsperstrip=std::max<int>(1,8192/(width*bpp/8)); //ca. 8 kb per strip (adobe tiff specs recomendation)
TIFFSetField(tfile,TIFFTAG_ROWSPERSTRIP,rowsperstrip);
TIFFSetField(tfile,TIFFTAG_SAMPLEFORMAT,fmt);
unsigned int stripcount=static_cast<int>(ceil( height/static_cast<Real>(rowsperstrip)));
@@ -549,9 +549,9 @@ TIFF* MapIOTiffHandler::open_subimage_stream(std::istream& location,const TIF& f
void MapIOTiffHandler::load_image_data(TIFF* tfile, img::ImageHandle& image, const TIF& formattif)
{
- uint32_t width,height,rps;
+ UINTNN_T width,height,rps;
uint16 bpp,spp,plc,ori,reso=RESUNIT_NONE,fmt=SAMPLEFORMAT_UINT;
- uint32_t* sbc;
+ UINTNN_T* sbc;
float xpos=0.0,ypos=0.0;
float xreso=1.0,yreso=1.0;
@@ -652,7 +652,7 @@ void MapIOTiffHandler::load_image_data(TIFF* tfile, img::ImageHandle& image, co
detail::do_tiff_read<uint16,short,img::image_state::WordSpatialImageState>(buf,rowcount,width,is,current_row,spp);
} else if(bpp==32) {
uint rowcount = cread/(width*4*spp);
- detail::do_tiff_read<uint32_t,short,img::image_state::WordSpatialImageState>(buf,rowcount,width,is,current_row,spp);
+ detail::do_tiff_read<UINTNN_T,short,img::image_state::WordSpatialImageState>(buf,rowcount,width,is,current_row,spp);
}
img::Progress::Instance().AdvanceProgress(this);
}
@@ -726,9 +726,9 @@ void MapIOTiffHandler::load_image_data(TIFF* tfile, img::ImageHandle& image, co
} else if(bpp==32) {
uint rowcount = cread/(width*4*spp);
if(fmt==SAMPLEFORMAT_INT){
- detail::do_tiff_read<int32_t,Real,img::image_state::RealSpatialImageState>(buf,rowcount,width,isr,current_row,spp);
+ detail::do_tiff_read<INTNN_T,Real,img::image_state::RealSpatialImageState>(buf,rowcount,width,isr,current_row,spp);
}else if(fmt==SAMPLEFORMAT_UINT){
- detail::do_tiff_read<uint32_t,Real,img::image_state::RealSpatialImageState>(buf,rowcount,width,isr,current_row,spp);
+ detail::do_tiff_read<UINTNN_T,Real,img::image_state::RealSpatialImageState>(buf,rowcount,width,isr,current_row,spp);
}else if(fmt==SAMPLEFORMAT_IEEEFP){
detail::do_tiff_read<float,Real,img::image_state::RealSpatialImageState>(buf,rowcount,width,isr,current_row,spp);
}else if(fmt==SAMPLEFORMAT_COMPLEXINT){
@@ -743,7 +743,7 @@ void MapIOTiffHandler::load_image_data(TIFF* tfile, img::ImageHandle& image, co
if(fmt==SAMPLEFORMAT_IEEEFP){
detail::do_tiff_read<Real,Real,img::image_state::RealSpatialImageState>(buf,rowcount,width,isr,current_row,spp);
}else if(fmt==SAMPLEFORMAT_COMPLEXINT){
- detail::do_tiff_read<detail::complexint32_t,Complex,img::image_state::ComplexSpatialImageState>(buf,rowcount,width,isc,current_row,spp);
+ detail::do_tiff_read<detail::COMPLEXINTNN_T,Complex,img::image_state::ComplexSpatialImageState>(buf,rowcount,width,isc,current_row,spp);
}else if(fmt==SAMPLEFORMAT_COMPLEXIEEEFP){
detail::do_tiff_read<std::complex<float>,Complex,img::image_state::ComplexSpatialImageState>(buf,rowcount,width,isc,current_row,spp);
}else{
diff --git a/modules/io/src/img/tiff_util.cc b/modules/io/src/img/tiff_util.cc
index fd1cf3f25d5a5c3af71a5cd9467cca35041b6832..105ebf73becf4ea763190c52d1fdec59402eca7f 100644
--- a/modules/io/src/img/tiff_util.cc
+++ b/modules/io/src/img/tiff_util.cc
@@ -41,7 +41,7 @@ void tiff_warning_handler(const char *mod, const char* fmt, va_list ap)
LOG_INFO(mod << ": " << message);
}
-int32_t CustomTIFFReadProcIStream(void* thandle, void* tdata, int32_t tsize)
+INTNN_T CustomTIFFReadProcIStream(void* thandle, void* tdata, INTNN_T tsize)
{
std::istream* file= reinterpret_cast<std::istream*>(thandle);
char* data= reinterpret_cast<char*>(tdata);
@@ -49,29 +49,29 @@ int32_t CustomTIFFReadProcIStream(void* thandle, void* tdata, int32_t tsize)
return file->gcount();
}
-int32_t CustomTIFFReadProcOStream(void* thandle, void* tdata, int32_t tsize)
+INTNN_T CustomTIFFReadProcOStream(void* thandle, void* tdata, INTNN_T tsize)
{
assert(false);
return -1;
}
-int32_t CustomTIFFWriteProcIStream(void* thandle, void* tdata, int32_t tsize)
+INTNN_T CustomTIFFWriteProcIStream(void* thandle, void* tdata, INTNN_T tsize)
{
assert(false);
return -1;
}
-int32_t CustomTIFFWriteProcOStream(void* thandle, void* tdata, int32_t tsize)
+INTNN_T CustomTIFFWriteProcOStream(void* thandle, void* tdata, INTNN_T tsize)
{
std::ostream* file= reinterpret_cast<std::ostream*>(thandle);
char* data= reinterpret_cast<char*>(tdata);
- int32_t before = file->tellp();
+ INTNN_T before = file->tellp();
file->write(data,tsize);
- int32_t after = file->tellp();
+ INTNN_T after = file->tellp();
return after-before;
}
-uint32_t CustomTIFFSeekProcIStream(void* thandle, uint32_t toff, int dir)
+UINTNN_T CustomTIFFSeekProcIStream(void* thandle, UINTNN_T toff, int dir)
{
std::istream* stream= reinterpret_cast<std::istream*>(thandle);
@@ -89,7 +89,7 @@ uint32_t CustomTIFFSeekProcIStream(void* thandle, uint32_t toff, int dir)
return stream->rdstate();
}
-uint32_t CustomTIFFSeekProcOStream(void* thandle, uint32_t toff, int dir)
+UINTNN_T CustomTIFFSeekProcOStream(void* thandle, UINTNN_T toff, int dir)
{
std::ostream* stream= reinterpret_cast<std::ostream*>(thandle);
@@ -111,33 +111,33 @@ int CustomTIFFCloseProc(void* thandle)
return 0;
}
-uint32_t CustomTIFFSizeProcIStream(void* thandle)
+UINTNN_T CustomTIFFSizeProcIStream(void* thandle)
{
std::istream* stream= reinterpret_cast<std::istream*>(thandle);
- uint32_t curr_pos = stream->tellg();
+ UINTNN_T curr_pos = stream->tellg();
stream->seekg(0,std::ios::end);
- uint32_t size = stream->tellg();
+ UINTNN_T size = stream->tellg();
stream->seekg(curr_pos,std::ios::beg);
return size;
}
-uint32_t CustomTIFFSizeProcOStream(void* thandle)
+UINTNN_T CustomTIFFSizeProcOStream(void* thandle)
{
std::ostream* stream= reinterpret_cast<std::ostream*>(thandle);
- uint32_t curr_pos = stream->tellp();
+ UINTNN_T curr_pos = stream->tellp();
stream->seekp(0,std::ios::end);
- uint32_t size = stream->tellp();
+ UINTNN_T size = stream->tellp();
stream->seekp(curr_pos,std::ios::beg);
return size;
}
-int CustomTIFFMapFileProc(void* thandle, void** tdata, uint32* toff)
+int CustomTIFFMapFileProc(void* thandle, void** tdata, UINTNN* toff)
{
assert(false);
return(0);
}
-void CustomTIFFUnmapFileProc(void* thandle, void* tdata, uint32 toff)
+void CustomTIFFUnmapFileProc(void* thandle, void* tdata, UINTNN toff)
{
assert(false);
}
diff --git a/modules/io/src/img/tiff_util.hh b/modules/io/src/img/tiff_util.hh
index 66393291b1d80f64feedb4082239d0b492f01160..b2aca3386a39f3587ba4fb31eb892147932940b7 100644
--- a/modules/io/src/img/tiff_util.hh
+++ b/modules/io/src/img/tiff_util.hh
@@ -27,6 +27,17 @@
#include <ost/img/alg/normalizer_factory.hh>
#include <ost/io/img/image_format.hh>
+#if defined(TIFFLIB_VERSION) && TIFFLIB_VERSION >= 20111221
+# define INTNN_T int64_t
+# define UINTNN uint64
+# define UINTNN_T uint64_t
+# define COMPLEXINTNN_T complexint64_t
+#else
+# define INTNN_T int32_t
+# define UINTNN uint32
+# define UINTNN_T uint32_t
+# define COMPLEXINTNN_T complexint32_t
+#endif
namespace ost { namespace io { namespace detail {
/// \internal
@@ -49,7 +60,7 @@ struct tiff_warning_handler_wrapper {
};
/// \internal
-class complexint32_t:public std::complex<int32_t>{
+class COMPLEXINTNN_T:public std::complex<INTNN_T>{
public:
operator std::complex<Real>()
@@ -79,33 +90,33 @@ public:
};
/// \internal
-int32_t CustomTIFFReadProcIStream(void* thandle, void* tdata, int32_t tsize);
+INTNN_T CustomTIFFReadProcIStream(void* thandle, void* tdata, INTNN_T tsize);
/// \internal
-int32_t CustomTIFFReadProcIStream(void* thandle, void* tdata, int32_t tsize);
+INTNN_T CustomTIFFReadProcIStream(void* thandle, void* tdata, INTNN_T tsize);
/// \internal
-int32_t CustomTIFFReadProcOStream(void* thandle, void* tdata, int32_t tsize);
+INTNN_T CustomTIFFReadProcOStream(void* thandle, void* tdata, INTNN_T tsize);
/// \internal
-int32_t CustomTIFFWriteProcIStream(void* thandle, void* tdata, int32_t tsize);
+INTNN_T CustomTIFFWriteProcIStream(void* thandle, void* tdata, INTNN_T tsize);
/// \internal
-int32_t CustomTIFFWriteProcOStream(void* thandle, void* tdata, int32_t tsize);
+INTNN_T CustomTIFFWriteProcOStream(void* thandle, void* tdata, INTNN_T tsize);
/// \internal
-uint32_t CustomTIFFSeekProcIStream(void* thandle, uint32_t toff, int dir);
+UINTNN_T CustomTIFFSeekProcIStream(void* thandle, UINTNN_T toff, int dir);
/// \internal
-uint32_t CustomTIFFSeekProcOStream(void* thandle, uint32_t toff, int dir);
+UINTNN_T CustomTIFFSeekProcOStream(void* thandle, UINTNN_T toff, int dir);
/// \internal
int CustomTIFFCloseProc(void* thandle);
/// \internal
-uint32_t CustomTIFFSizeProcIStream(void* thandle);
+UINTNN_T CustomTIFFSizeProcIStream(void* thandle);
/// \internal
-uint32_t CustomTIFFSizeProcOStream(void* thandle);
+UINTNN_T CustomTIFFSizeProcOStream(void* thandle);
/// \internal
-int CustomTIFFMapFileProc(void* thandle, void** tdata, uint32* toff);
+int CustomTIFFMapFileProc(void* thandle, void** tdata, UINTNN* toff);
/// \internal
-void CustomTIFFUnmapFileProc(void* thandle, void* tdata, uint32 toff);
+void CustomTIFFUnmapFileProc(void* thandle, void* tdata, UINTNN toff);
/// \internal
template<typename IN_TYPE,typename OUT_TYPE, class IST>
-void do_tiff_read(tdata_t buf,uint16 rps, uint32_t width, IST* is,int& current_row, int spp)
+void do_tiff_read(tdata_t buf,uint16 rps, UINTNN_T width, IST* is,int& current_row, int spp)
{
IN_TYPE* dp = static_cast<IN_TYPE*>(buf);
for(uint r=0;r<rps;r++) {
@@ -118,7 +129,7 @@ void do_tiff_read(tdata_t buf,uint16 rps, uint32_t width, IST* is,int& current_r
/// \internal
template<typename IN_TYPE,typename OUT_TYPE, class IST>
-void do_tiff_write(TIFF *tif, IST* is,uint32_t rowsperstrip,uint32_t width,uint32_t height, uint32_t strip,const img::NormalizerPtr& nptr)
+void do_tiff_write(TIFF *tif, IST* is,UINTNN_T rowsperstrip,UINTNN_T width,UINTNN_T height, UINTNN_T strip,const img::NormalizerPtr& nptr)
{
uint datalength=rowsperstrip*width;
if((strip+1)*rowsperstrip>height){
diff --git a/modules/io/src/io_manager.cc b/modules/io/src/io_manager.cc
index 12e714fd63a0170d32c676bf60bde007571ff6f6..6edc7fe430dd928159152bed7ebea0bde53aeb44 100644
--- a/modules/io/src/io_manager.cc
+++ b/modules/io/src/io_manager.cc
@@ -21,6 +21,7 @@
#include <ost/io/mol/entity_io_crd_handler.hh>
#include <ost/io/mol/entity_io_sdf_handler.hh>
#include <ost/io/mol/entity_io_mae_handler.hh>
+#include <ost/io/mol/entity_io_mmcif_handler.hh>
#include <ost/io/seq/fasta_io_handler.hh>
#include <ost/io/seq/pir_io_handler.hh>
#include <ost/io/seq/promod_io_handler.hh>
@@ -38,11 +39,13 @@
# include <ost/io/img/map_io_jpk_handler.hh>
# include <ost/io/img/map_io_nanoscope_handler.hh>
# include <ost/io/img/map_io_df3_handler.hh>
+# include <ost/io/img/map_io_ipl_handler.hh>
#endif
namespace ost { namespace io {
IOManager::IOManager()
{
+ RegisterFactory(EntityIOHandlerFactoryBaseP(new EntityIOMMCIFHandlerFactory));
RegisterFactory(EntityIOHandlerFactoryBaseP(new EntityIOPDBHandlerFactory));
RegisterFactory(EntityIOHandlerFactoryBaseP(new EntityIOCRDHandlerFactory));
RegisterFactory(EntityIOHandlerFactoryBaseP(new EntityIOSDFHandlerFactory));
@@ -63,7 +66,8 @@ IOManager::IOManager()
RegisterFactory(MapIOHandlerFactoryBasePtr(new MapIOJpkHandlerFactory));
RegisterFactory(MapIOHandlerFactoryBasePtr(new MapIODatHandlerFactory));
RegisterFactory(MapIOHandlerFactoryBasePtr(new MapIONanoscopeHandlerFactory));
- RegisterFactory(MapIOHandlerFactoryBasePtr(new MapIODF3HandlerFactory));
+ RegisterFactory(MapIOHandlerFactoryBasePtr(new MapIODF3HandlerFactory));
+ RegisterFactory(MapIOHandlerFactoryBasePtr(new MapIOIPLHandlerFactory));
#endif
}
diff --git a/modules/io/src/mol/CMakeLists.txt b/modules/io/src/mol/CMakeLists.txt
index 1201eb58fcff984f0bf0b5887a29f011ed6fd7ac..cb80b67a9600ed5ec3f98e19a5669dcb4b1f1a1b 100644
--- a/modules/io/src/mol/CMakeLists.txt
+++ b/modules/io/src/mol/CMakeLists.txt
@@ -5,6 +5,7 @@ pdb_reader.cc
entity_io_pdb_handler.cc
pdb_writer.cc
entity_io_sdf_handler.cc
+entity_io_mmcif_handler.cc
sdf_reader.cc
sdf_writer.cc
save_entity.cc
@@ -15,16 +16,21 @@ chemdict_parser.cc
io_profile.cc
dcd_io.cc
star_parser.cc
+mmcif_reader.cc
+mmcif_info.cc
PARENT_SCOPE
)
set(OST_IO_MOL_HEADERS
chemdict_parser.hh
star_parser.hh
+mmcif_reader.hh
+mmcif_info.hh
io_profile.hh
dcd_io.hh
entity_io_crd_handler.hh
entity_io_mae_handler.hh
+entity_io_mmcif_handler.hh
entity_io_handler.hh
pdb_reader.hh
entity_io_pdb_handler.hh
diff --git a/modules/io/src/mol/chemdict_parser.cc b/modules/io/src/mol/chemdict_parser.cc
index 5934b8341cf3220addbca4eaccd313984c7ecb39..a44dc733803bf7b805d52b839c8d756b3941f929 100644
--- a/modules/io/src/mol/chemdict_parser.cc
+++ b/modules/io/src/mol/chemdict_parser.cc
@@ -93,7 +93,18 @@ void ChemdictParser::OnDataItem(const StarDataItem& item)
<< compound_->GetID() << std::endl;
}
}
-
+ } else if (item.GetName()==StringRef("pdbx_type", 9)) {
+ String type=item.GetValue().str();
+ for (String::iterator i=type.begin(), e=type.end(); i!=e; ++i) {
+ *i=toupper(*i);
+ }
+ std::map<String, mol::ChemType>::iterator i=xtm_.find(type);
+ if (i!=xtm_.end()) {
+ compound_->SetChemType(i->second);
+ } else {
+ std::cout << "unknown pdbx_type '" << type << "' for compound "
+ << compound_->GetID() << std::endl;
+ }
} else if (item.GetName()==StringRef("formula", 7)) {
compound_->SetFormula(item.GetValue().str());
if (compound_->GetFormula()=="H2 O") {
@@ -136,6 +147,7 @@ void ChemdictParser::OnEndData()
}
std::map<String, mol::ChemClass> ChemdictParser::tm_=std::map<String, mol::ChemClass>();
+std::map<String, mol::ChemType> ChemdictParser::xtm_=std::map<String, mol::ChemType>();
void ChemdictParser::InitTypeMap()
{
@@ -168,4 +180,20 @@ void ChemdictParser::InitTypeMap()
tm_["WATER"]=mol::ChemClass(mol::ChemClass::WATER);
}
+void ChemdictParser::InitPDBXTypeMap()
+{
+ if (!xtm_.empty())
+ return;
+ xtm_["HETAI"]=mol::ChemType(mol::ChemType::IONS);
+ xtm_["HETAIN"]=mol::ChemType(mol::ChemType::NONCANONICALMOLS);
+ xtm_["ATOMS"]=mol::ChemType(mol::ChemType::SACCHARIDES);
+ xtm_["ATOMN"]=mol::ChemType(mol::ChemType::NUCLEOTIDES);
+ xtm_["ATOMP"]=mol::ChemType(mol::ChemType::AMINOACIDS);
+ xtm_["HETAC"]=mol::ChemType(mol::ChemType::COENZYMES);
+ xtm_["HETIC"]=mol::ChemType(mol::ChemType::WATERCOORDIONS);
+ xtm_["HETAD"]=mol::ChemType(mol::ChemType::DRUGS);
+ xtm_["HETAS"]=mol::ChemType(mol::ChemType::WATERS);
+ xtm_["?"]=mol::ChemType(mol::ChemType::UNKNOWN);
+}
+
}}
diff --git a/modules/io/src/mol/chemdict_parser.hh b/modules/io/src/mol/chemdict_parser.hh
index 4df2f4e2ddc0e7425c7c10704d88d39acb1198c9..51142744c37de1e419f39395db04edc926801982 100644
--- a/modules/io/src/mol/chemdict_parser.hh
+++ b/modules/io/src/mol/chemdict_parser.hh
@@ -25,6 +25,7 @@
#include <ost/mol/chem_class.hh>
+#include <ost/mol/chem_type.hh>
#include <ost/io/mol/star_parser.hh>
#include <ost/conop/compound_lib.hh>
@@ -43,6 +44,7 @@ public:
last_(0), loop_type_(DONT_KNOW), dialect_(dialect)
{
this->InitTypeMap();
+ this->InitPDBXTypeMap();
}
virtual bool OnBeginData(const StringRef& data_name);
@@ -62,6 +64,7 @@ public:
}
private:
void InitTypeMap();
+ void InitPDBXTypeMap();
conop::CompoundLibPtr lib_;
conop::CompoundPtr compound_;
typedef enum {
@@ -80,6 +83,7 @@ private:
int indices_[10];
bool insert_;
static std::map<String, mol::ChemClass> tm_;
+ static std::map<String, mol::ChemType> xtm_;
std::map<String, int> atom_map_;
LoopType loop_type_;
conop::AtomSpec atom_;
@@ -90,4 +94,4 @@ private:
}}
-#endif
\ No newline at end of file
+#endif
diff --git a/modules/io/src/mol/dcd_io.cc b/modules/io/src/mol/dcd_io.cc
index e5f48a93d4486e2de8c358ebb310dfb589f3d9e6..15a290279063e9c2dd7dc9948f55c0d0d70437e6 100644
--- a/modules/io/src/mol/dcd_io.cc
+++ b/modules/io/src/mol/dcd_io.cc
@@ -141,17 +141,41 @@ size_t calc_frame_size(bool skip_flag, bool gap_flag, size_t num_atoms)
return frame_size;
}
+
bool read_frame(std::istream& istream, const DCDHeader& header,
size_t frame_size, bool skip_flag, bool gap_flag,
bool swap_flag, std::vector<float>& xlist,
- std::vector<geom::Vec3>& frame)
+ std::vector<geom::Vec3>& frame,
+ uint frame_num,geom::Vec3& cell_size,geom::Vec3& cell_angles)
{
char dummy[4];
- if(skip_flag) istream.seekg(14*4,std::ios_base::cur);
+ //if(skip_flag) istream.seekg(14*4,std::ios_base::cur);
+ if(skip_flag){
+ istream.read(dummy,sizeof(dummy));
+ double x,y,z,a,b,c;
+ istream.read(reinterpret_cast<char*>(&x),sizeof(double));
+ istream.read(reinterpret_cast<char*>(&a),sizeof(double));
+ istream.read(reinterpret_cast<char*>(&y),sizeof(double));
+ istream.read(reinterpret_cast<char*>(&b),sizeof(double));
+ istream.read(reinterpret_cast<char*>(&c),sizeof(double));
+ istream.read(reinterpret_cast<char*>(&z),sizeof(double));
+ istream.read(dummy,sizeof(dummy));
+ cell_size[0]=x;
+ cell_size[1]=y;
+ cell_size[2]=z;
+ cell_angles[0]=acos(a);
+ cell_angles[1]=acos(b);
+ cell_angles[2]=acos(c);
+ if(a!=0.0||b!=0.0||c!=0.0){
+ LOG_ERROR("LoadCHARMMTraj: periodic cell not parallelepipedic, cell angles might be wrong, handle carefully")
+ }
+ }
+
// read each frame
if(!istream) {
/* premature EOF */
- LOG_ERROR("LoadCHARMMTraj: premature end of file, frames read");
+ LOG_ERROR("LoadCHARMMTraj: premature end of file while trying to read frame "
+ << frame_num << "Nothing left to be read");
return false;
}
// x coord
@@ -162,7 +186,12 @@ bool read_frame(std::istream& istream, const DCDHeader& header,
for(uint j=0;j<frame.size();++j) {
frame[j].x=xlist[j];
}
-
+ if(!istream) {
+ /* premature EOF */
+ LOG_ERROR("LoadCHARMMTraj: premature end of file while trying to read frame "
+ << frame_num << ". No y coordinates");
+ return false;
+ }
// y coord
if(gap_flag) istream.read(dummy,sizeof(dummy));
istream.read(reinterpret_cast<char*>(&xlist[0]),sizeof(float)*xlist.size());
@@ -171,7 +200,12 @@ bool read_frame(std::istream& istream, const DCDHeader& header,
for(uint j=0;j<frame.size();++j) {
frame[j].y=xlist[j];
}
-
+ if(!istream) {
+ /* premature EOF */
+ LOG_ERROR("LoadCHARMMTraj: premature end of file while trying to read frame "
+ << frame_num << ". No z coordinates");
+ return false;
+ }
// z coord
if(gap_flag) istream.read(dummy,sizeof(dummy));
istream.read(reinterpret_cast<char*>(&xlist[0]),sizeof(float)*xlist.size());
@@ -180,10 +214,26 @@ bool read_frame(std::istream& istream, const DCDHeader& header,
for(uint j=0;j<frame.size();++j) {
frame[j].z=xlist[j];
}
+ if(!istream) {
+ /* premature EOF */
+ LOG_ERROR("LoadCHARMMTraj: premature end of file while trying to read frame "
+ << frame_num);
+ return false;
+ }
return true;
}
-
+bool read_frame(std::istream& istream, const DCDHeader& header,
+ size_t frame_size, bool skip_flag, bool gap_flag,
+ bool swap_flag, std::vector<float>& xlist,
+ std::vector<geom::Vec3>& frame,uint frame_num)
+{
+ geom::Vec3 cell_size=geom::Vec3(),cell_angles=geom::Vec3();
+ return read_frame(istream,header, frame_size,skip_flag, gap_flag,
+ swap_flag, xlist,frame,frame_num, cell_size, cell_angles);
+}
+
+
mol::CoordGroupHandle load_dcd(const mol::AtomHandleList& alist, // this atom list is already sorted!
const String& trj_fn,
unsigned int stride)
@@ -199,10 +249,6 @@ mol::CoordGroupHandle load_dcd(const mol::AtomHandleList& alist, // this atom li
DCDHeader header;
bool swap_flag=false, skip_flag=false, gap_flag=false;
read_dcd_header(istream, header, swap_flag, skip_flag, gap_flag);
- LOG_DEBUG("LoadCHARMMTraj: " << header.num << " trajectories with "
- << header.atom_count << " atoms (" << header.f_atom_count
- << " fixed) each");
-
if(alist.size() != static_cast<size_t>(header.t_atom_count)) {
LOG_ERROR("LoadCHARMMTraj: atom count missmatch: " << alist.size()
<< " in coordinate file, " << header.t_atom_count
@@ -213,26 +259,31 @@ mol::CoordGroupHandle load_dcd(const mol::AtomHandleList& alist, // this atom li
mol::CoordGroupHandle cg=CreateCoordGroup(alist);
std::vector<geom::Vec3> clist(header.t_atom_count);
std::vector<float> xlist(header.t_atom_count);
+ geom::Vec3 cell_size, cell_angles;
size_t frame_size=calc_frame_size(skip_flag, gap_flag, xlist.size());
int i=0;
for(;i<header.num;i+=stride) {
+ std::cout << i << " " << header.num << std::endl;
if (!read_frame(istream, header, frame_size, skip_flag, gap_flag,
- swap_flag, xlist, clist)) {
+ swap_flag, xlist, clist, i,cell_size,cell_angles)) {
break;
}
- cg.AddFrame(clist);
+ if(skip_flag) {
+ cg.AddFrame(clist,cell_size,cell_angles);
+ }
+ else cg.AddFrame(clist);
// skip frames (defined by stride)
if(stride>1) istream.seekg(frame_size*(stride-1),std::ios_base::cur);
}
-
istream.get();
if(!istream.eof()) {
LOG_VERBOSE("LoadCHARMMTraj: unexpected trailing file data, bytes read: "
<< istream.tellg());
}
- LOG_VERBOSE("Loaded " << cg.GetFrameCount() << " frames with " << cg.GetAtomCount() << " atoms each");
+ LOG_VERBOSE("Loaded " << cg.GetFrameCount() << " frames with "
+ << cg.GetAtomCount() << " atoms each");
return cg;
}
@@ -263,6 +314,7 @@ public:
}
virtual void AddFrame(const std::vector<geom::Vec3>& coords) {}
+ virtual void AddFrame(const std::vector<geom::Vec3>& coords,const geom::Vec3& box_size,const geom::Vec3& box_angles) {}
virtual void InsertFrame(int pos, const std::vector<geom::Vec3>& coords) {}
private:
@@ -296,7 +348,7 @@ void DCDCoordSource::FetchFrame(uint frame)
stream_.seekg(pos,std::ios_base::beg);
std::vector<float> xlist(header_.t_atom_count);
if (!read_frame(stream_, header_, frame_size, skip_flag_, gap_flag_,
- swap_flag_, xlist, *frame_.get())) {
+ swap_flag_, xlist, *frame_.get(), frame)) {
}
}
diff --git a/modules/io/src/mol/entity_io_mae_handler.cc b/modules/io/src/mol/entity_io_mae_handler.cc
index a60b913f378db4b65a6043dfdf7959ef155d236a..6a5306b055c44f7d6c6ccc82f5defa8c1acd1d35 100644
--- a/modules/io/src/mol/entity_io_mae_handler.cc
+++ b/modules/io/src/mol/entity_io_mae_handler.cc
@@ -143,7 +143,13 @@ void MAEReader::Import(mol::EntityHandle& ent)
else if(line2=="r_m_z_coord") i_atom_zpos=pid;
else if(line2=="s_m_pdb_residue_name") i_res_name=pid;
else if(line2=="i_m_residue_number") i_res_num=pid;
- else if(line2=="s_m_pdb_segment_name") i_chain_name=pid;
+ else if(line2=="s_m_chain_name") i_chain_name=pid;
+ else if(line2=="s_m_pdb_segment_name") {
+ // only use this one if s_m_chain_name is not present
+ if(i_chain_name<0) {
+ i_chain_name=pid;
+ }
+ }
}
}
}
diff --git a/modules/io/src/mol/entity_io_mmcif_handler.cc b/modules/io/src/mol/entity_io_mmcif_handler.cc
new file mode 100644
index 0000000000000000000000000000000000000000..23e9ff3c52a1fd2652b1bbf7c1b7995eac487a11
--- /dev/null
+++ b/modules/io/src/mol/entity_io_mmcif_handler.cc
@@ -0,0 +1,98 @@
+//------------------------------------------------------------------------------
+// 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
+//------------------------------------------------------------------------------
+/*
+ Author: Marco Biasini, Ansgar Philippsen
+ */
+#include <iostream>
+#include <sstream>
+#include <iomanip>
+
+#include <boost/algorithm/string.hpp>
+#include <boost/filesystem/convenience.hpp>
+#include <boost/format.hpp>
+#include <boost/lexical_cast.hpp>
+
+#include <ost/log.hh>
+#include <ost/io/io_exception.hh>
+#include "entity_io_mmcif_handler.hh"
+#include <ost/profile.hh>
+#include <ost/io/mol/mmcif_reader.hh>
+namespace ost { namespace io {
+
+using boost::format;
+
+
+bool EntityIOMMCIFHandler::RequiresBuilder() const
+{
+ return true;
+}
+
+
+void EntityIOMMCIFHandler::Export(const mol::EntityView& ent,
+ const boost::filesystem::path& loc) const
+{
+}
+
+void EntityIOMMCIFHandler::Import(mol::EntityHandle& ent,
+ std::istream& stream)
+{
+ MMCifReader reader(stream,ent,
+ IOProfileRegistry::Instance().GetDefault());
+ reader.Parse();
+}
+
+void EntityIOMMCIFHandler::Export(const mol::EntityView& ent,
+ std::ostream& stream) const
+{
+}
+
+void EntityIOMMCIFHandler::Import(mol::EntityHandle& ent,
+ const boost::filesystem::path& loc)
+{
+ std::string filename=loc.string();
+ MMCifReader reader(filename, ent,
+ IOProfileRegistry::Instance().GetDefault());
+ reader.Parse();
+}
+
+bool EntityIOMMCIFHandler::ProvidesImport(const boost::filesystem::path& loc,
+ const String& type)
+{
+ if (type=="auto") {
+ String match_suf_string=loc.string();
+ std::transform(match_suf_string.begin(),match_suf_string.end(),
+ match_suf_string.begin(),tolower);
+ if(detail::FilenameEndsWith(match_suf_string,".cif") ||
+ detail::FilenameEndsWith(match_suf_string,".cif.gz")){
+ return true;
+ }
+ }
+ return type=="cif";
+}
+
+bool EntityIOMMCIFHandler::ProvidesExport(const boost::filesystem::path& loc,
+ const String& type)
+{
+ return false;
+}
+
+
+}} // ns
+
+
diff --git a/modules/io/src/mol/entity_io_mmcif_handler.hh b/modules/io/src/mol/entity_io_mmcif_handler.hh
new file mode 100644
index 0000000000000000000000000000000000000000..2fa262156d4867f665a8fc3f4d5ea8e71877f16f
--- /dev/null
+++ b/modules/io/src/mol/entity_io_mmcif_handler.hh
@@ -0,0 +1,59 @@
+//------------------------------------------------------------------------------
+// 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_IO_ENTITY_IO_PLUGIN_MMCIF_HH
+#define OST_IO_ENTITY_IO_PLUGIN_MMCIF_HH
+
+#include <vector>
+
+#include <ost/io/mol/entity_io_handler.hh>
+
+namespace ost { namespace io {
+
+
+class DLLEXPORT_OST_IO EntityIOMMCIFHandler: public EntityIOHandler {
+public:
+ virtual void Import(mol::EntityHandle& ent,
+ const boost::filesystem::path& loc);
+
+ virtual void Export(const mol::EntityView& ent,
+ const boost::filesystem::path& loc) const;
+
+ virtual void Import(mol::EntityHandle& ent, std::istream& stream);
+
+ virtual void Export(const mol::EntityView& ent, std::ostream& stream) const;
+
+ static bool ProvidesImport(const boost::filesystem::path& loc,
+ const String& format="auto");
+ static bool ProvidesExport(const boost::filesystem::path& loc,
+ const String& format="auto");
+ virtual bool RequiresBuilder() const;
+
+ static String GetFormatName() { return String("mmCIF"); }
+ static String GetFormatDescription() {
+ return String("macromolecular Crystallographic Information File ");
+ }
+};
+
+
+typedef EntityIOHandlerFactory<EntityIOMMCIFHandler> EntityIOMMCIFHandlerFactory;
+
+
+}} // ns
+
+#endif
diff --git a/modules/io/src/mol/io_profile.hh b/modules/io/src/mol/io_profile.hh
index 91fe27b7793350e10d29d922cf0ca501a1697da5..b4802583a838156ef5aac62048c158b50bff65d3 100644
--- a/modules/io/src/mol/io_profile.hh
+++ b/modules/io/src/mol/io_profile.hh
@@ -27,13 +27,13 @@ namespace ost { namespace io {
struct DLLEXPORT IOProfile {
public:
- IOProfile(String d, bool sh, bool qm, bool ft, bool js, bool nh, bool co):
+ IOProfile(String d, bool sh, bool qm, bool ft, bool js, bool nh, bool co, bool bf):
dialect(d), strict_hydrogens(sh), quack_mode(qm), fault_tolerant(ft),
- join_spread_atom_records(js), no_hetatms(nh), calpha_only(co)
+ join_spread_atom_records(js), no_hetatms(nh), calpha_only(co), bond_feasibility_check(bf)
{ }
IOProfile(): dialect("PDB"), strict_hydrogens(true), quack_mode(false),
fault_tolerant(false), join_spread_atom_records(false), no_hetatms(false),
- calpha_only(false)
+ calpha_only(false), bond_feasibility_check(true)
{ }
virtual ~IOProfile() { }
@@ -44,11 +44,12 @@ public:
bool join_spread_atom_records;
bool no_hetatms;
bool calpha_only;
+ bool bond_feasibility_check;
IOProfile Copy()
{
return IOProfile(dialect, strict_hydrogens, quack_mode, fault_tolerant,
- join_spread_atom_records, no_hetatms, calpha_only);
+ join_spread_atom_records, no_hetatms, calpha_only, bond_feasibility_check);
}
virtual void PostImport(mol::EntityHandle ent) { }
};
@@ -61,7 +62,8 @@ inline std::ostream& operator<<(std::ostream& stream, const IOProfile& p)
<< (p.join_spread_atom_records ? "True" : "False") << ", no_hetatms="
<< (p.no_hetatms ? "True" : "False") << ", calpha_only="
<< (p.calpha_only ? "True" : "False") << ", fault_tolerant="
- << (p.fault_tolerant ? "True" : "False") << ")";
+ << (p.fault_tolerant ? "True" : "False") << ", bond_feasibility_check="
+ << (p.bond_feasibility_check ? "True" : "False") << ")";
return stream;
}
diff --git a/modules/io/src/mol/mmcif_info.cc b/modules/io/src/mol/mmcif_info.cc
new file mode 100644
index 0000000000000000000000000000000000000000..c8565a2e809ff1f84b182b9f73e4cacd1866c509
--- /dev/null
+++ b/modules/io/src/mol/mmcif_info.cc
@@ -0,0 +1,76 @@
+//------------------------------------------------------------------------------
+// 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
+//------------------------------------------------------------------------------
+
+#include <ost/io/io_exception.hh>
+#include <ost/io/mol/mmcif_info.hh>
+
+namespace ost { namespace io {
+
+void MMCifInfo::AddAuthorsToCitation(StringRef id, std::vector<String> list)
+{
+ // find citation
+ std::vector<MMCifInfoCitation>::iterator cit_it;
+ for (cit_it = citations_.begin(); cit_it != citations_.end(); ++cit_it) {
+ if (id == StringRef(cit_it->GetID().c_str(), cit_it->GetID().length())) {
+ cit_it->SetAuthorList(list);
+ return;
+ }
+ }
+
+ throw IOException("No citation for identifier '" + id.str() + "' found.");
+}
+
+
+
+MMCifInfoStructRefSeqPtr
+MMCifInfoStructRef::AddAlignedSeq(const String& aid, const String& chain_name,
+ int seq_begin, int seq_end, int db_begin,
+ int db_end)
+{
+ std::map<String, MMCifInfoStructRefSeqPtr>::const_iterator i=seqs_.find(aid);
+ if (i!=seqs_.end()) {
+ throw IOException("duplicate align_id for struct_ref '"+id_+"'");
+ }
+ MMCifInfoStructRefSeqPtr p(new MMCifInfoStructRefSeq(aid, chain_name,
+ seq_begin, seq_end,
+ db_begin, db_end));
+ seqs_[aid]=p;
+ return p;
+}
+
+
+MMCifInfoStructRefSeqPtr
+MMCifInfoStructRef::GetAlignedSeq(const String& aid) const
+{
+
+ std::map<String, MMCifInfoStructRefSeqPtr>::const_iterator i=seqs_.find(aid);
+ return i==seqs_.end() ? MMCifInfoStructRefSeqPtr() : i->second;
+}
+
+MMCifInfoStructRefSeqDifPtr
+MMCifInfoStructRefSeq::AddDif(int seq_rnum, int db_rnum, const String& details)
+{
+ MMCifInfoStructRefSeqDifPtr d(new MMCifInfoStructRefSeqDif(seq_rnum, db_rnum,
+ details));
+ difs_.push_back(d);
+ return d;
+}
+
+
+}} //ns
diff --git a/modules/io/src/mol/mmcif_info.hh b/modules/io/src/mol/mmcif_info.hh
new file mode 100644
index 0000000000000000000000000000000000000000..38e49f58bec9420e353088d8a7858908be887456
--- /dev/null
+++ b/modules/io/src/mol/mmcif_info.hh
@@ -0,0 +1,843 @@
+//------------------------------------------------------------------------------
+// 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_MMCIF_INFO_HH
+#define OST_MMCIF_INFO_HH
+
+#include <vector>
+#include <map>
+#include <boost/shared_ptr.hpp>
+#include <ost/geom/geom.hh>
+#include <ost/string_ref.hh>
+#include <ost/io/module_config.hh>
+
+namespace ost { namespace io {
+
+class DLLEXPORT_OST_IO MMCifInfoStructDetails {
+public:
+ /// \brief Create a details object.
+ MMCifInfoStructDetails(): entry_id_(""), title_(""), casp_flag_('\0'),
+ descriptor_(""), mass_(0.0), mass_method_(""), model_details_(""),
+ model_type_details_("") {};
+
+ /// \brief Set id.
+ ///
+ /// \param id id
+ void SetEntryID(String id) { entry_id_ = id; }
+ /// \brief Get id.
+ ///
+ /// \return id
+ String GetEntryID() const { return entry_id_; }
+
+ /// \brief Set CASP flag.
+ ///
+ /// \param flag flag
+ void SetCASPFlag(char flag) { casp_flag_ = flag; }
+ /// \brief Get CASP flag.
+ ///
+ /// \return flag
+ char GetCASPFlag() const { return casp_flag_; }
+
+ /// \brief Set descriptor.
+ ///
+ /// \param desc descriptor for an NDB structure or PDB COMPND record
+ void SetDescriptor(String desc) { descriptor_ = desc; }
+ /// \brief Get CASP flag.
+ ///
+ /// \return flag
+ String GetDescriptor() const { return descriptor_; }
+
+ /// \brief Set mass.
+ ///
+ /// \param mass molecular mass
+ void SetMass(Real mass) { mass_ = mass; }
+ /// \brief Get molecular weight.
+ ///
+ /// \return mass
+ Real GetMass() const { return mass_; }
+
+ /// \brief Set the method how the molecular weight was detected.
+ ///
+ /// \param method detection method
+ void SetMassMethod(String method) { mass_method_ = method; }
+ /// \brief Get the method how the molecular weight was determined.
+ ///
+ /// \return method
+ String GetMassMethod() const { return mass_method_; }
+
+ /// \brief Set the description about the production of this structure.
+ ///
+ /// \param desc explaination
+ void SetModelDetails(String desc) { model_details_ = desc; }
+ /// \brief Get the details how the structure was determined.
+ ///
+ /// \return details
+ String GetModelDetails() const { return model_details_; }
+
+ /// \brief Set a description for the type of the structure model.
+ ///
+ /// \param desc explaination
+ void SetModelTypeDetails(String desc) { model_type_details_ = desc; }
+ /// \brief Get the description for the type of the structure model.
+ ///
+ /// \return details
+ String GetModelTypeDetails() const { return model_type_details_; }
+
+ /// \brief Set a title for the data block.
+ ///
+ /// \param title title
+ void SetTitle(String title) { title_ = title; }
+ /// \brief Get the title of the structure model.
+ ///
+ /// \return title
+ String GetTitle() const { return title_; }
+
+ bool operator==(const MMCifInfoStructDetails& sd) const {
+ if (this->entry_id_ != sd.entry_id_) {
+ return false;
+ }
+ if (this->casp_flag_ != sd.casp_flag_) {
+ return false;
+ }
+ if (this->descriptor_ != sd.descriptor_) {
+ return false;
+ }
+ if (this->mass_ != sd.mass_) {
+ return false;
+ }
+ if (this->mass_method_ != sd.mass_method_) {
+ return false;
+ }
+ if (this->model_details_ != sd.model_details_) {
+ return false;
+ }
+ if (this->model_type_details_ != sd.model_type_details_) {
+ return false;
+ }
+ if (this->title_ != sd.title_) {
+ return false;
+ }
+
+ return true;
+ }
+
+ bool operator!=(const MMCifInfoStructDetails& sd) const {
+ return !this->operator == (sd);
+ }
+
+private:
+ String entry_id_;
+ String title_;
+ char casp_flag_;
+ String descriptor_;
+ Real mass_;
+ String mass_method_;
+ String model_details_;
+ String model_type_details_;
+};
+
+class DLLEXPORT_OST_IO MMCifInfoTransOp {
+public:
+ /// \brief Create an operation
+ MMCifInfoTransOp(): id_(""), type_("")
+ {
+ translation_ = geom::Vec3();
+ };
+
+ /// \brief Set id
+ ///
+ /// \param id id
+ void SetID(String id) { id_ = id; }
+ /// \brief Get id
+ ///
+ /// \return id
+ String GetID() const { return id_; }
+
+ /// \brief Set type
+ ///
+ /// \param type
+ void SetType(String type) { type_ = type; }
+ /// \brief Get type
+ ///
+ /// \return type
+ String GetType() const { return type_; }
+
+ /// \brief Set the translational vector
+ ///
+ /// \param
+ void SetVector(Real x, Real y, Real z)
+ {
+ translation_.SetX(x);
+ translation_.SetY(y);
+ translation_.SetZ(z);
+ }
+ /// \brief Get the translational vector
+ ///
+ /// \return vector
+ geom::Vec3 GetVector() const { return translation_; }
+
+ /// \brief Set the rotational matrix
+ ///
+ /// \param
+ void SetMatrix(Real i00, Real i01, Real i02,
+ Real i10, Real i11, Real i12,
+ Real i20, Real i21, Real i22)
+ {
+ rotation_ = geom::Mat3(i00,i01,i02, i10,i11,i12, i20,i21,i22);
+ }
+ /// \brief Get the rotational matrix
+ ///
+ /// \return matrix
+ geom::Mat3 GetMatrix() const { return rotation_; }
+
+ bool operator==(const MMCifInfoTransOp& op) const {
+ if (this->id_ != op.id_) {
+ return false;
+ }
+ if (this->type_ != op.type_) {
+ return false;
+ }
+ if (this->translation_ != op.translation_) {
+ return false;
+ }
+ if (this->rotation_ != op.rotation_) {
+ return false;
+ }
+
+ return true;
+ }
+
+ bool operator!=(const MMCifInfoTransOp& op) const {
+ return !this->operator==(op);
+ }
+
+private:
+ String id_; ///< identifier
+ String type_; ///< type of operation
+ geom::Vec3 translation_; ///< translational vector
+ geom::Mat3 rotation_; ///< rotational matrix
+};
+typedef boost::shared_ptr<MMCifInfoTransOp> MMCifInfoTransOpPtr;
+
+
+class DLLEXPORT_OST_IO MMCifInfoBioUnit {
+public:
+ /// \brief Create a biounit.
+ MMCifInfoBioUnit(): details_("") {};
+
+ /// \brief Set details
+ ///
+ /// \param details details
+ void SetDetails(String details) { details_ = details; }
+ /// \brief Get details
+ ///
+ /// \return details
+ String GetDetails() const { return details_; }
+
+ /// \brief Add a chain name
+ ///
+ /// \param chain chain name
+ void AddChain(String chain) { chains_.push_back(chain); }
+ /// \brief Get vector of chain names
+ ///
+ /// \return chains
+ const std::vector<String>& GetChainList() const { return chains_; }
+
+ /// \brief Add a set of operations
+ ///
+ /// \param operations vector of operations to be added
+ void AddOperations(std::vector<MMCifInfoTransOpPtr> operations)
+ {
+ operations_.push_back(operations);
+ }
+ /// \brief Get the list of operations
+ ///
+ /// \return vector of vectors of iterators.
+ const std::vector<std::vector<MMCifInfoTransOpPtr> >& GetOperations()
+ {
+ return operations_;
+ }
+
+ bool operator==(const MMCifInfoBioUnit& bu) const {
+ if (this->details_ != bu.details_) {
+ return false;
+ }
+ if (this->chains_ != bu.chains_) {
+ return false;
+ }
+ if (this->operations_.size() == bu.operations_.size()) {
+ std::vector<std::vector<MMCifInfoTransOpPtr> >::const_iterator th_ops_it;
+ std::vector<std::vector<MMCifInfoTransOpPtr> >::const_iterator bu_ops_it;
+ std::vector<MMCifInfoTransOpPtr>::const_iterator th_op_it;
+ std::vector<MMCifInfoTransOpPtr>::const_iterator bu_op_it;
+
+ for (th_ops_it = this->operations_.begin(),
+ bu_ops_it = bu.operations_.begin();
+ th_ops_it != this->operations_.end();
+ ++th_ops_it, ++bu_ops_it) {
+ if (th_ops_it->size() == bu_ops_it->size()) {
+ for (th_op_it = th_ops_it->begin(), bu_op_it = bu_ops_it->begin();
+ th_op_it != th_ops_it->end();
+ ++th_op_it, ++bu_op_it) {
+ if (*th_op_it != *bu_op_it) {
+ return false;
+ }
+ }
+ } else {
+ return false;
+ }
+ }
+ } else {
+ return false;
+ }
+
+ return true;
+ }
+
+ bool operator!=(const MMCifInfoBioUnit& bu) const {
+ return !this->operator==(bu);
+ }
+
+private:
+ String details_; ///< pdbx_struct_assembly.details
+ std::vector<String> chains_; ///< chains involved in this assembly
+ std::vector<std::vector<MMCifInfoTransOpPtr> > operations_;
+};
+
+class DLLEXPORT_OST_IO MMCifInfoCitation {
+public:
+ /// \brief Create a citation.
+ MMCifInfoCitation(): id_(""), where_(UNKNOWN), cas_(""), published_in_(""),
+ volume_(""), page_first_(""), page_last_(""), doi_(""), pubmed_(0),
+ year_(0), title_("") {};
+
+ /// \brief Set ID
+ ///
+ /// \param id ID
+ void SetID(String id) { id_ = id; }
+ /// \brief Get ID
+ ///
+ /// \return ID
+ String GetID() const { return id_; }
+
+ /// \brief Set a CAS identifier
+ ///
+ /// \param id CAS identifier
+ void SetCAS(String id) { cas_ = id; }
+ /// \brief Get a CAS identifier
+ ///
+ /// \return CAS identifier
+ String GetCAS() const { return cas_; }
+
+ /// \brief Set an ISBN code
+ ///
+ /// \param code ISBN code
+ void SetISBN(String code) { isbn_ = code; }
+
+ /// \brief Get an ISBN code
+ ///
+ /// \return ISBN code
+ String GetISBN() const { return isbn_; }
+
+ /// \brief Set a book title or journal name
+ ///
+ /// \param title where published
+ void SetPublishedIn(String title) { published_in_ = title; }
+
+ /// \brief Get a book title or journal name
+ ///
+ /// \return title
+ String GetPublishedIn() const { return published_in_; }
+
+ /// \brief Set a journal volume
+ ///
+ /// \param volume
+ void SetVolume(String volume) { volume_ = volume; }
+
+ /// \brief Get a journal volume
+ ///
+ /// \return volume
+ String GetVolume() const { return volume_; }
+
+ /// \brief Set the start page for a publication
+ ///
+ /// \param start
+ void SetPageFirst(String first) { page_first_ = first; }
+
+ /// \brief Get the start page of a publication
+ ///
+ /// \return first page
+ String GetPageFirst() const { return page_first_; }
+
+ /// \brief Set the end page for a publication
+ ///
+ /// \param end
+ void SetPageLast(String last) { page_last_ = last; }
+
+ /// \brief Get the last page of a publication
+ ///
+ /// \return last page
+ String GetPageLast() const { return page_last_; }
+
+ /// \brief Set the DOI of a document
+ ///
+ /// \param doi
+ void SetDOI(String doi) { doi_ = doi; }
+
+
+ /// \brief Get the DOI of a document
+ ///
+ /// \return DOI
+ String GetDOI() const { return doi_; }
+
+ /// \brief Set the PubMed accession number
+ ///
+ /// \param no
+ void SetPubMed(int no) { pubmed_ = no; }
+
+ /// \brief Get the PubMed accession number
+ ///
+ /// \return PubMed accession
+ int GetPubMed() const { return pubmed_; }
+
+ /// \brief Set the year of a publication
+ ///
+ /// \param year
+ void SetYear(int year) { year_ = year; }
+
+
+ /// \brief Get the year of a publication
+ ///
+ /// \return year
+ int GetYear() const { return year_; }
+
+
+ /// \brief Set the title of a publication
+ ///
+ /// \param title
+ void SetTitle(String title) { title_ = title; }
+
+ /// \brief Get the title of a publication
+ ///
+ /// \return title
+ String GetTitle() const { return title_; }
+
+ /// \brief Set the list of authors
+ ///
+ /// \param list
+ void SetAuthorList(std::vector<String> list) { authors_ = list; }
+
+ /// \brief Get the list of authors
+ ///
+ /// \return list
+ const std::vector<String>& GetAuthorList() const { return authors_; }
+
+ bool operator==(const MMCifInfoCitation& cit) const {
+ if (this->year_ != cit.year_) {
+ return false;
+ }
+ if (this->pubmed_ != cit.pubmed_) {
+ return false;
+ }
+ if (this->where_ != cit.where_) {
+ return false;
+ }
+ if (StringRef(this->id_.c_str(), this->id_.length()) !=
+ StringRef(cit.id_.c_str(), cit.id_.length())) {
+ return false;
+ }
+ if (StringRef(this->cas_.c_str(), this->cas_.length()) !=
+ StringRef(cit.cas_.c_str(), cit.cas_.length())) {
+ return false;
+ }
+ if (StringRef(this->isbn_.c_str(), this->isbn_.length()) !=
+ StringRef(cit.isbn_.c_str(), cit.isbn_.length())) {
+ return false;
+ }
+ if (StringRef(this->published_in_.c_str(), this->published_in_.length()) !=
+ StringRef(cit.published_in_.c_str(), cit.published_in_.length())) {
+ return false;
+ }
+ if (StringRef(this->volume_.c_str(), this->volume_.length()) !=
+ StringRef(cit.volume_.c_str(), cit.volume_.length())) {
+ return false;
+ }
+ if (StringRef(this->page_first_.c_str(), this->page_first_.length()) !=
+ StringRef(cit.page_first_.c_str(), cit.page_first_.length())) {
+ return false;
+ }
+ if (StringRef(this->page_last_.c_str(), this->page_last_.length()) !=
+ StringRef(cit.page_last_.c_str(), cit.page_last_.length())) {
+ return false;
+ }
+ if (StringRef(this->doi_.c_str(), this->doi_.length()) !=
+ StringRef(cit.doi_.c_str(), cit.doi_.length())) {
+ return false;
+ }
+ if (StringRef(this->title_.c_str(), this->title_.length()) !=
+ StringRef(cit.title_.c_str(), cit.title_.length())) {
+ return false;
+ }
+ if (this->authors_ != cit.authors_) {
+ return false;
+ }
+
+ return true;
+ }
+
+ bool operator!=(const MMCifInfoCitation& cit) const {
+ return !this->operator==(cit);
+ }
+
+private:
+ /// \enum types of citations
+ typedef enum {
+ JOURNAL,
+ BOOK,
+ UNKNOWN
+ } MMCifInfoCType;
+
+ String id_; ///< internal identifier
+ MMCifInfoCType where_; ///< journal or book?
+ String cas_; ///< CAS identifier
+ String isbn_; ///< ISBN no. of medium
+ String published_in_; ///< book title or full journal name
+ String volume_; ///< journal volume
+ String page_first_; ///< first page
+ String page_last_; ///< last page
+ String doi_; ///< DOI identifier
+ int pubmed_; ///< accession no.
+ int year_; ///< year of publication
+ String title_; ///< title of the publication
+ std::vector<String> authors_; ///< author information
+};
+
+/// \brief container class for information on obsolete entries
+///
+class DLLEXPORT_OST_IO MMCifInfoObsolete {
+public:
+ /// \brief Create an object of information baout an obsolete entry.
+ MMCifInfoObsolete(): date_(""), id_(UNKNOWN), pdb_id_(""),
+ replaced_pdb_id_("") {};
+
+ /// \brief Set date of replacement.
+ ///
+ /// \param date
+ void SetDate(String date) { date_ = date; }
+
+ /// \brief Get the date string.
+ ///
+ /// \return date as string.
+ String GetDate() { return date_; }
+
+ /// \brief Set type of entry.
+ ///
+ /// \param type
+ void SetID(StringRef type)
+ {
+ if (type == StringRef("OBSLTE", 6)) {
+ id_ = OBSLTE;
+ }
+ else if (type == StringRef("SPRSDE", 6)) {
+ id_ = SPRSDE;
+ }
+ }
+
+ /// \brief Get type of entry.
+ ///
+ /// \return type as string, starting with an upper case letter.
+ String GetID()
+ {
+ if (id_ == OBSLTE) {
+ return "Obsolete";
+ }
+ if (id_ == SPRSDE) {
+ return "Supersede";
+ }
+ return "Unknown";
+ }
+
+ /// \brief Set id of replacement.
+ ///
+ /// \param id
+ void SetPDBID(String id) { pdb_id_ = id; }
+
+ /// \brief Get id of replacement.
+ ///
+ /// \return id
+ String GetPDBID() { return pdb_id_; }
+
+ /// \brief Set id of replaced entry.
+ ///
+ /// \param id
+ void SetReplacedPDBID(String id) { replaced_pdb_id_ = id; }
+
+ /// \brief Get id of replaced entry.
+ ///
+ /// \return id
+ String GetReplacedPDBID() { return replaced_pdb_id_; }
+
+private:
+ /// \enum types of obsolete entries
+ typedef enum {
+ OBSLTE,
+ SPRSDE,
+ UNKNOWN
+ } MMCifObsoleteType;
+
+ String date_; ///< date of replacement
+ MMCifObsoleteType id_; ///< type of entry
+ String pdb_id_; ///< replacing entry
+ String replaced_pdb_id_; ///< replaced entry
+};
+
+class MMCifInfoStructRef;
+class MMCifInfoStructRefSeq;
+class MMCifInfoStructRefSeqDif;
+
+
+typedef boost::shared_ptr<MMCifInfoStructRef> MMCifInfoStructRefPtr;
+typedef boost::shared_ptr<MMCifInfoStructRefSeq> MMCifInfoStructRefSeqPtr;
+typedef boost::shared_ptr<MMCifInfoStructRefSeqDif> MMCifInfoStructRefSeqDifPtr;
+
+typedef std::vector<MMCifInfoStructRefPtr> MMCifInfoStructRefs;
+typedef std::vector<MMCifInfoStructRefSeqPtr> MMCifInfoStructRefSeqs;
+typedef std::vector<MMCifInfoStructRefSeqDifPtr> MMCifInfoStructRefSeqDifs;
+class DLLEXPORT_OST_IO MMCifInfoStructRef {
+public:
+ MMCifInfoStructRef(const String& id, const String& ent_id,
+ const String& db_name,
+ const String& db_ident, const String& db_access):
+ id_(id), ent_id_(ent_id), db_name_(db_name), db_ident_(db_ident),
+ db_access_(db_access)
+ { }
+ const String& GetID() const { return id_; }
+ const String& GetDBName() const { return db_name_; }
+ const String& GetDBID() const { return db_ident_; }
+ const String& GetEntityID() const { return ent_id_; }
+ const String& GetDBAccess() const { return db_access_; }
+ MMCifInfoStructRefSeqPtr AddAlignedSeq(const String& align_id,
+ const String& chain_name, int seq_begin,
+ int seq_end, int db_begin, int db_end);
+ MMCifInfoStructRefSeqPtr GetAlignedSeq(const String& align_id) const;
+ MMCifInfoStructRefSeqs GetAlignedSeqs() const
+ {
+ MMCifInfoStructRefSeqs seqs;
+ seqs.reserve(seqs_.size());
+ for (std::map<String, MMCifInfoStructRefSeqPtr>::const_iterator
+ i=seqs_.begin(), e=seqs_.end(); i!=e; ++i) {
+ seqs.push_back(i->second);
+ }
+ return seqs;
+ }
+private:
+ String id_;
+ String ent_id_;
+ String db_name_;
+ String db_ident_;
+ String db_access_;
+ std::map<String, MMCifInfoStructRefSeqPtr> seqs_;
+};
+
+class DLLEXPORT_OST_IO MMCifInfoStructRefSeq {
+public:
+ MMCifInfoStructRefSeq(const String& align_id, const String& chain_name,
+ int seq_begin, int seq_end,
+ int db_begin, int db_end):
+ id_(align_id), chain_name_(chain_name),
+ seq_begin_(seq_begin), seq_end_(seq_end), db_begin_(db_begin), db_end_(db_end)
+ { }
+
+ const String& GetID() const { return id_; }
+ const String& GetChainName() const { return chain_name_; }
+ int GetSeqBegin() const { return seq_begin_; }
+ int GetSeqEnd() const { return seq_end_; }
+ int GetDBBegin() const { return db_begin_; }
+ int GetDBEnd() const { return db_end_; }
+ MMCifInfoStructRefSeqDifPtr AddDif(int seq_num, int db_num,
+ const String& details);
+ const std::vector<MMCifInfoStructRefSeqDifPtr>& GetDifs() const { return difs_; }
+private:
+ String id_;
+ String chain_name_;
+ int seq_begin_;
+ int seq_end_;
+ int db_begin_;
+ int db_end_;
+ std::vector<MMCifInfoStructRefSeqDifPtr> difs_;
+};
+
+class DLLEXPORT_OST_IO MMCifInfoStructRefSeqDif {
+public:
+ MMCifInfoStructRefSeqDif(int seq_rnum, int db_rnum, const String& details):
+ seq_rnum_(seq_rnum), db_rnum_(db_rnum), details_(details) {}
+ int GetSeqRNum() const { return seq_rnum_;}
+ int GetDBRNum() const { return db_rnum_; }
+ const String& GetDetails() const { return details_; }
+private:
+ int seq_rnum_;
+ int db_rnum_;
+ String details_;
+};
+
+/// \brief container class for additional information from MMCif files
+///
+/// \section mmcif annotation information
+///
+/// MMCif files contain loads of additional information beside coordinates.
+/// This class is set up to capture some of it. In detail, we have:
+///
+/// \li citations
+/// \li biounits
+/// \li transformation information from asym. unit to biounit
+/// \li structure information
+/// \li resolution
+/// \li method
+class DLLEXPORT_OST_IO MMCifInfo {
+public:
+ /// \brief Create an info object.
+ MMCifInfo(): exptl_method_(""), resolution_(0.0f) {};
+
+ /// \brief Add an item to the list of citations
+ ///
+ /// \param citation to be added
+ void AddCitation(MMCifInfoCitation citation) // unit test
+ {
+ citations_.push_back(citation);
+ }
+
+ /// \brief Add a list of authors to a specific citation.
+ ///
+ /// \param id identifier of the citation to be modified.
+ /// \param list list of authors to be added.
+ void AddAuthorsToCitation(StringRef id, std::vector<String> list); //unit test
+
+ /// \brief Get the list of citations stored in an info object.
+ ///
+ /// \return vector of MMCifInfoCitation objects
+ const std::vector<MMCifInfoCitation>& GetCitations() const
+ {
+ return citations_;
+ }
+
+ /// \brief Set an experimental method.
+ ///
+ /// \param method Method description
+ void SetMethod(String method) { exptl_method_ = method; }
+
+ /// \brief Get an experimental method.
+ ///
+ /// \return Method description
+ const StringRef GetMethod() const
+ {
+ return StringRef(exptl_method_.c_str(), exptl_method_.length());
+ }
+
+ /// \brief Set resolution.
+ ///
+ /// \param res experiment resolution
+ void SetResolution(Real res) { resolution_ = res; }
+
+ /// \brief Get resolution.
+ ///
+ /// \return experiment resolution
+ Real GetResolution() const { return resolution_; }
+
+ /// \brief Add a biounit
+ ///
+ /// \param bu biounit to be added
+ void AddBioUnit(MMCifInfoBioUnit bu) // unit test
+ {
+ biounits_.push_back(bu);
+ }
+
+ /// \brief Get the list of biounits stored in an info object.
+ ///
+ /// \return vector of MMCifInfoBioUnit objects
+ const std::vector<MMCifInfoBioUnit>& GetBioUnits() const
+ {
+ return biounits_;
+ }
+
+ /// \brief Add a operation
+ ///
+ /// \param op operation to be added
+ void AddOperation(MMCifInfoTransOpPtr op) // unit test
+ {
+ transops_.push_back(op);
+ }
+
+ /// \brief Get the list of operations stored in an info object.
+ ///
+ /// \return vector of MMCifInfoTransOp objects
+ const std::vector<MMCifInfoTransOpPtr>& GetOperations() const
+ {
+ return transops_;
+ }
+
+ /// \brief Add a set of structure details
+ ///
+ /// \param details info block to be added
+ void SetStructDetails(MMCifInfoStructDetails details)
+ {
+ struct_details_ = details;
+ }
+
+ /// \brief Get the list of details about structures.
+ ///
+ /// \return vector of MMCifInfoStructDetails objects
+ const MMCifInfoStructDetails GetStructDetails() const
+ {
+ return struct_details_;
+ }
+
+ /// \brief Add a block of information on obsolete entries
+ ///
+ /// \param obsolete
+ void SetObsoleteInfo(MMCifInfoObsolete obsolete)
+ {
+ obsolete_ = obsolete;
+ }
+
+ /// \brief Get information on an obsolete entries
+ ///
+ /// \return MMCifInfoObsolete object
+ MMCifInfoObsolete GetObsoleteInfo() const
+ {
+ return obsolete_;
+ }
+ const MMCifInfoStructRefs& GetStructRefs() const { return struct_refs_; }
+ void SetStructRefs(const MMCifInfoStructRefs& sr) { struct_refs_=sr; }
+//protected:
+
+private:
+ // members
+ String exptl_method_;
+ Real resolution_;
+ MMCifInfoStructDetails struct_details_; ///< mmCIF struct category
+ MMCifInfoObsolete obsolete_; ///< obsolete/ superseded entry
+ std::vector<MMCifInfoCitation> citations_; ///< list of citations
+ std::vector<MMCifInfoBioUnit> biounits_; ///< list of biounits
+ std::vector<MMCifInfoTransOpPtr> transops_;
+ MMCifInfoStructRefs struct_refs_;
+};
+
+
+}} // ns
+
+#endif
diff --git a/modules/io/src/mol/mmcif_reader.cc b/modules/io/src/mol/mmcif_reader.cc
new file mode 100644
index 0000000000000000000000000000000000000000..409902ab4391a66860aeed24d9b9aa3d6a9720a9
--- /dev/null
+++ b/modules/io/src/mol/mmcif_reader.cc
@@ -0,0 +1,1638 @@
+//------------------------------------------------------------------------------
+// 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
+//------------------------------------------------------------------------------
+
+#include <ctype.h>
+
+#include <ost/profile.hh>
+#include <ost/log.hh>
+#include <ost/dyn_cast.hh>
+#include <ost/mol/xcs_editor.hh>
+#include <ost/conop/conop.hh>
+
+#include <ost/conop/rule_based_builder.hh>
+#include <ost/io/mol/mmcif_reader.hh>
+
+namespace ost { namespace io {
+
+
+bool is_undef(StringRef value)
+{
+ return value.size()==1 && (value[0]=='?' || value[0]=='.');
+}
+
+MMCifReader::MMCifReader(std::istream& stream, mol::EntityHandle& ent_handle,
+ const IOProfile& profile):
+ StarParser(stream, true), profile_(profile), ent_handle_(ent_handle)
+{
+ this->Init();
+}
+
+MMCifReader::MMCifReader(const String& filename, mol::EntityHandle& ent_handle,
+ const IOProfile& profile):
+ StarParser(filename, true), profile_(profile), ent_handle_(ent_handle)
+{
+ this->Init();
+}
+
+void MMCifReader::Init()
+{
+ warned_name_mismatch_ = false;
+ category_ = DONT_KNOW;
+ memset(category_counts_, 0, DONT_KNOW * sizeof(int));
+ chain_count_ = 0;
+ atom_count_ = 0;
+ residue_count_ = 0;
+ auth_chain_id_ = false;
+ seqres_can_ = false;
+ has_model_ = false;
+ restrict_chains_ = "";
+ subst_res_id_ = "";
+ curr_chain_ = mol::ChainHandle();
+ curr_residue_ = mol::ResidueHandle();
+ seqres_ = seq::CreateSequenceList();
+ read_seqres_ = false;
+ warned_rule_based_ = false;
+ info_ = MMCifInfo();
+}
+
+void MMCifReader::ClearState()
+{
+ curr_chain_ = mol::ChainHandle();
+ curr_residue_ = mol::ResidueHandle();
+ chain_count_ = 0;
+ residue_count_ = 0;
+ atom_count_ = 0;
+ category_ = DONT_KNOW;
+ warned_name_mismatch_ = false;
+ seqres_ = seq::CreateSequenceList();
+ info_ = MMCifInfo();
+ entity_desc_map_.clear();
+ authors_map_.clear();
+ bu_origin_map_.clear();
+ bu_assemblies_.clear();
+ helix_list_.clear();
+ strand_list_.clear();
+}
+
+void MMCifReader::SetRestrictChains(const String& restrict_chains)
+{
+ restrict_chains_ = restrict_chains;
+}
+
+bool MMCifReader::IsValidPDBIdent(const StringRef& pdbid)
+{
+ if (pdbid.length() == PDBID_LEN && isdigit(pdbid[0])) {
+ return true;
+ }
+ return false;
+}
+
+bool MMCifReader::OnBeginData(const StringRef& data_name)
+{
+ LOG_DEBUG("MCIFFReader: " << profile_);
+ Profile profile_import("MMCifReader::OnBeginData");
+
+ // check for PDB id
+ if (!this->IsValidPDBIdent(data_name)) {
+ throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
+ "No valid PDB id found for data block, read instead \'"
+ + data_name.str() + "\'",
+ this->GetCurrentLinenum()));
+ }
+
+ this->ClearState();
+
+ return true;
+}
+
+bool MMCifReader::OnBeginLoop(const StarLoopDesc& header)
+{
+ bool cat_available = false;
+ category_ = DONT_KNOW;
+ // set whole array to -1
+ memset(indices_, -1, MAX_ITEMS_IN_ROW * sizeof(int));
+ // walk through possible categories
+ if (header.GetCategory() == "atom_site") {
+ category_ = ATOM_SITE;
+ // mandatory items
+ this->TryStoreIdx(AUTH_ASYM_ID, "auth_asym_id", header);
+ this->TryStoreIdx(AS_ID, "id", header);
+ this->TryStoreIdx(LABEL_ALT_ID, "label_alt_id", header);
+ this->TryStoreIdx(LABEL_ASYM_ID, "label_asym_id", header);
+ this->TryStoreIdx(LABEL_ATOM_ID, "label_atom_id", header);
+ this->TryStoreIdx(LABEL_COMP_ID, "label_comp_id", header);
+ this->TryStoreIdx(LABEL_ENTITY_ID, "label_entity_id", header);
+ this->TryStoreIdx(LABEL_SEQ_ID, "label_seq_id", header);
+ this->TryStoreIdx(TYPE_SYMBOL, "type_symbol", header);
+ // assumed mandatory
+ this->TryStoreIdx(CARTN_X, "Cartn_x", header);
+ this->TryStoreIdx(CARTN_Y, "Cartn_y", header);
+ this->TryStoreIdx(CARTN_Z, "Cartn_z", header);
+ // optional
+ indices_[OCCUPANCY] = header.GetIndex("occupancy");
+ indices_[B_ISO_OR_EQUIV] = header.GetIndex("B_iso_or_equiv");
+ indices_[GROUP_PDB] = header.GetIndex("group_PDB");
+ indices_[AUTH_SEQ_ID] = header.GetIndex("auth_seq_id");
+ indices_[PDBX_PDB_INS_CODE] = header.GetIndex("pdbx_PDB_ins_code");
+ indices_[PDBX_PDB_MODEL_NUM] = header.GetIndex("pdbx_PDB_model_num");
+
+ // post processing
+ if (category_counts_[category_] > 0) {
+ if ((has_model_ && (indices_[PDBX_PDB_MODEL_NUM] == -1))||
+ (!has_model_ && (indices_[PDBX_PDB_MODEL_NUM] != -1))) {
+ throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
+ "Not all atom_site entries carry a model number.",
+ this->GetCurrentLinenum()));
+ }
+ }
+ cat_available = true;
+ } else if (header.GetCategory() == "entity") {
+ category_ = ENTITY;
+ // mandatory items
+ this->TryStoreIdx(E_ID, "id", header);
+ // optional
+ indices_[E_TYPE] = header.GetIndex("type");
+ indices_[PDBX_DESCRIPTION] = header.GetIndex("pdbx_description");
+ cat_available = true;
+ } else if (header.GetCategory() == "entity_poly") {
+ category_ = ENTITY_POLY;
+ // mandatory
+ this->TryStoreIdx(ENTITY_ID, "entity_id", header);
+ // optional
+ indices_[EP_TYPE] = header.GetIndex("type");
+ indices_[PDBX_SEQ_ONE_LETTER_CODE] =
+ header.GetIndex("pdbx_seq_one_letter_code");
+ indices_[PDBX_SEQ_ONE_LETTER_CODE_CAN] =
+ header.GetIndex("pdbx_seq_one_letter_code_can");
+ cat_available = true;
+ } else if (header.GetCategory() == "citation") {
+ category_ = CITATION;
+ // mandatory items
+ this->TryStoreIdx(CITATION_ID, "id", header);
+ // optional
+ indices_[ABSTRACT_ID_CAS] = header.GetIndex("abstract_id_CAS");
+ indices_[BOOK_ID_ISBN] = header.GetIndex("book_id_ISBN");
+ indices_[BOOK_TITLE] = header.GetIndex("book_title");
+ indices_[JOURNAL_ABBREV] = header.GetIndex("journal_abbrev");
+ indices_[YEAR] = header.GetIndex("year");
+ indices_[TITLE] = header.GetIndex("title");
+ indices_[JOURNAL_VOLUME] = header.GetIndex("journal_volume");
+ indices_[PAGE_FIRST] = header.GetIndex("page_first");
+ indices_[PAGE_LAST] = header.GetIndex("page_last");
+ indices_[PDBX_DATABASE_ID_DOI] = header.GetIndex("pdbx_database_id_DOI");
+ indices_[PDBX_DATABASE_ID_PUBMED] =
+ header.GetIndex("pdbx_database_id_PubMed");
+ cat_available = true;
+ } else if (header.GetCategory()=="citation_author") {
+ category_ = CITATION_AUTHOR;
+ // mandatory items
+ this->TryStoreIdx(AUTHOR_CITATION_ID, "citation_id", header);
+ this->TryStoreIdx(AUTHOR_NAME, "name", header);
+ this->TryStoreIdx(ORDINAL, "ordinal", header);
+ cat_available = true;
+ } else if (header.GetCategory() == "exptl") {
+ category_ = EXPTL;
+ // mandatory items
+ this->TryStoreIdx(CITATION_ID, "entry_id", header);
+ this->TryStoreIdx(METHOD, "method", header);
+ cat_available = true;
+ } else if (header.GetCategory() == "refine") {
+ category_ = REFINE;
+ // mandatory items
+ this->TryStoreIdx(REFINE_ENTRY_ID, "entry_id", header);
+ this->TryStoreIdx(LS_D_RES_HIGH, "ls_d_res_high", header);
+ this->TryStoreIdx(LS_D_RES_LOW, "ls_d_res_low", header);
+ cat_available = true;
+ } else if (header.GetCategory() == "pdbx_struct_assembly") {
+ category_ = PDBX_STRUCT_ASSEMBLY;
+ // mandatory items
+ this->TryStoreIdx(PSA_ID, "id", header);
+ // optional
+ indices_[PSA_DETAILS] = header.GetIndex("details");
+ //indices_[METHOD_DETAILS] = header.GetIndex("method_details");
+ cat_available = true;
+ } else if (header.GetCategory() == "pdbx_struct_assembly_gen") {
+ category_ = PDBX_STRUCT_ASSEMBLY_GEN;
+ // mandatory items
+ this->TryStoreIdx(ASSEMBLY_ID, "assembly_id", header);
+ this->TryStoreIdx(ASYM_ID_LIST, "asym_id_list", header);
+ this->TryStoreIdx(OPER_EXPRESSION, "oper_expression", header);
+ cat_available = true;
+ } else if (header.GetCategory() == "pdbx_struct_oper_list") {
+ category_ = PDBX_STRUCT_OPER_LIST;
+ // mandatory items
+ this->TryStoreIdx(PSOL_ID, "id", header);
+ this->TryStoreIdx(PSOL_TYPE, "type", header);
+ // optional items
+ indices_[VECTOR_1] = header.GetIndex("vector[1]");
+ indices_[VECTOR_2] = header.GetIndex("vector[2]");
+ indices_[VECTOR_3] = header.GetIndex("vector[3]");
+ indices_[MATRIX_1_1] = header.GetIndex("matrix[1][1]");
+ indices_[MATRIX_1_2] = header.GetIndex("matrix[1][2]");
+ indices_[MATRIX_1_3] = header.GetIndex("matrix[1][3]");
+ indices_[MATRIX_2_1] = header.GetIndex("matrix[2][1]");
+ indices_[MATRIX_2_2] = header.GetIndex("matrix[2][2]");
+ indices_[MATRIX_2_3] = header.GetIndex("matrix[2][3]");
+ indices_[MATRIX_3_1] = header.GetIndex("matrix[3][1]");
+ indices_[MATRIX_3_2] = header.GetIndex("matrix[3][2]");
+ indices_[MATRIX_3_3] = header.GetIndex("matrix[3][3]");
+ cat_available = true;
+ } else if (header.GetCategory() == "struct") {
+ category_ = STRUCT;
+ // mandatory items
+ this->TryStoreIdx(STRUCT_ENTRY_ID, "entry_id", header);
+ // optional items
+ indices_[PDBX_CASP_FLAG] = header.GetIndex("pdbx_CASP_flag");
+ indices_[PDBX_DESCRIPTOR] = header.GetIndex("pdbx_descriptor");
+ indices_[PDBX_FORMULA_WEIGHT] = header.GetIndex("pdbx_formula_weight");
+ indices_[PDBX_FORMULA_WEIGHT_METHOD]
+ = header.GetIndex("pdbx_formula_weight_method");
+ indices_[PDBX_MODEL_DETAILS] = header.GetIndex("pdbx_model_details");
+ indices_[PDBX_MODEL_TYPE_DETAILS]
+ = header.GetIndex("pdbx_model_type_details");
+ indices_[STRUCT_TITLE] = header.GetIndex("title");
+ cat_available = true;
+ } else if (header.GetCategory() == "struct_conf") {
+ category_ = STRUCT_CONF;
+ // mandatory items
+ this->TryStoreIdx(SC_BEG_LABEL_ASYM_ID, "beg_label_asym_id", header);
+ this->TryStoreIdx(SC_BEG_LABEL_COMP_ID, "beg_label_comp_id", header);
+ this->TryStoreIdx(SC_BEG_LABEL_SEQ_ID, "beg_label_seq_id", header);
+ this->TryStoreIdx(SC_CONF_TYPE_ID, "conf_type_id", header);
+ this->TryStoreIdx(SC_END_LABEL_ASYM_ID, "end_label_asym_id", header);
+ this->TryStoreIdx(SC_END_LABEL_COMP_ID, "end_label_comp_id", header);
+ this->TryStoreIdx(SC_END_LABEL_SEQ_ID, "end_label_seq_id", header);
+ this->TryStoreIdx(SC_ID, "id", header);
+ // optional items
+ indices_[SC_BEG_AUTH_ASYM_ID] = header.GetIndex("beg_auth_asym_id");
+ indices_[SC_END_AUTH_ASYM_ID] = header.GetIndex("end_auth_asym_id");
+ cat_available = true;
+ } else if (header.GetCategory() == "struct_sheet_range") {
+ category_ = STRUCT_SHEET_RANGE;
+ // mandatory items
+ this->TryStoreIdx(SSR_BEG_LABEL_ASYM_ID, "beg_label_asym_id", header);
+ this->TryStoreIdx(SSR_BEG_LABEL_COMP_ID, "beg_label_comp_id", header);
+ this->TryStoreIdx(SSR_BEG_LABEL_SEQ_ID, "beg_label_seq_id", header);
+ this->TryStoreIdx(SSR_END_LABEL_ASYM_ID, "end_label_asym_id", header);
+ this->TryStoreIdx(SSR_END_LABEL_COMP_ID, "end_label_comp_id", header);
+ this->TryStoreIdx(SSR_END_LABEL_SEQ_ID, "end_label_seq_id", header);
+ this->TryStoreIdx(SSR_SHEET_ID, "sheet_id", header);
+ this->TryStoreIdx(SSR_ID, "id", header);
+ // optional items
+ indices_[SSR_BEG_AUTH_ASYM_ID] = header.GetIndex("beg_auth_asym_id");
+ indices_[SSR_END_AUTH_ASYM_ID] = header.GetIndex("end_auth_asym_id");
+ cat_available = true;
+ } else if (header.GetCategory() == "pdbx_database_PDB_obs_spr") {
+ category_ = PDBX_DATABASE_PDB_OBS_SPR;
+ // mandatory items
+ this->TryStoreIdx(DATE, "date", header);
+ this->TryStoreIdx(PDPOS_ID, "id", header);
+ this->TryStoreIdx(PDB_ID, "pdb_id", header);
+ this->TryStoreIdx(REPLACE_PDB_ID, "replace_pdb_id", header);
+ cat_available = true;
+ } else if (header.GetCategory() == "struct_ref") {
+ category_ = STRUCT_REF;
+ this->TryStoreIdx(SR_ENTITY_ID, "entity_id", header);
+ this->TryStoreIdx(SR_ID, "id", header);
+ this->TryStoreIdx(SR_DB_NAME, "db_name", header);
+ this->TryStoreIdx(SR_DB_CODE, "db_code", header);
+ indices_[SR_DB_ACCESS]=header.GetIndex("pdbx_db_accession");
+ cat_available = true;
+ } else if (header.GetCategory() == "struct_ref_seq") {
+ category_ = STRUCT_REF_SEQ;
+ this->TryStoreIdx(SRS_ALIGN_ID, "align_id", header);
+ this->TryStoreIdx(SRS_STRUCT_REF_ID, "ref_id", header);
+ this->TryStoreIdx(SRS_ENT_ALIGN_BEG, "seq_align_beg", header);
+ this->TryStoreIdx(SRS_ENT_ALIGN_END, "seq_align_end", header);
+ this->TryStoreIdx(SRS_DB_ALIGN_BEG, "db_align_beg", header);
+ this->TryStoreIdx(SRS_DB_ALIGN_END, "db_align_end", header);
+ indices_[SRS_PDBX_STRAND_ID]=header.GetIndex("pdbx_strand_id");
+ cat_available = true;
+ } else if (header.GetCategory()=="struct_ref_seq_dif") {
+ category_ = STRUCT_REF_SEQ_DIF;
+ this->TryStoreIdx(SRSD_ALIGN_ID, "align_id", header);
+ this->TryStoreIdx(SRSD_SEQ_RNUM, "seq_num", header);
+ this->TryStoreIdx(SRSD_DB_RNUM, "pdbx_seq_db_seq_num", header);
+ indices_[SRSD_DETAILS]=header.GetIndex("details");
+ cat_available = true;
+ }
+ category_counts_[category_]++;
+ return cat_available;
+}
+
+mol::ResNum to_res_num(int num, char ins_code)
+{
+ return mol::ResNum(num, ins_code==' ' ? '\0' : ins_code);
+}
+
+bool MMCifReader::ParseAtomIdent(const std::vector<StringRef>& columns,
+ String& auth_chain_name,
+ String& cif_chain_name,
+ StringRef& res_name,
+ mol::ResNum& resnum,
+ bool& valid_res_num,
+ StringRef& atom_name,
+ char& alt_loc)
+{
+ // ATOM name
+ atom_name = columns[indices_[LABEL_ATOM_ID]];
+ if (profile_.calpha_only) {
+ if (atom_name != StringRef("CA", 2)) {
+ return false;
+ }
+ }
+ // CHAIN ID
+ auth_chain_name = columns[indices_[AUTH_ASYM_ID]].str();
+ cif_chain_name = columns[indices_[LABEL_ASYM_ID]].str();
+
+ if (restrict_chains_.size() > 0 &&
+ restrict_chains_.find(cif_chain_name) == String::npos) {
+ return false;
+ }
+
+ std::pair<bool, int> a_num = this->TryGetInt(columns[indices_[AS_ID]],
+ "atom_site.id",
+ profile_.fault_tolerant); // unit test
+
+ alt_loc = columns[indices_[LABEL_ALT_ID]][0];
+ res_name = columns[indices_[LABEL_COMP_ID]];
+ std::pair<bool, int> res_num;
+ if (columns[indices_[LABEL_SEQ_ID]][0] != '.') {
+ res_num =this->TryGetInt(columns[indices_[LABEL_SEQ_ID]],
+ "atom_site.label_seq_id",
+ profile_.fault_tolerant); // unit test
+ if (!res_num.first) { // unit test
+ if (profile_.fault_tolerant) {
+ return false;
+ }
+ }
+ valid_res_num = true;
+ } else {
+ valid_res_num = false;
+ return true;
+ }
+
+ resnum = to_res_num(res_num.second, ' ');
+
+ return true;
+}
+
+void MMCifReader::ParseAndAddAtom(const std::vector<StringRef>& columns)
+{
+ mol::XCSEditor editor=ent_handle_.EditXCS(mol::BUFFERED_EDIT); // potbl
+ char alt_loc=0;
+ String auth_chain_name;
+ String cif_chain_name;
+ StringRef res_name, atom_name;
+ mol::ResNum res_num(0);
+ bool valid_res_num = false;
+ if (indices_[PDBX_PDB_MODEL_NUM] != -1) {
+ if (has_model_) {
+ if (curr_model_ != TryGetInt(columns[indices_[PDBX_PDB_MODEL_NUM]],
+ "atom_site.pdbx_PDB_model_num")) {
+ return;
+ }
+ } else {
+ has_model_ = true;
+ curr_model_ = TryGetInt(columns[indices_[PDBX_PDB_MODEL_NUM]],
+ "atom_site.pdbx_PDB_model_num");
+ }
+ }
+
+ if (!this->ParseAtomIdent(columns,
+ auth_chain_name,
+ cif_chain_name,
+ res_name,
+ res_num,
+ valid_res_num,
+ atom_name,
+ alt_loc)) {// unit test
+ return;
+ }
+ Real occ = 1.00f, temp = 0;
+ geom::Vec3 apos;
+
+ for (int i = CARTN_X; i <= CARTN_Z; ++i) {
+ std::pair<bool, float> result = this->TryGetFloat(columns[indices_[i]],
+ "atom_site.cartn_[xyz]",
+ profile_.fault_tolerant);
+ if (!result.first) { // unit test
+ if (profile_.fault_tolerant) { // unit test
+ return;
+ }
+ }
+ apos[i - CARTN_X] = result.second;
+ }
+
+ if (indices_[OCCUPANCY] != -1) { // unit test
+ occ = this->TryGetReal(columns[indices_[OCCUPANCY]], "atom_site.occupancy");
+ }
+ if (indices_[B_ISO_OR_EQUIV] != -1) { // unit test
+ temp = this->TryGetReal(columns[indices_[B_ISO_OR_EQUIV]],
+ "atom_site.B_iso_or_equiv");
+ }
+
+ // determine element
+ String s_ele(columns[indices_[TYPE_SYMBOL]].str());
+
+ String aname(atom_name.str());
+ // some postprocessing
+ LOG_TRACE( "s_chain: [" << cif_chain_name << "]" );
+
+ // determine chain and residue update
+ bool update_chain = false;
+ bool update_residue = false;
+ if(!curr_chain_) { // unit test
+ update_chain=true;
+ update_residue=true;
+ } else if(curr_chain_.GetName() != cif_chain_name) { // unit test
+ update_chain=true;
+ update_residue=true;
+ }
+
+ if(!curr_residue_) { // unit test
+ update_residue=true;
+ } else if (!valid_res_num) {
+ if (indices_[AUTH_SEQ_ID] != -1 &&
+ indices_[PDBX_PDB_INS_CODE] != -1) {
+ if (subst_res_id_ !=
+ cif_chain_name +
+ columns[indices_[AUTH_SEQ_ID]].str() +
+ columns[indices_[PDBX_PDB_INS_CODE]].str()) {
+ update_residue=true;
+
+ subst_res_id_ = cif_chain_name +
+ columns[indices_[AUTH_SEQ_ID]].str() +
+ columns[indices_[PDBX_PDB_INS_CODE]].str();
+ }
+ } else {
+ throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
+ "Missing residue number information",
+ this->GetCurrentLinenum()));
+ }
+ } else if(curr_residue_.GetNumber() != res_num) { // unit test
+ update_residue=true;
+ }
+
+ if(update_chain) { // unit test
+ curr_chain_ = ent_handle_.FindChain(cif_chain_name);
+ if(!curr_chain_.IsValid()) { // unit test
+ LOG_DEBUG("new chain " << cif_chain_name);
+ curr_chain_=editor.InsertChain(cif_chain_name);
+ curr_chain_.SetStringProp("pdb_auth_chain_name", auth_chain_name);
+ ++chain_count_;
+ // store entity id
+ chain_id_pairs_.push_back(std::pair<mol::ChainHandle,String>(curr_chain_,
+ columns[indices_[LABEL_ENTITY_ID]].str()));
+ }
+ assert(curr_chain_.IsValid());
+ } else if (chain_id_pairs_.back().second != // unit test
+ columns[indices_[LABEL_ENTITY_ID]].str()) {
+ // check that label_entity_id stays the same
+ throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
+ "Change of 'atom_site.label_entity_id' item for chain " +
+ curr_chain_.GetName() + "! Expected: " + chain_id_pairs_.back().second +
+ ", found: " + columns[indices_[LABEL_ENTITY_ID]].str() + ".",
+ this->GetCurrentLinenum()));
+ }
+
+ if(update_residue) { // unit test
+ curr_residue_=mol::ResidueHandle();
+ if (valid_res_num && profile_.join_spread_atom_records) { // unit test
+ curr_residue_=curr_chain_.FindResidue(res_num);
+ }
+ if (!curr_residue_.IsValid()) { // unit test
+ LOG_DEBUG("new residue " << res_name << " " << res_num);
+ if (valid_res_num) {
+ curr_residue_ = editor.AppendResidue(curr_chain_,
+ res_name.str(),
+ res_num);
+ } else {
+ curr_residue_ = editor.AppendResidue(curr_chain_, res_name.str());
+ }
+ warned_name_mismatch_=false;
+ ++residue_count_;
+ }
+ assert(curr_residue_.IsValid());
+ }
+
+ // finally add atom
+ LOG_DEBUG("adding atom " << aname << " (" << s_ele << ") @" << apos);
+ mol::AtomHandle ah;
+ if (curr_residue_.GetName()!=res_name.str()) { // unit test
+ if (!profile_.fault_tolerant && alt_loc=='.') { // unit test
+ std::stringstream ss;
+ ss << "Residue with number " << res_num << " has more than one name.";
+ throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
+ ss.str(),
+ this->GetCurrentLinenum()));
+ }
+ if (!warned_name_mismatch_) { // unit test
+ if (alt_loc=='.') { // unit test
+ LOG_WARNING("Residue with number " << res_num << " has more than one "
+ "name. Ignoring atoms for everything but the first");
+ } else {
+ LOG_WARNING("Residue with number " << res_num
+ << " contains a microheterogeneity. Everything but atoms "
+ "for the residue '" << curr_residue_.GetName()
+ << "' will be ignored");
+ }
+ }
+ warned_name_mismatch_=true;
+ return;
+ }
+ if (alt_loc!='.') { // unit test
+ // Check if there is already a atom with the same name.
+ mol::AtomHandle me=curr_residue_.FindAtom(aname);
+ if (me.IsValid()) { // unit test
+ try {
+ editor.AddAltAtomPos(String(1, alt_loc), me, apos);
+ } catch (Error) {
+ LOG_INFO("Ignoring atom alt location since there is already an atom "
+ "with name " << aname << ", but without an alt loc");
+ return;
+ }
+ return;
+ } else {
+ ah = editor.InsertAltAtom(curr_residue_, aname,
+ String(1, alt_loc), apos, s_ele);
+ ++atom_count_;
+ }
+ } else {
+ mol::AtomHandle atom=curr_residue_.FindAtom(aname);
+ if (atom.IsValid() && !profile_.quack_mode) { // unit test
+ if (profile_.fault_tolerant) { // unit test
+ LOG_WARNING("duplicate atom '" << aname << "' in residue "
+ << curr_residue_);
+ return;
+ }
+ throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
+ "Duplicate atom '"+aname+
+ "' in residue "+
+ curr_residue_.GetQualifiedName(),
+ this->GetCurrentLinenum()));
+ }
+ ah = editor.InsertAtom(curr_residue_, aname, apos, s_ele);
+ ++atom_count_;
+ }
+ ah.SetBFactor(temp);
+
+ ah.SetOccupancy(occ);
+
+ // record type
+ ah.SetHetAtom(indices_[GROUP_PDB] == -1 ? false :
+ columns[indices_[GROUP_PDB]][0]=='H');
+
+}
+
+void MMCifReader::ParseEntity(const std::vector<StringRef>& columns)
+{
+ bool store = false; // is it worth storing this record?
+ MMCifEntityDesc desc;
+
+ // type
+ if (indices_[E_TYPE] != -1) {
+ desc.type = mol::ChainTypeFromString(columns[indices_[E_TYPE]]);
+ store = true;
+ }
+
+ // description
+ if (indices_[PDBX_DESCRIPTION] != -1) {
+ desc.details = columns[indices_[PDBX_DESCRIPTION]].str();
+ } else {
+ desc.details = "";
+ }
+
+ if (store) {
+ desc.seqres = "";
+ entity_desc_map_.insert(
+ MMCifEntityDescMap::value_type(columns[indices_[E_ID]].str(),
+ desc)
+ );
+ }
+}
+
+void MMCifReader::ParseEntityPoly(const std::vector<StringRef>& columns)
+{
+ // we assume that the entity cat. ALWAYS comes before the entity_poly cat.
+ // search entity
+ MMCifEntityDescMap::iterator edm_it =
+ entity_desc_map_.find(columns[indices_[ENTITY_ID]].str());
+
+ if (edm_it == entity_desc_map_.end()) {
+ throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
+ "'entity_poly' category defined before 'entity' for id '" +
+ columns[indices_[ENTITY_ID]].str() +
+ "' or missing.",
+ this->GetCurrentLinenum()));
+ }
+
+ // store type
+ if (indices_[EP_TYPE] != -1) {
+ edm_it->second.type = mol::ChainTypeFromString(columns[indices_[EP_TYPE]]);
+ }
+
+ // store seqres
+ if (edm_it->second.seqres.length() > 0) {
+ throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
+ "entity_poly.pdbx_seq_one_letter_code[_can] clash: sequence for entry '" +
+ columns[indices_[ENTITY_ID]].str() +
+ "' is already set to '" +
+ edm_it->second.seqres + "'.",
+ this->GetCurrentLinenum()));
+ }
+ if (read_seqres_) {
+ StringRef seqres;
+ if (seqres_can_) {
+ if (indices_[PDBX_SEQ_ONE_LETTER_CODE_CAN] != -1) {
+ seqres=columns[indices_[PDBX_SEQ_ONE_LETTER_CODE_CAN]];
+ edm_it->second.seqres = seqres.str_no_whitespace();
+ } else {
+ throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
+ "'entity_poly.pdbx_seq_one_letter_code_can' not available.'",
+ this->GetCurrentLinenum()));
+ }
+ } else if (indices_[PDBX_SEQ_ONE_LETTER_CODE] != -1) {
+ seqres=columns[indices_[PDBX_SEQ_ONE_LETTER_CODE]];
+ conop::BuilderP builder=conop::Conopology::Instance().GetBuilder("DEFAULT");
+ conop::RuleBasedBuilderPtr rbb=dyn_cast<conop::RuleBasedBuilder>(builder);
+ if (!rbb) {
+ if (!warned_rule_based_) {
+ LOG_WARNING("SEQRES import requires the rule-based builder. Ignoring "
+ "SEQRES records");
+ }
+ warned_rule_based_=true;
+ return;
+ }
+ conop::CompoundLibPtr comp_lib=rbb->GetCompoundLib();
+ edm_it->second.seqres = this->ConvertSEQRES(seqres.str_no_whitespace(),
+ comp_lib);
+ } else {
+ throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
+ "'entity_poly.pdbx_seq_one_letter_code' not available.'",
+ this->GetCurrentLinenum()));
+ }
+ }
+}
+
+String MMCifReader::ConvertSEQRES(const String& seqres,
+ conop::CompoundLibPtr comp_lib)
+{
+ String can_seqres;
+ for (String::const_iterator i=seqres.begin(), e=seqres.end(); i!=e; ++i) {
+ if (*i=='(') {
+ bool found_end_paren=false;
+ String tlc;
+ tlc.reserve(3);
+ while ((++i)!=seqres.end()) {
+ if (*i==')') {
+ found_end_paren=true;
+ break;
+ }
+ tlc.push_back(*i);
+ }
+ if (!found_end_paren) {
+ throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
+ "'entity_poly.pdbx_seq_one_letter_code' contains "
+ "unmatched '('", this->GetCurrentLinenum()));
+ }
+ conop::CompoundPtr compound=comp_lib->FindCompound(tlc,
+ conop::Compound::PDB);
+ if (!compound) {
+ if (tlc!="UNK") {
+
+ LOG_WARNING("unknown residue '" << tlc << "' in SEQRES record. "
+ "Setting one-letter-code to 'X'");
+ }
+ can_seqres.push_back('X');
+ continue;
+ }
+ if (compound->GetOneLetterCode()=='?') {
+ can_seqres.push_back('X');
+ } else {
+ can_seqres.push_back(compound->GetOneLetterCode());
+ }
+
+ } else {
+ can_seqres.push_back(*i);
+ }
+ }
+ return can_seqres;
+}
+
+void MMCifReader::ParseCitation(const std::vector<StringRef>& columns)
+{
+ // create citation object
+ MMCifInfoCitation cit = MMCifInfoCitation();
+ // just add info
+ cit.SetID(columns[indices_[CITATION_ID]].str());
+ if (indices_[ABSTRACT_ID_CAS] != -1) {
+ cit.SetCAS(columns[indices_[ABSTRACT_ID_CAS]].str());
+ }
+ if (indices_[BOOK_ID_ISBN] != -1) {
+ cit.SetISBN(columns[indices_[BOOK_ID_ISBN]].str());
+ }
+ if (indices_[BOOK_TITLE] != -1) {
+ if (columns[indices_[BOOK_TITLE]] != StringRef(".", 1)) {
+ cit.SetPublishedIn(columns[indices_[BOOK_TITLE]].str());
+ }
+ }
+ if (indices_[JOURNAL_ABBREV] != -1) {
+ if (columns[indices_[JOURNAL_ABBREV]] != StringRef(".", 1)) {
+ if (cit.GetPublishedIn().length() > 0) {
+ throw IOException(this->FormatDiagnostic(STAR_DIAG_WARNING,
+ "citation.book_title already occupies the 'published_in' field of this citation, cannot add " +
+ columns[indices_[JOURNAL_ABBREV]].str() +
+ ".",
+ this->GetCurrentLinenum()));
+ } else {
+ cit.SetPublishedIn(columns[indices_[JOURNAL_ABBREV]].str());
+ }
+ }
+ }
+ if (indices_[JOURNAL_VOLUME] != -1) {
+ cit.SetVolume(columns[indices_[JOURNAL_VOLUME]].str());
+ }
+ if (indices_[PAGE_FIRST] != -1) {
+ cit.SetPageFirst(columns[indices_[PAGE_FIRST]].str());
+ }
+ if (indices_[PAGE_LAST] != -1) {
+ cit.SetPageLast(columns[indices_[PAGE_LAST]].str());
+ }
+ if (indices_[PDBX_DATABASE_ID_DOI] != -1) {
+ cit.SetDOI(columns[indices_[PDBX_DATABASE_ID_DOI]].str());
+ }
+ if (indices_[PDBX_DATABASE_ID_PUBMED] != -1) {
+ if (columns[indices_[PDBX_DATABASE_ID_PUBMED]][0]!='?') {
+ cit.SetPubMed(this->TryGetInt(columns[indices_[PDBX_DATABASE_ID_PUBMED]],
+ "citation.pdbx_database_id_PubMed"));
+ }
+ }
+ if (indices_[YEAR] != -1) {
+ if (columns[indices_[YEAR]][0]!='?') {
+ cit.SetYear(this->TryGetInt(columns[indices_[YEAR]], "citation.year"));
+ }
+ }
+ if (indices_[TITLE] != -1) {
+ cit.SetTitle(columns[indices_[TITLE]].str());
+ }
+
+ // store citation (wo author, yet)
+ info_.AddCitation(cit);
+}
+
+void MMCifReader::ParseCitationAuthor(const std::vector<StringRef>& columns)
+{
+ // get/ pack values
+ MMCifCitationAuthorMap::iterator atm_it;
+ std::vector<String> at_vec;
+ std::vector<int> pos_vec;
+ atm_it = authors_map_.find(columns[indices_[AUTHOR_CITATION_ID]].str());
+ if (atm_it != authors_map_.end()) {
+ at_vec = atm_it->second.second;
+ pos_vec = atm_it->second.first;
+ }
+ at_vec.push_back(columns[indices_[AUTHOR_NAME]].str());
+ pos_vec.push_back(this->TryGetInt(columns[indices_[ORDINAL]],
+ "citation_author.ordinal"));
+
+ // sort new author into right position
+ std::vector<int>::iterator pos_it;
+ std::vector<String>::iterator atv_it;
+ int ti;
+ String ts;
+ pos_it = pos_vec.end();
+ atv_it = at_vec.end();
+ --pos_it;
+ --atv_it;
+ for (; pos_it != pos_vec.begin(); --pos_it, --atv_it) {
+ if (*pos_it < *(pos_it-1)) {
+ ti = *pos_it;
+ *pos_it = *(pos_it-1);
+ *(pos_it-1) = ti;
+ ts = *atv_it;
+ *atv_it = *(atv_it-1);
+ *(atv_it-1) = ts;
+ }
+ else {
+ break;
+ }
+ }
+
+ // store new values in map
+ if (atm_it != authors_map_.end()) {
+ atm_it->second.second = at_vec;
+ atm_it->second.first = pos_vec;
+ } else {
+ authors_map_.insert(MMCifCitationAuthorMap::value_type(
+ columns[indices_[AUTHOR_CITATION_ID]].str(),
+ std::pair<std::vector<int>, std::vector<String> >(pos_vec, at_vec)
+ ));
+ }
+}
+
+void MMCifReader::ParseExptl(const std::vector<StringRef>& columns)
+{
+ info_.SetMethod(columns[indices_[METHOD]].str());
+}
+
+void MMCifReader::ParseRefine(const std::vector<StringRef>& columns)
+{
+ StringRef col=columns[indices_[LS_D_RES_HIGH]];
+ if (col.size()!=1 || (col[0]!='?' && col[0]!='.')) {
+ info_.SetResolution(this->TryGetReal(columns[indices_[LS_D_RES_HIGH]],
+ "refine.ls_d_res_high"));
+ }
+}
+
+void MMCifReader::ParsePdbxStructAssembly(const std::vector<StringRef>& columns)
+{
+ if (indices_[PSA_DETAILS] != -1) {
+ bu_origin_map_.insert(std::pair<String,
+ String>(columns[indices_[PSA_ID]].str(),
+ columns[indices_[PSA_DETAILS]].str()));
+ } else {
+ bu_origin_map_.insert(std::pair<String,
+ String>(columns[indices_[PSA_ID]].str(),
+ "?"));
+ }
+}
+
+void MMCifReader::StoreExpression(const char* l, const char* s,
+ bool& is_range, int lborder,
+ std::vector<String>& single_block)
+{
+ std::stringstream ss;
+ int rborder;
+
+ if (l != s) {
+ if (is_range) {
+ is_range = false;
+ rborder = this->TryGetInt(StringRef(l, s-l),
+ "pdbx_struct_assembly_gen.oper_expression");
+ for (lborder += 1; lborder < rborder; lborder++) {
+ ss << lborder;
+ single_block.push_back(ss.str());
+ ss.str("");
+ }
+ }
+ single_block.push_back(String(l, s-l));
+ }
+}
+
+void MMCifReader::StoreRange(const char*& l, const char* s, bool& is_range,
+ int& lborder, std::vector<String>& single_block)
+{
+ if (is_range) {
+ throw IOException(this->FormatDiagnostic(STAR_DIAG_WARNING,
+ "pdbx_struct_assembly_gen.oper_expression is missing a right border for a range expression.",
+ this->GetCurrentLinenum()));
+ }
+ is_range = true;
+ if (l != s) {
+ lborder = this->TryGetInt(StringRef(l, s-l),
+ "pdbx_struct_assembly_gen.oper_expression");
+ single_block.push_back(String(l, s-l));
+ }
+ l = s+1;
+}
+
+std::vector<std::vector<String> > MMCifReader::UnPackOperExperession(StringRef expression)
+{
+ std::vector<std::vector<String> > unpacked;
+ std::vector<String> single_block;
+ int lborder;
+ bool is_range = false;
+ std::stringstream ss;
+ const char* s = expression.begin();
+ const char* e = expression.end();
+ const char* l = expression.begin();
+
+ if (*s == '(') {
+ ++s;
+ ++l;
+ // multiple blocks
+ while (s != e) {
+ if (*s == ',') {
+ StoreExpression(l, s, is_range, lborder, single_block);
+ l = s+1;
+ } else if (*s == '-') {
+ StoreRange(l, s, is_range, lborder, single_block);
+ } else if (*s == '(') {
+ ++l;
+ } else if (*s == ')') {
+ StoreExpression(l, s, is_range, lborder, single_block);
+ l = s+1;
+ if (single_block.size() > 0) {
+ unpacked.push_back(single_block);
+ }
+ single_block.clear();
+ }
+ ++s;
+ }
+ } else {
+ // single block
+ while (s != e) {
+ if (*s == ',') {
+ StoreExpression(l, s, is_range, lborder, single_block);
+ l = s+1;
+ } else if (*s == '-') {
+ StoreRange(l, s, is_range, lborder, single_block);
+ }
+ ++s;
+ }
+ StoreExpression(l, s, is_range, lborder, single_block);
+
+ if (is_range) {
+ throw IOException(this->FormatDiagnostic(STAR_DIAG_WARNING,
+ "pdbx_struct_assembly_gen.oper_expression is missing a right border for a range expression.",
+ this->GetCurrentLinenum()));
+ }
+ unpacked.push_back(single_block);
+ }
+
+ return unpacked;
+}
+
+void MMCifReader::ParsePdbxStructAssemblyGen(const std::vector<StringRef>& columns)
+{
+ MMCifBioUAssembly assembly;
+ assembly.biounit = MMCifInfoBioUnit();
+
+ assembly.biounit.SetDetails(columns[indices_[ASSEMBLY_ID]].str());
+
+ std::vector<StringRef> tmp_chains=columns[indices_[ASYM_ID_LIST]].split(',');
+ std::vector<StringRef>::const_iterator tc_it;
+ for (tc_it = tmp_chains.begin(); tc_it != tmp_chains.end(); ++tc_it) {
+ assembly.biounit.AddChain(tc_it->str());
+ }
+
+ assembly.operations =
+ this->UnPackOperExperession(columns[indices_[OPER_EXPRESSION]]);
+
+ bu_assemblies_.push_back(assembly);
+}
+
+void MMCifReader::ParsePdbxStructOperList(const std::vector<StringRef>& columns)
+{
+ MMCifInfoTransOpPtr op(new MMCifInfoTransOp);
+
+ op->SetID(columns[indices_[PSOL_ID]].str());
+ op->SetType(columns[indices_[PSOL_TYPE]].str());
+
+ if ((indices_[VECTOR_1] != -1)&&
+ (indices_[VECTOR_2] != -1)&&
+ (indices_[VECTOR_3] != -1)) {
+ op->SetVector(this->TryGetReal(columns[indices_[VECTOR_1]],
+ "pdbx_struct_oper_list.vector[1]"),
+ this->TryGetReal(columns[indices_[VECTOR_2]],
+ "pdbx_struct_oper_list.vector[2]"),
+ this->TryGetReal(columns[indices_[VECTOR_3]],
+ "pdbx_struct_oper_list.vector[3]"));
+ }
+
+ if ((indices_[MATRIX_1_1] != -1)&&
+ (indices_[MATRIX_1_2] != -1)&&
+ (indices_[MATRIX_1_3] != -1)&&
+ (indices_[MATRIX_2_1] != -1)&&
+ (indices_[MATRIX_2_2] != -1)&&
+ (indices_[MATRIX_2_3] != -1)&&
+ (indices_[MATRIX_3_1] != -1)&&
+ (indices_[MATRIX_3_2] != -1)&&
+ (indices_[MATRIX_3_3] != -1)) {
+ op->SetMatrix(this->TryGetReal(columns[indices_[MATRIX_1_1]],
+ "pdbx_struct_oper_list.matrix[1][1]"),
+ this->TryGetReal(columns[indices_[MATRIX_1_2]],
+ "pdbx_struct_oper_list.matrix[1][2]"),
+ this->TryGetReal(columns[indices_[MATRIX_1_3]],
+ "pdbx_struct_oper_list.matrix[1][3]"),
+ this->TryGetReal(columns[indices_[MATRIX_2_1]],
+ "pdbx_struct_oper_list.matrix[2][1]"),
+ this->TryGetReal(columns[indices_[MATRIX_2_2]],
+ "pdbx_struct_oper_list.matrix[2][2]"),
+ this->TryGetReal(columns[indices_[MATRIX_2_3]],
+ "pdbx_struct_oper_list.matrix[2][3]"),
+ this->TryGetReal(columns[indices_[MATRIX_3_1]],
+ "pdbx_struct_oper_list.matrix[3][1]"),
+ this->TryGetReal(columns[indices_[MATRIX_3_2]],
+ "pdbx_struct_oper_list.matrix[3][2]"),
+ this->TryGetReal(columns[indices_[MATRIX_3_3]],
+ "pdbx_struct_oper_list.matrix[3][3]"));
+ }
+
+ info_.AddOperation(op);
+}
+
+void MMCifReader::ParseStruct(const std::vector<StringRef>& columns)
+{
+ MMCifInfoStructDetails details = MMCifInfoStructDetails();
+
+ details.SetEntryID(columns[indices_[STRUCT_ENTRY_ID]].str());
+
+ if (indices_[STRUCT_TITLE] != -1) {
+ details.SetTitle(columns[indices_[STRUCT_TITLE]].str());
+ }
+
+ if ((indices_[PDBX_CASP_FLAG] != -1) &&
+ (columns[indices_[PDBX_CASP_FLAG]][0] != '?')) {
+ details.SetCASPFlag(columns[indices_[PDBX_CASP_FLAG]][0]);
+ }
+
+ if (indices_[PDBX_DESCRIPTOR] != -1) {
+ details.SetDescriptor(columns[indices_[PDBX_DESCRIPTOR]].str());
+ }
+
+ if (indices_[PDBX_FORMULA_WEIGHT] != -1) {
+ details.SetMass(this->TryGetReal(columns[indices_[PDBX_FORMULA_WEIGHT]],
+ "struct.pdbx_formula_weight"));
+ }
+
+ if (indices_[PDBX_FORMULA_WEIGHT_METHOD] != -1) {
+ details.SetMassMethod(columns[indices_[PDBX_FORMULA_WEIGHT_METHOD]].str());
+ }
+
+ if ((indices_[PDBX_MODEL_DETAILS] != -1) &&
+ (columns[indices_[PDBX_MODEL_DETAILS]][0] != '?')) {
+ details.SetModelDetails(columns[indices_[PDBX_MODEL_DETAILS]].str());
+ }
+
+ if ((indices_[PDBX_MODEL_TYPE_DETAILS] != -1) &&
+ (columns[indices_[PDBX_MODEL_TYPE_DETAILS]][0] != '?')) {
+ details.SetModelTypeDetails(
+ columns[indices_[PDBX_MODEL_TYPE_DETAILS]].str());
+ }
+
+ info_.SetStructDetails(details);
+}
+
+MMCifReader::MMCifSecStructElement MMCifReader::DetermineSecStructType(
+ const StringRef& type) const
+{
+ if (type == StringRef("HELX_P", 6)) {
+ return MMCIF_HELIX;
+ } else if (type == StringRef("HELX_OT_P", 9)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_RH_P", 9)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_RH_OT_P", 12)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_RH_AL_P", 12)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_RH_GA_P", 12)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_RH_OM_P", 12)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_RH_PI_P", 12)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_RH_27_P", 12)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_RH_3T_P", 12)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_RH_PP_P", 12)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_LH_P", 9)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_LH_OT_P", 12)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_LH_AL_P", 12)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_LH_GA_P", 12)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_LH_OM_P", 12)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_LH_PI_P", 12)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_LH_27_P", 12)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_LH_3T_P", 12)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_LH_PP_P", 12)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_N", 6)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_OT_N", 9)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_RH_N", 9)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_RH_OT_N", 12)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_RH_A_N", 11)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_RH_B_N", 11)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_RH_Z_N", 11)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_LH_N", 9)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_LH_OT_N", 12)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_LH_A_N", 11)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_LH_B_N", 11)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_LH_Z_N", 11)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("TURN_P", 6)) {
+ return MMCIF_TURN;
+ }
+ else if (type == StringRef("TURN_OT_P", 9)) {
+ return MMCIF_TURN;
+ }
+ else if (type == StringRef("TURN_TY1_P", 10)) {
+ return MMCIF_TURN;
+ }
+ else if (type == StringRef("TURN_TY1P_P", 11)) {
+ return MMCIF_TURN;
+ }
+ else if (type == StringRef("TURN_TY2_P", 10)) {
+ return MMCIF_TURN;
+ }
+ else if (type == StringRef("TURN_TY2P_P", 11)) {
+ return MMCIF_TURN;
+ }
+ else if (type == StringRef("TURN_TY3_P", 10)) {
+ return MMCIF_TURN;
+ }
+ else if (type == StringRef("TURN_TY3P_P", 11)) {
+ return MMCIF_TURN;
+ }
+ else if (type == StringRef("STRN", 4)) {
+ return MMCIF_STRAND;
+ }
+
+ throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
+ "Unknown secondary structure class found: "+
+ type.str(),
+ this->GetCurrentLinenum()));
+}
+
+void MMCifReader::ParseStructConf(const std::vector<StringRef>& columns)
+{
+ StringRef chain_name;
+ int s_res_num;
+ int e_res_num;
+
+ // fetch chain name, first
+ if(auth_chain_id_) {
+ if (indices_[SC_BEG_AUTH_ASYM_ID] != -1) {
+ chain_name = columns[indices_[SC_BEG_AUTH_ASYM_ID]];
+ } else {
+ throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
+"Chain name by author requested but 'struct_conf.beg_auth_asym_id' is not set.",
+ this->GetCurrentLinenum()));
+ }
+ } else {
+ chain_name = columns[indices_[SC_BEG_LABEL_ASYM_ID]];
+ }
+
+ if (restrict_chains_.size() == 0 ||
+ restrict_chains_.find(chain_name.str()) != String::npos) {
+ // fetch start and end
+ s_res_num = this->TryGetInt(columns[indices_[SC_BEG_LABEL_SEQ_ID]],
+ "struct_conf.beg_label_seq_id");
+ e_res_num = this->TryGetInt(columns[indices_[SC_END_LABEL_SEQ_ID]],
+ "struct_conf.end_label_seq_id");
+ MMCifHSEntry hse = {to_res_num(s_res_num, ' '),
+ to_res_num(e_res_num, ' '),
+ chain_name.str()};
+
+ MMCifSecStructElement type =
+ DetermineSecStructType(columns[indices_[SC_CONF_TYPE_ID]]);
+ if (type == MMCIF_HELIX) {
+ helix_list_.push_back(hse);
+ } else if (type == MMCIF_STRAND) {
+ strand_list_.push_back(hse);
+ }
+ }
+}
+
+void MMCifReader::ParseStructSheetRange(const std::vector<StringRef>& columns)
+{
+ StringRef chain_name;
+ int s_res_num;
+ int e_res_num;
+
+ if(auth_chain_id_) {
+ if (indices_[SSR_BEG_AUTH_ASYM_ID] != -1) {
+ chain_name = columns[indices_[SSR_BEG_AUTH_ASYM_ID]];
+ } else {
+ throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
+"Chain name by author requested but 'struct_sheet_range.beg_auth_asym_id' is not set.",
+ this->GetCurrentLinenum()));
+ }
+ } else {
+ chain_name = columns[indices_[SSR_BEG_LABEL_ASYM_ID]];
+ }
+
+ // restrict_chains feature not unit tested, since its about to be changed in
+ // the future
+ if (restrict_chains_.size() == 0 ||
+ restrict_chains_.find(chain_name.str()) != String::npos) {
+
+ s_res_num = this->TryGetInt(columns[indices_[SSR_BEG_LABEL_SEQ_ID]],
+ "struct_sheet_range.beg_label_seq_id");
+ e_res_num = this->TryGetInt(columns[indices_[SSR_END_LABEL_SEQ_ID]],
+ "struct_sheet_range.end_label_seq_id");
+
+ MMCifHSEntry hse = {to_res_num(s_res_num, ' '),
+ to_res_num(e_res_num, ' '),
+ chain_name.str()};
+ strand_list_.push_back(hse);
+ }
+}
+
+void MMCifReader::ParsePdbxDatabasePdbObsSpr(const std::vector<StringRef>&
+ columns)
+{
+ MMCifInfoObsolete obs_data = MMCifInfoObsolete();
+
+ obs_data.SetDate(columns[indices_[DATE]].str());
+ obs_data.SetID(columns[indices_[PDPOS_ID]]);
+ obs_data.SetPDBID(columns[indices_[PDB_ID]].str());
+ obs_data.SetReplacedPDBID(columns[indices_[REPLACE_PDB_ID]].str());
+
+ info_.SetObsoleteInfo(obs_data);
+}
+
+void MMCifReader::OnDataRow(const StarLoopDesc& header,
+ const std::vector<StringRef>& columns)
+{
+ switch(category_) {
+ case ATOM_SITE:
+ LOG_TRACE("processing atom_site entry");
+ this->ParseAndAddAtom(columns);
+ break;
+ case ENTITY:
+ LOG_TRACE("processing entity entry");
+ this->ParseEntity(columns);
+ break;
+ case ENTITY_POLY:
+ LOG_TRACE("processing entity_poly entry");
+ this->ParseEntityPoly(columns);
+ break;
+ case CITATION:
+ LOG_TRACE("processing citation entry");
+ this->ParseCitation(columns);
+ break;
+ case CITATION_AUTHOR:
+ LOG_TRACE("processing citation_author entry")
+ this->ParseCitationAuthor(columns);
+ break;
+ case EXPTL:
+ LOG_TRACE("processing exptl entry")
+ this->ParseExptl(columns);
+ break;
+ case REFINE:
+ LOG_TRACE("processing refine entry")
+ this->ParseRefine(columns);
+ break;
+ case PDBX_STRUCT_ASSEMBLY:
+ LOG_TRACE("processing pdbx_struct_assembly entry")
+ this->ParsePdbxStructAssembly(columns);
+ break;
+ case PDBX_STRUCT_ASSEMBLY_GEN:
+ LOG_TRACE("processing pdbx_struct_assembly_gen entry")
+ this->ParsePdbxStructAssemblyGen(columns);
+ break;
+ case PDBX_STRUCT_OPER_LIST:
+ LOG_TRACE("processing pdbx_struct_oper_list entry")
+ this->ParsePdbxStructOperList(columns);
+ break;
+ case STRUCT:
+ LOG_TRACE("processing struct entry")
+ this->ParseStruct(columns);
+ break;
+ case STRUCT_CONF:
+ LOG_TRACE("processing struct_conf entry")
+ this->ParseStructConf(columns);
+ break;
+ case STRUCT_SHEET_RANGE:
+ LOG_TRACE("processing struct_sheet_range entry")
+ this->ParseStructSheetRange(columns);
+ break;
+ case PDBX_DATABASE_PDB_OBS_SPR:
+ LOG_TRACE("processing pdbx_database_PDB_obs_spr entry")
+ this->ParsePdbxDatabasePdbObsSpr(columns);
+ break;
+ case STRUCT_REF:
+ LOG_TRACE("processing struct_ref entry");
+ this->ParseStructRef(columns);
+ break;
+ case STRUCT_REF_SEQ:
+ LOG_TRACE("processing struct_ref entry");
+ this->ParseStructRefSeq(columns);
+ break;
+ case STRUCT_REF_SEQ_DIF:
+ LOG_TRACE("processing struct_ref entry");
+ this->ParseStructRefSeqDif(columns);
+ break;
+ default:
+ throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
+ "Uncatched category '"+ header.GetCategory() +"' found.",
+ this->GetCurrentLinenum()));
+ return;
+ }
+}
+
+void MMCifReader::AssignSecStructure(mol::EntityHandle ent)
+{
+ for (MMCifHSVector::const_iterator i=helix_list_.begin(), e=helix_list_.end();
+ i!=e; ++i) {
+ mol::ChainHandle chain = ent.FindChain(i->chain_name);
+ if (!chain.IsValid()) {
+ LOG_INFO("ignoring helix record for unknown chain " + i->chain_name);
+ continue;
+ }
+ mol::SecStructure alpha(mol::SecStructure::ALPHA_HELIX);
+ // some PDB files contain helix/strand entries that are adjacent to each
+ // other. To avoid visual artifacts, we effectively shorten the first of
+ // the two secondary structure segments to insert one residue of coil
+ // conformation.
+ mol::ResNum start = i->start, end = i->end;
+ if (helix_list_.end() != i+1 && // unit test
+ (*(i+1)).start.GetNum() <= end.GetNum()+1 &&
+ (*(i+1)).end.GetNum() > end.GetNum()) {
+ end = mol::ResNum((*(i+1)).start.GetNum()-2);
+ }
+ chain.AssignSecondaryStructure(alpha, start, end);
+ }
+
+ for (MMCifHSVector::const_iterator i=strand_list_.begin(),
+ e=strand_list_.end();
+ i!=e; ++i) {
+ mol::ChainHandle chain=ent.FindChain(i->chain_name);
+ if (!chain.IsValid()) {
+ LOG_INFO("ignoring strand record for unknown chain " + i->chain_name);
+ continue;
+ }
+ mol::SecStructure extended(mol::SecStructure::EXTENDED);
+ mol::ResNum start = i->start, end = i->end;
+ // see comment for helix assignment
+ if (strand_list_.end() != i+1 && // unit test
+ (*(i+1)).start.GetNum() <= end.GetNum()+1 &&
+ (*(i+1)).end.GetNum() > end.GetNum()) {
+ end=mol::ResNum((*(i+1)).start.GetNum()-2);
+ }
+ chain.AssignSecondaryStructure(extended, start, end);
+ }
+}
+
+
+void MMCifReader::ParseStructRef(const std::vector<StringRef>& columns)
+{
+ String ent_id=columns[indices_[SR_ENTITY_ID]].str();
+ String db_name=columns[indices_[SR_DB_NAME]].str();
+ String db_code=columns[indices_[SR_DB_CODE]].str();
+ String id=columns[indices_[SR_ID]].str();
+ String db_access;
+ if (indices_[SR_DB_ACCESS]!=-1) {
+ db_access=columns[indices_[SR_DB_ACCESS]].str();
+ }
+ MMCifInfoStructRefPtr sr(new MMCifInfoStructRef(id, ent_id, db_name,
+ db_code, db_access));
+ struct_refs_.push_back(sr);
+}
+
+void MMCifReader::ParseStructRefSeq(const std::vector<StringRef>& columns)
+{
+ String aln_id=columns[indices_[SRS_ALIGN_ID]].str();
+ String sr_id=columns[indices_[SRS_STRUCT_REF_ID]].str();
+ String chain_name;
+ if (indices_[SRS_PDBX_STRAND_ID]!=-1) {
+ chain_name=columns[indices_[SRS_PDBX_STRAND_ID]].str();
+ }
+ std::pair<bool,int> dbbeg=this->TryGetInt(columns[indices_[SRS_DB_ALIGN_BEG]],
+ "_struct_ref_seq.db_align_beg",
+ profile_.fault_tolerant);
+ std::pair<bool,int> dbend=this->TryGetInt(columns[indices_[SRS_DB_ALIGN_END]],
+ "_struct_ref_seq.db_align_end",
+ profile_.fault_tolerant);
+ std::pair<bool,int> entbeg=this->TryGetInt(columns[indices_[SRS_ENT_ALIGN_BEG]],
+ "_struct_ref_seq.seq_align_beg",
+ profile_.fault_tolerant);
+ std::pair<bool,int> entend=this->TryGetInt(columns[indices_[SRS_ENT_ALIGN_END]],
+ "_struct_ref_seq.seq_align_END",
+ profile_.fault_tolerant);
+ if (!(dbbeg.first && dbend.first && entbeg.first && entend.first)) {
+ return;
+ }
+ bool found=false;
+ for (MMCifInfoStructRefs::iterator i=struct_refs_.begin(),
+ e=struct_refs_.end(); i!=e; ++i) {
+ if ((*i)->GetID()==sr_id) {
+ (*i)->AddAlignedSeq(aln_id, chain_name, entbeg.second, entend.second,
+ dbbeg.second, dbend.second);
+ found=true;
+ break;
+ }
+ }
+ if (!found) {
+ if (profile_.fault_tolerant) {
+ LOG_ERROR("struct_ref_seq.ref_id points to inexistent struct_ref '"
+ << sr_id << "'");
+ return;
+ }
+ std::stringstream ss;
+ ss << "struct_ref_seq.ref_id points to inexistent struct_ref '";
+ ss << sr_id << "'";
+ throw IOException(ss.str());
+ }
+}
+
+void MMCifReader::ParseStructRefSeqDif(const std::vector<StringRef>& columns)
+{
+ String aln_id=columns[indices_[SRSD_ALIGN_ID]].str();
+ std::pair<bool,int> db_rnum(true, -1);
+ if (!is_undef(columns[indices_[SRSD_DB_RNUM]])) {
+ db_rnum=this->TryGetInt(columns[indices_[SRSD_DB_RNUM]],
+ "_struct_ref_seq_dif.pdbx_seq_db_seq_num",
+ profile_.fault_tolerant);
+
+ }
+ std::pair<bool,int> seq_rnum(true, -1);
+ if (!is_undef(columns[indices_[SRSD_SEQ_RNUM]])) {
+ seq_rnum=this->TryGetInt(columns[indices_[SRSD_SEQ_RNUM]],
+ "_struct_ref_seq_dif.seq_num",
+ profile_.fault_tolerant);
+
+ }
+ if (!seq_rnum.first || !db_rnum.first) {
+ return;
+ }
+ String details;
+ if (indices_[SRSD_DETAILS]!=-1) {
+ details=columns[indices_[SRSD_DETAILS]].str();
+ }
+ bool found=false;
+ for (MMCifInfoStructRefs::iterator i=struct_refs_.begin(),
+ e=struct_refs_.end(); i!=e; ++i) {
+ if (MMCifInfoStructRefSeqPtr s=(*i)->GetAlignedSeq(aln_id)) {
+ s->AddDif(seq_rnum.second, db_rnum.second, details);
+ found=true;
+ break;
+ }
+ }
+ if (!found) {
+ if (profile_.fault_tolerant) {
+ LOG_ERROR("struct_ref_seq_dif.align_id points to inexistent "
+ "struct_ref_seq '" << aln_id << "'");
+ return;
+ }
+ std::stringstream ss;
+ ss << "struct_ref_seq.ref_id points to inexistent struct_ref '";
+ ss << aln_id << "'";
+ throw IOException(ss.str());
+ }
+}
+
+void MMCifReader::OnEndData()
+{
+ mol::XCSEditor editor=ent_handle_.EditXCS(mol::BUFFERED_EDIT);
+
+ // process chain types
+ std::vector<std::pair<mol::ChainHandle, String> >::const_iterator css;
+ MMCifEntityDescMap::const_iterator edm_it;
+ for (css = chain_id_pairs_.begin(); css != chain_id_pairs_.end(); ++css) {
+ edm_it = entity_desc_map_.find(css->second);
+
+ if (edm_it != entity_desc_map_.end()) {
+ editor.SetChainType(css->first, edm_it->second.type);
+ editor.SetChainDescription(css->first, edm_it->second.details);
+ if (edm_it->second.seqres.length() > 0) {
+ seqres_.AddSequence(seq::CreateSequence(css->first.GetName(),
+ edm_it->second.seqres));
+ } else if (edm_it->second.type!=mol::CHAINTYPE_WATER) {
+ // mark everything that doesn't have SEQRES as ligand and isn't of type
+ // water as ligand
+ mol::ChainHandle chain=css->first;
+ mol::ResidueHandleList residues=chain.GetResidueList();
+ for (mol::ResidueHandleList::iterator
+ i=residues.begin(), e=residues.end(); i!=e; ++i) {
+ (*i).SetIsLigand(true);
+ }
+ }
+ } else {
+ LOG_WARNING("No entity description found for atom_site.label_entity_id '"
+ << css->second << "'");
+ }
+ }
+
+ // process citations (couple with authors
+ // iterate citations
+ MMCifCitationAuthorMap::const_iterator atm_it;
+ for (atm_it = authors_map_.begin(); atm_it != authors_map_.end(); ++atm_it) {
+ info_.AddAuthorsToCitation(StringRef(atm_it->first.c_str(),
+ atm_it->first.length()),
+ atm_it->second.second);
+ }
+
+ bool found;
+ MMCifBioUAssemblyVector::iterator bua_it;
+ std::vector<std::vector<String> >::const_iterator aol_it;
+ std::vector<String>::const_iterator aob_it;
+ std::vector<MMCifInfoTransOpPtr> operation_list;
+ std::map<String, String>::const_iterator buom_it;
+ std::vector<MMCifInfoTransOpPtr> operations = info_.GetOperations();
+ info_.SetStructRefs(struct_refs_);
+ std::vector<MMCifInfoTransOpPtr>::const_iterator buop_it;
+ for (bua_it = bu_assemblies_.begin();
+ bua_it != bu_assemblies_.end();
+ ++bua_it) {
+ // pair with pdbx_struct_assembly entry
+ buom_it = bu_origin_map_.find(bua_it->biounit.GetDetails());
+ if (buom_it == bu_origin_map_.end()) {
+ throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
+ "No pdbx_struct_assembly.id '"+
+ bua_it->biounit.GetDetails() +
+ "' found as requested by pdbx_struct_assembly_gen."));
+ }
+ bua_it->biounit.SetDetails(buom_it->second);
+
+ // pair with pdbx_struct_oper_list
+ for (aol_it = bua_it->operations.begin();
+ aol_it != bua_it->operations.end();
+ ++aol_it) {
+ operation_list.clear();
+ for (aob_it = aol_it->begin(); aob_it != aol_it->end(); aob_it++) {
+ found = false;
+ for (buop_it = operations.begin();
+ buop_it != operations.end();
+ ++buop_it) {
+ if ((*buop_it)->GetID() == *aob_it) {
+ operation_list.push_back(*buop_it);
+ found = true;
+ break;
+ }
+ }
+ if (!found) {
+ throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
+ "No pdbx_struct_oper_list.id '"+
+ *aob_it +
+ "' found as requested by pdbx_struct_assembly_gen."));
+ }
+ }
+ bua_it->biounit.AddOperations(operation_list);
+ }
+ info_.AddBioUnit(bua_it->biounit);
+ }
+ bu_assemblies_.clear();
+
+ // create secondary structure from struct_conf info
+ this->AssignSecStructure(ent_handle_);
+
+ LOG_INFO("imported "
+ << chain_count_ << " chains, "
+ << residue_count_ << " residues, "
+ << atom_count_ << " atoms;"
+ << helix_list_.size() << " helices and "
+ << strand_list_.size() << " strands");
+}
+
+}}
diff --git a/modules/io/src/mol/mmcif_reader.hh b/modules/io/src/mol/mmcif_reader.hh
new file mode 100644
index 0000000000000000000000000000000000000000..e9ff3b893f0e8ade4cce29838b79fb8ab89cf871
--- /dev/null
+++ b/modules/io/src/mol/mmcif_reader.hh
@@ -0,0 +1,598 @@
+//------------------------------------------------------------------------------
+// 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_MMCIF_READER_HH
+#define OST_MMCIF_READER_HH
+
+#include <map>
+
+#include <ost/geom/geom.hh>
+#include <ost/seq/sequence_list.hh>
+#include <ost/mol/residue_handle.hh>
+#include <ost/mol/chain_type.hh>
+#include <ost/conop/compound_lib.hh>
+#include <ost/io/mol/io_profile.hh>
+#include <ost/io/io_exception.hh>
+#include <ost/io/mol/star_parser.hh>
+#include <ost/io/mol/mmcif_info.hh>
+
+namespace ost { namespace io {
+
+/// \brief reader for the mmcif file format
+///
+/// \section mmcif_format mmcif format description/ coverage
+///
+/// mmcif is an instance of the \link StarParser STAR format\endlink to store
+/// entries of the PDB. The following data categories should be covered by this
+/// reader:
+///
+/// \li atom_site
+/// \li entity
+/// \li entity_poly
+/// \li citation
+/// \li citation_author
+/// \li exptl
+/// \li refine
+/// \li pdbx_struct_assembly
+/// \li pdbx_struct_assembly_gen
+/// \li pdbx_struct_oper_list
+/// \li struct
+/// \li struct_conf
+/// \li struct_sheet_range
+/// \li pdbx_database_PDB_obs_spr
+class DLLEXPORT_OST_IO MMCifReader : public StarParser {
+public:
+ /// \brief create a MMCifReader
+ ///
+ /// \param stream input stream
+ MMCifReader(std::istream& stream, mol::EntityHandle& ent_handle,
+ const IOProfile& profile);
+
+ /// \brief create a MMCifReader
+ ///
+ /// \param filename input file
+ MMCifReader(const String& filename, mol::EntityHandle& ent_handle,
+ const IOProfile& profile);
+
+ /// \brief Initialise the reader.
+ ///
+ /// \param loc Location of the file
+ void Init();
+
+ /// \brief Set up a fresh instance
+ void ClearState();
+
+ /// \brief Set names of restricted chains for the reader.
+ ///
+ /// \param restrict_chains chain name
+ void SetRestrictChains(const String& restrict_chains);
+
+ /// \brief Toggle reading of canonical sequence residues
+ /// (entity_poly.pdbx_seq_one_letter_code_can instead of
+ /// entity_poly.pdbx_seq_one_letter_code). This flag is exclusive.
+ ///
+ /// \param flag True for reading canonical sequences.
+ void SetReadCanonicalSeqRes(bool flag)
+ {
+ seqres_can_ = flag;
+ }
+
+ const String& GetRestrictChains() const
+ {
+ return restrict_chains_;
+ }
+
+ /// \brief Enable or disable reading of auth_chain_id instead aof label_chain
+ /// id (default)
+ ///
+ /// \param id enable (true) or disable (false) reading of auth_chain_id.
+ void SetAuthChainID(bool id)
+ {
+ auth_chain_id_ = id;
+ }
+
+ /// \brief check mmcif input to be read. Substitutional function for
+ /// \link StarParser StarParser\endlink.
+ ///
+ /// \param data_name value of the data_ tag
+ ///
+ /// \return true, if the blockcode (PDB id) is valid, false otherwise
+ virtual bool OnBeginData(const StringRef& data_name);
+
+ /// \brief check if a current loop is to be parsed
+ ///
+ /// \param header categories of the upcoming loop block
+ ///
+ /// \return bool
+ virtual bool OnBeginLoop(const StarLoopDesc& header); // tested
+
+ /// \brief read a row of data
+ ///
+ /// \param header categories and items
+ /// \param columns data
+ virtual void OnDataRow(const StarLoopDesc& header,
+ const std::vector<StringRef>& columns);
+
+ /// \brief Finalise parsing.
+ virtual void OnEndData();
+
+ /// \brief Return sequences
+ ///
+ /// \return List of sequences
+ seq::SequenceList GetSeqRes() const {
+ return seqres_;
+ }
+
+ /// \brief Toggle reading of SEQRES
+ ///
+ /// \param flag True enables, False disables reading SEQRES
+ void SetReadSeqRes(bool flag)
+ {
+ read_seqres_ = flag;
+ }
+
+ /// \brief Check if reading of SEQRES is enabled
+ ///
+ /// \return True if reading of SEQRES is enabled
+ bool GetReadSeqRes() const
+ {
+ return read_seqres_;
+ }
+
+ /// \brief Get additional information of the mmCIF file.
+ ///
+ /// \return MMCitfInfo object
+ const MMCifInfo& GetInfo() { return info_; }
+
+protected:
+ /// \brief Store an item index from loop header in preparation for reading a
+ /// row. Throws an exception if the item does not exist.
+ ///
+ /// \param mapping position the item index is stored at
+ /// \param item exact item name to fetch
+ /// \param header loop header to pull index from
+ void TryStoreIdx(const int mapping,
+ const String& item,
+ const StarLoopDesc& header)
+ {
+ indices_[mapping] = header.GetIndex(item);
+
+ if (indices_[mapping] == -1) {
+ throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
+ "No item '" + item +
+ "' found in '" +
+ header.GetCategory()+
+ "' header",
+ this->GetCurrentLinenum()));
+ }
+ } // tested
+
+ /// \brief Check a PDB id to be of length 4 and start with a digit
+ ///
+ /// \param pdbid putative PDB id
+ ///
+ /// \return true for a valid id, false otherwise
+ bool IsValidPDBIdent(const StringRef& pdbid);
+
+ /// \brief fetch values identifying atoms
+ ///
+ /// \param[in] columns data row
+ /// \param[out] chain_name takes atom_site.label_asym_id or, if
+ /// auth_chain_id_ is set, atom_site.auth_asym_id as a chain name
+ /// \param[out] res_name fetches atom_site.label_comp_id
+ /// \param[out] resnum gets atom_site.label_seq_id if available, consecutive
+ /// numbers, otherwise
+ /// \param[out] valid_res_num shows if we have a valid residue number or if
+ /// we have to invent our own
+ /// \param[out] atom_name corresponds to label_atom_id
+ /// \param[out] alt_loc gets first letter of atom_site.label_alt_id
+ bool ParseAtomIdent(const std::vector<StringRef>& columns,
+ String& auth_chain_name,
+ String& cif_chain_name,
+ StringRef& res_name,
+ mol::ResNum& resnum,
+ bool& valid_res_num,
+ StringRef& atom_name,
+ char& alt_loc);
+
+ /// \brief Fetch atom information and store it.
+ ///
+ /// \param columns data row
+ void ParseAndAddAtom(const std::vector<StringRef>& columns);
+
+ /// \brief Fetch mmCIF entity information
+ ///
+ /// \param columns data row
+ void ParseEntity(const std::vector<StringRef>& columns);
+
+ /// \brief Fetch mmCIF entity_poly information
+ ///
+ /// \param columns data row
+ void ParseEntityPoly(const std::vector<StringRef>& columns);
+
+ /// \brief Fetch mmCIF citation information
+ ///
+ /// \param columns data row
+ void ParseCitation(const std::vector<StringRef>& columns);
+
+ const MMCifInfoStructRefs& GetStructRefs() const { return struct_refs_; }
+ /// \brief convert the seqres data item to canonical form.
+ ///
+ /// The seqres sequence lists non-standard residues in paranthesis. For
+ /// proper handling of our sequence classes, these need to be converted to
+ /// one-letter-codes. Ideally, we would use the canonical SEQRES. This is
+ /// not possible, however, since the PDB assigns multiple one letter codes
+ /// to some of the residues. To be consistent, we have to do the conversion on
+ /// our own.
+ String ConvertSEQRES(const String& seqres, conop::CompoundLibPtr compound_lib);
+ /// \brief Fetch mmCIF citation_author information
+ ///
+ /// \param columns data row
+ void ParseCitationAuthor(const std::vector<StringRef>& columns);
+
+ /// \ brief parse a row in the struct_ref category
+ void ParseStructRef(const std::vector<StringRef>& columns);
+
+ /// \brief parse row in the struct_ref_seq category
+ void ParseStructRefSeq(const std::vector<StringRef>& columns);
+
+ /// \brief parse row in the struct_ref_seq_dif category
+ void ParseStructRefSeqDif(const std::vector<StringRef>& columns);
+ /// \brief Fetch mmCIF exptl information
+ ///
+ /// \param columns data row
+ void ParseExptl(const std::vector<StringRef>& columns);
+
+ /// \brief Fetch mmCIF refine information
+ ///
+ /// \param columns data row
+ void ParseRefine(const std::vector<StringRef>& columns);
+
+ /// \brief Fetch mmCIF pdbx_struct_assembly information
+ ///
+ /// \param columns data row
+ void ParsePdbxStructAssembly(const std::vector<StringRef>& columns);
+
+ /// \brief Fetch mmCIF pdbx_struct_assembly_gen information
+ ///
+ /// \param columns data row
+ void ParsePdbxStructAssemblyGen(const std::vector<StringRef>& columns);
+
+ std::vector<std::vector<String> > UnPackOperExperession(StringRef expression);
+
+ void StoreExpression(const char* l, const char* s,
+ bool& is_range, int lborder,
+ std::vector<String>& single_block);
+
+ void StoreRange(const char*& l, const char* s, bool& is_range, int& lborder,
+ std::vector<String>& single_block);
+
+ /// \brief Fetch mmCIF pdbx_struct_oper_list information
+ ///
+ /// \param columns data row
+ void ParsePdbxStructOperList(const std::vector<StringRef>& columns);
+
+ /// \brief Fetch mmCIF struct information
+ ///
+ /// \param columns data row
+ void ParseStruct(const std::vector<StringRef>& columns);
+
+ /// \brief Fetch mmCIF struct_conf (secondary structure) information
+ ///
+ /// \param columns data row
+ void ParseStructConf(const std::vector<StringRef>& columns);
+
+ /// \brief Fetch mmCIF struct_sheet_range (beta sheets) information
+ ///
+ /// \param columns data row
+ void ParseStructSheetRange(const std::vector<StringRef>& columns);
+
+ /// \brief Fetch mmCIF pdbx_database_PDB_obs_spr information
+ ///
+ /// \param columns data row
+ void ParsePdbxDatabasePdbObsSpr(const std::vector<StringRef>& columns);
+
+ /// \struct types of secondary structure
+ typedef enum {
+ MMCIF_HELIX,
+ MMCIF_STRAND,
+ MMCIF_TURN
+ } MMCifSecStructElement;
+
+ /// \brief Check whether an element was classified sheet or helix
+ ///
+ /// \param type Type to be classified
+ MMCifSecStructElement DetermineSecStructType(const StringRef& type) const;
+
+ /// \brief Transform data from struct_conf entry into secondary structure
+ ///
+ /// \param ent Entity to assign secondary structure to
+ void AssignSecStructure(mol::EntityHandle ent);
+
+private:
+ /// \enum magic numbers of this class
+ typedef enum {
+ PDBID_LEN=4, ///< length of a PDB id
+ MAX_ITEMS_IN_ROW=18, ///< count for possible items in a loop row
+ } MMCifMagicNos;
+
+ /// \enum items of the atom_site category
+ typedef enum {
+ AUTH_ASYM_ID, ///< chain name by author as in PDB
+ AS_ID, ///< atom serial id
+ LABEL_ALT_ID, ///< AltLoc
+ LABEL_ASYM_ID, ///< chain name by PDB
+ LABEL_ATOM_ID,
+ LABEL_COMP_ID,
+ LABEL_ENTITY_ID, ///< link to category entity
+ LABEL_SEQ_ID, ///< residue no.
+ AUTH_SEQ_ID, ///< residue no. by author
+ TYPE_SYMBOL, ///< chemical element
+ CARTN_X, ///< Coordinates ||IMPORTANT: This 3 entries have to stay
+ CARTN_Y, ///< Coordinates ||together for the reader to work!
+ CARTN_Z, ///< Coordinates ||
+ OCCUPANCY,
+ B_ISO_OR_EQUIV,
+ PDBX_PDB_INS_CODE,
+ GROUP_PDB, ///< record name
+ PDBX_PDB_MODEL_NUM ///< model no. (especially NMR structures)
+ } AtomSiteItems;
+
+ /// \enum items of the entity category
+ typedef enum {
+ E_ID, ///< unique identifier
+ E_TYPE, ///< polymer, non-polymer or water
+ PDBX_DESCRIPTION ///< special aspects of the entity
+ } EntityItems;
+
+ /// \enum items of the entity_poly category
+ typedef enum {
+ ENTITY_ID, ///< pointer to entity.id
+ EP_TYPE, ///< type of polymer
+ PDBX_SEQ_ONE_LETTER_CODE, ///< sequence, 1-letter code
+ PDBX_SEQ_ONE_LETTER_CODE_CAN ///< canonical sequence, 1-letter code
+ } EntityPolyItems;
+
+ /// \enum items of the citation category
+ typedef enum {
+ CITATION_ID, ///< unique identifier
+ ABSTRACT_ID_CAS, ///< CAS identifier
+ BOOK_ID_ISBN, ///< ISBN code assigned, if book cited
+ BOOK_TITLE, ///< title of book storing the citation
+ JOURNAL_ABBREV, ///< abbreviated journal title for articles
+ JOURNAL_VOLUME, ///< volume of cited journal
+ PAGE_FIRST, ///< first page of citation
+ PAGE_LAST, ///< last page of citation
+ PDBX_DATABASE_ID_DOI, ///< Document Object Identifier of doi.org
+ PDBX_DATABASE_ID_PUBMED, ///< Ascession number of PubMed
+ YEAR, ///< year of the citation
+ TITLE ///< title of the citation
+ } CitationItems;
+
+ /// \enum items of the citation_author category
+ typedef enum {
+ AUTHOR_CITATION_ID, ///< link to CITATION_ID
+ AUTHOR_NAME, ///< name of an author
+ ORDINAL ///< position in author list
+ } CitationAuthorItems;
+
+ /// \enum items of the exptl category
+ typedef enum {
+ EXPTL_ENTRY_ID, ///< identifier
+ METHOD ///< method of the experiment
+ } ExptlItems;
+
+ /// \enum items of the refine category
+ typedef enum {
+ REFINE_ENTRY_ID, ///< id
+ LS_D_RES_HIGH, ///< crystal resolution
+ LS_D_RES_LOW
+ } RefineItems;
+
+ /// \enum items of the pdbx_struct_assembly category
+ typedef enum {
+ PSA_DETAILS, ///< special aspects of the assembly
+ PSA_ID, ///< unique identifier
+ METHOD_DETAILS ///< details about assembly computation
+ } PdbxStructAssemblyItems;
+
+ // \enum items of the struct_ref category
+ typedef enum {
+ SR_ENTITY_ID,
+ SR_ID,
+ SR_DB_CODE,
+ SR_DB_NAME,
+ SR_DB_ACCESS
+ } StructRefItems;
+
+ /// \enum items of the struct_ref_seq category
+ typedef enum {
+ SRS_ALIGN_ID,
+ SRS_STRUCT_REF_ID,
+ SRS_PDBX_STRAND_ID,
+ SRS_DB_ALIGN_BEG,
+ SRS_DB_ALIGN_END,
+ SRS_ENT_ALIGN_BEG,
+ SRS_ENT_ALIGN_END
+ } StructRefSeqItems;
+
+ /// \enum items of the struct_ref_seq_dif category
+ typedef enum {
+ SRSD_ALIGN_ID,
+ SRSD_SEQ_RNUM,
+ SRSD_DB_RNUM,
+ SRSD_DETAILS
+ } StructRefSeqDifItems;
+ /// \enum items of the pdbx_struct_assembly_gen category
+ typedef enum {
+ ASSEMBLY_ID, ///< link to pdbx_struct_assembly.id
+ ASYM_ID_LIST, ///< list of chains
+ OPER_EXPRESSION ///< list of pdbx_struct_oper_list.ids
+ } PdbxStructAssemblyGenItems;
+
+ /// \enum items of the pdbx_struct_oper_list category
+ typedef enum {
+ PSOL_ID, ///< unique identifier
+ PSOL_TYPE, ///< type of operation
+ VECTOR_1, ///< vector component
+ VECTOR_2, ///< vector component
+ VECTOR_3, ///< vector component
+ MATRIX_1_1, ///< matrix component
+ MATRIX_1_2, ///< matrix component
+ MATRIX_1_3, ///< matrix component
+ MATRIX_2_1, ///< matrix component
+ MATRIX_2_2, ///< matrix component
+ MATRIX_2_3, ///< matrix component
+ MATRIX_3_1, ///< matrix component
+ MATRIX_3_2, ///< matrix component
+ MATRIX_3_3 ///< matrix component
+ } PdbxStructOperListItems;
+
+ /// \enum items of the struct category
+ typedef enum {
+ STRUCT_ENTRY_ID, ///< name of the structure
+ PDBX_CASP_FLAG, ///< CASP/ CASD-NMR/ other contest target
+ PDBX_DESCRIPTOR, ///< descriptor for NDB structure/ PDB COMPND record
+ PDBX_FORMULA_WEIGHT, ///< mass in daltons
+ PDBX_FORMULA_WEIGHT_METHOD, ///< how mass was determined
+ PDBX_MODEL_DETAILS, ///< methodology
+ PDBX_MODEL_TYPE_DETAILS, ///< type of structure model
+ STRUCT_TITLE ///< title for the data block
+ } StructItems;
+
+ /// \enum items of the struct_conf category
+ typedef enum {
+ SC_BEG_AUTH_ASYM_ID, ///< Starting residue (atom_site.auth_asym_id)
+ SC_BEG_LABEL_ASYM_ID, ///< Starting residue (atom_site.label_asym_id)
+ SC_BEG_LABEL_COMP_ID, ///< Starting residue (atom_site.label_comp_id)
+ SC_BEG_LABEL_SEQ_ID, ///< Starting residue (atom_site.label_seq_id)
+ SC_CONF_TYPE_ID, ///< Pointer to struct_conf_type.id
+ SC_END_AUTH_ASYM_ID, ///< Ending residue, points to atom_site.auth_asym_id
+ SC_END_LABEL_ASYM_ID, ///< Ending residue, points to atom_site.label_asym_id
+ SC_END_LABEL_COMP_ID, ///< Ending residue, points to atom_site.label_comp_id
+ SC_END_LABEL_SEQ_ID, ///< Ending residue, points to atom_site.label_seq_id
+ SC_ID, ///< Unique identifier
+ } StructConfItems;
+
+ /// \enum items of the struct_sheet_range category
+ typedef enum {
+ SSR_BEG_LABEL_ASYM_ID, ///< start, chain name (atom_site.label_asym_id)
+ SSR_BEG_LABEL_COMP_ID, ///< start, atom_site.label_comp_id
+ SSR_BEG_LABEL_SEQ_ID, ///< start, residue number (atom_site.label_seq_id)
+ SSR_END_LABEL_ASYM_ID, ///< end, chain name (atom_site.label_asym_id)
+ SSR_END_LABEL_COMP_ID, ///< end, atom_site.label_comp_id
+ SSR_END_LABEL_SEQ_ID, ///< end, residue number (atom_site.label_seq_id)
+ SSR_SHEET_ID, ///< unique identifier
+ SSR_ID, ///< link to struct_sheet.id
+ SSR_BEG_AUTH_ASYM_ID, ///< alternative start, (atom_site.auth_asym_id)
+ SSR_END_AUTH_ASYM_ID, ///< alternative end, (atom_site.auth_asym_id)
+ } StructSheetRangeItems;
+
+ /// \enum items of the pdbx_database_PDB_obs_spr category
+ typedef enum {
+ DATE, ///< date of replacement
+ PDPOS_ID, ///< type of obsolete of this entry
+ PDB_ID, ///< NEW PDB ID
+ REPLACE_PDB_ID, ///< OLD PDB ID
+ } PdbxDatabasePDBObsSpr;
+
+ /// \enum categories of the mmcif format
+ typedef enum {
+ ATOM_SITE,
+ ENTITY,
+ ENTITY_POLY,
+ CITATION,
+ CITATION_AUTHOR,
+ EXPTL,
+ REFINE,
+ PDBX_STRUCT_ASSEMBLY,
+ PDBX_STRUCT_ASSEMBLY_GEN,
+ PDBX_STRUCT_OPER_LIST,
+ STRUCT,
+ STRUCT_CONF,
+ STRUCT_SHEET_RANGE,
+ PDBX_DATABASE_PDB_OBS_SPR,
+ STRUCT_REF,
+ STRUCT_REF_SEQ,
+ STRUCT_REF_SEQ_DIF,
+ DONT_KNOW
+ } MMCifCategory;
+
+ /// \struct keeping track of entity information
+ typedef struct {
+ mol::ChainType type; ///< characterise entity
+ String details; ///< description of this entity
+ String seqres; ///< chain of monomers
+ } MMCifEntityDesc;
+ typedef std::map<String, MMCifEntityDesc> MMCifEntityDescMap;
+
+ /// \struct assembly information
+ typedef struct {
+ MMCifInfoBioUnit biounit;
+ std::vector<std::vector<String> > operations; ///< list of links to
+ /// MMCifBioUOperation
+ } MMCifBioUAssembly;
+ typedef std::vector<MMCifBioUAssembly> MMCifBioUAssemblyVector;
+
+ typedef std::map<String, std::pair<std::vector<int>, std::vector<String> > >
+ MMCifCitationAuthorMap;
+
+ /// \struct store struct_conf info (secondary structure)
+ typedef struct {
+ mol::ResNum start;
+ mol::ResNum end;
+ String chain_name;
+ } MMCifHSEntry;
+ typedef std::vector<MMCifHSEntry> MMCifHSVector;
+
+ // members
+ MMCifCategory category_;
+ int category_counts_[DONT_KNOW+1]; ///< overall no. of atom_site loops
+ int indices_[MAX_ITEMS_IN_ROW]; ///< map items to values in loops
+ const IOProfile& profile_;
+ mol::EntityHandle& ent_handle_;
+ String restrict_chains_;
+ bool auth_chain_id_; ///< use chain IDs given by authors rather than pdb
+ bool seqres_can_; ///< read canonical 1-letter residues?
+ mol::ChainHandle curr_chain_;
+ mol::ResidueHandle curr_residue_;
+ int chain_count_;
+ int residue_count_;
+ int atom_count_;
+ bool warned_name_mismatch_;
+ bool warned_rule_based_;
+ String subst_res_id_; ///< work around for missing label_seq_id's
+ bool has_model_; ///< keep track of models through different atom_sites
+ int curr_model_; ///< if we have pdbx_PDB_model_num, store no.
+ std::vector<std::pair<mol::ChainHandle, String> > chain_id_pairs_;
+ ///< chain and label_entity_id
+ MMCifEntityDescMap entity_desc_map_; ///< stores entity items
+ seq::SequenceList seqres_;
+ bool read_seqres_;
+ MMCifInfo info_; ///< info container
+ MMCifCitationAuthorMap authors_map_;
+ MMCifBioUAssemblyVector bu_assemblies_;
+ std::map<String, String> bu_origin_map_; ///< pdbx_struct_assembly.details
+ MMCifHSVector helix_list_; ///< for storing struct_conf sec.struct. data
+ MMCifHSVector strand_list_; ///< for storing struct_conf sec.struct. data
+ MMCifInfoStructRefs struct_refs_;
+};
+
+}}
+
+#endif
diff --git a/modules/io/src/mol/pdb_reader.cc b/modules/io/src/mol/pdb_reader.cc
index 65078588a0fe28bdbf2a2cafa982a4be7452a5f8..287c605f6b3003c02aeed0eafecaeb5e363c5b4e 100644
--- a/modules/io/src/mol/pdb_reader.cc
+++ b/modules/io/src/mol/pdb_reader.cc
@@ -102,6 +102,9 @@ void PDBReader::Init(const boost::filesystem::path& loc)
hard_end_=false;
skip_next_=false;
data_continues_=false;
+ old_key_="";
+ mol_id_=std::make_pair(false, 0);
+
}
void PDBReader::ThrowFaultTolerant(const String& msg) {
@@ -114,7 +117,7 @@ void PDBReader::ThrowFaultTolerant(const String& msg) {
void PDBReader::ParseCompndEntry (const StringRef& line, int line_num)
{
- if (line.size()<20) {
+ if (line.size()<12) {
if (profile_.fault_tolerant) {
LOG_WARNING("invalid COMPND record on line " << line_num
<< ": record is too short");
@@ -147,11 +150,22 @@ void PDBReader::ParseCompndEntry (const StringRef& line, int line_num)
}
if((entry.find(':')!=entry.end())){
std::vector<StringRef> fields=entry.split(':');
- key=fields[0].trim();
- old_key_=key.str();
- data=fields[1].trim();
+ key=fields[0].trim();
+ old_key_=key.str();
+ if (fields.size()>1) {
+ data=fields[1].trim();
+ }
+
if(data.size()<1){
+ if (!(key.str()=="MOL_ID")&&!(key.str()=="CHAIN")){
+ LOG_WARNING("skipping unsupported COMPND record on line " << line_num<< ": record value"<< key.str()<<" too small");
+ if (data_continues_) {
+ skip_next_=true;
+ } else {
+ return;
+ }
+ }
ThrowFaultTolerant(str(format("invalid COMPND record on line %d, record after ':' too small")%line_num));
}
data_continues_=true;
@@ -179,7 +193,7 @@ void PDBReader::ParseCompndEntry (const StringRef& line, int line_num)
}
//currently only these are parsed
if (!(key.str()=="MOL_ID")&&!(key.str()=="CHAIN")){
- LOG_TRACE("reading COMPND record on line " << line_num<< "is not supported");
+ LOG_INFO("reading COMPND record on line " << line_num<< "is not supported");
if (data_continues_) {
skip_next_=true;
} else {
@@ -470,7 +484,9 @@ void PDBReader::AssignMolIds(mol::EntityHandle ent) {
if (chain) {
chain.SetIntProp("mol_id", compnd_iterator->mol_id);
}else{
- std::stringstream ss("could not map COMPND record MOL_ID onto chain");
+ LOG_WARNING("failed to assign MOL_ID to chain: "<<*chain_iterator <<std::endl);
+ std::stringstream ss;
+ ss << "could not map COMPND record MOL_ID onto chain";
ss <<*chain_iterator;
ThrowFaultTolerant(ss.str());
}
@@ -481,9 +497,13 @@ void PDBReader::AssignMolIds(mol::EntityHandle ent) {
mol::ChainHandleList ch_list=ent.GetChainList();
for (mol::ChainHandleList::const_iterator chain=ch_list.begin();
chain!=ch_list.end(); ++chain) {
+ //~ skip HETATM only chains!!
if(chain->IsValid()){
if (!chain->HasProp("mol_id")) {
- ThrowFaultTolerant("found chain without MOL_ID");
+ std::stringstream ss;
+ ss << "found chain without MOL_ID: ";
+ ss << chain->GetName();
+ LOG_WARNING(ss.str());
}
}
}
@@ -583,14 +603,6 @@ bool PDBReader::ParseAtomIdent(const StringRef& line, int line_num,
}
}
- std::pair<bool, int> a_num=line.substr(6, 5).ltrim().to_int();
- if (!a_num.first) {
- if (!(profile_.fault_tolerant)) {
- throw IOException(str(format("invalid atom number on line %d") %line_num));
- }
- LOG_WARNING("invalid atom number on line " << line_num);
- }
-
alt_loc=line[16];
res_name=line.substr(17, charmm_style_ ? 4 : 3).trim();
std::pair<bool, int> res_num=line.substr(22, 4).ltrim().to_int();;
@@ -694,10 +706,10 @@ void PDBReader::ParseAndAddAtom(const StringRef& line, int line_num,
occ=std::make_pair(true, Real(1.0));
temp=std::make_pair(true, Real(0.0));
if (line.length()>=60) {
- charge=line.substr(54,6).ltrim().to_float();
+ charge=line.substr(55,7).ltrim().to_float();
}
- if (line.length()>=66) {
- radius=line.substr(60, 6).ltrim().to_float();
+ if (line.length()>=68) {
+ radius=line.substr(63,6).ltrim().to_float();
}
} else {
if (line.length()>=60) {
@@ -772,7 +784,7 @@ void PDBReader::ParseAndAddAtom(const StringRef& line, int line_num,
assert(curr_residue_.IsValid());
}
// finally add atom
- LOG_DEBUG("adding atom " << aname << " (" << s_ele << ") @" << apos);
+ LOG_DEBUG("adding atom " << aname << " (" << s_ele << " '" << alt_loc << "'" << ") @" << apos);
mol::AtomHandle ah;
if (curr_residue_.GetName()!=res_name.str()) {
if (!profile_.fault_tolerant && alt_loc==' ') {
@@ -781,26 +793,30 @@ void PDBReader::ParseAndAddAtom(const StringRef& line, int line_num,
<< "residue with number " << res_num << " has more than one name.";
throw IOException(ss.str());
}
- if (!warned_name_mismatch_) {
- if (alt_loc==' ') {
- LOG_WARNING("Residue with number " << res_num << " has more than one name."
- "Ignoring atoms for everything but the first");
- } else {
- LOG_WARNING("Residue with number " << res_num
- << " contains a microheterogeneity. Everything but atoms for "
- << "the residue '" << curr_residue_.GetName()
- << "' will be ignored");
+ if(!profile_.quack_mode) {
+ if (!warned_name_mismatch_) {
+ if (alt_loc==' ') {
+ LOG_WARNING("Residue with number " << res_num << " has more than one name. "
+ "Ignoring atoms for everything but the first");
+ } else {
+ LOG_WARNING("Residue with number " << res_num
+ << " contains a microheterogeneity. Everything but atoms for "
+ << "the residue '" << curr_residue_.GetName()
+ << "' will be ignored");
+ }
}
+ warned_name_mismatch_=true;
+ return;
}
- warned_name_mismatch_=true;
- return;
}
- if (alt_loc!=' ') {
+ Real b=temp.first ? temp.second : 0.0;
+ Real o=occ.first ? occ.second : 1.0;
+ if (!profile_.quack_mode && alt_loc!=' ') {
// Check if there is already a atom with the same name.
mol::AtomHandle me=curr_residue_.FindAtom(aname);
if (me.IsValid()) {
try {
- editor.AddAltAtomPos(String(1, alt_loc), me, apos);
+ editor.AddAltAtomPos(String(1, alt_loc), me, apos, o, b);
} catch (Error) {
LOG_INFO("Ignoring atom alt location since there is already an atom "
"with name " << aname << ", but without an alt loc");
@@ -809,7 +825,7 @@ void PDBReader::ParseAndAddAtom(const StringRef& line, int line_num,
return;
} else {
ah=editor.InsertAltAtom(curr_residue_, aname,
- String(1, alt_loc), apos, s_ele);
+ String(1, alt_loc), apos, s_ele, o, b);
++atom_count_;
}
} else {
@@ -831,12 +847,8 @@ void PDBReader::ParseAndAddAtom(const StringRef& line, int line_num,
ah.SetRadius(radius.second);
}
}
- if (temp.first) {
- ah.SetBFactor(temp.second);
- }
- if (occ.first) {
- ah.SetOccupancy(occ.second);
- }
+ ah.SetBFactor(b);
+ ah.SetOccupancy(o);
if (charge.first) {
ah.SetCharge(charge.second);
}
diff --git a/modules/io/src/mol/pdb_writer.cc b/modules/io/src/mol/pdb_writer.cc
index 2b4379ae33c60476b043bb5df40cd927e3a6acbe..fdae17a5110b741790e5c4c4c791b78cb67edbe6 100644
--- a/modules/io/src/mol/pdb_writer.cc
+++ b/modules/io/src/mol/pdb_writer.cc
@@ -20,9 +20,14 @@
Author: Marco Biasini
*/
#include <locale>
-#include <boost/format.hpp>
+
#include <string.h>
+#include <boost/format.hpp>
+#include <boost/iostreams/filter/gzip.hpp>
+#include <boost/filesystem/convenience.hpp>
+#include <boost/algorithm/string.hpp>
+
#include <ost/io/io_exception.hh>
#include <ost/mol/atom_handle.hh>
#include <ost/mol/residue_handle.hh>
@@ -73,7 +78,12 @@ void write_atom(std::ostream& ostr, FormattedLine& line,
geom::Vec3 p=atom.GetPos();
line( 0, 6)=record_name;
- line( 6, 5)=fmt::LPaddedInt(atomnum);
+ // Avoid writing out atomnumbers larger than 5 digits
+ if (atomnum > 99999) {
+ line( 6, 5)=fmt::LPadded("*****");
+ } else {
+ line( 6, 5)=fmt::LPaddedInt(atomnum);
+ }
String atom_name=atom.GetName();
if (atom_name.size()>4) {
throw IOException("Atom name '"+atom.GetQualifiedName()+
@@ -125,8 +135,8 @@ void write_atom(std::ostream& ostr, FormattedLine& line,
line(46, 8)=fmt::LPaddedFloat(p[2], 3);
if (is_pqr) {
- line(54, 6)=fmt::LPaddedFloat(atom.GetCharge(), 2);
- line(60, 6)=fmt::LPaddedFloat(atom.GetRadius(), 2);
+ line(55, 7)=fmt::LPaddedFloat(atom.GetCharge(), 4);
+ line(63, 6)=fmt::LPaddedFloat(atom.GetRadius(), 4);
} else {
line(54, 6)=fmt::LPaddedFloat(atom.GetOccupancy(), 2);
Real bfac=atom.GetBFactor();
@@ -162,8 +172,8 @@ void write_atom(std::ostream& ostr, FormattedLine& line,
line(54, 6)=fmt::LPaddedFloat(atom.GetCharge(), 2);
line(60, 6)=fmt::LPaddedFloat(atom.GetRadius(), 2);
} else {
- line(54, 6)=fmt::LPaddedFloat(atom.GetOccupancy(), 2);
- Real bfac=atom.GetBFactor();
+ line(54, 6)=fmt::LPaddedFloat(atom.GetAltOcc(*i), 2);
+ Real bfac=atom.GetAltBFactor(*i);
if (bfac>999.99) {
line(60, 6)=fmt::LPaddedFloat(999.99, 2);
} else {
@@ -332,7 +342,7 @@ PDBWriter::PDBWriter(std::ostream& stream, const IOProfile& profile):
multi_model_(false), charmm_style_(profile.dialect=="CHARMM"), is_pqr_(false),
profile_(profile)
{
-
+ out_.push(outstream_);
}
PDBWriter::PDBWriter(const boost::filesystem::path& filename,
@@ -346,19 +356,34 @@ PDBWriter::PDBWriter(const boost::filesystem::path& filename,
charmm_style_(profile.dialect=="CHARMM"), is_pqr_(false),
profile_(profile), filename_("")
{
+ if (boost::iequals(".pqr", boost::filesystem::extension(filename))) {
+ is_pqr_=true;
+ }
+ if (boost::iequals(".gz", boost::filesystem::extension(filename))) {
+ out_.push(boost::iostreams::gzip_compressor());
+ }
+ out_.push(outstream_);
}
PDBWriter::PDBWriter(const String& filename, const IOProfile& profile):
outfile_(filename.c_str()), outstream_(outfile_), mol_count_(0), line_(80),
multi_model_(false), charmm_style_(profile.dialect=="CHARMM"),
is_pqr_(false), profile_(profile), filename_(filename)
-{}
+{
+ if (boost::iequals(".pqr", boost::filesystem::extension(filename))) {
+ is_pqr_=true;
+ }
+ if (boost::iequals(".gz", boost::filesystem::extension(filename))) {
+ out_.push(boost::iostreams::gzip_compressor());
+ }
+ out_.push(outstream_);
+}
void PDBWriter::WriteModelLeader()
{
++mol_count_;
if (multi_model_) {
- outstream_ << "MODEL " << mol_count_ << std::endl;
+ out_ << "MODEL " << mol_count_ << std::endl;
} else if (mol_count_>1) {
throw IOException("Trying to write several models into one file with ");
}
@@ -367,14 +392,14 @@ void PDBWriter::WriteModelLeader()
void PDBWriter::WriteModelTrailer()
{
if (multi_model_) {
- outstream_ << "ENDMDL" << std::endl;
+ out_ << "ENDMDL" << std::endl;
}
}
template <typename H>
void PDBWriter::WriteModel(H ent)
{
- if (!outstream_) {
+ if (!out_) {
if (!filename_.empty()) {
std::stringstream ss;
ss << "Can't write PDB to file '" << filename_ << "'";
@@ -384,10 +409,10 @@ void PDBWriter::WriteModel(H ent)
}
ForcePOSIX posix;
this->WriteModelLeader();
- PDBWriterImpl writer(outstream_,line_, atom_indices_, charmm_style_);
+ PDBWriterImpl writer(out_, line_, atom_indices_, charmm_style_);
writer.SetIsPQR(is_pqr_);
ent.Apply(writer);
- PDBConectWriterImpl con_writer(outstream_,atom_indices_);
+ PDBConectWriterImpl con_writer(out_, atom_indices_);
ent.Apply(con_writer);
this->WriteModelTrailer();
}
@@ -410,7 +435,7 @@ void PDBWriter::Write(const mol::AtomHandleList& atoms)
mol::ChainHandle last_chain;
for (mol::AtomHandleList::const_iterator i=atoms.begin(),
e=atoms.end(); i!=e; ++i, ++counter) {
- write_atom(outstream_, line_, *i, counter, is_pqr_, charmm_style_);
+ write_atom(out_, line_, *i, counter, is_pqr_, charmm_style_);
}
this->WriteModelTrailer();
}
@@ -418,7 +443,7 @@ void PDBWriter::Write(const mol::AtomHandleList& atoms)
PDBWriter::~PDBWriter()
{
- outstream_ << "END ";
+ out_ << "END ";
}
}}
diff --git a/modules/io/src/mol/pdb_writer.hh b/modules/io/src/mol/pdb_writer.hh
index b0e70a89f5e3478fdf572798b93a517f4988e173..d12b3219f5cd509cebefea9f1444cdd028ae7b60 100644
--- a/modules/io/src/mol/pdb_writer.hh
+++ b/modules/io/src/mol/pdb_writer.hh
@@ -43,7 +43,9 @@ class EntityHandle;
namespace io {
+
class DLLEXPORT_OST_IO PDBWriter {
+ typedef boost::iostreams::filtering_stream<boost::iostreams::output> OutStream;
public:
PDBWriter(const String& filename,
const IOProfile& profile);
@@ -76,6 +78,7 @@ private:
bool is_pqr_;
IOProfile profile_;
String filename_;
+ OutStream out_;
};
}}
diff --git a/modules/io/src/mol/star_parser.cc b/modules/io/src/mol/star_parser.cc
index cee3a1c38f1fffbd51536fb7cca44b4322edcc45..0de35fec5072aff97c421fa8a9de409b8cb2011b 100644
--- a/modules/io/src/mol/star_parser.cc
+++ b/modules/io/src/mol/star_parser.cc
@@ -20,33 +20,44 @@
/*
Author: Marco Biasini
*/
+#include <boost/iostreams/filter/gzip.hpp>
+
#include <cassert>
#include <sstream>
+#include <ost/log.hh>
#include <ost/io/io_exception.hh>
#include <ost/io/mol/star_parser.hh>
namespace ost { namespace io {
StarParser::StarParser(std::istream& stream, bool items_as_row):
- stream_(stream), filename_("<stream>"), line_num_(0),
+ filename_("<stream>"), line_num_(0),
has_current_line_(false), current_line_(),
items_row_header_(), file_open_(true), items_row_columns_(),
items_row_values_()
{
items_as_row_ = items_as_row;
-
- if (!fstream_) {
+
+ if (!stream) {
file_open_ = false;
}
+
+ stream_.push(stream);
}
StarParser::StarParser(const String& filename, bool items_as_row):
- fstream_(filename.c_str()), stream_(fstream_), filename_(filename),
+ fstream_(filename.c_str()), filename_(filename),
line_num_(0), has_current_line_(false), current_line_(),
items_row_header_(), file_open_(true), items_row_columns_(),
items_row_values_()
{
- items_as_row_ = items_as_row;
+ items_as_row_=items_as_row;
+ if (filename.length() >= 3 &&
+ filename.substr(filename.length() - 3) == ".gz") {
+ stream_.push(boost::iostreams::gzip_decompressor());
+ }
+
+ stream_.push(fstream_);
if (!fstream_) {
file_open_ = false;
@@ -75,6 +86,18 @@ String StarParser::FormatDiagnostic(StarDiagType type, const String& message,
return ss.str();
}
+Real StarParser::TryGetReal(const StringRef& data, const String& name) const
+{
+ std::pair<bool, Real> value = data.to_float();
+ if (!value.first) {
+ throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
+ "Expecting real number for " +
+ name + ", found '" + data.str() +
+ "' instead.", line_num_));
+ }
+ return value.second;
+}
+
float StarParser::TryGetFloat(const StringRef& data, const String& name) const
{
std::pair<bool, float> value = data.to_float();
@@ -87,6 +110,28 @@ float StarParser::TryGetFloat(const StringRef& data, const String& name) const
return value.second;
}
+std::pair<bool, float> StarParser::TryGetFloat(const StringRef& data,
+ const String& name,
+ bool may_fail) const
+{
+ std::pair<bool, float> value = data.to_float();
+ if (!value.first) {
+ if (!may_fail) {
+ throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
+ "Expecting floating point value for " +
+ name + ", found '" + data.str() +
+ "' instead.", line_num_));
+ }
+ else {
+ LOG_WARNING(this->FormatDiagnostic(STAR_DIAG_WARNING,
+ "Expecting floating point value for " +
+ name + ", found '" + data.str() +
+ "' instead.", line_num_));
+ }
+ }
+ return value;
+}
+
int StarParser::TryGetInt(const StringRef& data, const String& name) const
{
std::pair<bool, int> value = data.to_int();
@@ -99,6 +144,27 @@ int StarParser::TryGetInt(const StringRef& data, const String& name) const
return value.second;
}
+std::pair<bool, int> StarParser::TryGetInt(const StringRef& data,
+ const String& name,
+ bool may_fail) const
+{
+ std::pair<bool, int> value = data.to_int();
+ if (!value.first) {
+ if (!may_fail) {
+ throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
+ "Expecting integer value for " +
+ name + ", found '" + data.str() +
+ "' instead.", line_num_));
+ } else {
+ LOG_WARNING(this->FormatDiagnostic(STAR_DIAG_WARNING,
+ "Expecting integer value for " +
+ name + ", found '" + data.str() +
+ "' instead.", line_num_));
+ }
+ }
+ return value;
+}
+
bool StarParser::TryGetBool(const StringRef& data, const String& name) const
{
if (data.length() == 1) {
@@ -343,7 +409,7 @@ void StarParser::ParseDataItem()
StarParser::SplitLine(line, nv);
if (nv.size()==1) {
// remember identifier.
- String identifier=line.str();
+ String identifier=line.trim().str();
String value;
while (this->NextLine(line)) {
diff --git a/modules/io/src/mol/star_parser.hh b/modules/io/src/mol/star_parser.hh
index b0ef784b76c5633487e7c113398d8c6e8751bf03..c5febf7fb3c2672c2381cdac72c178e9e93beb9a 100644
--- a/modules/io/src/mol/star_parser.hh
+++ b/modules/io/src/mol/star_parser.hh
@@ -23,6 +23,8 @@
/*
Author: Marco Biasini
*/
+#include <boost/iostreams/filtering_stream.hpp>
+
#include <iostream>
#include <fstream>
#include <vector>
@@ -148,6 +150,14 @@ public:
/// OnBeginData() returned true.
virtual void OnEndData() { }
+ /// \brief try to convert a value to Real, on failure raise an exception.
+ ///
+ /// \param data value to be converted
+ /// \param name to be included in the message
+ ///
+ /// \return converted value
+ Real TryGetReal(const StringRef& data, const String& name) const;
+
/// \brief try to convert a value to float, on failure raise an exception.
///
/// \param data value to be converted
@@ -156,6 +166,17 @@ public:
/// \return converted value
float TryGetFloat(const StringRef& data, const String& name) const;
+ /// \brief try to convert a value to float, on failure raise an exception.
+ ///
+ /// \param data value to be converted
+ /// \param name to be included in the message
+ /// \param may_fail decides if an exception is raised (false) or not (true)
+ ///
+ /// \return converted value
+ std::pair<bool, float> TryGetFloat(const StringRef& data,
+ const String& name,
+ bool may_fail) const;
+
/// \brief try to convert a value to integer, on failure raise an exception.
///
/// \param data value to be converted
@@ -164,6 +185,17 @@ public:
/// \return converted value
int TryGetInt(const StringRef& data, const String& name) const;
+ /// \brief try to convert a value to integer, exception can be turned off.
+ ///
+ /// \param data value to be converted
+ /// \param name to be included in the message
+ /// \param may_fail decides if an exception is raised (false) or not (true)
+ ///
+ /// \return pair with value and indicator if conversion worked
+ std::pair<bool, int> TryGetInt(const StringRef& data,
+ const String& name,
+ bool may_fail) const;
+
/// \brief try to convert a value to bool, on failure raise an exception.
///
/// \param data value to be converted
@@ -238,7 +270,7 @@ private:
void DiagnoseUnknown();
bool ParseMultilineValue(String& value, bool skip=false);
std::ifstream fstream_;
- std::istream& stream_;
+ boost::iostreams::filtering_stream<boost::iostreams::input> stream_;
String filename_;
int line_num_;
bool has_current_line_;
diff --git a/modules/io/tests/CMakeLists.txt b/modules/io/tests/CMakeLists.txt
index f10be7bc4857bbe2d04bb896849f9d677707cfa0..98f075bd9785c1c051f642e3be91dd2e125cc62f 100644
--- a/modules/io/tests/CMakeLists.txt
+++ b/modules/io/tests/CMakeLists.txt
@@ -1,5 +1,6 @@
set(OST_IO_UNIT_TESTS
test_io_pdb.py
+ test_io_mmcif.py
test_clustal.cc
test_io_pdb.cc
test_io_crd.cc
@@ -8,6 +9,8 @@ set(OST_IO_UNIT_TESTS
test_iomanager.cc
tests.cc
test_star_parser.cc
+ test_mmcif_reader.cc
+ test_mmcif_info.cc
)
if (ENABLE_IMG)
list(APPEND OST_IO_UNIT_TESTS test_io_img.cc)
@@ -16,6 +19,9 @@ ost_unittest(MODULE io
SOURCES "${OST_IO_UNIT_TESTS}"
LINK ost_mol ost_seq)
-add_executable(test_mae_standalone test_mae_standalone.cc)
-target_link_libraries(test_mae_standalone ost_mol)
-target_link_libraries(test_mae_standalone ost_io)
+if(NOT ENABLE_STATIC)
+ add_executable(test_mae_standalone test_mae_standalone.cc)
+ target_link_libraries(test_mae_standalone ost_mol)
+ target_link_libraries(test_mae_standalone ost_io)
+ target_link_libraries(test_mae_standalone ${Boost_REGEX_LIBRARY})
+endif()
diff --git a/modules/io/tests/test_io_img.cc b/modules/io/tests/test_io_img.cc
index d8165dd76203ba7fcb1fc8e00fcce5a7df290a62..890a7a9c29a22beb57b4c7c0aa0ffb04273f8777 100644
--- a/modules/io/tests/test_io_img.cc
+++ b/modules/io/tests/test_io_img.cc
@@ -34,6 +34,7 @@
#include <ost/io/img/map_io_dat_handler.hh>
#include <ost/io/img/map_io_jpk_handler.hh>
#include <ost/io/img/map_io_nanoscope_handler.hh>
+#include <ost/io/img/map_io_ipl_handler.hh>
#include <ost/img/alg/normalizer_factory.hh>
using namespace ost;
@@ -46,17 +47,16 @@ BOOST_AUTO_TEST_CASE(test_io_img)
{
//float tests
boost::test_tools::close_at_tolerance<Real> close_test(::boost::test_tools::percent_tolerance(0.001));
- ost::img::ImageHandle testimage=ost::img::CreateImage(ost::img::Extent(ost::img::Point(0,0),ost::img::Point(3,3)));
+ ost::img::ImageHandle testimage=ost::img::CreateImage(ost::img::Extent(ost::img::Point(0,0),ost::img::Point(4,3)));
int counter=0;
for (img::ExtentIterator i(testimage.GetExtent()); !i.AtEnd(); ++i, ++counter) {
testimage.SetReal(i, counter);
}
- testimage+=0.01; //if all values are > 0.0 we can use close_at_tolerance
+ testimage+=5.01; //if all values are > 0.0 we can use close_at_tolerance
const String fname("temp_img.tmp");
std::map<String,ImageFormatBase*> float_formats;
float_formats["DX"]=new DX;
float_formats["Situs"]=new Situs;
- float_formats["DAT (float)"]=new DAT(false,OST_FLOAT_FORMAT);
float_formats["CCP4 (float)"]=new MRC;
float_formats["MRC (float)"]=new MRC(false,MRC_OLD_FORMAT);
float_formats["SPIDER"]= new Spider;
@@ -82,7 +82,7 @@ BOOST_AUTO_TEST_CASE(test_io_img)
}
//int 16 formats
std::map<String,ImageFormatBase*> int_formats;
- int_formats["DAT (16 bit)"]=new DAT(true,OST_BIT16_FORMAT);
+ int_formats["IPL (16 bit)"]=new IPL(true,OST_BIT16_FORMAT);
int_formats["TIF (16 bit)"]=new TIF;
int_formats["JPK (16 bit)"]=new JPK;
// int_formats["DF3"]=new DF3(true);
@@ -108,9 +108,33 @@ BOOST_AUTO_TEST_CASE(test_io_img)
delete it->second;
}
+ //int 32 formats
+ std::map<String,ImageFormatBase*> int32_formats;
+ int32_formats["IPL (32 bit)"]=new IPL(true,OST_BIT32_FORMAT);
+ for(std::map<String,ImageFormatBase*>::iterator it=int32_formats.begin();it!=int32_formats.end();++it){
+ ost::io::SaveImage(testimage,fname,*(it->second));
+ ost::img::ImageHandle loadedimage=ost::io::LoadImage(fname,*(it->second));
+ ost::img::alg::Normalizer norm=ost::img::alg::CreateLinearRangeNormalizer(testimage,0.0,4294967295.0);
+ ost::img::ImageHandle scaled_image=testimage.Apply(norm);
+ bool failed=false;
+ ost::img::ExtentIterator eit(scaled_image.GetExtent());
+ for(;!eit.AtEnd();++eit) {
+ if( static_cast<uint>(scaled_image.GetReal(eit))!=static_cast<uint>(loadedimage.GetReal(eit))){
+ failed=true;
+ break;
+ }
+ }
+ if(failed){
+ BOOST_ERROR("Image IO failed for plugin " << it->first << " at point "
+ << ost::img::Point(eit)<< ". Should be "
+ << static_cast<uint>(scaled_image.GetReal(eit)) << ", but "
+ << static_cast<uint>(loadedimage.GetReal(eit)) << " found.");
+ }
+ delete it->second;
+ }
+
//byte formats
std::map<String,ImageFormatBase*> byte_formats;
- byte_formats["DAT (byte)"]=new DAT(true,OST_BIT8_FORMAT);
byte_formats["PNG"]=new PNG;
byte_formats["JPK (byte)"]= new JPK(true,OST_BIT8_FORMAT);
byte_formats["TIF (byte)"]= new TIF(true,OST_BIT8_FORMAT);
@@ -134,4 +158,70 @@ BOOST_AUTO_TEST_CASE(test_io_img)
}
}
+BOOST_AUTO_TEST_CASE(test_io_img_dat)
+{
+ // test for the dat file format using a square image (non square images not supported by dat)
+ //float test
+ boost::test_tools::close_at_tolerance<Real> close_test(::boost::test_tools::percent_tolerance(0.001));
+ ost::img::ImageHandle testimage=ost::img::CreateImage(ost::img::Extent(ost::img::Point(0,0),ost::img::Point(3,3)));
+ int counter=0;
+ for (img::ExtentIterator i(testimage.GetExtent()); !i.AtEnd(); ++i, ++counter) {
+ testimage.SetReal(i, counter);
+ }
+ testimage+=5.01; //if all values are > 0.0 we can use close_at_tolerance
+ const String fname("temp_img.tmp");
+ ost::io::SaveImage(testimage,fname,DAT(false,OST_FLOAT_FORMAT));
+ ost::img::ImageHandle loadedimage=ost::io::LoadImage(fname,DAT(false,OST_FLOAT_FORMAT));
+ bool failed=false;
+ ost::img::ExtentIterator eit(testimage.GetExtent());
+ for(;!eit.AtEnd();++eit) {
+ if( ! close_test(testimage.GetReal(eit),loadedimage.GetReal(eit))){
+ failed=true;
+ break;
+ }
+ }
+ if(failed){
+ BOOST_ERROR("Image IO failed for plugin DAT (float) at point " << ost::img::Point(eit)<< ". The values are: " << testimage.GetReal(eit)<< ","<< loadedimage.GetReal(eit) );
+ }
+ //int 16 format
+ ost::io::SaveImage(testimage,fname,DAT(true,OST_BIT16_FORMAT));
+ loadedimage=ost::io::LoadImage(fname,DAT(true,OST_BIT16_FORMAT));
+ ost::img::alg::Normalizer norm=ost::img::alg::CreateLinearRangeNormalizer(testimage,0.0,65535.0);
+ ost::img::ImageHandle scaled_image=testimage.Apply(norm);
+ failed=false;
+ eit=ost::img::ExtentIterator(testimage.GetExtent());
+ for(;!eit.AtEnd();++eit) {
+ if( static_cast<int>(scaled_image.GetReal(eit))!=static_cast<int>(loadedimage.GetReal(eit))){
+ failed=true;
+ break;
+ }
+ }
+ if(failed){
+ BOOST_ERROR("Image IO failed for plugin DAT (int16) at point "
+ << ost::img::Point(eit)<< ". Should be "
+ << static_cast<int>(scaled_image.GetReal(eit)) << ", but "
+ << static_cast<int>(loadedimage.GetReal(eit)) << " found.");
+ }
+
+ //byte format
+ ost::io::SaveImage(testimage,fname,DAT(true,OST_BIT8_FORMAT));
+ loadedimage=ost::io::LoadImage(fname,DAT(true,OST_BIT8_FORMAT));
+ norm=ost::img::alg::CreateLinearRangeNormalizer(testimage,0.0,255.0);
+ scaled_image=testimage.Apply(norm);
+ failed=false;
+ eit=ost::img::ExtentIterator(testimage.GetExtent());
+ for(;!eit.AtEnd();++eit) {
+ if( static_cast<int>(scaled_image.GetReal(eit))!=static_cast<int>(loadedimage.GetReal(eit))){
+ failed=true;
+ break;
+ }
+ }
+ if(failed){
+ BOOST_ERROR("Image IO failed for plugin DAT (int8) at point "
+ << ost::img::Point(eit)<< ". Should be "
+ << static_cast<int>(scaled_image.GetReal(eit)) << ", but "
+ << static_cast<int>(loadedimage.GetReal(eit)) << " found.");
+ }
+}
+
BOOST_AUTO_TEST_SUITE_END()
diff --git a/modules/io/tests/test_io_mmcif.py b/modules/io/tests/test_io_mmcif.py
new file mode 100644
index 0000000000000000000000000000000000000000..94eb063301b5e56f697c7d67f43452c023b38f56
--- /dev/null
+++ b/modules/io/tests/test_io_mmcif.py
@@ -0,0 +1,223 @@
+import unittest
+from ost import *
+
+class TestMMCifInfo(unittest.TestCase):
+ def setUp(self):
+ pass
+
+ def test_mmcifinfo_citation(self):
+ c = io.MMCifInfoCitation()
+ # test ID setting/ getting
+ c.SetID('ID')
+ self.assertEquals(c.GetID(), 'ID')
+ # test CAS setting/ getting
+ c.SetCAS('FOO')
+ self.assertEquals(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')
+ # test published_in setting/ getting
+ c.SetPublishedIn('Best Book Ever')
+ self.assertEquals(c.GetPublishedIn(), 'Best Book Ever')
+ # test volume setting/ getting
+ c.SetVolume('3')
+ self.assertEquals(c.GetVolume(), '3')
+ # test page setting/ getting
+ c.SetPageFirst('1')
+ self.assertEquals(c.GetPageFirst(), '1')
+ c.SetPageLast('10')
+ self.assertEquals(c.GetPageLast(), '10')
+ # test doi setting/ getting
+ c.SetDOI('HERE')
+ self.assertEquals(c.GetDOI(), 'HERE')
+ # test PubMed setting/ getting
+ c.SetPubMed(815)
+ self.assertEquals(c.GetPubMed(), 815)
+ # test year setting/ getting
+ c.SetYear(815)
+ self.assertEquals(c.GetYear(), 815)
+ # test title setting/ getting
+ c.SetTitle('Foo')
+ self.assertEquals(c.GetTitle(), 'Foo')
+ # test auhtors setting/ getting
+ s = ost.StringList()
+ s.append('Foo')
+ c.SetAuthorList(s)
+ s2 = c.GetAuthorList()
+ self.assertEquals(s2[0], 'Foo')
+
+ i = io.MMCifInfo()
+ i.SetMethod('Deep-Fry')
+ i.SetResolution(2.0)
+ i.AddCitation(c)
+ s.append('Bar')
+ i.AddAuthorsToCitation('ID', s)
+
+ cl = i.GetCitations()
+ self.assertEquals(len(cl), 1)
+ al = cl[0].GetAuthorList()
+ self.assertEquals(len(al), 2)
+ self.assertEquals(al[0], 'Foo')
+ self.assertEquals(al[1], 'Bar')
+
+ self.assertEquals(i.GetMethod(), 'Deep-Fry')
+ self.assertEquals(i.GetResolution(), 2.0)
+
+
+ def test_mmcifinfo_biounit(self):
+ b = io.MMCifInfoBioUnit()
+ b.SetDetails('Details')
+ self.assertEquals(b.GetDetails(), 'Details')
+ b.AddChain('A')
+ cl = b.GetChainList()
+ self.assertEquals(cl[0], 'A')
+
+ i = io.MMCifInfo()
+ i.AddBioUnit(b)
+
+ bl = i.GetBioUnits()
+ self.assertEquals(len(bl), 1)
+
+
+ def test_mmcifinfo_transoperation(self):
+ o = io.MMCifInfoTransOp()
+ o.SetID("1")
+ self.assertEquals(o.GetID(), '1')
+ o.SetType("identity operation")
+ self.assertEquals(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)
+ o.SetMatrix(1, 2, 3, 4, 5, 6, 7, 8, 9)
+ self.assertEquals(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')
+
+ b = io.MMCifInfoBioUnit()
+ b.AddOperations(ol)
+ oll = b.GetOperations()
+ self.assertEquals(oll[0][0].GetID(), '1')
+
+ def test_mmcifinfo_biounit_pdbize(self):
+ ent, seqres, info = io.LoadMMCIF("testfiles/mmcif/3T6C.cif.gz",
+ seqres=True,
+ info=True)
+ pdb_ent = info.GetBioUnits()[0].PDBize(ent)
+ pdb_seqres_ent = info.GetBioUnits()[0].PDBize(ent, seqres)
+
+ # chains
+ self.assertEquals(str(pdb_ent.GetChainList()[0]), 'A')
+ self.assertEquals(str(pdb_ent.GetChainList()[1]), 'B')
+ self.assertEquals(str(pdb_ent.GetChainList()[2]), '_')
+ self.assertEquals(str(pdb_ent.GetChainList()[3]), '-')
+ self.assertEquals(str(pdb_ent.GetChainList()[4]), 'C')
+ self.assertEquals(str(pdb_ent.GetChainList()[5]), 'D')
+ self.assertEquals(str(pdb_ent.GetChainList()[6]), 'E')
+ self.assertEquals(str(pdb_ent.GetChainList()[7]), 'F')
+ self.assertEquals(str(pdb_ent.GetChainList()[8]), 'G')
+ self.assertEquals(str(pdb_ent.GetChainList()[9]), 'H')
+ # size of chains
+ self.assertEquals(len(pdb_ent.GetChainList()[0].GetResidueList()), 415)
+ self.assertEquals(len(pdb_ent.GetChainList()[1].GetResidueList()), 414)
+ self.assertEquals(len(pdb_ent.GetChainList()[2].GetResidueList()), 64)
+ self.assertEquals(len(pdb_ent.GetChainList()[3].GetResidueList()), 3816)
+ self.assertEquals(len(pdb_ent.GetChainList()[4].GetResidueList()), 415)
+ self.assertEquals(len(pdb_ent.GetChainList()[5].GetResidueList()), 414)
+ self.assertEquals(len(pdb_ent.GetChainList()[6].GetResidueList()), 415)
+ self.assertEquals(len(pdb_ent.GetChainList()[7].GetResidueList()), 414)
+ self.assertEquals(len(pdb_ent.GetChainList()[8].GetResidueList()), 415)
+ self.assertEquals(len(pdb_ent.GetChainList()[9].GetResidueList()), 414)
+
+ self.assertEquals(str(pdb_seqres_ent.GetChainList()[0]), 'A')
+ self.assertEquals(str(pdb_seqres_ent.GetChainList()[1]), 'B')
+ self.assertEquals(str(pdb_seqres_ent.GetChainList()[2]), '_')
+ self.assertEquals(str(pdb_seqres_ent.GetChainList()[3]), '-')
+ self.assertEquals(str(pdb_seqres_ent.GetChainList()[4]), 'C')
+ self.assertEquals(str(pdb_seqres_ent.GetChainList()[5]), 'D')
+ self.assertEquals(str(pdb_seqres_ent.GetChainList()[6]), 'E')
+ self.assertEquals(str(pdb_seqres_ent.GetChainList()[7]), 'F')
+ self.assertEquals(str(pdb_seqres_ent.GetChainList()[8]), 'G')
+ self.assertEquals(str(pdb_seqres_ent.GetChainList()[9]), 'H')
+
+ self.assertEquals(len(pdb_seqres_ent.GetChainList()[0].GetResidueList()),
+ 415)
+ self.assertEquals(len(pdb_seqres_ent.GetChainList()[1].GetResidueList()),
+ 414)
+ self.assertEquals(len(pdb_seqres_ent.GetChainList()[2].GetResidueList()),
+ 64)
+ self.assertEquals(len(pdb_seqres_ent.GetChainList()[3].GetResidueList()),
+ 3816)
+ self.assertEquals(len(pdb_seqres_ent.GetChainList()[4].GetResidueList()),
+ 415)
+ self.assertEquals(len(pdb_seqres_ent.GetChainList()[5].GetResidueList()),
+ 414)
+ self.assertEquals(len(pdb_seqres_ent.GetChainList()[6].GetResidueList()),
+ 415)
+ self.assertEquals(len(pdb_seqres_ent.GetChainList()[7].GetResidueList()),
+ 414)
+ self.assertEquals(len(pdb_seqres_ent.GetChainList()[8].GetResidueList()),
+ 415)
+ self.assertEquals(len(pdb_seqres_ent.GetChainList()[9].GetResidueList()),
+ 414)
+
+ def test_mmcifinfo_structdetails(self):
+ d = io.MMCifInfoStructDetails()
+
+ d.SetEntryID('1BAR')
+ d.SetTitle('A Title')
+ d.SetCASPFlag('N')
+ d.SetDescriptor('FooBar')
+ d.SetMass(1.0)
+ 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')
+
+ 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(),
+ 'Created with SwissModel')
+ self.assertEquals(i.GetStructDetails().GetModelTypeDetails(), 'Average')
+
+ def test_mmcifinfo_obsolete(self):
+ obs = io.MMCifInfoObsolete()
+ obs.SetDate('2011-08-31')
+ 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')
+
+ 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')
+
+if __name__== '__main__':
+ from ost import testutils
+ testutils.RunTests()
+
+
diff --git a/modules/io/tests/test_io_pdb.cc b/modules/io/tests/test_io_pdb.cc
index 6a055b83fe0624cf9cb783162bc1028039b055ed..47f858f8eb26f61b3e7e775c201fbbfd2d73f160 100644
--- a/modules/io/tests/test_io_pdb.cc
+++ b/modules/io/tests/test_io_pdb.cc
@@ -27,6 +27,8 @@
#include <ost/io/mol/entity_io_pdb_handler.hh>
#include <ost/io/pdb_reader.hh>
#include <ost/io/pdb_writer.hh>
+#include <ost/log.hh>
+
#include <ost/io/io_exception.hh>
#define BOOST_TEST_DYN_LINK
#include <boost/test/unit_test.hpp>
@@ -37,7 +39,6 @@ using namespace ost::io;
BOOST_AUTO_TEST_SUITE( io )
-
BOOST_AUTO_TEST_CASE(test_pdb_import_handler)
{
String fname("testfiles/test_in.pdb");
@@ -135,11 +136,53 @@ BOOST_AUTO_TEST_CASE(test_parse_compnd_record4)
//COMPND CHAIN record misses B chain
BOOST_AUTO_TEST_CASE(test_parse_compnd_record5)
{
+ Logger::Instance().PushVerbosityLevel(0);
+
String fname("testfiles/pdb/1AKE_noBchain.pdb");
PDBReader reader(fname, IOProfile());
mol::EntityHandle ent=mol::CreateEntity();
+ BOOST_CHECK_NO_THROW(reader.Import(ent));
+
+ mol::ChainHandle ch = ent.FindChain("A");
+ BOOST_CHECK(ch.HasProp("mol_id")==true);
+ BOOST_CHECK(ch.GetIntProp("mol_id")==1);
+
+ ch = ent.FindChain("B");
+ BOOST_CHECK(ch.HasProp("mol_id")==false);
+}
+
+//chain I in MOL_ID record but no chain I
+BOOST_AUTO_TEST_CASE(test_parse_compnd_record6)
+{
+ Logger::Instance().PushVerbosityLevel(0);
+ String fname("testfiles/pdb/1oax.pdb");
+ PDBReader reader(fname, IOProfile());
+ mol::EntityHandle ent=mol::CreateEntity();
+
BOOST_CHECK_THROW(reader.Import(ent), IOException);
+
+}
+
+// has an empy MOLECULE record (unsupported ATM anyway, but crashed ost)
+BOOST_AUTO_TEST_CASE(test_parse_compnd_record7)
+{
+ Logger::Instance().PushVerbosityLevel(0);
+ String fname("testfiles/pdb/2p6a.pdb");
+ PDBReader reader(fname, IOProfile());
+ mol::EntityHandle ent=mol::CreateEntity();
+
+ reader.Import(ent);
+ mol::ChainHandle ch = ent.FindChain("A");
+ BOOST_CHECK(ch.HasProp("mol_id")==true);
+ BOOST_CHECK(ch.GetIntProp("mol_id")==1);
+ ch = ent.FindChain("D");
+ BOOST_CHECK(ch.HasProp("mol_id")==true);
+ BOOST_CHECK(ch.GetIntProp("mol_id")==2);
+
+ ch = ent.FindChain("E");
+ BOOST_CHECK(ch.HasProp("mol_id")==true);
+ BOOST_CHECK(ch.GetIntProp("mol_id")==3);
}
@@ -386,6 +429,25 @@ BOOST_AUTO_TEST_CASE(deuterium_import)
BOOST_CHECK(ent.FindResidue("A", 297).IsPeptideLinking());
}
+BOOST_AUTO_TEST_CASE(bzdng_318)
+{
+ String fname("testfiles/pdb/bzdng-318.pdb");
+ PDBReader reader(fname, IOProfile());
+ mol::EntityHandle ent=mol::CreateEntity();
+ reader.Import(ent);
+ // we use conopology to mark amino acids as peptide-linking.
+ conop::Conopology& conop_inst=conop::Conopology::Instance();
+ conop_inst.ConnectAll(conop_inst.GetBuilder(), ent);
+ {
+ PDBWriter writer(std::string("testfiles/pdb/bzdng-318-out.pdb"),
+ IOProfile());
+ writer.Write(ent);
+ }
+
+ BOOST_CHECK(compare_files("testfiles/pdb/bzdng-318.pdb",
+ "testfiles/pdb/bzdng-318-out.pdb"));
+}
+
BOOST_AUTO_TEST_CASE(faulty_lines)
{
String fname("testfiles/pdb/faulty.pdb");
@@ -419,6 +481,64 @@ BOOST_AUTO_TEST_CASE(write_atom)
" 1.00128.00 C ");
}
+BOOST_AUTO_TEST_CASE(write_atom_100000)
+{
+ char c_names[] = "ABCDEFGHIJ";
+ std::stringstream out;
+ PDBWriter writer(out, IOProfile());
+
+ mol::EntityHandle ent=mol::CreateEntity();
+ mol::XCSEditor edi=ent.EditXCS();
+ mol::ChainHandle ch;
+ mol::ResidueHandle r;
+ mol::AtomHandle a;
+
+ for (unsigned long i = 0; i < 10; ++i) {
+ ch=edi.InsertChain(String(1, c_names[i]));
+ for (unsigned long j = 1; j < 1000; ++j) {
+ r=edi.AppendResidue(ch, "ARG");
+ a=edi.InsertAtom(r,"N", geom::Vec3(26.861, 50.841, 38.803), "N");
+ a.SetOccupancy(1.0);
+ a.SetBFactor(128.0);
+ a=edi.InsertAtom(r,"CA", geom::Vec3(27.437, 49.969, 37.786), "C");
+ a.SetOccupancy(1.0);
+ a.SetBFactor(128.0);
+ a=edi.InsertAtom(r,"C", geom::Vec3(26.336, 48.959, 37.429), "C");
+ a.SetOccupancy(1.0);
+ a.SetBFactor(128.0);
+ a=edi.InsertAtom(r,"O", geom::Vec3(25.745, 48.313, 38.312), "O");
+ a.SetOccupancy(1.0);
+ a.SetBFactor(128.0);
+ a=edi.InsertAtom(r,"CB", geom::Vec3(28.653, 49.266, 38.349), "C");
+ a.SetOccupancy(1.0);
+ a.SetBFactor(128.0);
+ a=edi.InsertAtom(r,"CG", geom::Vec3(29.870, 50.188, 38.416), "C");
+ a.SetOccupancy(1.0);
+ a.SetBFactor(128.0);
+ a=edi.InsertAtom(r,"CD", geom::Vec3(31.033, 49.532, 39.173), "C");
+ a.SetOccupancy(1.0);
+ a.SetBFactor(128.0);
+ a=edi.InsertAtom(r,"NE", geom::Vec3(32.318, 50.244, 39.125), "N");
+ a.SetOccupancy(1.0);
+ a.SetBFactor(128.0);
+ a=edi.InsertAtom(r,"CZ", geom::Vec3(33.462, 49.750, 39.679), "C");
+ a.SetOccupancy(1.0);
+ a.SetBFactor(128.0);
+ a=edi.InsertAtom(r,"NH1", geom::Vec3(33.522, 48.572, 40.308), "N");
+ a.SetOccupancy(1.0);
+ a.SetBFactor(128.0);
+ a=edi.InsertAtom(r,"NH2", geom::Vec3(34.610, 50.427, 39.597), "N");
+ a.SetOccupancy(1.0);
+ a.SetBFactor(128.0);
+ }
+ }
+
+ writer.Write(ent);
+ String s=out.str();
+ BOOST_CHECK_EQUAL(s.substr(8099844, 5), "99999");
+ BOOST_CHECK_EQUAL(s.substr(8099925, 5), "*****");
+}
+
BOOST_AUTO_TEST_CASE(write_hetatom)
{
std::stringstream out;
@@ -798,7 +918,7 @@ BOOST_AUTO_TEST_CASE(charmm_rname)
{
PDBWriter writer(String("testfiles/pdb/charmm_rname-out.pdb"),
IOProfile("CHARMM", true, false, false,
- false, false, false));
+ false, false, false, true));
mol::EntityHandle ent=mol::CreateEntity();
mol::XCSEditor edi=ent.EditXCS();
@@ -818,7 +938,7 @@ BOOST_AUTO_TEST_CASE(charmm_longcname)
{
PDBWriter writer(String("testfiles/pdb/charmm_longcname-out.pdb"),
IOProfile("CHARMM", true, false, false,
- false, false, false));
+ false, false, false, true));
mol::EntityHandle ent=mol::CreateEntity();
mol::XCSEditor edi=ent.EditXCS();
@@ -838,7 +958,7 @@ BOOST_AUTO_TEST_CASE(write_charmm_ter)
{
PDBWriter writer(String("testfiles/pdb/charmm_ter-out.pdb"),
IOProfile("CHARMM", true, false, false,
- false, false, false));
+ false, false, false, true));
mol::EntityHandle ent=mol::CreateEntity();
mol::XCSEditor edi=ent.EditXCS();
@@ -855,4 +975,88 @@ BOOST_AUTO_TEST_CASE(write_charmm_ter)
"testfiles/pdb/charmm_ter-out.pdb"));
}
+BOOST_AUTO_TEST_CASE(test_pqr_import_handler)
+{
+ String fname("testfiles/test_in.pqr");
+
+ mol::EntityHandle eh=mol::CreateEntity();
+ EntityIOPDBHandler pdbh;
+
+ BOOST_CHECK(EntityIOPDBHandler::ProvidesImport(fname));
+ BOOST_CHECK(EntityIOPDBHandler::ProvidesImport("test_in.PQR"));
+
+ BOOST_CHECK(EntityIOPDBHandler::ProvidesExport(fname));
+ BOOST_CHECK(EntityIOPDBHandler::ProvidesExport("test_in.PQR"));
+
+ pdbh.Import(eh,"testfiles/pdb/simple.pqr");
+}
+
+
+BOOST_AUTO_TEST_CASE(test_pqr_read_atom)
+{
+ String fname("testfiles/pdb/simple.pqr");
+ PDBReader reader(fname, IOProfile());
+ mol::EntityHandle ent=mol::CreateEntity();
+ reader.Import(ent);
+ BOOST_REQUIRE_EQUAL(ent.GetChainCount(), 1);
+ BOOST_REQUIRE_EQUAL(ent.GetResidueCount(), 5);
+ BOOST_REQUIRE_EQUAL(ent.GetAtomCount(), 91);
+ mol::AtomHandle a1=ent.FindAtom(" ", mol::ResNum(1), "N");
+ BOOST_REQUIRE(a1.IsValid());
+ BOOST_CHECK_EQUAL(a1.GetName(), "N");
+ BOOST_CHECK_EQUAL(a1.GetResidue().GetName(), "MET");
+ BOOST_CHECK_EQUAL(a1.GetResidue().GetChain().GetName(), " ");
+
+
+ BOOST_CHECK_EQUAL(a1.GetPos(), geom::Vec3(21.6, 35.3, 56.7));
+ BOOST_CHECK_EQUAL(a1.GetElement(), "");
+ BOOST_CHECK_EQUAL(a1.IsHetAtom(), false);
+ BOOST_CHECK_CLOSE(a1.GetCharge(), Real(-0.3755), Real(1e-4));
+ BOOST_CHECK_CLOSE(a1.GetRadius(), Real(2.0005), Real(1e-4));
+
+ mol::AtomHandle a2=ent.FindAtom(" ", mol::ResNum(2), "CZ");
+ BOOST_REQUIRE(a2.IsValid());
+ BOOST_CHECK_EQUAL(a2.GetName(), "CZ");
+ BOOST_CHECK_EQUAL(a2.GetResidue().GetName(), "ARG");
+ BOOST_CHECK_EQUAL(a2.GetResidue().GetChain().GetName(), " ");
+
+ BOOST_CHECK_EQUAL(a2.GetPos(), geom::Vec3(23.9, 28.7, 56.5));
+ BOOST_CHECK_EQUAL(a2.GetElement(), "");
+ BOOST_CHECK_EQUAL(a2.IsHetAtom(), false);
+ BOOST_CHECK_CLOSE(a2.GetCharge(), Real(0.2507), Real(1e-4));
+ BOOST_CHECK_CLOSE(a2.GetRadius(), Real(1.7503), Real(1e-4));
+}
+
+BOOST_AUTO_TEST_CASE(test_pqr_write_atom)
+{
+ std::stringstream out;
+ PDBWriter writer(out, IOProfile());
+ writer.SetIsPQR(true);
+
+ mol::EntityHandle ent=mol::CreateEntity();
+ mol::XCSEditor edi=ent.EditXCS();
+ mol::ChainHandle ch=edi.InsertChain("A");
+ mol::ResidueHandle r=edi.AppendResidue(ch, "GLY");
+
+ mol::AtomHandle a=edi.InsertAtom(r, "CA", geom::Vec3(32.0, -128.0, -2.5), "C");
+ a.SetOccupancy(1.0);
+ a.SetBFactor(128.0);
+ a.SetCharge(-0.6543);
+ a.SetRadius(1.2345);
+ mol::AtomHandle a2=edi.InsertAtom(r, "CA", geom::Vec3(32.0, -128.0, -2.5), "C");
+ a2.SetOccupancy(1.0);
+ a2.SetBFactor(128.0);
+ a2.SetCharge(0.1234);
+ a2.SetRadius(2.5432);
+ writer.Write(ent);
+ String s=out.str();
+ BOOST_CHECK_EQUAL(s.substr(0, 54),
+ "ATOM 1 CA GLY A 1 32.000-128.000 -2.500");
+ BOOST_CHECK_EQUAL(s.substr(54, 26),
+ " -0.6543 1.2345 C ");
+
+ PDBWriter fwriter(String("testfiles/pdb/pqr_atom-out.pqr"), IOProfile());
+ BOOST_CHECK_EQUAL(fwriter.IsPQR(), true);
+}
+
BOOST_AUTO_TEST_SUITE_END()
diff --git a/modules/io/tests/test_io_pdb.py b/modules/io/tests/test_io_pdb.py
index c8bb3902dbd45b1fb08aea68b81982662d3178a1..348fde1d929669405e612cb92d3a274ceb5636f1 100644
--- a/modules/io/tests/test_io_pdb.py
+++ b/modules/io/tests/test_io_pdb.py
@@ -11,7 +11,23 @@ class TestPDB(unittest.TestCase):
ch = e.FindChain("A");
self.assertEquals(ch.GetIntProp("mol_id"), 1)
+class TestPDB(unittest.TestCase):
+ def setUp(self):
+ pass
+
+ def test_compnd_parser(self):
+ profiles=io.IOProfiles()
+ profiles['NO_FEAS_CHECK']=io.IOProfile(bond_feasibility_check=False)
+
+ e=io.LoadPDB('testfiles/pdb/simple_defective.pdb', restrict_chains="A",profile='NO_FEAS_CHECK')
+
+ res=e.FindResidue('A',3)
+
+ self.assertTrue(mol.BondExists(res.FindAtom("CA"),res.FindAtom("CB")))
+
if __name__== '__main__':
- unittest.main()
+ from ost import testutils
+ testutils.RunTests()
+
diff --git a/modules/io/tests/test_mmcif_info.cc b/modules/io/tests/test_mmcif_info.cc
new file mode 100644
index 0000000000000000000000000000000000000000..23a28205ea74f2e15eb9cd793e16113d137da425
--- /dev/null
+++ b/modules/io/tests/test_mmcif_info.cc
@@ -0,0 +1,201 @@
+//------------------------------------------------------------------------------
+// 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
+//------------------------------------------------------------------------------
+
+#include <ost/io/io_exception.hh>
+#include <ost/io/mol/mmcif_info.hh>
+
+#define BOOST_AUTO_TEST_DYN_LINK
+#include <boost/test/unit_test.hpp>
+
+
+using namespace ost;
+using namespace ost::io;
+
+BOOST_AUTO_TEST_SUITE( io );
+
+BOOST_AUTO_TEST_CASE(mmcif_info_obsolete)
+{
+ BOOST_MESSAGE(" Running mmcif_info_obsolete tests...");
+
+ MMCifInfoObsolete obs = MMCifInfoObsolete();
+
+ obs.SetDate("2011-08-31");
+ obs.SetID(StringRef("OBSLTE", 6));
+ obs.SetPDBID("1FOO");
+ obs.SetReplacedPDBID("1BAR");
+
+ BOOST_CHECK(obs.GetDate() == "2011-08-31");
+ BOOST_CHECK(obs.GetID() == "Obsolete");
+ BOOST_CHECK(obs.GetPDBID() == "1FOO");
+ BOOST_CHECK(obs.GetReplacedPDBID() == "1BAR");
+
+ obs.SetID(StringRef("SPRSDE", 6));
+ BOOST_CHECK(obs.GetID() == "Supersede");
+
+ BOOST_MESSAGE(" done.");
+}
+
+BOOST_AUTO_TEST_CASE(mmcif_info_citation)
+{
+ BOOST_MESSAGE(" Running mmcif_info_citation tests...");
+
+ MMCifInfoCitation cit = MMCifInfoCitation();
+ std::vector<String> author_list;
+
+ author_list.push_back("Kabel, H.");
+
+ cit.SetID("ID");
+ cit.SetCAS("FOO");
+ cit.SetISBN("0-0-0-0-0");
+ cit.SetPublishedIn("Journal of Uncanny Science");
+ cit.SetVolume("3");
+ cit.SetPageFirst("1");
+ cit.SetPageLast("10");
+ cit.SetDOI("HERE");
+ cit.SetPubMed(815);
+ cit.SetYear(815);
+ cit.SetTitle("Foo");
+ cit.SetAuthorList(author_list);
+ author_list.clear();
+
+ BOOST_CHECK(cit.GetID() == "ID");
+ BOOST_CHECK(cit.GetCAS() == "FOO");
+ BOOST_CHECK(cit.GetISBN() == "0-0-0-0-0");
+ BOOST_CHECK(cit.GetPublishedIn() == "Journal of Uncanny Science");
+ BOOST_CHECK(cit.GetVolume() == "3");
+ BOOST_CHECK(cit.GetPageFirst() == "1");
+ BOOST_CHECK(cit.GetPageLast() == "10");
+ BOOST_CHECK(cit.GetDOI() == "HERE");
+ BOOST_CHECK(cit.GetPubMed() == 815);
+ BOOST_CHECK(cit.GetYear() == 815);
+ BOOST_CHECK(cit.GetTitle() == "Foo");
+ author_list = cit.GetAuthorList();
+ BOOST_CHECK(author_list.back() == "Kabel, H.");
+
+ BOOST_MESSAGE(" done.");
+ BOOST_MESSAGE(" trying to add everything to an info object");
+ MMCifInfo info = MMCifInfo();
+ info.AddCitation(cit);
+ std::vector<MMCifInfoCitation> citations = info.GetCitations();
+ BOOST_CHECK(citations.size() == 1);
+ BOOST_CHECK(citations.back() == cit);
+ BOOST_CHECK_THROW(info.AddAuthorsToCitation(StringRef("Foo", 3),
+ author_list),
+ IOException);
+ BOOST_MESSAGE(" done.");
+}
+
+BOOST_AUTO_TEST_CASE(mmcif_info_biounit)
+{
+ BOOST_MESSAGE(" Running mmcif_info_biounit tests...");
+
+ MMCifInfoBioUnit bu = MMCifInfoBioUnit();
+
+ bu.SetDetails("author_defined_assembly");
+ bu.AddChain("A");
+
+ BOOST_CHECK(bu.GetDetails() == "author_defined_assembly");
+ BOOST_CHECK(bu.GetChainList().back() == "A");
+
+ MMCifInfo info = MMCifInfo();
+ info.AddBioUnit(bu);
+ std::vector<MMCifInfoBioUnit> biounits = info.GetBioUnits();
+ BOOST_CHECK(biounits.size() == 1);
+ BOOST_CHECK(biounits.back() == bu);
+
+ BOOST_MESSAGE(" done.");
+}
+
+BOOST_AUTO_TEST_CASE(mmcif_info_transoperation)
+{
+ BOOST_MESSAGE(" Running mmcif_info_transoperation tests...");
+
+ MMCifInfoTransOpPtr op(new MMCifInfoTransOp);
+
+ op->SetID("1");
+ op->SetType("identity operation");
+ op->SetVector(1, 2, 3);
+ op->SetMatrix(1, 2, 3, 4, 5, 6, 7 ,8, 9);
+
+ BOOST_CHECK(op->GetID() == "1");
+ BOOST_CHECK(op->GetVector() == geom::Vec3(1, 2, 3));
+ BOOST_CHECK(op->GetMatrix() == geom::Mat3(1, 2, 3, 4, 5, 6, 7, 8, 9));
+ BOOST_CHECK(op->GetType() == "identity operation");
+
+ MMCifInfo info = MMCifInfo();
+ info.AddOperation(op);
+ BOOST_CHECK(info.GetOperations().back() == op);
+
+ std::vector<MMCifInfoTransOpPtr> ops;
+ ops.push_back(*(info.GetOperations().begin()));
+ MMCifInfoBioUnit bu = MMCifInfoBioUnit();
+ bu.AddOperations(ops);
+ BOOST_CHECK((*(bu.GetOperations().begin()->begin())) == op);
+
+ BOOST_MESSAGE(" done.");
+}
+
+BOOST_AUTO_TEST_CASE(mmcif_info_structdetails)
+{
+ BOOST_MESSAGE(" Running mmcif_info_structdetails tests...");
+
+ MMCifInfoStructDetails sd = MMCifInfoStructDetails();
+
+ sd.SetEntryID("1BAR");
+ sd.SetTitle("More than a structure");
+ sd.SetCASPFlag('Y');
+ sd.SetDescriptor("ADENYLATE KINASE");
+ sd.SetMass(1.0);
+ sd.SetMassMethod("Good Guess");
+ sd.SetModelDetails("Even more guessing");
+ sd.SetModelTypeDetails("MINIMIZED AVERAGE");
+
+ BOOST_CHECK(sd.GetEntryID() == "1BAR");
+ BOOST_CHECK(sd.GetTitle() == "More than a structure");
+ BOOST_CHECK(sd.GetCASPFlag() == 'Y');
+ BOOST_CHECK(sd.GetDescriptor() == "ADENYLATE KINASE");
+ BOOST_CHECK_CLOSE(sd.GetMass(), 1.0f, 0.001f);
+ BOOST_CHECK(sd.GetMassMethod() == "Good Guess");
+ BOOST_CHECK(sd.GetModelDetails() == "Even more guessing");
+ BOOST_CHECK(sd.GetModelTypeDetails() == "MINIMIZED AVERAGE");
+
+ MMCifInfo info = MMCifInfo();
+ info.SetStructDetails(sd);
+ BOOST_CHECK(info.GetStructDetails() == sd);
+
+ BOOST_MESSAGE(" done.");
+}
+
+BOOST_AUTO_TEST_CASE(mmcif_info)
+{
+ BOOST_MESSAGE(" Running mmcif_info tests...");
+
+ MMCifInfo info = MMCifInfo();
+
+ info.SetMethod("Cooking.");
+ info.SetResolution(1.9f);
+
+ BOOST_CHECK(info.GetMethod() == StringRef("Cooking.", 8));
+ BOOST_CHECK_CLOSE(info.GetResolution(), 1.9f, 0.001f);
+
+ BOOST_MESSAGE(" done.");
+}
+
+
+BOOST_AUTO_TEST_SUITE_END();
diff --git a/modules/io/tests/test_mmcif_reader.cc b/modules/io/tests/test_mmcif_reader.cc
new file mode 100644
index 0000000000000000000000000000000000000000..fff6bbb2e6d6d2596f69f6a223aeeb957f84a50d
--- /dev/null
+++ b/modules/io/tests/test_mmcif_reader.cc
@@ -0,0 +1,1270 @@
+//------------------------------------------------------------------------------
+// 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
+//------------------------------------------------------------------------------
+
+#include <fstream>
+#include <ost/platform.hh>
+#include <ost/io/io_exception.hh>
+#include <ost/io/mol/mmcif_reader.hh>
+#include <ost/conop/conop.hh>
+#include <ost/conop/rule_based_builder.hh>
+
+#define BOOST_AUTO_TEST_DYN_LINK
+#include <boost/test/unit_test.hpp>
+
+
+using namespace ost;
+using namespace ost::io;
+
+class TestMMCifReaderProtected : MMCifReader {
+public:
+ TestMMCifReaderProtected(std::istream& stream, mol::EntityHandle& ent_handle):
+ MMCifReader(stream, ent_handle, IOProfile())
+ { }
+
+ TestMMCifReaderProtected(std::istream& stream, mol::EntityHandle& ent_handle,
+ const IOProfile& profile):
+ MMCifReader(stream, ent_handle, profile)
+ { }
+
+ TestMMCifReaderProtected(const String& filename,
+ mol::EntityHandle& ent_handle):
+ MMCifReader(filename, ent_handle, IOProfile())
+ { }
+
+ using MMCifReader::OnBeginLoop;
+ using MMCifReader::OnEndData;
+ using MMCifReader::IsValidPDBIdent;
+ using MMCifReader::ParseAtomIdent;
+ using MMCifReader::ParseAndAddAtom;
+ using MMCifReader::ParseEntity;
+ using MMCifReader::ParseEntityPoly;
+ using MMCifReader::ParseCitation;
+ using MMCifReader::ParseRefine;
+ using MMCifReader::ParsePdbxStructAssemblyGen;
+ using MMCifReader::ParsePdbxStructAssembly;
+ using MMCifReader::ParsePdbxStructOperList;
+ using MMCifReader::ParseStruct;
+ using MMCifReader::ParseStructConf;
+ using MMCifReader::ParseStructSheetRange;
+ using MMCifReader::TryStoreIdx;
+ using MMCifReader::SetRestrictChains;
+ using MMCifReader::SetReadSeqRes;
+ using MMCifReader::SetReadCanonicalSeqRes;
+ using MMCifReader::ClearState;
+ using MMCifReader::ConvertSEQRES;
+ using MMCifReader::GetInfo;
+ using MMCifReader::DetermineSecStructType;
+ using MMCifReader::MMCifSecStructElement;
+ using MMCifReader::MMCIF_HELIX;
+ using MMCifReader::MMCIF_TURN;
+ using MMCifReader::MMCIF_STRAND;
+ using MMCifReader::SetAuthChainID;
+};
+
+void SetAtomSiteHeader(StarLoopDesc* mmcif_h)
+{
+ mmcif_h->Clear();
+ mmcif_h->SetCategory(StringRef("atom_site", 9));
+ mmcif_h->Add(StringRef("auth_asym_id", 12));
+ mmcif_h->Add(StringRef("id", 2));
+ mmcif_h->Add(StringRef("label_alt_id", 12));
+ mmcif_h->Add(StringRef("label_asym_id", 13));
+ mmcif_h->Add(StringRef("label_atom_id", 13));
+ mmcif_h->Add(StringRef("label_comp_id", 13));
+ mmcif_h->Add(StringRef("label_entity_id", 15));
+ mmcif_h->Add(StringRef("label_seq_id", 12));
+ mmcif_h->Add(StringRef("type_symbol", 11));
+ mmcif_h->Add(StringRef("Cartn_x", 7));
+ mmcif_h->Add(StringRef("Cartn_y", 7));
+ mmcif_h->Add(StringRef("Cartn_z", 7));
+}
+
+BOOST_AUTO_TEST_SUITE( io );
+
+BOOST_AUTO_TEST_CASE(mmcif_isvalidpdbident)
+{
+ mol::EntityHandle eh=mol::CreateEntity();
+
+ // on changing the tests for a PDB id in mmcif files, extend this unit test
+ BOOST_MESSAGE(" Running mmcif_isvalidpdbident tests...");
+ std::ifstream s("testfiles/mmcif/atom_site.mmcif");
+ TestMMCifReaderProtected tmmcif_p(s, eh);
+ StringRef id = StringRef("1FOO", 4);
+ BOOST_MESSAGE(" Testing valid id ('"+ id.str() +"')...");
+ BOOST_CHECK(tmmcif_p.IsValidPDBIdent(id));
+ BOOST_MESSAGE(" done.");
+ id = StringRef("this is to long for a PDB id", 28);
+ BOOST_MESSAGE(" Testing oversized PDB id ('"+ id.str() +"')...");
+ BOOST_CHECK(!tmmcif_p.IsValidPDBIdent(id));
+ BOOST_MESSAGE(" done.");
+ id = StringRef("nFOO", 4);
+ BOOST_MESSAGE(" Testing PDB id with missing number ('"+ id.str() +"')...");
+ BOOST_CHECK(!tmmcif_p.IsValidPDBIdent(id));
+ BOOST_MESSAGE(" done.");
+}
+
+BOOST_AUTO_TEST_CASE(mmcif_trystoreidx)
+{
+ mol::EntityHandle eh = mol::CreateEntity();
+
+ BOOST_MESSAGE(" Running mmcif_trystoreidx tests...");
+ std::ifstream s("testfiles/mmcif/atom_site.mmcif");
+ TestMMCifReaderProtected tmmcif_p(s, eh, IOProfile());
+ StarLoopDesc mmcif_h;
+ mmcif_h.SetCategory(StringRef("Foo", 3));
+ // negative
+ BOOST_CHECK_THROW(tmmcif_p.TryStoreIdx(0, "bar", mmcif_h), IOException);
+ // positive
+ mmcif_h.Add(StringRef("bar", 3));
+ BOOST_CHECK_NO_THROW(tmmcif_p.TryStoreIdx(0, "bar", mmcif_h));
+}
+
+BOOST_AUTO_TEST_CASE(mmcif_convert_seqres)
+{
+ SetPrefixPath(getenv("OST_ROOT"));
+ String lib_path=GetSharedDataPath()+"/compounds.chemlib";
+ conop::CompoundLibPtr compound_lib=conop::CompoundLib::Load(lib_path);
+ if (!compound_lib) {
+ std::cout << "WARNING: skipping SEQRES import unit test. "
+ << "Rule-based builder is required" << std::endl;
+ return;
+ }
+ conop::RuleBasedBuilderPtr rbb(new conop::RuleBasedBuilder(compound_lib));
+ conop::Conopology::Instance().RegisterBuilder(rbb, "RBB");
+ conop::Conopology::Instance().SetDefaultBuilder("RBB");
+ mol::EntityHandle eh=mol::CreateEntity();
+
+ TestMMCifReaderProtected tmmcif_p("testfiles/mmcif/atom_site.mmcif", eh);
+ std::vector<StringRef> columns;
+ StarLoopDesc tmmcif_h;
+ BOOST_CHECK_EQUAL(tmmcif_p.ConvertSEQRES("A(MSE)Y", compound_lib), "AMY");
+ BOOST_CHECK_THROW(tmmcif_p.ConvertSEQRES("A(MSEY", compound_lib),
+ IOException);
+ conop::Conopology::Instance().SetDefaultBuilder("HEURISTIC");
+}
+
+BOOST_AUTO_TEST_CASE(mmcif_onbeginloop)
+{
+ mol::EntityHandle eh=mol::CreateEntity();
+
+ // add more tests on new mandatory items
+ BOOST_MESSAGE(" Running mmcif_onbeginloop tests...");
+ std::ifstream s("testfiles/mmcif/atom_site.mmcif");
+ MMCifReader mmcif_p(s, eh, IOProfile());
+ StarLoopDesc mmcif_h;
+ BOOST_MESSAGE(" testing atom_site items...");
+ mmcif_h.SetCategory(StringRef("atom_site", 9));
+ BOOST_MESSAGE(" auth_asym_id");
+ BOOST_CHECK_THROW(mmcif_p.OnBeginLoop(mmcif_h), IOException);
+ mmcif_h.Add(StringRef("auth_asym_id", 12));
+ BOOST_MESSAGE(" id");
+ BOOST_CHECK_THROW(mmcif_p.OnBeginLoop(mmcif_h), IOException);
+ mmcif_h.Add(StringRef("id", 2));
+ BOOST_MESSAGE(" label_alt_id");
+ BOOST_CHECK_THROW(mmcif_p.OnBeginLoop(mmcif_h), IOException);
+ mmcif_h.Add(StringRef("label_alt_id", 12));
+ BOOST_MESSAGE(" label_asym_id");
+ BOOST_CHECK_THROW(mmcif_p.OnBeginLoop(mmcif_h), IOException);
+ mmcif_h.Add(StringRef("label_asym_id", 13));
+ BOOST_MESSAGE(" label_atom_id");
+ BOOST_CHECK_THROW(mmcif_p.OnBeginLoop(mmcif_h), IOException);
+ mmcif_h.Add(StringRef("label_atom_id", 13));
+ BOOST_MESSAGE(" label_comp_id");
+ BOOST_CHECK_THROW(mmcif_p.OnBeginLoop(mmcif_h), IOException);
+ mmcif_h.Add(StringRef("label_comp_id", 13));
+ BOOST_MESSAGE(" label_entity_id");
+ BOOST_CHECK_THROW(mmcif_p.OnBeginLoop(mmcif_h), IOException);
+ mmcif_h.Add(StringRef("label_entity_id", 15));
+ BOOST_MESSAGE(" label_seq_id");
+ BOOST_CHECK_THROW(mmcif_p.OnBeginLoop(mmcif_h), IOException);
+ mmcif_h.Add(StringRef("label_seq_id", 12));
+ BOOST_MESSAGE(" type_symbol");
+ BOOST_CHECK_THROW(mmcif_p.OnBeginLoop(mmcif_h), IOException);
+ mmcif_h.Add(StringRef("type_symbol", 11));
+ BOOST_MESSAGE(" Cartn_x");
+ BOOST_CHECK_THROW(mmcif_p.OnBeginLoop(mmcif_h), IOException);
+ mmcif_h.Add(StringRef("Cartn_x", 7));
+ BOOST_MESSAGE(" Cartn_y");
+ BOOST_CHECK_THROW(mmcif_p.OnBeginLoop(mmcif_h), IOException);
+ mmcif_h.Add(StringRef("Cartn_y", 7));
+ BOOST_MESSAGE(" Cartn_z");
+ BOOST_CHECK_THROW(mmcif_p.OnBeginLoop(mmcif_h), IOException);
+ mmcif_h.Add(StringRef("Cartn_z", 7));
+ BOOST_CHECK_NO_THROW(mmcif_p.OnBeginLoop(mmcif_h));
+ BOOST_MESSAGE(" done.");
+ mmcif_h.Clear();
+ BOOST_MESSAGE(" testing entity items...");
+ mmcif_h.SetCategory(StringRef("entity", 6));
+ BOOST_MESSAGE(" id");
+ BOOST_CHECK_THROW(mmcif_p.OnBeginLoop(mmcif_h), IOException);
+ mmcif_h.Add(StringRef("id", 2));
+ BOOST_CHECK_NO_THROW(mmcif_p.OnBeginLoop(mmcif_h));
+ BOOST_MESSAGE(" done.");
+ BOOST_MESSAGE(" done.");
+}
+
+BOOST_AUTO_TEST_CASE(mmcif_parse_models)
+{
+ BOOST_MESSAGE(" Running mmcif_parse_models tests...");
+ IOProfile profile;
+
+ // positive w models
+ BOOST_MESSAGE(" true positive test for models...");
+ {
+ mol::EntityHandle eh = mol::CreateEntity();
+ MMCifReader mmcif_p("testfiles/mmcif/model_truepos.mmcif", eh, profile);
+ BOOST_CHECK_NO_THROW(mmcif_p.Parse());
+ BOOST_REQUIRE_EQUAL(eh.GetChainCount(), 2);
+ BOOST_REQUIRE_EQUAL(eh.GetResidueCount(), 2);
+ BOOST_REQUIRE_EQUAL(eh.GetAtomCount(), 26);
+ }
+ BOOST_MESSAGE(" done.");
+
+ // positive wo models atom_site.mmcif
+ BOOST_MESSAGE(" test absent atom_site.pdbx_PDB_model_num entry...");
+ {
+ mol::EntityHandle eh = mol::CreateEntity();
+ MMCifReader mmcif_p("testfiles/mmcif/atom_site.mmcif", eh, profile);
+ BOOST_CHECK_NO_THROW(mmcif_p.Parse());
+ }
+ BOOST_MESSAGE(" done.");
+ // negative, more than 1 atom_site category
+ BOOST_MESSAGE(" testing more than one atom_site block...");
+ {
+ mol::EntityHandle eh = mol::CreateEntity();
+ MMCifReader mmcif_p("testfiles/mmcif/model_multi_atom_site.mmcif", eh,
+ profile);
+ BOOST_CHECK_THROW(mmcif_p.Parse(), IOException);
+ }
+ {
+ mol::EntityHandle eh = mol::CreateEntity();
+ MMCifReader mmcif_p("testfiles/mmcif/model_multi_atom_site_inverted.mmcif",
+ eh, profile);
+ BOOST_CHECK_THROW(mmcif_p.Parse(), IOException);
+ }
+ BOOST_MESSAGE(" done.");
+
+ BOOST_MESSAGE(" testing single model with model no. entry...");
+ {
+ // build dummy header
+ mol::EntityHandle eh = mol::CreateEntity();
+ StarLoopDesc tmmcif_h;
+ TestMMCifReaderProtected tmmcif_p("testfiles/mmcif/atom_site.mmcif", eh);
+ SetAtomSiteHeader(&tmmcif_h);
+ tmmcif_p.OnBeginLoop(tmmcif_h);
+ tmmcif_h.Add(StringRef("pdbx_PDB_model_num", 18));
+ BOOST_CHECK_THROW(tmmcif_p.OnBeginLoop(tmmcif_h), IOException);
+ }
+ BOOST_MESSAGE(" done.");
+
+ BOOST_MESSAGE(" done.");
+}
+
+BOOST_AUTO_TEST_CASE(mmcif_changing_label_entity_id)
+{
+ BOOST_MESSAGE(" Running mmcif_changing_label_entity_id tests...");
+ IOProfile profile;
+
+ // positive
+ BOOST_MESSAGE(" true positive test...");
+ {
+ mol::EntityHandle eh = mol::CreateEntity();
+ MMCifReader mmcif_p("testfiles/mmcif/atom_site.mmcif", eh, profile);
+ BOOST_CHECK_NO_THROW(mmcif_p.Parse());
+ }
+ BOOST_MESSAGE(" done.");
+
+ // negative
+ BOOST_MESSAGE(" true negative test...");
+ {
+ mol::EntityHandle eh = mol::CreateEntity();
+ MMCifReader mmcif_p("testfiles/mmcif/changing_label_entity_id.mmcif", eh,
+ profile);
+ BOOST_CHECK_THROW(mmcif_p.Parse(), IOException);
+ }
+ BOOST_MESSAGE(" done.");
+
+ BOOST_MESSAGE(" done.");
+}
+
+BOOST_AUTO_TEST_CASE(mmcif_unknown_entity_type)
+{
+ BOOST_MESSAGE(" Running mmcif_unknown_entity_type tests...");
+
+ mol::EntityHandle eh = mol::CreateEntity();
+ std::vector<StringRef> columns;
+ TestMMCifReaderProtected tmmcif_p("testfiles/mmcif/atom_site.mmcif", eh);
+ StarLoopDesc tmmcif_h;
+
+ // build dummy header
+ tmmcif_h.SetCategory(StringRef("entity", 6));
+ tmmcif_h.Add(StringRef("id", 2));
+ tmmcif_h.Add(StringRef("type", 4));
+ tmmcif_p.OnBeginLoop(tmmcif_h);
+
+ // positive
+ BOOST_MESSAGE(" known type...");
+ // build datarow
+ columns.push_back(StringRef("1", 1));
+ columns.push_back(StringRef("polymer", 7));
+ BOOST_CHECK_NO_THROW(tmmcif_p.ParseEntity(columns));
+ columns.pop_back();
+ columns.push_back(StringRef("non-polymer", 11));
+ BOOST_CHECK_NO_THROW(tmmcif_p.ParseEntity(columns));
+ columns.pop_back();
+ columns.push_back(StringRef("water", 5));
+ BOOST_CHECK_NO_THROW(tmmcif_p.ParseEntity(columns));
+ BOOST_MESSAGE(" done.");
+
+ // negative
+ BOOST_MESSAGE(" unknown type...");
+ columns.pop_back();
+ columns.push_back(StringRef("foo", 3));
+ BOOST_CHECK_THROW(tmmcif_p.ParseEntity(columns), std::runtime_error);
+ BOOST_MESSAGE(" done.");
+
+ BOOST_MESSAGE(" done.");
+}
+
+BOOST_AUTO_TEST_CASE(mmcif_entity_tests)
+{
+ BOOST_MESSAGE(" Running mmcif_entity_tests...");
+ mol::ChainHandle ch;
+ IOProfile profile;
+
+ // positive
+ BOOST_MESSAGE(" fetching chain type...");
+ {
+ mol::EntityHandle eh = mol::CreateEntity();
+ MMCifReader mmcif_p("testfiles/mmcif/atom_site.mmcif", eh, profile);
+ mmcif_p.Parse();
+ ch = eh.FindChain("A");
+ BOOST_CHECK(ch.IsValid());
+ BOOST_CHECK(ch.GetType() == mol::CHAINTYPE_POLY_PEPTIDE_L);
+ ch = eh.FindChain("C");
+ BOOST_CHECK(ch.IsValid());
+ BOOST_CHECK(ch.GetType() == mol::CHAINTYPE_POLY_PEPTIDE_L);
+ ch = eh.FindChain("O");
+ BOOST_CHECK(ch.IsValid());
+ BOOST_CHECK(ch.GetType() == mol::CHAINTYPE_WATER);
+ }
+ BOOST_MESSAGE(" done.");
+ // negative: no entity description
+ BOOST_MESSAGE(" check missing entity description...");
+ {
+ mol::EntityHandle eh = mol::CreateEntity();
+ MMCifReader mmcif_p("testfiles/mmcif/model_truepos.mmcif",
+ eh,
+ profile);
+ mmcif_p.Parse();
+ ch = eh.FindChain("A");
+ BOOST_CHECK(ch.IsValid());
+ BOOST_CHECK(ch.GetType() == mol::CHAINTYPE_UNKNOWN);
+ ch = eh.FindChain("B");
+ BOOST_CHECK(ch.IsValid());
+ BOOST_CHECK(ch.GetType() == mol::CHAINTYPE_UNKNOWN);
+ }
+ BOOST_MESSAGE(" done.");
+ BOOST_MESSAGE(" fetch details...");
+ {
+ mol::EntityHandle eh = mol::CreateEntity();
+ MMCifReader mmcif_p("testfiles/mmcif/atom_site.mmcif", eh, profile);
+ mmcif_p.Parse();
+ ch = eh.FindChain("A");
+ BOOST_CHECK(ch.IsValid());
+ BOOST_CHECK(ch.GetDescription() == "Very important information.");
+ }
+ BOOST_MESSAGE(" done.");
+
+ BOOST_MESSAGE(" done.");
+}
+
+BOOST_AUTO_TEST_CASE(mmcif_entity_poly_tests)
+{
+ conop::Conopology::Instance().SetDefaultBuilder("RBB");
+ BOOST_MESSAGE(" Running mmcif_entity_poly_tests...");
+ mol::ChainHandle ch;
+ IOProfile profile;
+ StarLoopDesc tmmcif_h;
+
+ mol::EntityHandle eh = mol::CreateEntity();
+ MMCifReader mmcif_p("testfiles/mmcif/atom_site.mmcif", eh, profile);
+
+ mmcif_p.SetReadSeqRes(true);
+ mmcif_p.Parse();
+
+ seq::SequenceList seqres = mmcif_p.GetSeqRes();
+ seq::SequenceHandle curr = seqres.FindSequence("A");
+ BOOST_CHECK(curr.GetString() == "VTI");
+
+ BOOST_MESSAGE(" testing missing corresponding entity entry...");
+ {
+ mol::EntityHandle eh = mol::CreateEntity();
+ std::vector<StringRef> columns;
+ TestMMCifReaderProtected tmmcif_p("testfiles/mmcif/atom_site.mmcif", eh);
+
+ tmmcif_h.SetCategory(StringRef("entity_poly", 11));
+ tmmcif_h.Add(StringRef("entity_id", 9));
+ tmmcif_p.OnBeginLoop(tmmcif_h);
+
+ columns.push_back(StringRef("1", 1));
+ BOOST_CHECK_THROW(tmmcif_p.ParseEntityPoly(columns), IOException);
+ }
+ BOOST_MESSAGE(" done.");
+ BOOST_MESSAGE(" testing type recognition...");
+ {
+ TestMMCifReaderProtected tmmcif_p("testfiles/mmcif/atom_site.mmcif", eh);
+ std::vector<StringRef> columns;
+
+ // create corresponding entity entry
+ tmmcif_h.Clear();
+ tmmcif_h.SetCategory(StringRef("entity", 6));
+ tmmcif_h.Add(StringRef("id", 2));
+ tmmcif_h.Add(StringRef("type", 4));
+ tmmcif_p.OnBeginLoop(tmmcif_h);
+ columns.push_back(StringRef("1", 1));
+ columns.push_back(StringRef("polymer", 7));
+ tmmcif_p.ParseEntity(columns);
+ columns.pop_back();
+ columns.pop_back();
+
+ // build dummy entity_poly header
+ tmmcif_h.Clear();
+ tmmcif_h.SetCategory(StringRef("entity_poly", 11));
+ tmmcif_h.Add(StringRef("entity_id", 9));
+ tmmcif_h.Add(StringRef("type", 4));
+ tmmcif_p.OnBeginLoop(tmmcif_h);
+
+ columns.push_back(StringRef("1", 1));
+ columns.push_back(StringRef("polypeptide(D)", 14));
+ BOOST_CHECK_NO_THROW(tmmcif_p.ParseEntityPoly(columns));
+ columns.pop_back();
+ columns.push_back(StringRef("polypeptide(L)", 14));
+ BOOST_CHECK_NO_THROW(tmmcif_p.ParseEntityPoly(columns));
+ columns.pop_back();
+ columns.push_back(StringRef("polydeoxyribonucleotide", 23));
+ BOOST_CHECK_NO_THROW(tmmcif_p.ParseEntityPoly(columns));
+ columns.pop_back();
+ columns.push_back(StringRef("polyribonucleotide", 18));
+ BOOST_CHECK_NO_THROW(tmmcif_p.ParseEntityPoly(columns));
+ columns.pop_back();
+ columns.push_back(StringRef("polysaccharide(D)", 17));
+ BOOST_CHECK_NO_THROW(tmmcif_p.ParseEntityPoly(columns));
+ columns.pop_back();
+ columns.push_back(StringRef("polysaccharide(L)", 17));
+ BOOST_CHECK_NO_THROW(tmmcif_p.ParseEntityPoly(columns));
+ columns.pop_back();
+columns.push_back(StringRef("polydeoxyribonucleotide/polyribonucleotide hybrid",
+ 49));
+ BOOST_CHECK_NO_THROW(tmmcif_p.ParseEntityPoly(columns));
+ columns.pop_back();
+ columns.push_back(StringRef("other", 5));
+ BOOST_CHECK_NO_THROW(tmmcif_p.ParseEntityPoly(columns));
+ columns.pop_back();
+ columns.pop_back();
+ columns.push_back(StringRef("badbadprion", 11));
+ BOOST_CHECK_THROW(tmmcif_p.ParseEntityPoly(columns), IOException);
+ columns.pop_back();
+ }
+ BOOST_MESSAGE(" done.");
+ BOOST_MESSAGE(" testing pdbx_seq_one_letter_code reading...");
+ {
+ TestMMCifReaderProtected tmmcif_p("testfiles/mmcif/atom_site.mmcif", eh);
+ std::vector<StringRef> columns;
+
+ tmmcif_h.Clear();
+ tmmcif_h.SetCategory(StringRef("entity", 6));
+ tmmcif_h.Add(StringRef("id", 2));
+ tmmcif_h.Add(StringRef("type", 4));
+ tmmcif_p.OnBeginLoop(tmmcif_h);
+ columns.push_back(StringRef("1", 1));
+ columns.push_back(StringRef("polymer", 7));
+ tmmcif_p.ParseEntity(columns);
+ columns.pop_back();
+ columns.pop_back();
+
+ tmmcif_h.Clear();
+ tmmcif_h.SetCategory(StringRef("entity_poly", 11));
+ tmmcif_h.Add(StringRef("entity_id", 9));
+ tmmcif_h.Add(StringRef("type", 4));
+ tmmcif_h.Add(StringRef("pdbx_seq_one_letter_code", 24));
+ tmmcif_p.OnBeginLoop(tmmcif_h);
+
+ columns.push_back(StringRef("1", 1));
+ columns.push_back(StringRef("other", 5));
+ columns.push_back(StringRef("ABRND", 5));
+ tmmcif_p.SetReadSeqRes(true);
+ tmmcif_p.SetReadCanonicalSeqRes(true);
+ BOOST_CHECK_THROW(tmmcif_p.ParseEntityPoly(columns), IOException);
+ tmmcif_p.SetReadCanonicalSeqRes(false);
+ BOOST_CHECK_NO_THROW(tmmcif_p.ParseEntityPoly(columns));
+ BOOST_CHECK_THROW(tmmcif_p.ParseEntityPoly(columns), IOException);
+ }
+ BOOST_MESSAGE(" done.");
+ BOOST_MESSAGE(" testing pdbx_seq_one_letter_code_can reading...");
+ {
+ TestMMCifReaderProtected tmmcif_p("testfiles/mmcif/atom_site.mmcif", eh);
+ std::vector<StringRef> columns;
+
+ tmmcif_h.Clear();
+ tmmcif_h.SetCategory(StringRef("entity", 6));
+ tmmcif_h.Add(StringRef("id", 2));
+ tmmcif_h.Add(StringRef("type", 4));
+ tmmcif_p.OnBeginLoop(tmmcif_h);
+ columns.push_back(StringRef("1", 1));
+ columns.push_back(StringRef("polymer", 7));
+ tmmcif_p.ParseEntity(columns);
+ columns.pop_back();
+ columns.pop_back();
+
+ tmmcif_h.Clear();
+ tmmcif_h.SetCategory(StringRef("entity_poly", 11));
+ tmmcif_h.Add(StringRef("entity_id", 9));
+ tmmcif_h.Add(StringRef("type", 4));
+ tmmcif_h.Add(StringRef("pdbx_seq_one_letter_code_can", 28));
+ tmmcif_p.OnBeginLoop(tmmcif_h);
+ tmmcif_p.SetReadCanonicalSeqRes(false);
+ columns.push_back(StringRef("1", 1));
+ columns.push_back(StringRef("other", 5));
+ columns.push_back(StringRef("ABRND", 5));
+ tmmcif_p.SetReadSeqRes(true);
+ BOOST_CHECK_THROW(tmmcif_p.ParseEntityPoly(columns), IOException);
+ tmmcif_p.SetReadCanonicalSeqRes(true);
+ BOOST_CHECK_NO_THROW(tmmcif_p.ParseEntityPoly(columns));
+ BOOST_CHECK_THROW(tmmcif_p.ParseEntityPoly(columns), IOException);
+ }
+ BOOST_MESSAGE(" done.");
+
+ BOOST_MESSAGE(" done.");
+ conop::Conopology::Instance().SetDefaultBuilder("HEURISTIC");
+}
+
+BOOST_AUTO_TEST_CASE(mmcif_citation_tests)
+{
+ BOOST_MESSAGE(" Running mmcif_citation_tests...");
+ //build dummy citation
+ mol::EntityHandle eh;
+ TestMMCifReaderProtected tmmcif_p("testfiles/mmcif/atom_site.mmcif", eh);
+ StarLoopDesc tmmcif_h;
+ std::vector<StringRef> columns;
+
+ tmmcif_h.SetCategory(StringRef("citation", 8));
+ tmmcif_h.Add(StringRef("id", 2));
+ tmmcif_h.Add(StringRef("book_title", 10));
+ tmmcif_h.Add(StringRef("journal_abbrev", 14));
+ tmmcif_p.OnBeginLoop(tmmcif_h);
+
+ columns.push_back(StringRef("Foo", 3));
+ columns.push_back(StringRef("The Guide", 9));
+ columns.push_back(StringRef(".", 1));
+
+ BOOST_CHECK_NO_THROW(tmmcif_p.ParseCitation(columns));
+
+ columns.pop_back();
+ columns.pop_back();
+ columns.push_back(StringRef(".", 1));
+ columns.push_back(StringRef("Hitch", 5));
+
+ BOOST_CHECK_NO_THROW(tmmcif_p.ParseCitation(columns));
+
+ columns.pop_back();
+ columns.pop_back();
+ columns.push_back(StringRef("The Guide", 9));
+ columns.push_back(StringRef("Hitch", 5));
+
+ BOOST_CHECK_THROW(tmmcif_p.ParseCitation(columns), IOException);
+
+ BOOST_MESSAGE(" done.");
+}
+
+BOOST_AUTO_TEST_CASE(mmcif_citation_author_tests)
+{
+ BOOST_MESSAGE(" Running mmcif_citation_author_tests...");
+
+ mol::EntityHandle eh = mol::CreateEntity();
+ std::ifstream s("testfiles/mmcif/atom_site.mmcif");
+ IOProfile profile;
+ MMCifReader mmcif_p(s, eh, profile);
+ BOOST_CHECK_NO_THROW(mmcif_p.Parse());
+
+ std::vector<String> authors =
+ mmcif_p.GetInfo().GetCitations().back().GetAuthorList();
+
+ BOOST_CHECK(authors.size() == 3);
+ BOOST_CHECK(authors[0] == "Whiskers, P.D.");
+ BOOST_CHECK(authors[1] == "McCheese, B.M.");
+ BOOST_CHECK(authors[2] == "Van Hummel, J.F.");
+
+ BOOST_MESSAGE(" done.");
+}
+
+BOOST_AUTO_TEST_CASE(mmcif_struct_ref)
+{
+ mol::EntityHandle eh = mol::CreateEntity();
+ std::ifstream s("testfiles/mmcif/struct_ref.cif");
+ IOProfile profile;
+ MMCifReader mmcif_p(s, eh, profile);
+ mmcif_p.Parse();
+ MMCifInfoStructRefs refs=mmcif_p.GetInfo().GetStructRefs();
+ BOOST_CHECK_EQUAL(refs.size(), 1);
+ MMCifInfoStructRefPtr sr1=refs[0];
+ BOOST_CHECK_EQUAL(sr1->GetDBName(), "UNP");
+ BOOST_CHECK_EQUAL(sr1->GetDBID(), "BLA2_BACCE");
+ BOOST_CHECK_EQUAL(sr1->GetDBAccess(), "P04190");
+ BOOST_CHECK_EQUAL(sr1->GetID(), "1");
+ MMCifInfoStructRefSeqs seqs=sr1->GetAlignedSeqs();
+ BOOST_CHECK_EQUAL(seqs.size(), 2);
+ BOOST_CHECK_EQUAL(seqs[0]->GetID(), "1");
+ BOOST_CHECK_EQUAL(seqs[0]->GetChainName(), "A");
+ BOOST_CHECK_EQUAL(seqs[0]->GetSeqBegin(), 1);
+ BOOST_CHECK_EQUAL(seqs[0]->GetSeqEnd(), 19);
+ BOOST_CHECK_EQUAL(seqs[0]->GetDBBegin(), 31);
+ BOOST_CHECK_EQUAL(seqs[0]->GetDBEnd(), 49);
+ BOOST_CHECK_EQUAL(seqs[1]->GetID(), "13");
+ BOOST_CHECK_EQUAL(seqs[1]->GetChainName(), "B");
+ BOOST_CHECK_EQUAL(seqs[1]->GetSeqBegin(), 1);
+ BOOST_CHECK_EQUAL(seqs[1]->GetSeqEnd(), 19);
+ BOOST_CHECK_EQUAL(seqs[1]->GetDBBegin(), 31);
+ BOOST_CHECK_EQUAL(seqs[1]->GetDBEnd(), 49);
+ MMCifInfoStructRefSeqDifs diffs=seqs[0]->GetDifs();
+ BOOST_CHECK_EQUAL(diffs.size(), 1);
+ BOOST_CHECK_EQUAL(diffs[0]->GetSeqRNum(), 91);
+ BOOST_CHECK_EQUAL(diffs[0]->GetDetails(), "ENGINEERED MUTATION");
+}
+
+BOOST_AUTO_TEST_CASE(mmcif_refine_tests)
+{
+ BOOST_MESSAGE(" Running mmcif_refine_tests...");
+ BOOST_MESSAGE(" positive test...");
+ {
+ mol::EntityHandle eh = mol::CreateEntity();
+ std::ifstream s("testfiles/mmcif/atom_site.mmcif");
+ IOProfile profile;
+ MMCifReader mmcif_p(s, eh, profile);
+ BOOST_CHECK_NO_THROW(mmcif_p.Parse());
+ BOOST_CHECK_CLOSE(mmcif_p.GetInfo().GetResolution(), 2.0f, 0.001f);
+ }
+ BOOST_MESSAGE(" done.");
+ BOOST_MESSAGE(" capturing fishy data lines...");
+ {
+ mol::EntityHandle eh;
+ TestMMCifReaderProtected tmmcif_p("testfiles/mmcif/atom_site.mmcif", eh);
+ StarLoopDesc tmmcif_h;
+ std::vector<StringRef> columns;
+
+ tmmcif_h.SetCategory(StringRef("refine", 6));
+ tmmcif_h.Add(StringRef("entry_id", 8));
+ tmmcif_h.Add(StringRef("ls_d_res_high", 13));
+ tmmcif_h.Add(StringRef("ls_d_res_low", 12));
+ tmmcif_p.OnBeginLoop(tmmcif_h);
+
+ columns.push_back(StringRef("1Foo", 4));
+ columns.push_back(StringRef("Foo", 3));
+ columns.push_back(StringRef("1", 1));
+
+ BOOST_CHECK_THROW(tmmcif_p.ParseRefine(columns), IOException);
+ }
+ BOOST_MESSAGE(" done.");
+ BOOST_MESSAGE(" done.");
+}
+
+BOOST_AUTO_TEST_CASE(mmcif_biounit_tests)
+{
+ BOOST_MESSAGE(" Running mmcif_biounit_tests...");
+ //build dummy biounit
+ mol::EntityHandle eh = mol::CreateEntity();
+ TestMMCifReaderProtected tmmcif_p("testfiles/mmcif/atom_site.mmcif", eh);
+ StarLoopDesc tmmcif_h;
+ std::vector<StringRef> columns;
+
+ tmmcif_h.SetCategory(StringRef("pdbx_struct_assembly_gen", 24));
+ tmmcif_h.Add(StringRef("assembly_id", 11));
+ tmmcif_h.Add(StringRef("asym_id_list", 12));
+ tmmcif_h.Add(StringRef("oper_expression", 15));
+ tmmcif_p.OnBeginLoop(tmmcif_h);
+
+ columns.push_back(StringRef("1", 1));
+ columns.push_back(StringRef("A", 1));
+ columns.push_back(StringRef("1", 1));
+
+ BOOST_CHECK_NO_THROW(tmmcif_p.ParsePdbxStructAssemblyGen(columns));
+ BOOST_CHECK_THROW(tmmcif_p.OnEndData(), IOException);
+
+ tmmcif_h.Clear();
+ tmmcif_h.SetCategory(StringRef("pdbx_struct_assembly", 20));
+ tmmcif_h.Add(StringRef("id", 2));
+ columns.pop_back();
+ columns.pop_back();
+ columns.pop_back();
+ columns.push_back(StringRef("1", 1));
+ tmmcif_p.OnBeginLoop(tmmcif_h);
+ tmmcif_p.ParsePdbxStructAssembly(columns);
+
+ tmmcif_h.Clear();
+ tmmcif_h.SetCategory(StringRef("pdbx_struct_assembly_gen", 24));
+ tmmcif_h.Add(StringRef("assembly_id", 11));
+ tmmcif_h.Add(StringRef("asym_id_list", 12));
+ tmmcif_h.Add(StringRef("oper_expression", 15));
+ tmmcif_p.OnBeginLoop(tmmcif_h);
+
+ columns.pop_back();
+ columns.push_back(StringRef("1", 1));
+ columns.push_back(StringRef("A", 1));
+ columns.push_back(StringRef("1", 1));
+
+ BOOST_CHECK_NO_THROW(tmmcif_p.ParsePdbxStructAssemblyGen(columns));
+ BOOST_CHECK_THROW(tmmcif_p.OnEndData(), IOException);
+
+ tmmcif_h.Clear();
+ tmmcif_h.SetCategory(StringRef("pdbx_struct_assembly_gen", 24));
+ tmmcif_h.Add(StringRef("assembly_id", 11));
+ tmmcif_h.Add(StringRef("asym_id_list", 12));
+ tmmcif_h.Add(StringRef("oper_expression", 15));
+ tmmcif_p.OnBeginLoop(tmmcif_h);
+
+ columns.pop_back();
+ columns.push_back(StringRef("1-Z", 3));
+ BOOST_CHECK_THROW(tmmcif_p.ParsePdbxStructAssemblyGen(columns), IOException);
+
+ columns.pop_back();
+ columns.push_back(StringRef("--", 3));
+ BOOST_CHECK_THROW(tmmcif_p.ParsePdbxStructAssemblyGen(columns), IOException);
+
+ columns.pop_back();
+ columns.push_back(StringRef("A-3", 3));
+ BOOST_CHECK_THROW(tmmcif_p.ParsePdbxStructAssemblyGen(columns), IOException);
+
+ tmmcif_h.Clear();
+ tmmcif_h.SetCategory(StringRef("pdbx_struct_oper_list", 21));
+ tmmcif_h.Add(StringRef("id", 2));
+ tmmcif_h.Add(StringRef("type", 4));
+ tmmcif_h.Add(StringRef("vector[1]", 9));
+ tmmcif_h.Add(StringRef("vector[2]", 9));
+ tmmcif_h.Add(StringRef("vector[3]", 9));
+ tmmcif_h.Add(StringRef("matrix[1][1]", 12));
+ tmmcif_h.Add(StringRef("matrix[1][2]", 12));
+ tmmcif_h.Add(StringRef("matrix[1][3]", 12));
+ tmmcif_h.Add(StringRef("matrix[2][1]", 12));
+ tmmcif_h.Add(StringRef("matrix[2][2]", 12));
+ tmmcif_h.Add(StringRef("matrix[2][3]", 12));
+ tmmcif_h.Add(StringRef("matrix[3][1]", 12));
+ tmmcif_h.Add(StringRef("matrix[3][2]", 12));
+ tmmcif_h.Add(StringRef("matrix[3][3]", 12));
+
+ tmmcif_p.OnBeginLoop(tmmcif_h);
+
+ columns.pop_back();
+ columns.pop_back();
+ columns.pop_back();
+ columns.push_back(StringRef("1", 1));
+ columns.push_back(StringRef("Nan", 3));
+ columns.push_back(StringRef("1", 1));
+ columns.push_back(StringRef("A", 1));
+ columns.push_back(StringRef("3", 1));
+ BOOST_CHECK_THROW(tmmcif_p.ParsePdbxStructOperList(columns), IOException);
+
+ columns.pop_back();
+ columns.pop_back();
+ columns.pop_back();
+ columns.pop_back();
+ columns.pop_back();
+ columns.push_back(StringRef("1", 1));
+ columns.push_back(StringRef("Nan", 3));
+ columns.push_back(StringRef("1", 1));
+ columns.push_back(StringRef("2", 1));
+ columns.push_back(StringRef("3", 1));
+ columns.push_back(StringRef("1", 1));
+ columns.push_back(StringRef("2", 1));
+ columns.push_back(StringRef("3", 1));
+ columns.push_back(StringRef("1", 1));
+ columns.push_back(StringRef("2", 1));
+ columns.push_back(StringRef("3", 1));
+ columns.push_back(StringRef("1", 1));
+ columns.push_back(StringRef("A", 1));
+ columns.push_back(StringRef("3", 1));
+ BOOST_CHECK_THROW(tmmcif_p.ParsePdbxStructOperList(columns), IOException);
+
+ BOOST_MESSAGE(" done.");
+}
+
+BOOST_AUTO_TEST_CASE(mmcif_struct_tests)
+{
+ BOOST_MESSAGE(" Running mmcif_struct_tests...");
+
+ mol::EntityHandle eh = mol::CreateEntity();
+ TestMMCifReaderProtected tmmcif_p("testfiles/mmcif/atom_site.mmcif", eh);
+ StarLoopDesc tmmcif_h;
+ std::vector<StringRef> columns;
+
+ tmmcif_h.SetCategory(StringRef("struct", 6));
+ tmmcif_h.Add(StringRef("entry_id", 8));
+ tmmcif_h.Add(StringRef("pdbx_CASP_flag", 14));
+ tmmcif_h.Add(StringRef("pdbx_model_details", 18));
+ tmmcif_h.Add(StringRef("pdbx_model_type_details", 23));
+ tmmcif_h.Add(StringRef("pdbx_formula_weight", 19));
+ tmmcif_p.OnBeginLoop(tmmcif_h);
+
+ columns.push_back(StringRef("1BAR", 4));
+ columns.push_back(StringRef("?", 1));
+ columns.push_back(StringRef("?", 1));
+ columns.push_back(StringRef("?", 1));
+ columns.push_back(StringRef("1.0", 3));
+ BOOST_CHECK_NO_THROW(tmmcif_p.ParseStruct(columns));
+
+ MMCifInfoStructDetails sd = MMCifInfoStructDetails();
+ sd = tmmcif_p.GetInfo().GetStructDetails();
+
+ BOOST_CHECK(sd.GetCASPFlag() == '\0');
+ BOOST_CHECK(sd.GetModelDetails() == "");
+ BOOST_CHECK(sd.GetModelTypeDetails() == "");
+
+ columns.pop_back();
+ columns.push_back(StringRef("A", 1));
+ BOOST_CHECK_THROW(tmmcif_p.ParseStruct(columns), IOException);
+
+ BOOST_MESSAGE(" done.");
+}
+
+BOOST_AUTO_TEST_CASE(mmcif_struct_conf_tests)
+{
+ BOOST_MESSAGE(" Running mmcif_struct_conf_tests...");
+ mol::EntityHandle eh = mol::CreateEntity();
+ TestMMCifReaderProtected tmmcif_p("testfiles/mmcif/atom_site.mmcif", eh);
+
+ BOOST_MESSAGE(" testing type validation");
+ StringRef type = StringRef("HELX_P", 6);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifReaderProtected::MMCIF_HELIX);
+ type = StringRef("HELX_OT_P", 9);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifReaderProtected::MMCIF_HELIX);
+ type = StringRef("HELX_RH_P", 9);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifReaderProtected::MMCIF_HELIX);
+ type = StringRef("HELX_RH_OT_P", 12);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifReaderProtected::MMCIF_HELIX);
+ type = StringRef("HELX_RH_AL_P", 12);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifReaderProtected::MMCIF_HELIX);
+ type = StringRef("HELX_RH_GA_P", 12);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifReaderProtected::MMCIF_HELIX);
+ type = StringRef("HELX_RH_OM_P", 12);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifReaderProtected::MMCIF_HELIX);
+ type = StringRef("HELX_RH_PI_P", 12);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifReaderProtected::MMCIF_HELIX);
+ type = StringRef("HELX_RH_27_P", 12);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifReaderProtected::MMCIF_HELIX);
+ type = StringRef("HELX_RH_3T_P", 12);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifReaderProtected::MMCIF_HELIX);
+ type = StringRef("HELX_RH_PP_P", 12);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifReaderProtected::MMCIF_HELIX);
+ type = StringRef("HELX_LH_P", 9);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifReaderProtected::MMCIF_HELIX);
+ type = StringRef("HELX_LH_OT_P", 12);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifReaderProtected::MMCIF_HELIX);
+ type = StringRef("HELX_LH_AL_P", 12);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifReaderProtected::MMCIF_HELIX);
+ type = StringRef("HELX_LH_GA_P", 12);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifReaderProtected::MMCIF_HELIX);
+ type = StringRef("HELX_LH_OM_P", 12);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifReaderProtected::MMCIF_HELIX);
+ type = StringRef("HELX_LH_PI_P", 12);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifReaderProtected::MMCIF_HELIX);
+ type = StringRef("HELX_LH_27_P", 12);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifReaderProtected::MMCIF_HELIX);
+ type = StringRef("HELX_LH_3T_P", 12);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifReaderProtected::MMCIF_HELIX);
+ type = StringRef("HELX_LH_PP_P", 12);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifReaderProtected::MMCIF_HELIX);
+ type = StringRef("HELX_N", 6);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifReaderProtected::MMCIF_HELIX);
+ type = StringRef("HELX_OT_N", 9);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifReaderProtected::MMCIF_HELIX);
+ type = StringRef("HELX_RH_N", 9);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifReaderProtected::MMCIF_HELIX);
+ type = StringRef("HELX_RH_OT_N", 12);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifReaderProtected::MMCIF_HELIX);
+ type = StringRef("HELX_RH_A_N", 11);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifReaderProtected::MMCIF_HELIX);
+ type = StringRef("HELX_RH_B_N", 11);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifReaderProtected::MMCIF_HELIX);
+ type = StringRef("HELX_RH_Z_N", 11);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifReaderProtected::MMCIF_HELIX);
+ type = StringRef("HELX_LH_N", 9);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifReaderProtected::MMCIF_HELIX);
+ type = StringRef("HELX_LH_OT_N", 12);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifReaderProtected::MMCIF_HELIX);
+ type = StringRef("HELX_LH_A_N", 11);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifReaderProtected::MMCIF_HELIX);
+ type = StringRef("HELX_LH_B_N", 11);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifReaderProtected::MMCIF_HELIX);
+ type = StringRef("HELX_LH_Z_N", 11);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifReaderProtected::MMCIF_HELIX);
+ type = StringRef("TURN_P", 6);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifReaderProtected::MMCIF_TURN);
+ type = StringRef("TURN_OT_P", 9);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifReaderProtected::MMCIF_TURN);
+ type = StringRef("TURN_TY1_P", 10);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifReaderProtected::MMCIF_TURN);
+ type = StringRef("TURN_TY1P_P", 11);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifReaderProtected::MMCIF_TURN);
+ type = StringRef("TURN_TY2_P", 10);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifReaderProtected::MMCIF_TURN);
+ type = StringRef("TURN_TY2P_P", 11);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifReaderProtected::MMCIF_TURN);
+ type = StringRef("TURN_TY3_P", 10);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifReaderProtected::MMCIF_TURN);
+ type = StringRef("TURN_TY3P_P", 11);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifReaderProtected::MMCIF_TURN);
+ type = StringRef("STRN", 4);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifReaderProtected::MMCIF_STRAND);
+ type = StringRef("Foo", 3);
+ BOOST_CHECK_THROW(tmmcif_p.DetermineSecStructType(type), IOException);
+
+ BOOST_MESSAGE(" done.");
+
+ BOOST_MESSAGE(" testing auth_chain_id switch...");
+ StarLoopDesc tmmcif_h;
+ {
+ std::vector<StringRef> columns;
+ tmmcif_h.SetCategory(StringRef("struct_conf", 11));
+ tmmcif_h.Add(StringRef("beg_label_asym_id", 17));
+ tmmcif_h.Add(StringRef("beg_label_comp_id", 17));
+ tmmcif_h.Add(StringRef("beg_label_seq_id", 16));
+ tmmcif_h.Add(StringRef("conf_type_id", 12));
+ tmmcif_h.Add(StringRef("end_label_asym_id", 17));
+ tmmcif_h.Add(StringRef("end_label_comp_id", 17));
+ tmmcif_h.Add(StringRef("end_label_seq_id", 16));
+ tmmcif_h.Add(StringRef("id", 2));
+ tmmcif_h.Add(StringRef("beg_auth_asym_id", 16));
+ tmmcif_p.OnBeginLoop(tmmcif_h);
+ columns.push_back(StringRef("A", 1));
+ columns.push_back(StringRef("ARG", 3));
+ columns.push_back(StringRef("1", 1));
+ columns.push_back(StringRef("HELX_RH_AL_P", 12));
+ columns.push_back(StringRef("A", 1));
+ columns.push_back(StringRef("ARG", 3));
+ columns.push_back(StringRef("2", 1));
+ columns.push_back(StringRef("DHLX1", 5));
+ columns.push_back(StringRef("A", 1));
+ tmmcif_p.SetAuthChainID(true);
+ BOOST_CHECK_NO_THROW(tmmcif_p.ParseStructConf(columns));
+ tmmcif_p.SetAuthChainID(false);
+ BOOST_CHECK_NO_THROW(tmmcif_p.ParseStructConf(columns));
+ tmmcif_h.Clear();
+ tmmcif_h.SetCategory(StringRef("struct_conf", 11));
+ tmmcif_h.Add(StringRef("beg_label_asym_id", 17));
+ tmmcif_h.Add(StringRef("beg_label_comp_id", 17));
+ tmmcif_h.Add(StringRef("beg_label_seq_id", 16));
+ tmmcif_h.Add(StringRef("conf_type_id", 12));
+ tmmcif_h.Add(StringRef("end_label_asym_id", 17));
+ tmmcif_h.Add(StringRef("end_label_comp_id", 17));
+ tmmcif_h.Add(StringRef("end_label_seq_id", 16));
+ tmmcif_h.Add(StringRef("id", 2));
+ tmmcif_p.OnBeginLoop(tmmcif_h);
+ columns.pop_back();
+ tmmcif_p.SetAuthChainID(true);
+ BOOST_CHECK_THROW(tmmcif_p.ParseStructConf(columns), IOException);
+ }
+ tmmcif_p.SetAuthChainID(false);
+ BOOST_MESSAGE(" done.");
+
+ BOOST_MESSAGE(" done.");
+}
+
+BOOST_AUTO_TEST_CASE(mmcif_struct_sheet_range_tests)
+{
+ BOOST_MESSAGE(" Running mmcif_struct_sheet_range_tests...");
+ mol::EntityHandle eh = mol::CreateEntity();
+ TestMMCifReaderProtected tmmcif_p("testfiles/mmcif/atom_site.mmcif", eh);
+
+ BOOST_MESSAGE(" testing auth_chain_id switch...");
+ StarLoopDesc tmmcif_h;
+ std::vector<StringRef> columns;
+ tmmcif_h.SetCategory(StringRef("struct_sheet_range", 18));
+ tmmcif_h.Add(StringRef("sheet_id", 8));
+ tmmcif_h.Add(StringRef("beg_label_asym_id", 17));
+ tmmcif_h.Add(StringRef("beg_label_comp_id", 17));
+ tmmcif_h.Add(StringRef("beg_label_seq_id", 16));
+ tmmcif_h.Add(StringRef("end_label_asym_id", 17));
+ tmmcif_h.Add(StringRef("end_label_comp_id", 17));
+ tmmcif_h.Add(StringRef("end_label_seq_id", 16));
+ tmmcif_h.Add(StringRef("id", 2));
+ tmmcif_h.Add(StringRef("beg_auth_asym_id", 16));
+ tmmcif_p.OnBeginLoop(tmmcif_h);
+ columns.push_back(StringRef("Sheet1", 6));
+ columns.push_back(StringRef("A", 1));
+ columns.push_back(StringRef("ARG", 3));
+ columns.push_back(StringRef("1", 1));
+ columns.push_back(StringRef("A", 1));
+ columns.push_back(StringRef("ARG", 3));
+ columns.push_back(StringRef("2", 1));
+ columns.push_back(StringRef("DSTRAND", 7));
+ columns.push_back(StringRef("A", 1));
+ tmmcif_p.SetAuthChainID(true);
+ BOOST_CHECK_NO_THROW(tmmcif_p.ParseStructSheetRange(columns));
+ tmmcif_p.SetAuthChainID(false);
+ BOOST_CHECK_NO_THROW(tmmcif_p.ParseStructSheetRange(columns));
+ tmmcif_h.Clear();
+ tmmcif_h.SetCategory(StringRef("struct_sheet_range", 11));
+ tmmcif_h.Add(StringRef("sheet_id", 8));
+ tmmcif_h.Add(StringRef("beg_label_asym_id", 17));
+ tmmcif_h.Add(StringRef("beg_label_comp_id", 17));
+ tmmcif_h.Add(StringRef("beg_label_seq_id", 16));
+ tmmcif_h.Add(StringRef("end_label_asym_id", 17));
+ tmmcif_h.Add(StringRef("end_label_comp_id", 17));
+ tmmcif_h.Add(StringRef("end_label_seq_id", 16));
+ tmmcif_h.Add(StringRef("id", 2));
+ tmmcif_p.OnBeginLoop(tmmcif_h);
+ columns.pop_back();
+ tmmcif_p.SetAuthChainID(true);
+ BOOST_CHECK_THROW(tmmcif_p.ParseStructSheetRange(columns), IOException);
+ tmmcif_p.SetAuthChainID(false);
+ BOOST_MESSAGE(" done.");
+
+
+
+ BOOST_MESSAGE(" done.");
+}
+
+BOOST_AUTO_TEST_CASE(mmcif_parseatomident)
+{
+ BOOST_MESSAGE(" Running mmcif_parseatomident tests...");
+
+ mol::EntityHandle eh = mol::CreateEntity();
+
+ std::ifstream s("testfiles/mmcif/atom_site.mmcif");
+ IOProfile profile;
+ StarLoopDesc tmmcif_h;
+ TestMMCifReaderProtected tmmcif_p(s, eh, profile);
+ std::vector<StringRef> columns;
+ String cif_chain_name;
+ String auth_chain_name;
+ StringRef res_name;
+ mol::ResNum resnum(0);
+ bool valid_res_num = false;
+ char alt_loc;
+ StringRef atom_name;
+
+ BOOST_MESSAGE(" testing valid line");
+ BOOST_MESSAGE(" done.");
+ // negative
+ //cols.push_back(StringRef("ATOM", 4));
+ //BOOST_CHECK_THROW(tmmcif_p.ParseAtomIdent(cols,
+ // chain_name,
+ // res_name,
+ // resnum,
+ // atom_name,
+ // alt_loc), IOException);
+ // positive
+ //StarLoopDesc tmmcif_h;
+ //tmmcif_h.SetCategory(StringRef("atom_site", 9));
+ // build header
+ //mmcif_h.Add(StringRef("AUTH_ASYM_ID", 12));
+ /*
+ this->TryStoreIdx(AUTH_ASYM_ID, "auth_asym_id", header);
+ this->TryStoreIdx(ID, "id", header);
+ this->TryStoreIdx(LABEL_ALT_ID, "label_alt_id", header);
+ this->TryStoreIdx(LABEL_ASYM_ID, "label_asym_id", header);
+ this->TryStoreIdx(LABEL_ATOM_ID, "label_atom_id", header);
+ this->TryStoreIdx(LABEL_COMP_ID, "label_comp_id", header);
+ this->TryStoreIdx(LABEL_ENTITY_ID, "label_entity_id", header);
+ this->TryStoreIdx(LABEL_SEQ_ID, "label_seq_id", header);
+ this->TryStoreIdx(TYPE_SYMBOL, "type_symbol", header);
+ this->TryStoreIdx(CARTN_X, "Cartn_x", header);
+ this->TryStoreIdx(CARTN_Y, "Cartn_y", header);
+ this->TryStoreIdx(CARTN_Z, "Cartn_z", header);
+*/
+
+ BOOST_MESSAGE(" testing profile to read calpha only");
+ {
+ profile.calpha_only = true;
+ // set up dummy header to pre-set indices
+ SetAtomSiteHeader(&tmmcif_h);
+ tmmcif_p.OnBeginLoop(tmmcif_h);
+ // create CA dummy line
+ columns.push_back(StringRef("A", 1));
+ columns.push_back(StringRef("2", 1));
+ columns.push_back(StringRef(".", 1));
+ columns.push_back(StringRef("A", 1));
+ columns.push_back(StringRef("CA", 2));
+ columns.push_back(StringRef("VAL", 3));
+ columns.push_back(StringRef("1", 1)); // label_entity_id
+ columns.push_back(StringRef("11", 2)); // label_seq_id
+ columns.push_back(StringRef("C", 1)); // type_symbol
+ columns.push_back(StringRef("25.369", 6)); // Cartn_x
+ columns.push_back(StringRef("30.691", 6)); // Cartn_y
+ columns.push_back(StringRef("11.795", 6)); // Cartn_z
+ BOOST_CHECK_EQUAL(tmmcif_p.ParseAtomIdent(columns, auth_chain_name,
+ cif_chain_name, res_name,
+ resnum, valid_res_num, atom_name,
+ alt_loc), true);
+ columns.pop_back();
+ columns.pop_back();
+ columns.pop_back();
+ columns.pop_back();
+ columns.pop_back();
+ columns.pop_back();
+ columns.pop_back();
+ columns.pop_back();
+ columns.push_back(StringRef("CB", 2));
+ columns.push_back(StringRef("VAL", 3));
+ columns.push_back(StringRef("1", 1)); // label_entity_id
+ columns.push_back(StringRef("11", 2)); // label_seq_id
+ columns.push_back(StringRef("C", 1)); // type_symbol
+ columns.push_back(StringRef("25.369", 6)); // Cartn_x
+ columns.push_back(StringRef("30.691", 6)); // Cartn_y
+ columns.push_back(StringRef("11.795", 6)); // Cartn_z
+ BOOST_CHECK_EQUAL(tmmcif_p.ParseAtomIdent(columns, auth_chain_name,
+ cif_chain_name, res_name,
+ resnum, valid_res_num, atom_name,
+ alt_loc), false);
+ }
+ BOOST_MESSAGE(" done.");
+
+ BOOST_MESSAGE(" done.");
+}
+
+/*
+BOOST_AUTO_TEST_CASE(mmcif_parseandaddatom)
+{
+ mol::EntityHandle eh = mol::CreateEntity();
+
+ BOOST_MESSAGE(" Running mmcif_parseandaddatom tests...");
+ std::ifstream s("testfiles/mmcif/atom_site.mmcif");
+ TestMMCifReaderProtected tmmcif_p(s, eh, IOProfile());
+ std::vector<StringRef> cols;
+
+ //BOOST_MESSAGE(" testing short atom_site entry");
+ //cols.push_back(StringRef("ATOM", 4));
+ //BOOST_CHECK_THROW(tmmcif_p.ParseAndAddAtom(cols), IOException);
+ //BOOST_MESSAGE(" done.");
+}
+*/
+
+BOOST_AUTO_TEST_CASE(mmcif_testreader)
+{
+ BOOST_MESSAGE(" Running mmcif_testreader tests...");
+ mol::EntityHandle eh = mol::CreateEntity();
+ std::ifstream s("testfiles/mmcif/atom_site.mmcif");
+ IOProfile profile;
+ MMCifReader mmcif_p(s, eh, profile);
+
+ mmcif_p.SetRestrictChains("A O C");
+
+ BOOST_MESSAGE(" testing Parse()...");
+ BOOST_CHECK_NO_THROW(mmcif_p.Parse());
+
+ BOOST_REQUIRE_EQUAL(eh.GetChainCount(), 3);
+ BOOST_REQUIRE_EQUAL(eh.GetResidueCount(), 14);
+ BOOST_REQUIRE_EQUAL(eh.GetAtomCount(), 35);
+
+ mol::ChainHandle ch = eh.FindChain("A");
+ BOOST_CHECK(ch.IsValid());
+ BOOST_MESSAGE(" done.");
+
+ BOOST_MESSAGE(" testing numbering water...");
+ ch = eh.FindChain("O");
+ BOOST_CHECK(ch.IsValid());
+ mol::ResidueHandleList rl = ch.GetResidueList();
+ mol::ResidueHandleList::const_iterator rs;
+ int i = 1;
+ for (rs = rl.begin(); rs != rl.end(); ++rs, ++i) {
+ BOOST_CHECK_EQUAL(rs->GetNumber().GetNum(), i);
+ }
+ BOOST_MESSAGE(" done.");
+
+ BOOST_MESSAGE(" testing secondary structure...");
+ // pick chains, iterate residues, check for correct sec.struct.
+ ch = eh.FindChain("A");
+ rl = ch.GetResidueList();
+ BOOST_CHECK_EQUAL(rl[0].GetSecStructure().IsHelical(), true);
+ BOOST_CHECK_EQUAL(rl[1].GetSecStructure().IsHelical(), true);
+ BOOST_CHECK_EQUAL(rl[2].GetSecStructure().IsExtended(), true);
+ ch = eh.FindChain("C");
+ rl = ch.GetResidueList();
+ BOOST_CHECK_EQUAL(rl[0].GetSecStructure().IsExtended(), true);
+ BOOST_MESSAGE(" done.");
+
+ BOOST_MESSAGE(" reading data fields which should not fail...");
+ BOOST_CHECK(mmcif_p.GetInfo().GetMethod().str() == "Deep-fry");
+ BOOST_CHECK(mmcif_p.GetInfo().GetBioUnits().back().GetDetails() ==
+ "author_defined_assembly");
+ BOOST_CHECK(mmcif_p.GetInfo().GetBioUnits().back().GetChainList().back() ==
+ "F");
+ MMCifInfoBioUnit bu = mmcif_p.GetInfo().GetBioUnits().back();
+ BOOST_CHECK(bu.GetOperations().back().back()->GetType() ==
+ "identity operation");
+ MMCifInfoStructDetails sd = mmcif_p.GetInfo().GetStructDetails();
+ BOOST_CHECK(sd.GetEntryID() == "1BAR");
+ BOOST_CHECK(sd.GetTitle() == "A Title");
+ BOOST_CHECK(sd.GetCASPFlag() == 'Y');
+ BOOST_CHECK(sd.GetDescriptor() == "ADENYLATE KINASE");
+ BOOST_CHECK_CLOSE(sd.GetMass(), 1.0f, 0.001f);
+ BOOST_CHECK(sd.GetMassMethod() == "Good Guess");
+ BOOST_CHECK(sd.GetModelDetails() == "Even better guessing");
+ BOOST_CHECK(sd.GetModelTypeDetails() == "Guess");
+ MMCifInfoObsolete obs = mmcif_p.GetInfo().GetObsoleteInfo();
+ BOOST_CHECK(obs.GetDate() == "2011-08-31");
+ BOOST_CHECK(obs.GetID() == "Obsolete");
+ BOOST_CHECK(obs.GetPDBID() == "1FOO");
+ BOOST_CHECK(obs.GetReplacedPDBID() == "2BAR");
+ BOOST_MESSAGE(" done.");
+
+ BOOST_MESSAGE(" done.");
+}
+
+BOOST_AUTO_TEST_SUITE_END();
diff --git a/modules/io/tests/testfiles/mmcif/3T6C.cif.gz b/modules/io/tests/testfiles/mmcif/3T6C.cif.gz
new file mode 100644
index 0000000000000000000000000000000000000000..afda31f696dd24fcbecee1d652b7431b93d5dca4
Binary files /dev/null and b/modules/io/tests/testfiles/mmcif/3T6C.cif.gz differ
diff --git a/modules/io/tests/testfiles/mmcif/atom_site.mmcif b/modules/io/tests/testfiles/mmcif/atom_site.mmcif
new file mode 100644
index 0000000000000000000000000000000000000000..ce890cf9d3be305019cbc431726433df8a06beee
--- /dev/null
+++ b/modules/io/tests/testfiles/mmcif/atom_site.mmcif
@@ -0,0 +1,195 @@
+data_1BAR
+
+# this file is also used in the mmcif_parse_models tests for a true negative
+# test, hence it is not allowed to carry atom_site.pdbx_PDB_model_num entries
+
+# this file is also used in the mmcif_mmcif_chaintype_setting test for a true
+# positive test, hence the entity category is not to be changed
+
+_pdbx_database_PDB_obs_spr.id OBSLTE
+_pdbx_database_PDB_obs_spr.date 2011-08-31
+_pdbx_database_PDB_obs_spr.pdb_id 1FOO
+_pdbx_database_PDB_obs_spr.replace_pdb_id 2BAR
+
+loop_
+_entity.id
+_entity.type
+_entity.pdbx_description
+1 polymer
+; Very important information.
+;
+5 water .
+
+_entity_poly.entity_id 1
+_entity_poly.type 'polypeptide(L)'
+_entity_poly.nstd_linkage no
+_entity_poly.nstd_monomer no
+_entity_poly.pdbx_seq_one_letter_code 'VTI'
+
+loop_
+_citation.id
+_citation.abstract_id_CAS
+_citation.title
+_citation.journal_volume
+_citation.journal_full
+_citation.page_first
+_citation.page_last
+_citation.pdbx_database_id_DOI
+_citation.pdbx_database_id_PubMed
+_citation.year
+primary 58-08-2 'Very important, but we won't tell' 1 'Some Journal' 0 10 0815 0815 2011
+
+# the authors are not ordered on purpose for unit tests
+loop_
+_citation_author.citation_id
+_citation_author.ordinal
+_citation_author.name
+ primary 1 'Whiskers, P.D.'
+ primary 3 'Van Hummel, J.F.'
+ primary 2 'McCheese, B.M.'
+
+_exptl.entry_id experiment1
+_exptl.method 'Deep-fry'
+
+_refine.entry_id '1BAR'
+_refine.ls_d_res_high 2.0
+_refine.ls_d_res_low 1.5
+
+# biounit begin
+loop_
+_pdbx_struct_assembly.id
+_pdbx_struct_assembly.details
+_pdbx_struct_assembly.method_details
+_pdbx_struct_assembly.oligomeric_details
+_pdbx_struct_assembly.oligomeric_count
+1 author_defined_assembly ? monomeric 1
+2 author_defined_assembly ? monomeric 1
+
+loop_
+_pdbx_struct_assembly_gen.assembly_id
+_pdbx_struct_assembly_gen.oper_expression
+_pdbx_struct_assembly_gen.asym_id_list
+1 1 A,C,E
+2 1 B,D,F
+
+_pdbx_struct_oper_list.id 1
+_pdbx_struct_oper_list.type 'identity operation'
+_pdbx_struct_oper_list.name 1_555
+_pdbx_struct_oper_list.symmetry_operation x,y,z
+_pdbx_struct_oper_list.matrix[1][1] 1.0000000000
+_pdbx_struct_oper_list.matrix[1][2] 0.0000000000
+_pdbx_struct_oper_list.matrix[1][3] 0.0000000000
+_pdbx_struct_oper_list.vector[1] 1.1000000000
+_pdbx_struct_oper_list.matrix[2][1] 0.0000000000
+_pdbx_struct_oper_list.matrix[2][2] 1.0000000000
+_pdbx_struct_oper_list.matrix[2][3] 0.0000000000
+_pdbx_struct_oper_list.vector[2] 0.5000000000
+_pdbx_struct_oper_list.matrix[3][1] 0.0000000000
+_pdbx_struct_oper_list.matrix[3][2] 0.0000000000
+_pdbx_struct_oper_list.matrix[3][3] 1.0000000000
+_pdbx_struct_oper_list.vector[3] 23.3000000000
+# biounit end
+
+_struct.entry_id 1BAR
+_struct.title 'A Title'
+_struct.pdbx_CASP_flag Y
+_struct.pdbx_descriptor 'ADENYLATE KINASE'
+_struct.pdbx_formula_weight 1.0
+_struct.pdbx_formula_weight_method 'Good Guess'
+_struct.pdbx_model_details 'Even better guessing'
+_struct.pdbx_model_type_details 'Guess'
+
+# do not change anything, here
+loop_
+_struct_conf.id
+_struct_conf.conf_type_id
+_struct_conf.beg_label_comp_id
+_struct_conf.beg_label_asym_id
+_struct_conf.beg_label_seq_id
+_struct_conf.end_label_comp_id
+_struct_conf.end_label_asym_id
+_struct_conf.end_label_seq_id
+_struct_conf.details
+HELX1 HELX_RH_AL_P VAL A 11 THR A 12 .
+STRN1 STRN ILE A 13 ILE A 13 .
+HELX1 HELX_RH_AL_P ILE Z 1 ILE Z 1 .
+
+loop_
+_struct_sheet_range.sheet_id
+_struct_sheet_range.id
+_struct_sheet_range.beg_label_comp_id
+_struct_sheet_range.beg_label_asym_id
+_struct_sheet_range.beg_label_seq_id
+_struct_sheet_range.end_label_comp_id
+_struct_sheet_range.end_label_asym_id
+_struct_sheet_range.end_label_seq_id
+sheet_1 strand_a APS C 1 APS C 1
+
+loop_
+_atom_site.group_PDB
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.label_alt_id
+_atom_site.label_entity_id
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.B_iso_or_equiv
+_atom_site.footnote_id
+_atom_site.auth_seq_id
+_atom_site.id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.auth_asym_id
+ATOM N N VAL A 11 . 1 25.369 30.691 11.795 1.00 17.93 . 11 1 ? A
+ATOM C CA VAL A 11 . 1 25.970 31.965 12.332 1.00 17.75 . 11 2 ? A
+ATOM C C VAL A 11 . 1 25.569 32.010 13.808 1.00 17.83 . 11 3 ? A
+ATOM O O VAL A 11 . 1 24.735 31.190 14.167 1.00 17.53 . 11 4 ? A
+ATOM C CB VAL A 11 . 1 25.379 33.146 11.540 1.00 17.66 . 11 5 ? A
+ATOM C CG1 VAL A 11 . 1 25.584 33.034 10.030 1.00 18.86 . 11 6 ? A
+ATOM C CG2 VAL A 11 . 1 23.933 33.309 11.872 1.00 17.12 . 11 7 ? A
+ATOM N N THR A 12 . 1 26.095 32.930 14.590 1.00 18.97 4 12 8 ? A
+ATOM C CA THR A 12 . 1 25.734 32.995 16.032 1.00 19.80 4 12 9 ? A
+ATOM C C THR A 12 . 1 24.695 34.106 16.113 1.00 20.92 4 12 10 ? A
+ATOM O O THR A 12 . 1 24.869 35.118 15.421 1.00 21.84 4 12 11 ? A
+ATOM C CB THR A 12 . 1 26.911 33.346 17.018 1.00 20.51 4 12 12 ? A
+ATOM O OG1 THR A 12 3 1 27.946 33.921 16.183 0.50 20.29 4 12 13 ? A
+ATOM O OG1 THR A 12 4 1 27.769 32.142 17.103 0.50 20.59 4 12 14 ? A
+ATOM C CG2 THR A 12 3 1 27.418 32.181 17.878 0.50 20.47 4 12 15 ? A
+ATOM C CG2 THR A 12 4 1 26.489 33.778 18.426 0.50 20.00 4 12 16 ? A
+ATOM N N ILE A 13 . 1 23.664 33.855 16.884 1.00 22.08 . 13 17 ? A
+ATOM C CA ILE A 13 . 1 22.623 34.850 17.093 1.00 23.44 . 13 18 ? A
+ATOM C C ILE A 13 . 1 22.657 35.113 18.610 1.00 25.77 . 13 19 ? A
+ATOM O O ILE A 13 . 1 23.123 34.250 19.406 1.00 26.28 . 13 20 ? A
+ATOM C CB ILE A 13 . 1 21.236 34.463 16.492 1.00 22.67 . 13 21 ? A
+ATOM C CG1 ILE A 13 . 1 20.478 33.469 17.371 1.00 22.14 . 13 22 ? A
+ATOM C CG2 ILE A 13 . 1 21.357 33.986 15.016 1.00 21.75 . 13 23 ? A
+# - - - - data truncated for brevity - - - -
+HETATM C C1 APS C 1 1 1 4.171 29.012 7.116 0.58 17.27 1 300 101 ? A
+HETATM C C2 APS C 1 1 1 4.949 27.758 6.793 0.58 16.95 1 300 102 ? A
+HETATM O O3 APS C 1 1 1 4.800 26.678 7.393 0.58 16.85 1 300 103 ? A
+HETATM N N4 APS C 1 1 1 5.930 27.841 5.869 0.58 16.43 1 300 104 ? A
+# - - - - data truncated for brevity - - - -
+# chain to be ignored by 'restrict_chains' feature
+ATOM N N ILE Z 1 . 1 23.664 33.855 16.884 1.00 22.08 . 1 17 ? Z
+ATOM C CA ILE Z 1 . 1 22.623 34.850 17.093 1.00 23.44 . 1 18 ? Z
+ATOM C C ILE Z 1 . 1 22.657 35.113 18.610 1.00 25.77 . 1 19 ? Z
+ATOM O O ILE Z 1 . 1 23.123 34.250 19.406 1.00 26.28 . 1 20 ? Z
+ATOM C CB ILE Z 1 . 1 21.236 34.463 16.492 1.00 22.67 . 1 21 ? Z
+ATOM C CG1 ILE Z 1 . 1 20.478 33.469 17.371 1.00 22.14 . 1 22 ? Z
+ATOM C CG2 ILE Z 1 . 1 21.357 33.986 15.016 1.00 21.75 . 1 23 ? Z
+#
+# H2O
+HETATM O O HOH O . . 5 -5.322 10.972 9.720 0.95 7.25 . 2001 2731 ? B
+HETATM O O HOH O . . 5 4.148 4.008 12.383 0.64 14.61 . 2002 2732 ? B
+HETATM O O HOH O . . 5 -2.238 5.875 8.525 0.92 15.43 . 2003 2733 ? B
+HETATM O O HOH O . . 5 0.114 4.343 8.960 0.45 20.65 . 2004 2734 ? B
+HETATM O O HOH O . . 5 1.045 9.537 8.846 0.98 4.03 . 2005 2735 ? B
+HETATM O O HOH O . . 5 -0.532 11.899 9.196 1.00 4.09 . 2006 2736 ? B
+HETATM O O HOH O . . 5 0.936 18.270 7.581 0.97 5.52 . 2007 2737 ? B
+HETATM O O HOH O . . 5 -6.561 13.498 9.629 1.00 8.03 . 2008 2738 ? B
+HETATM O O HOH O . . 5 -11.465 18.494 11.144 0.81 14.02 . 2009 2739 ? B
+HETATM O O HOH O . . 5 12.795 11.508 13.991 0.90 35.55 . 2010 2740 ? B
diff --git a/modules/io/tests/testfiles/mmcif/changing_label_entity_id.mmcif b/modules/io/tests/testfiles/mmcif/changing_label_entity_id.mmcif
new file mode 100644
index 0000000000000000000000000000000000000000..c19da79d7f7e6c5bbdb1f4f8f473d92ebce2d69d
--- /dev/null
+++ b/modules/io/tests/testfiles/mmcif/changing_label_entity_id.mmcif
@@ -0,0 +1,26 @@
+data_1BAR
+
+# this file is also used in the mmcif_parse_models tests for a true negative
+# test, hence it is not allowed to carry atom_site.pdbx_PDB_model_num entries
+
+loop_
+_atom_site.group_PDB
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_seq_id
+_atom_site.label_alt_id
+_atom_site.label_entity_id
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.B_iso_or_equiv
+_atom_site.footnote_id
+_atom_site.auth_seq_id
+_atom_site.id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.auth_asym_id
+ATOM N N VAL A 11 . 1 25.369 30.691 11.795 1.00 17.93 . 11 1 ? A
+ATOM C CA VAL A 11 . 2 25.970 31.965 12.332 1.00 17.75 . 11 2 ? A
diff --git a/modules/io/tests/testfiles/mmcif/model_multi_atom_site.mmcif b/modules/io/tests/testfiles/mmcif/model_multi_atom_site.mmcif
new file mode 100644
index 0000000000000000000000000000000000000000..760e7556496ab0d41268fe46f8aaab2d6418b3b0
--- /dev/null
+++ b/modules/io/tests/testfiles/mmcif/model_multi_atom_site.mmcif
@@ -0,0 +1,120 @@
+data_1MBA
+# derived from 2JSP
+
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_entity_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.auth_seq_id
+_atom_site.auth_comp_id
+_atom_site.auth_asym_id
+_atom_site.auth_atom_id
+_atom_site.pdbx_PDB_model_num
+ATOM 1 N N . ALA A 1 1 ? 13.847 16.632 5.806 1 ALA A N 1
+ATOM 2 C CA . ALA A 1 1 ? 14.050 15.239 5.351 1 ALA A CA 1
+ATOM 3 C C . ALA A 1 1 ? 15.057 15.051 4.185 1 ALA A C 1
+ATOM 4 O O . ALA A 1 1 ? 16.242 14.860 4.448 1 ALA A O 1
+ATOM 5 C CB . ALA A 1 1 ? 12.682 14.599 5.070 1 ALA A CB 1
+ATOM 6 H H1 . ALA A 1 1 ? 14.344 17.346 5.293 1 ALA A H1 1
+ATOM 7 H HA . ALA A 1 1 ? 14.425 14.660 6.196 1 ALA A HA 1
+ATOM 8 H HB1 . ALA A 1 1 ? 12.168 15.166 4.295 1 ALA A HB1 1
+ATOM 9 H HB2 . ALA A 1 1 ? 12.824 13.571 4.734 1 ALA A HB2 1
+ATOM 10 H HB3 . ALA A 1 1 ? 12.085 14.603 5.981 1 ALA A HB3 1
+ATOM 11 N N . VAL B 1 2 ? 14.602 15.209 2.935 2 VAL A N 1
+ATOM 12 C CA . VAL B 1 2 ? 15.402 15.012 1.699 2 VAL A CA 1
+ATOM 13 C C . VAL B 1 2 ? 14.579 15.343 0.431 2 VAL A C 1
+ATOM 14 O O . VAL B 1 2 ? 14.518 16.503 0.039 2 VAL A O 1
+ATOM 15 C CB . VAL B 1 2 ? 16.165 13.656 1.685 2 VAL A CB 1
+ATOM 16 C CG1 . VAL B 1 2 ? 15.292 12.399 1.812 2 VAL A CG1 1
+ATOM 17 C CG2 . VAL B 1 2 ? 17.136 13.551 0.504 2 VAL A CG2 1
+ATOM 18 H H . VAL B 1 2 ? 13.617 15.489 2.821 2 VAL A H 1
+ATOM 19 H HA . VAL B 1 2 ? 16.285 15.650 1.689 2 VAL A HA 1
+ATOM 20 H HB . VAL B 1 2 ? 16.859 13.653 2.526 2 VAL A HB 1
+ATOM 21 H HG11 . VAL B 1 2 ? 15.925 11.512 1.791 2 VAL A HG11 1
+ATOM 22 H HG12 . VAL B 1 2 ? 14.743 12.431 2.754 2 VAL A HG12 1
+ATOM 23 H HG13 . VAL B 1 2 ? 14.586 12.361 0.982 2 VAL A HG13 1
+ATOM 24 H HG21 . VAL B 1 2 ? 17.872 14.353 0.565 2 VAL A HG21 1
+ATOM 25 H HG22 . VAL B 1 2 ? 17.645 12.588 0.536 2 VAL A HG22 1
+ATOM 26 H HG23 . VAL B 1 2 ? 16.583 13.637 -0.431 2 VAL A HG23 1
+#
+ATOM 1 N N . ALA A 1 1 ? 13.847 16.632 5.806 1 ALA A N 2
+ATOM 2 C CA . ALA A 1 1 ? 14.050 15.239 5.351 1 ALA A CA 2
+ATOM 3 C C . ALA A 1 1 ? 15.057 15.051 4.185 1 ALA A C 2
+ATOM 4 O O . ALA A 1 1 ? 16.242 14.860 4.448 1 ALA A O 2
+ATOM 5 C CB . ALA A 1 1 ? 12.682 14.599 5.070 1 ALA A CB 2
+ATOM 6 H H1 . ALA A 1 1 ? 14.344 17.346 5.293 1 ALA A H1 2
+ATOM 7 H HA . ALA A 1 1 ? 14.425 14.660 6.196 1 ALA A HA 2
+ATOM 8 H HB1 . ALA A 1 1 ? 12.168 15.166 4.295 1 ALA A HB1 2
+ATOM 9 H HB2 . ALA A 1 1 ? 12.824 13.571 4.734 1 ALA A HB2 2
+ATOM 10 H HB3 . ALA A 1 1 ? 12.085 14.603 5.981 1 ALA A HB3 2
+ATOM 11 N N . VAL B 1 2 ? 14.602 15.209 2.935 2 VAL A N 2
+ATOM 12 C CA . VAL B 1 2 ? 15.402 15.012 1.699 2 VAL A CA 2
+ATOM 13 C C . VAL B 1 2 ? 14.579 15.343 0.431 2 VAL A C 2
+ATOM 14 O O . VAL B 1 2 ? 14.518 16.503 0.039 2 VAL A O 2
+ATOM 15 C CB . VAL B 1 2 ? 16.165 13.656 1.685 2 VAL A CB 2
+ATOM 16 C CG1 . VAL B 1 2 ? 15.292 12.399 1.812 2 VAL A CG1 2
+ATOM 17 C CG2 . VAL B 1 2 ? 17.136 13.551 0.504 2 VAL A CG2 2
+ATOM 18 H H . VAL B 1 2 ? 13.617 15.489 2.821 2 VAL A H 2
+ATOM 19 H HA . VAL B 1 2 ? 16.285 15.650 1.689 2 VAL A HA 2
+ATOM 20 H HB . VAL B 1 2 ? 16.859 13.653 2.526 2 VAL A HB 2
+ATOM 21 H HG11 . VAL B 1 2 ? 15.925 11.512 1.791 2 VAL A HG11 2
+ATOM 22 H HG12 . VAL B 1 2 ? 14.743 12.431 2.754 2 VAL A HG12 2
+ATOM 23 H HG13 . VAL B 1 2 ? 14.586 12.361 0.982 2 VAL A HG13 2
+ATOM 24 H HG21 . VAL B 1 2 ? 17.872 14.353 0.565 2 VAL A HG21 2
+ATOM 25 H HG22 . VAL B 1 2 ? 17.645 12.588 0.536 2 VAL A HG22 2
+ATOM 26 H HG23 . VAL B 1 2 ? 16.583 13.637 -0.431 2 VAL A HG23 2
+# additional atom_site block
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_entity_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.auth_seq_id
+_atom_site.auth_comp_id
+_atom_site.auth_asym_id
+_atom_site.auth_atom_id
+ATOM 1 N N . ALA A 1 1 ? 13.847 16.632 5.806 1 ALA A N
+ATOM 2 C CA . ALA A 1 1 ? 14.050 15.239 5.351 1 ALA A CA
+ATOM 3 C C . ALA A 1 1 ? 15.057 15.051 4.185 1 ALA A C
+ATOM 4 O O . ALA A 1 1 ? 16.242 14.860 4.448 1 ALA A O
+ATOM 5 C CB . ALA A 1 1 ? 12.682 14.599 5.070 1 ALA A CB
+ATOM 6 H H1 . ALA A 1 1 ? 14.344 17.346 5.293 1 ALA A H1
+ATOM 7 H HA . ALA A 1 1 ? 14.425 14.660 6.196 1 ALA A HA
+ATOM 8 H HB1 . ALA A 1 1 ? 12.168 15.166 4.295 1 ALA A HB1
+ATOM 9 H HB2 . ALA A 1 1 ? 12.824 13.571 4.734 1 ALA A HB2
+ATOM 10 H HB3 . ALA A 1 1 ? 12.085 14.603 5.981 1 ALA A HB3
+ATOM 11 N N . VAL B 1 2 ? 14.602 15.209 2.935 2 VAL A N
+ATOM 12 C CA . VAL B 1 2 ? 15.402 15.012 1.699 2 VAL A CA
+ATOM 13 C C . VAL B 1 2 ? 14.579 15.343 0.431 2 VAL A C
+ATOM 14 O O . VAL B 1 2 ? 14.518 16.503 0.039 2 VAL A O
+ATOM 15 C CB . VAL B 1 2 ? 16.165 13.656 1.685 2 VAL A CB
+ATOM 16 C CG1 . VAL B 1 2 ? 15.292 12.399 1.812 2 VAL A CG1
+ATOM 17 C CG2 . VAL B 1 2 ? 17.136 13.551 0.504 2 VAL A CG2
+ATOM 18 H H . VAL B 1 2 ? 13.617 15.489 2.821 2 VAL A H
+ATOM 19 H HA . VAL B 1 2 ? 16.285 15.650 1.689 2 VAL A HA
+ATOM 20 H HB . VAL B 1 2 ? 16.859 13.653 2.526 2 VAL A HB
+ATOM 21 H HG11 . VAL B 1 2 ? 15.925 11.512 1.791 2 VAL A HG11
+ATOM 22 H HG12 . VAL B 1 2 ? 14.743 12.431 2.754 2 VAL A HG12
+ATOM 23 H HG13 . VAL B 1 2 ? 14.586 12.361 0.982 2 VAL A HG13
+ATOM 24 H HG21 . VAL B 1 2 ? 17.872 14.353 0.565 2 VAL A HG21
+ATOM 25 H HG22 . VAL B 1 2 ? 17.645 12.588 0.536 2 VAL A HG22
+ATOM 26 H HG23 . VAL B 1 2 ? 16.583 13.637 -0.431 2 VAL A HG23
diff --git a/modules/io/tests/testfiles/mmcif/model_multi_atom_site_inverted.mmcif b/modules/io/tests/testfiles/mmcif/model_multi_atom_site_inverted.mmcif
new file mode 100644
index 0000000000000000000000000000000000000000..58d22a61f34a1fe561bd2881d7db5211e7a148f3
--- /dev/null
+++ b/modules/io/tests/testfiles/mmcif/model_multi_atom_site_inverted.mmcif
@@ -0,0 +1,124 @@
+data_1MBA
+# derived from 2JSP
+
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_entity_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.auth_seq_id
+_atom_site.auth_comp_id
+_atom_site.auth_asym_id
+_atom_site.auth_atom_id
+ATOM 1 N N . ALA A 1 1 ? 13.847 16.632 5.806 1 ALA A N
+ATOM 2 C CA . ALA A 1 1 ? 14.050 15.239 5.351 1 ALA A CA
+ATOM 3 C C . ALA A 1 1 ? 15.057 15.051 4.185 1 ALA A C
+ATOM 4 O O . ALA A 1 1 ? 16.242 14.860 4.448 1 ALA A O
+ATOM 5 C CB . ALA A 1 1 ? 12.682 14.599 5.070 1 ALA A CB
+ATOM 6 H H1 . ALA A 1 1 ? 14.344 17.346 5.293 1 ALA A H1
+ATOM 7 H HA . ALA A 1 1 ? 14.425 14.660 6.196 1 ALA A HA
+ATOM 8 H HB1 . ALA A 1 1 ? 12.168 15.166 4.295 1 ALA A HB1
+ATOM 9 H HB2 . ALA A 1 1 ? 12.824 13.571 4.734 1 ALA A HB2
+ATOM 10 H HB3 . ALA A 1 1 ? 12.085 14.603 5.981 1 ALA A HB3
+ATOM 11 N N . VAL B 1 2 ? 14.602 15.209 2.935 2 VAL A N
+ATOM 12 C CA . VAL B 1 2 ? 15.402 15.012 1.699 2 VAL A CA
+ATOM 13 C C . VAL B 1 2 ? 14.579 15.343 0.431 2 VAL A C
+ATOM 14 O O . VAL B 1 2 ? 14.518 16.503 0.039 2 VAL A O
+ATOM 15 C CB . VAL B 1 2 ? 16.165 13.656 1.685 2 VAL A CB
+ATOM 16 C CG1 . VAL B 1 2 ? 15.292 12.399 1.812 2 VAL A CG1
+ATOM 17 C CG2 . VAL B 1 2 ? 17.136 13.551 0.504 2 VAL A CG2
+ATOM 18 H H . VAL B 1 2 ? 13.617 15.489 2.821 2 VAL A H
+ATOM 19 H HA . VAL B 1 2 ? 16.285 15.650 1.689 2 VAL A HA
+ATOM 20 H HB . VAL B 1 2 ? 16.859 13.653 2.526 2 VAL A HB
+ATOM 21 H HG11 . VAL B 1 2 ? 15.925 11.512 1.791 2 VAL A HG11
+ATOM 22 H HG12 . VAL B 1 2 ? 14.743 12.431 2.754 2 VAL A HG12
+ATOM 23 H HG13 . VAL B 1 2 ? 14.586 12.361 0.982 2 VAL A HG13
+ATOM 24 H HG21 . VAL B 1 2 ? 17.872 14.353 0.565 2 VAL A HG21
+ATOM 25 H HG22 . VAL B 1 2 ? 17.645 12.588 0.536 2 VAL A HG22
+ATOM 26 H HG23 . VAL B 1 2 ? 16.583 13.637 -0.431 2 VAL A HG23
+
+# additional atom_site block
+
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_entity_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.auth_seq_id
+_atom_site.auth_comp_id
+_atom_site.auth_asym_id
+_atom_site.auth_atom_id
+_atom_site.pdbx_PDB_model_num
+ATOM 1 N N . ALA A 1 1 ? 13.847 16.632 5.806 1 ALA A N 1
+ATOM 2 C CA . ALA A 1 1 ? 14.050 15.239 5.351 1 ALA A CA 1
+ATOM 3 C C . ALA A 1 1 ? 15.057 15.051 4.185 1 ALA A C 1
+ATOM 4 O O . ALA A 1 1 ? 16.242 14.860 4.448 1 ALA A O 1
+ATOM 5 C CB . ALA A 1 1 ? 12.682 14.599 5.070 1 ALA A CB 1
+ATOM 6 H H1 . ALA A 1 1 ? 14.344 17.346 5.293 1 ALA A H1 1
+ATOM 7 H HA . ALA A 1 1 ? 14.425 14.660 6.196 1 ALA A HA 1
+ATOM 8 H HB1 . ALA A 1 1 ? 12.168 15.166 4.295 1 ALA A HB1 1
+ATOM 9 H HB2 . ALA A 1 1 ? 12.824 13.571 4.734 1 ALA A HB2 1
+ATOM 10 H HB3 . ALA A 1 1 ? 12.085 14.603 5.981 1 ALA A HB3 1
+ATOM 11 N N . VAL B 1 2 ? 14.602 15.209 2.935 2 VAL A N 1
+ATOM 12 C CA . VAL B 1 2 ? 15.402 15.012 1.699 2 VAL A CA 1
+ATOM 13 C C . VAL B 1 2 ? 14.579 15.343 0.431 2 VAL A C 1
+ATOM 14 O O . VAL B 1 2 ? 14.518 16.503 0.039 2 VAL A O 1
+ATOM 15 C CB . VAL B 1 2 ? 16.165 13.656 1.685 2 VAL A CB 1
+ATOM 16 C CG1 . VAL B 1 2 ? 15.292 12.399 1.812 2 VAL A CG1 1
+ATOM 17 C CG2 . VAL B 1 2 ? 17.136 13.551 0.504 2 VAL A CG2 1
+ATOM 18 H H . VAL B 1 2 ? 13.617 15.489 2.821 2 VAL A H 1
+ATOM 19 H HA . VAL B 1 2 ? 16.285 15.650 1.689 2 VAL A HA 1
+ATOM 20 H HB . VAL B 1 2 ? 16.859 13.653 2.526 2 VAL A HB 1
+ATOM 21 H HG11 . VAL B 1 2 ? 15.925 11.512 1.791 2 VAL A HG11 1
+ATOM 22 H HG12 . VAL B 1 2 ? 14.743 12.431 2.754 2 VAL A HG12 1
+ATOM 23 H HG13 . VAL B 1 2 ? 14.586 12.361 0.982 2 VAL A HG13 1
+ATOM 24 H HG21 . VAL B 1 2 ? 17.872 14.353 0.565 2 VAL A HG21 1
+ATOM 25 H HG22 . VAL B 1 2 ? 17.645 12.588 0.536 2 VAL A HG22 1
+ATOM 26 H HG23 . VAL B 1 2 ? 16.583 13.637 -0.431 2 VAL A HG23 1
+#
+ATOM 1 N N . ALA A 1 1 ? 13.847 16.632 5.806 1 ALA A N 2
+ATOM 2 C CA . ALA A 1 1 ? 14.050 15.239 5.351 1 ALA A CA 2
+ATOM 3 C C . ALA A 1 1 ? 15.057 15.051 4.185 1 ALA A C 2
+ATOM 4 O O . ALA A 1 1 ? 16.242 14.860 4.448 1 ALA A O 2
+ATOM 5 C CB . ALA A 1 1 ? 12.682 14.599 5.070 1 ALA A CB 2
+ATOM 6 H H1 . ALA A 1 1 ? 14.344 17.346 5.293 1 ALA A H1 2
+ATOM 7 H HA . ALA A 1 1 ? 14.425 14.660 6.196 1 ALA A HA 2
+ATOM 8 H HB1 . ALA A 1 1 ? 12.168 15.166 4.295 1 ALA A HB1 2
+ATOM 9 H HB2 . ALA A 1 1 ? 12.824 13.571 4.734 1 ALA A HB2 2
+ATOM 10 H HB3 . ALA A 1 1 ? 12.085 14.603 5.981 1 ALA A HB3 2
+ATOM 11 N N . VAL B 1 2 ? 14.602 15.209 2.935 2 VAL A N 2
+ATOM 12 C CA . VAL B 1 2 ? 15.402 15.012 1.699 2 VAL A CA 2
+ATOM 13 C C . VAL B 1 2 ? 14.579 15.343 0.431 2 VAL A C 2
+ATOM 14 O O . VAL B 1 2 ? 14.518 16.503 0.039 2 VAL A O 2
+ATOM 15 C CB . VAL B 1 2 ? 16.165 13.656 1.685 2 VAL A CB 2
+ATOM 16 C CG1 . VAL B 1 2 ? 15.292 12.399 1.812 2 VAL A CG1 2
+ATOM 17 C CG2 . VAL B 1 2 ? 17.136 13.551 0.504 2 VAL A CG2 2
+ATOM 18 H H . VAL B 1 2 ? 13.617 15.489 2.821 2 VAL A H 2
+ATOM 19 H HA . VAL B 1 2 ? 16.285 15.650 1.689 2 VAL A HA 2
+ATOM 20 H HB . VAL B 1 2 ? 16.859 13.653 2.526 2 VAL A HB 2
+ATOM 21 H HG11 . VAL B 1 2 ? 15.925 11.512 1.791 2 VAL A HG11 2
+ATOM 22 H HG12 . VAL B 1 2 ? 14.743 12.431 2.754 2 VAL A HG12 2
+ATOM 23 H HG13 . VAL B 1 2 ? 14.586 12.361 0.982 2 VAL A HG13 2
+ATOM 24 H HG21 . VAL B 1 2 ? 17.872 14.353 0.565 2 VAL A HG21 2
+ATOM 25 H HG22 . VAL B 1 2 ? 17.645 12.588 0.536 2 VAL A HG22 2
+ATOM 26 H HG23 . VAL B 1 2 ? 16.583 13.637 -0.431 2 VAL A HG23 2
+
+
diff --git a/modules/io/tests/testfiles/mmcif/model_truepos.mmcif b/modules/io/tests/testfiles/mmcif/model_truepos.mmcif
new file mode 100644
index 0000000000000000000000000000000000000000..9f1e39f16319bb4e9290c31d9896f209ecb15796
--- /dev/null
+++ b/modules/io/tests/testfiles/mmcif/model_truepos.mmcif
@@ -0,0 +1,78 @@
+data_1TPM
+# derived from 2JSP
+
+# this file is also used in the mmcif_mmcif_chaintype_setting test for a true
+# negative test, hence no entity category may be added
+
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_entity_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.auth_seq_id
+_atom_site.auth_comp_id
+_atom_site.auth_asym_id
+_atom_site.auth_atom_id
+_atom_site.pdbx_PDB_model_num
+ATOM 1 N N . ALA A 1 1 ? 13.847 16.632 5.806 1 ALA A N 1
+ATOM 2 C CA . ALA A 1 1 ? 14.050 15.239 5.351 1 ALA A CA 1
+ATOM 3 C C . ALA A 1 1 ? 15.057 15.051 4.185 1 ALA A C 1
+ATOM 4 O O . ALA A 1 1 ? 16.242 14.860 4.448 1 ALA A O 1
+ATOM 5 C CB . ALA A 1 1 ? 12.682 14.599 5.070 1 ALA A CB 1
+ATOM 6 H H1 . ALA A 1 1 ? 14.344 17.346 5.293 1 ALA A H1 1
+ATOM 7 H HA . ALA A 1 1 ? 14.425 14.660 6.196 1 ALA A HA 1
+ATOM 8 H HB1 . ALA A 1 1 ? 12.168 15.166 4.295 1 ALA A HB1 1
+ATOM 9 H HB2 . ALA A 1 1 ? 12.824 13.571 4.734 1 ALA A HB2 1
+ATOM 10 H HB3 . ALA A 1 1 ? 12.085 14.603 5.981 1 ALA A HB3 1
+ATOM 11 N N . VAL B 1 2 ? 14.602 15.209 2.935 2 VAL A N 1
+ATOM 12 C CA . VAL B 1 2 ? 15.402 15.012 1.699 2 VAL A CA 1
+ATOM 13 C C . VAL B 1 2 ? 14.579 15.343 0.431 2 VAL A C 1
+ATOM 14 O O . VAL B 1 2 ? 14.518 16.503 0.039 2 VAL A O 1
+ATOM 15 C CB . VAL B 1 2 ? 16.165 13.656 1.685 2 VAL A CB 1
+ATOM 16 C CG1 . VAL B 1 2 ? 15.292 12.399 1.812 2 VAL A CG1 1
+ATOM 17 C CG2 . VAL B 1 2 ? 17.136 13.551 0.504 2 VAL A CG2 1
+ATOM 18 H H . VAL B 1 2 ? 13.617 15.489 2.821 2 VAL A H 1
+ATOM 19 H HA . VAL B 1 2 ? 16.285 15.650 1.689 2 VAL A HA 1
+ATOM 20 H HB . VAL B 1 2 ? 16.859 13.653 2.526 2 VAL A HB 1
+ATOM 21 H HG11 . VAL B 1 2 ? 15.925 11.512 1.791 2 VAL A HG11 1
+ATOM 22 H HG12 . VAL B 1 2 ? 14.743 12.431 2.754 2 VAL A HG12 1
+ATOM 23 H HG13 . VAL B 1 2 ? 14.586 12.361 0.982 2 VAL A HG13 1
+ATOM 24 H HG21 . VAL B 1 2 ? 17.872 14.353 0.565 2 VAL A HG21 1
+ATOM 25 H HG22 . VAL B 1 2 ? 17.645 12.588 0.536 2 VAL A HG22 1
+ATOM 26 H HG23 . VAL B 1 2 ? 16.583 13.637 -0.431 2 VAL A HG23 1
+#
+ATOM 1 N N . ALA A 1 1 ? 13.847 16.632 5.806 1 ALA A N 2
+ATOM 2 C CA . ALA A 1 1 ? 14.050 15.239 5.351 1 ALA A CA 2
+ATOM 3 C C . ALA A 1 1 ? 15.057 15.051 4.185 1 ALA A C 2
+ATOM 4 O O . ALA A 1 1 ? 16.242 14.860 4.448 1 ALA A O 2
+ATOM 5 C CB . ALA A 1 1 ? 12.682 14.599 5.070 1 ALA A CB 2
+ATOM 6 H H1 . ALA A 1 1 ? 14.344 17.346 5.293 1 ALA A H1 2
+ATOM 7 H HA . ALA A 1 1 ? 14.425 14.660 6.196 1 ALA A HA 2
+ATOM 8 H HB1 . ALA A 1 1 ? 12.168 15.166 4.295 1 ALA A HB1 2
+ATOM 9 H HB2 . ALA A 1 1 ? 12.824 13.571 4.734 1 ALA A HB2 2
+ATOM 10 H HB3 . ALA A 1 1 ? 12.085 14.603 5.981 1 ALA A HB3 2
+ATOM 11 N N . VAL B 1 2 ? 14.602 15.209 2.935 2 VAL A N 2
+ATOM 12 C CA . VAL B 1 2 ? 15.402 15.012 1.699 2 VAL A CA 2
+ATOM 13 C C . VAL B 1 2 ? 14.579 15.343 0.431 2 VAL A C 2
+ATOM 14 O O . VAL B 1 2 ? 14.518 16.503 0.039 2 VAL A O 2
+ATOM 15 C CB . VAL B 1 2 ? 16.165 13.656 1.685 2 VAL A CB 2
+ATOM 16 C CG1 . VAL B 1 2 ? 15.292 12.399 1.812 2 VAL A CG1 2
+ATOM 17 C CG2 . VAL B 1 2 ? 17.136 13.551 0.504 2 VAL A CG2 2
+ATOM 18 H H . VAL B 1 2 ? 13.617 15.489 2.821 2 VAL A H 2
+ATOM 19 H HA . VAL B 1 2 ? 16.285 15.650 1.689 2 VAL A HA 2
+ATOM 20 H HB . VAL B 1 2 ? 16.859 13.653 2.526 2 VAL A HB 2
+ATOM 21 H HG11 . VAL B 1 2 ? 15.925 11.512 1.791 2 VAL A HG11 2
+ATOM 22 H HG12 . VAL B 1 2 ? 14.743 12.431 2.754 2 VAL A HG12 2
+ATOM 23 H HG13 . VAL B 1 2 ? 14.586 12.361 0.982 2 VAL A HG13 2
+ATOM 24 H HG21 . VAL B 1 2 ? 17.872 14.353 0.565 2 VAL A HG21 2
+ATOM 25 H HG22 . VAL B 1 2 ? 17.645 12.588 0.536 2 VAL A HG22 2
+ATOM 26 H HG23 . VAL B 1 2 ? 16.583 13.637 -0.431 2 VAL A HG23 2
diff --git a/modules/io/tests/testfiles/mmcif/struct_ref.cif b/modules/io/tests/testfiles/mmcif/struct_ref.cif
new file mode 100644
index 0000000000000000000000000000000000000000..1d87ec60bb9b4cbca7c25ce02255be58a3f31896
--- /dev/null
+++ b/modules/io/tests/testfiles/mmcif/struct_ref.cif
@@ -0,0 +1,47 @@
+data_2bfl
+# taken from 2bfl.cif
+_struct_ref.id 1
+_struct_ref.db_name UNP
+_struct_ref.db_code BLA2_BACCE
+_struct_ref.entity_id 1
+_struct_ref.pdbx_seq_one_letter_code ?
+_struct_ref.pdbx_align_begin ?
+_struct_ref.biol_id .
+_struct_ref.pdbx_db_accession P04190
+#
+loop_
+_struct_ref_seq.align_id
+_struct_ref_seq.ref_id
+_struct_ref_seq.pdbx_PDB_id_code
+_struct_ref_seq.pdbx_strand_id
+_struct_ref_seq.seq_align_beg
+_struct_ref_seq.pdbx_seq_align_beg_ins_code
+_struct_ref_seq.seq_align_end
+_struct_ref_seq.pdbx_seq_align_end_ins_code
+_struct_ref_seq.pdbx_db_accession
+_struct_ref_seq.db_align_beg
+_struct_ref_seq.pdbx_db_align_beg_ins_code
+_struct_ref_seq.db_align_end
+_struct_ref_seq.pdbx_db_align_end_ins_code
+_struct_ref_seq.pdbx_auth_seq_align_beg
+_struct_ref_seq.pdbx_auth_seq_align_end
+1 1 2BFL A 1 ? 19 ? P04190 31 ? 49 ? 27 45
+13 1 2BFL B 1 ? 19 ? P04190 31 ? 49 ? 27 45
+#
+loop_
+_struct_ref_seq_dif.align_id
+_struct_ref_seq_dif.pdbx_pdb_id_code
+_struct_ref_seq_dif.mon_id
+_struct_ref_seq_dif.pdbx_pdb_strand_id
+_struct_ref_seq_dif.seq_num
+_struct_ref_seq_dif.pdbx_pdb_ins_code
+_struct_ref_seq_dif.pdbx_seq_db_name
+_struct_ref_seq_dif.pdbx_seq_db_accession_code
+_struct_ref_seq_dif.db_mon_id
+_struct_ref_seq_dif.pdbx_seq_db_seq_num
+_struct_ref_seq_dif.details
+_struct_ref_seq_dif.pdbx_auth_seq_num
+_struct_ref_seq_dif.pdbx_ordinal
+1 2BFL CYS A 91 ? UNP P04190 ARG 121 'ENGINEERED MUTATION' 121 1
+13 2BFL CYS B 91 ? UNP P04190 ARG 121 'ENGINEERED MUTATION' 121 2
+
diff --git a/modules/io/tests/testfiles/pdb/1oax.pdb b/modules/io/tests/testfiles/pdb/1oax.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..8a61950e8a0970d2b719b35c65465907ff0b6f3d
--- /dev/null
+++ b/modules/io/tests/testfiles/pdb/1oax.pdb
@@ -0,0 +1,24 @@
+
+COMPND MOL_ID: 1;
+COMPND 2 MOLECULE: IMMUNOGLOBULIN E;
+COMPND 3 CHAIN: H, I, J, K;
+COMPND 4 FRAGMENT: FV REGION, RESIDUES 1-122;
+COMPND 5 ENGINEERED: YES;
+COMPND 6 MOL_ID: 2;
+COMPND 7 MOLECULE: IMMUNOGLOBULIN E;
+COMPND 8 CHAIN: L, M, N, O;
+COMPND 9 FRAGMENT: FV REGION, RESIDUES 1-110;
+COMPND 10 ENGINEERED: YES
+
+ATOM 961 CB ALA H 122 24.405 78.113 110.762 1.00 46.85 C
+TER 962 ALA H 122
+ATOM 1923 CB ALA J 122 -18.810 34.607 14.909 1.00 46.23 C
+TER 1924 ALA J 122
+ATOM 2722 CD2 LEU L 109 61.832 51.079 106.030 1.00 43.23 C
+TER 2723 LEU L 109
+ATOM 3521 CD2 LEU M 109 2.184 -0.589 68.108 1.00 43.23 C
+TER 3522 LEU M 109
+ATOM 4320 CD2 LEU N 109 7.889 -2.865 19.656 1.00 43.22 C
+TER 4321 LEU N 109
+ATOM 5113 CD2 LEU O 109 59.692 56.678 57.399 1.00 43.23 C
+TER 5114 LEU O 109
diff --git a/modules/io/tests/testfiles/pdb/2p6a.pdb b/modules/io/tests/testfiles/pdb/2p6a.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..19935ba86c1e7b632bd02a2c50ac89a726f0e9cb
--- /dev/null
+++ b/modules/io/tests/testfiles/pdb/2p6a.pdb
@@ -0,0 +1,25 @@
+COMPND MOL_ID: 1;
+COMPND 2 MOLECULE: INHIBIN BETA A CHAIN;
+COMPND 3 CHAIN: A, B;
+COMPND 4 SYNONYM: ACTIVIN BETA-A CHAIN, ERYTHROID DIFFERENTIATION
+COMPND 5 PROTEIN, EDF;
+COMPND 6 ENGINEERED: YES;
+COMPND 7 MOL_ID: 2;
+COMPND 8 MOLECULE: FOLLISTATIN;
+COMPND 9 CHAIN: D, C;
+COMPND 10 SYNONYM: FS, ACTIVIN-BINDING PROTEIN;
+COMPND 11 ENGINEERED: YES;
+COMPND 12 MOL_ID: 3;
+COMPND 13 MOLECULE:;
+COMPND 14 CHAIN: E;
+COMPND 15 ENGINEERED: YES
+ATOM 882 OXT SER A 116 15.399 37.353 44.611 1.00 73.37 O
+TER 883 SER A 116
+ATOM 3870 OXT SER B 116 13.780 40.357 30.274 1.00 27.95 O
+TER 3871 SER B 116
+ATOM 2987 OE2 GLU D 299 33.348 36.499 4.332 1.00 81.88 O
+TER 2988 GLU D 299
+ATOM 5905 CB ILE C 290 46.026 -9.354 55.435 1.00233.79 C
+TER 5906 ILE C 290
+ATOM 5956 CB ALA E 10 30.651 13.129 53.296 1.00191.07 C
+TER 5957 ALA E 10
diff --git a/modules/io/tests/testfiles/pdb/bzdng-318.pdb b/modules/io/tests/testfiles/pdb/bzdng-318.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..8008e84b1abbeeeed341e7e91745c5327923b633
--- /dev/null
+++ b/modules/io/tests/testfiles/pdb/bzdng-318.pdb
@@ -0,0 +1,4 @@
+ATOM 1 CA ALYS A 9 31.209 -9.896 12.154 0.62 22.96 C
+ATOM 1 CA BLYS A 9 31.213 -9.902 12.145 0.38 24.64 C
+TER 2 LYS A 9
+END
\ No newline at end of file
diff --git a/modules/io/tests/testfiles/pdb/simple.pqr b/modules/io/tests/testfiles/pdb/simple.pqr
new file mode 100644
index 0000000000000000000000000000000000000000..57b48919b6f94b1ace9a91597b0c301b0b6adf23
--- /dev/null
+++ b/modules/io/tests/testfiles/pdb/simple.pqr
@@ -0,0 +1,100 @@
+REMARK 1 PQR file generated by PDB2PQR (Version 1.4.0)
+REMARK 1
+REMARK 1 Forcefield Used: parse
+REMARK 1
+REMARK 5 Gap in backbone detected between LEU A 3 and MET A 255!
+REMARK 5 Gap in backbone detected between MET B 1 and SER B 256!
+REMARK 5
+REMARK 6 Total charge on this protein: 1.0000 e
+REMARK 6
+ATOM 1 N MET 1 21.600 35.300 56.700 -0.3755 2.0005
+ATOM 2 CA MET 1 20.601 35.494 57.793 0.3300 2.0000
+ATOM 3 C MET 1 19.654 34.300 57.789 0.5500 1.7000
+ATOM 4 O MET 1 18.447 34.456 57.595 -0.5500 1.4000
+ATOM 5 CB MET 1 19.789 36.783 57.639 0.0000 2.0000
+ATOM 6 CG MET 1 20.629 38.055 57.606 0.2650 2.0000
+ATOM 7 SD MET 1 21.638 38.325 59.084 -0.5300 1.8500
+ATOM 8 CE MET 1 23.233 37.697 58.529 0.2650 2.0000
+ATOM 9 HE1 MET 1 23.125 37.266 57.634 0.0000 0.0000
+ATOM 10 HE2 MET 1 23.881 38.455 58.461 0.0000 0.0000
+ATOM 11 HE3 MET 1 23.571 37.025 59.187 0.0000 0.0000
+ATOM 12 H2 MET 1 22.177 34.580 56.869 0.3300 0.0000
+ATOM 13 H3 MET 1 21.135 35.294 55.831 0.3300 0.0000
+ATOM 14 HG2 MET 1 21.223 38.027 56.761 0.0000 0.0000
+ATOM 15 HG3 MET 1 19.996 38.856 57.448 0.0000 0.0000
+ATOM 16 H MET 1 22.175 36.206 56.703 0.3300 0.0000
+ATOM 17 HA MET 1 21.099 35.502 58.665 0.0000 0.0000
+ATOM 18 HB3 MET 1 19.138 36.853 58.408 0.0000 0.0000
+ATOM 19 HB2 MET 1 19.255 36.733 56.783 0.0000 0.0000
+ATOM 20 N ARG 2 20.202 33.112 58.011 -0.4000 1.5000
+ATOM 21 CA ARG 2 19.396 31.903 58.033 -0.0000 2.0000
+ATOM 22 C ARG 2 18.608 31.739 59.328 0.5500 1.7000
+ATOM 23 O ARG 2 17.651 30.965 59.381 -0.5500 1.4000
+ATOM 24 CB ARG 2 20.284 30.681 57.801 0.0000 2.0000
+ATOM 25 CG ARG 2 20.665 30.488 56.342 0.0000 2.0000
+ATOM 26 CD ARG 2 21.557 29.281 56.154 0.3500 2.0000
+ATOM 27 NE ARG 2 22.931 29.557 56.551 -0.3500 1.5000
+ATOM 28 CZ ARG 2 23.900 28.700 56.500 0.2507 1.7503
+ATOM 29 NH1 ARG 2 23.640 27.417 56.130 -0.7000 1.5000
+ATOM 30 NH2 ARG 2 25.132 28.980 56.893 -0.7000 1.5000
+ATOM 31 HG3 ARG 2 21.156 31.294 56.019 0.0000 0.0000
+ATOM 32 HA ARG 2 18.738 31.934 57.260 0.0000 0.0000
+ATOM 33 HE ARG 2 23.157 30.486 56.860 0.4500 1.0000
+ATOM 34 HG2 ARG 2 19.838 30.356 55.799 0.0000 0.0000
+ATOM 35 HH22 ARG 2 25.859 28.300 56.895 0.4000 1.0000
+ATOM 36 HH21 ARG 2 25.336 29.925 57.170 0.4000 1.0000
+ATOM 37 H ARG 2 21.227 33.124 58.163 0.4000 1.0000
+ATOM 38 HD3 ARG 2 21.537 29.027 55.190 0.0000 0.0000
+ATOM 39 HD2 ARG 2 21.197 28.537 56.711 0.0000 0.0000
+ATOM 40 HH12 ARG 2 24.383 26.727 56.133 0.4000 1.0000
+ATOM 41 HH11 ARG 2 22.728 27.161 55.829 0.4000 1.0000
+ATOM 42 HB3 ARG 2 19.790 29.875 58.100 0.0000 0.0000
+ATOM 43 HB2 ARG 2 21.118 30.797 58.325 0.0000 0.0000
+ATOM 44 N LEU 3 19.003 32.473 60.366 -0.4000 1.5000
+ATOM 45 CA LEU 3 18.330 32.402 61.664 -0.0000 2.0000
+ATOM 46 C LEU 3 17.884 33.787 62.117 0.5500 1.7000
+ATOM 47 O LEU 3 17.853 34.091 63.308 -0.5500 1.4000
+ATOM 48 CB LEU 3 19.269 31.793 62.710 0.0000 2.0000
+ATOM 49 CG LEU 3 19.695 30.340 62.501 0.0000 2.0000
+ATOM 50 CD1 LEU 3 20.585 29.897 63.648 0.0000 2.0000
+ATOM 51 CD2 LEU 3 18.461 29.459 62.420 0.0000 2.0000
+ATOM 52 HD22 LEU 3 17.888 29.751 61.653 0.0000 0.0000
+ATOM 53 HD23 LEU 3 18.736 28.507 62.283 0.0000 0.0000
+ATOM 54 HD21 LEU 3 17.938 29.533 63.270 0.0000 0.0000
+ATOM 55 H LEU 3 19.817 33.091 60.179 0.4000 1.0000
+ATOM 56 HD13 LEU 3 20.084 29.973 64.512 0.0000 0.0000
+ATOM 57 HD12 LEU 3 20.863 28.945 63.510 0.0000 0.0000
+ATOM 58 HD11 LEU 3 21.400 30.478 63.686 0.0000 0.0000
+ATOM 59 HA LEU 3 17.516 31.820 61.570 0.0000 0.0000
+ATOM 60 HG LEU 3 20.197 30.269 61.643 0.0000 0.0000
+ATOM 61 HB3 LEU 3 18.811 31.845 63.597 0.0000 0.0000
+ATOM 62 HB2 LEU 3 20.102 32.347 62.730 0.0000 0.0000
+ATOM 63 N MET 255 29.709 5.069 60.642 -0.4000 1.5000
+ATOM 64 CA MET 255 28.701 5.164 59.592 -0.0000 2.0000
+ATOM 65 C MET 255 27.302 4.748 60.005 0.5500 1.7000
+ATOM 66 O MET 255 27.057 3.586 60.326 -0.5500 1.4000
+ATOM 67 CB MET 255 29.146 4.331 58.399 0.0000 2.0000
+ATOM 68 CG MET 255 30.558 4.642 57.948 0.2650 2.0000
+ATOM 69 SD MET 255 31.116 3.394 56.790 -0.5300 1.8500
+ATOM 70 CE MET 255 31.526 2.062 57.912 0.2650 2.0000
+ATOM 71 HG2 MET 255 30.571 5.563 57.524 0.0000 0.0000
+ATOM 72 HE1 MET 255 32.437 1.708 57.695 0.0000 0.0000
+ATOM 73 HE2 MET 255 31.518 2.401 58.854 0.0000 0.0000
+ATOM 74 HE3 MET 255 30.854 1.325 57.820 0.0000 0.0000
+ATOM 75 HB2 MET 255 29.096 3.355 58.642 0.0000 0.0000
+ATOM 76 HG3 MET 255 31.163 4.679 58.762 0.0000 0.0000
+ATOM 77 H MET 255 26.414 14.773 61.903 0.4000 1.0000
+ATOM 78 HA MET 255 28.661 6.140 59.286 0.0000 0.0000
+ATOM 79 HB3 MET 255 28.520 4.500 57.628 0.0000 0.0000
+ATOM 80 N SER 256 26.376 5.699 59.965 -0.4000 1.5000
+ATOM 81 CA SER 256 24.998 5.430 60.347 -0.0000 2.0000
+ATOM 82 C SER 256 24.040 5.839 59.231 0.1000 1.7000
+ATOM 83 O SER 256 24.543 6.294 58.186 -0.5500 1.4000
+ATOM 84 CB SER 256 24.664 6.188 61.642 0.0000 2.0000
+ATOM 85 OG SER 256 25.569 5.836 62.681 -0.4900 1.4000
+ATOM 86 OXT SER 256 22.811 5.701 59.408 -0.5500 1.4000
+ATOM 87 H SER 256 26.714 6.626 59.646 0.4000 1.0000
+ATOM 88 HA SER 256 24.898 4.440 60.490 0.0000 0.0000
+ATOM 89 HB3 SER 256 23.741 5.949 61.922 0.0000 0.0000
+ATOM 90 HB2 SER 256 24.734 7.163 61.468 0.0000 0.0000
+ATOM 91 HG SER 256 26.464 6.235 62.490 0.4900 1.0000
diff --git a/modules/io/tests/testfiles/pdb/simple_defective.pdb b/modules/io/tests/testfiles/pdb/simple_defective.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..725b68dbad3e82a101122f3f301f8a254e9a4aab
--- /dev/null
+++ b/modules/io/tests/testfiles/pdb/simple_defective.pdb
@@ -0,0 +1,67 @@
+HELIX 1 1 ARG A 15 GLU A 28 1 14
+HELIX 2 2 ASN A 38 GLY A 50 1 13
+SHEET 1 A 7 ALA A 53 ALA A 57 0
+SHEET 2 A 7 ALA A 30 ASP A 36 1 N ILE A 34 O CYS A 54
+CRYST1 67.465 67.465 191.044 90.00 90.00 120.00 P 31 2 1 12
+ATOM 1 N MET A 1 21.609 35.384 56.705 1.00 41.48 N
+ATOM 2 CA MET A 1 20.601 35.494 57.793 1.00 41.58 C
+ATOM 3 C MET A 1 19.654 34.300 57.789 1.00 39.51 C
+ATOM 4 O MET A 1 18.447 34.456 57.595 1.00 38.98 O
+ATOM 5 CB MET A 1 19.789 36.783 57.639 1.00 45.90 C
+ATOM 6 CG MET A 1 20.629 38.055 57.606 1.00 51.18 C
+ATOM 7 SD MET A 1 21.638 38.325 59.084 1.00 55.83 S
+ATOM 8 CE MET A 1 23.233 37.697 58.529 1.00 54.59 C
+ATOM 9 N ARG A 2 20.202 33.112 58.011 1.00 36.39 N
+ATOM 10 CA ARG A 2 19.396 31.903 58.033 1.00 34.35 C
+ATOM 11 C ARG A 2 18.608 31.739 59.328 1.00 34.20 C
+ATOM 12 O ARG A 2 17.651 30.965 59.381 1.00 32.64 O
+ATOM 13 CB ARG A 2 20.284 30.681 57.801 1.00 33.48 C
+ATOM 14 CG ARG A 2 20.665 30.488 56.342 1.00 31.69 C
+ATOM 15 CD ARG A 2 21.557 29.281 56.154 1.00 29.91 C
+ATOM 16 NE ARG A 2 22.931 29.557 56.551 1.00 28.95 N
+ATOM 17 CZ ARG A 2 23.901 28.653 56.528 1.00 30.21 C
+ATOM 18 NH1 ARG A 2 23.640 27.417 56.130 1.00 32.54 N
+ATOM 19 NH2 ARG A 2 25.132 28.980 56.893 1.00 29.14 N
+ATOM 20 N LEU A 3 19.003 32.473 60.366 1.00 35.07 N
+ATOM 21 CA LEU A 3 18.330 32.402 61.664 1.00 34.70 C
+ATOM 22 C LEU A 3 17.884 33.787 62.117 1.00 35.41 C
+ATOM 23 O LEU A 3 17.853 34.091 63.308 1.00 35.91 O
+ATOM 24 CB LEU A 3 19.269 31.793 102.710 1.00 31.47 C
+ATOM 25 CG LEU A 3 19.695 30.340 62.501 1.00 29.10 C
+ATOM 26 CD1 LEU A 3 20.585 29.897 63.648 1.00 26.97 C
+ATOM 27 CD2 LEU A 3 18.461 29.459 62.420 1.00 27.95 C
+ATOM 1881 N MET A 255 29.709 5.069 60.642 1.00 26.34 N
+ATOM 1882 CA MET A 255 28.701 5.164 59.592 1.00 27.93 C
+ATOM 1883 C MET A 255 27.302 4.748 60.005 1.00 27.64 C
+ATOM 1884 O MET A 255 27.057 3.586 60.326 1.00 29.54 O
+ATOM 1885 CB MET A 255 29.146 4.331 58.399 1.00 28.54 C
+ATOM 1886 CG MET A 255 30.558 4.642 57.948 1.00 30.99 C
+ATOM 1887 SD MET A 255 31.116 3.394 56.790 1.00 34.74 S
+ATOM 1888 CE MET A 255 31.526 2.062 57.912 1.00 35.45 C
+ATOM 1889 N SER A 256 26.376 5.699 59.965 1.00 26.90 N
+ATOM 1890 CA SER A 256 24.998 5.430 60.347 1.00 28.27 C
+ATOM 1891 C SER A 256 24.040 5.839 59.231 1.00 28.44 C
+ATOM 1892 O SER A 256 24.543 6.294 58.186 1.00 28.92 O
+ATOM 1893 CB SER A 256 24.664 6.188 61.642 1.00 28.64 C
+ATOM 1894 OG SER A 256 25.569 5.836 62.681 1.00 28.28 O
+ATOM 1895 OXT SER A 256 22.811 5.701 59.408 1.00 27.92 O
+TER 1896 SER A 256
+ATOM 1897 N MET B 1 22.333 -31.975 81.215 1.00 44.89 N
+ATOM 1898 CA MET B 1 23.104 -30.998 82.028 1.00 43.40 C
+ATOM 1899 C MET B 1 24.121 -30.191 81.211 1.00 40.48 C
+ATOM 1900 O MET B 1 25.266 -30.614 81.040 1.00 38.97 O
+ATOM 1901 CB MET B 1 23.828 -31.727 83.164 1.00 48.82 C
+ATOM 1902 CG MET B 1 23.086 -31.723 84.500 1.00 55.57 C
+ATOM 1903 SD MET B 1 21.607 -32.746 84.539 1.00 63.93 S
+ATOM 1904 CE MET B 1 21.996 -33.836 85.950 1.00 64.69 C
+ATOM 3785 N SER B 256 17.566 -6.734 64.432 1.00 23.90 N
+ATOM 3786 CA SER B 256 18.942 -6.278 64.584 1.00 23.46 C
+ATOM 3787 C SER B 256 19.884 -7.335 64.032 1.00 23.50 C
+ATOM 3788 O SER B 256 19.390 -8.439 63.723 1.00 25.09 O
+ATOM 3789 CB SER B 256 19.253 -6.025 66.064 1.00 22.10 C
+ATOM 3790 OG SER B 256 18.279 -5.173 66.635 1.00 18.70 O
+ATOM 3791 OXT SER B 256 21.095 -7.051 63.923 1.00 22.97 O
+TER 3792 SER B 256
+HETATM 3793 O HOH 1 14.659 7.548 75.525 1.00 6.25 O
+HETATM 3794 O HOH 2 29.166 1.788 77.529 1.00 15.43 O
+END
diff --git a/modules/mol/alg/pymod/CMakeLists.txt b/modules/mol/alg/pymod/CMakeLists.txt
index 0ffb3f65183cb217c5fcfe6b1093a884ea42bca9..000e754817bce15b4e118a6ad65de253d9af8763 100644
--- a/modules/mol/alg/pymod/CMakeLists.txt
+++ b/modules/mol/alg/pymod/CMakeLists.txt
@@ -3,12 +3,16 @@ set(OST_MOL_ALG_PYMOD_SOURCES
export_svd_superpose.cc
export_clash.cc
export_trajectory_analysis.cc
+ export_structure_analysis.cc
)
set(OST_MOL_ALG_PYMOD_MODULES
"__init__.py"
views.py
superpose.py
+ trajectory_analysis.py
+ structure_analysis.py
+ helix_kinks.py
)
if (ENABLE_IMG)
@@ -19,7 +23,7 @@ if (ENABLE_IMG)
)
endif()
-
-pymod(NAME mol_alg OUTPUT_DIR ost/mol/alg CPP ${OST_MOL_ALG_PYMOD_SOURCES}
- PY ${OST_MOL_ALG_PYMOD_MODULES})
-
+if (NOT ENABLE_STATIC)
+ pymod(NAME mol_alg OUTPUT_DIR ost/mol/alg CPP ${OST_MOL_ALG_PYMOD_SOURCES}
+ PY ${OST_MOL_ALG_PYMOD_MODULES})
+endif()
diff --git a/modules/mol/alg/pymod/__init__.py b/modules/mol/alg/pymod/__init__.py
index 98fe346c5a07b1e28571832929b535ab0588adb3..3d7901d005e4328a1c730c1fd2e5a493360cce16 100644
--- a/modules/mol/alg/pymod/__init__.py
+++ b/modules/mol/alg/pymod/__init__.py
@@ -1,3 +1,5 @@
from _ost_mol_alg import *
from ost.mol.alg.superpose import *
-
+import ost.mol.alg.trajectory_analysis
+import ost.mol.alg.structure_analysis
+import ost.mol.alg.helix_kinks
diff --git a/modules/mol/alg/pymod/export_structure_analysis.cc b/modules/mol/alg/pymod/export_structure_analysis.cc
new file mode 100644
index 0000000000000000000000000000000000000000..85fbc230d34a1a568b1565672278b61a85a1b5b6
--- /dev/null
+++ b/modules/mol/alg/pymod/export_structure_analysis.cc
@@ -0,0 +1,35 @@
+//------------------------------------------------------------------------------
+// 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
+//------------------------------------------------------------------------------
+#include <boost/python.hpp>
+using namespace boost::python;
+
+#include <ost/mol/alg/structure_analysis.hh>
+
+using namespace ost;
+using namespace ost::mol::alg;
+
+void export_StructureAnalysis()
+{
+ def("GetPosListFromView",&GetPosListFromView, (arg("view")));
+#if OST_IMG_ENABLED
+ def("CalculateAverageAgreementWithDensityMap",&CalculateAverageAgreementWithDensityMap,(arg("pos_list"),arg("density_map")));
+ def("CalculateAgreementWithDensityMap",&CalculateAgreementWithDensityMap,(arg("pos_list"),arg("density_map")));
+#endif
+ def("WrapEntityInPeriodicCell",&WrapEntityInPeriodicCell,(arg("Entity"),arg("cell_center"),arg("nasis_vec")));
+}
diff --git a/modules/mol/alg/pymod/export_trajectory_analysis.cc b/modules/mol/alg/pymod/export_trajectory_analysis.cc
index 31377016a874dc6dcc42cc702d11a3a4058f0934..4db2668e91832d72952b12b637ad7141a7117ff3 100644
--- a/modules/mol/alg/pymod/export_trajectory_analysis.cc
+++ b/modules/mol/alg/pymod/export_trajectory_analysis.cc
@@ -43,7 +43,13 @@ void export_TrajectoryAnalysis()
def("AnalyzeDihedralAngle",&AnalyzeDihedralAngle, (arg("traj"), arg("atom"), arg("atom"), arg("atom"), arg("atom"), arg("stride")=1));
def("AnalyzeDistanceBetwCenterOfMass",&AnalyzeDistanceBetwCenterOfMass, (arg("traj"), arg("selection"), arg("selection"), arg("stride")=1));
def("AnalyzeRMSD",&AnalyzeRMSD, (arg("traj"), arg("reference_view"), arg("selection"), arg("stride")=1));
+ def("AnalyzeRMSF",&AnalyzeRMSF, (arg("traj"), arg("selection"), arg("first")=0, arg("last")=-1, arg("stride")=1));
def("AnalyzeMinDistance", &AnalyzeMinDistance, (arg("traj"), arg("view1"), arg("view2"), arg("stride")=1));
def("AnalyzeMinDistanceBetwCenterOfMassAndView", &AnalyzeMinDistanceBetwCenterOfMassAndView, (arg("traj"), arg("view_cm"), arg("view_atoms"), arg("stride")=1));
def("AnalyzeAromaticRingInteraction", &AnalyzeAromaticRingInteraction, (arg("traj"), arg("view_ring1"), arg("view_ring2"), arg("stride")=1));
+ def("AnalyzeAlphaHelixAxis", &AnalyzeAlphaHelixAxis, (arg("traj"), arg("protein_segment"), arg("directions"), arg("centers"), arg("stride")=1));
+ def("AnalyzeBestFitLine", &AnalyzeBestFitLine, (arg("traj"), arg("protein_segment"), arg("directions"), arg("centers"), arg("stride")=1));
+ def("AnalyzeBestFitPlane", &AnalyzeBestFitPlane, (arg("traj"), arg("protein_segment"), arg("normals"), arg("origins"), arg("stride")=1));
+ def("AnalyzeHelicity", &AnalyzeHelicity, (arg("traj"), arg("protein_segment"), arg("stride")=1));
+ def("CreateMeanStructure", &CreateMeanStructure, (arg("traj"), arg("selection"), arg("from")=0, arg("to")=-1, arg("stride")=1 ));
}
diff --git a/modules/mol/alg/pymod/helix_kinks.py b/modules/mol/alg/pymod/helix_kinks.py
new file mode 100644
index 0000000000000000000000000000000000000000..d57196bc5dc92d55e7b6f1abe6a7479b333b4fd2
--- /dev/null
+++ b/modules/mol/alg/pymod/helix_kinks.py
@@ -0,0 +1,150 @@
+"""
+Functions to calculate helix kinks: bend, face shift and wobbla angles
+
+Author: Niklaus Johner
+"""
+
+import os
+import ost
+
+def __FindProline(sele,proline):
+ if not sele.IsValid():
+ 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'
+ raise RuntimeError
+ proline=proline.residues[0]
+ proline_ca=proline.FindAtom('CA')
+ if not proline_ca.IsValid():
+ print 'proline has no CA atom'
+ raise RuntimeError
+ return (proline,proline_ca)
+ proline.GetNumber().num
+
+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'
+ for res in pre_proline.residues:
+ print res
+ print 'post-proline residues'
+ for res in post_proline.residues:
+ 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'
+ raise RuntimeError
+ return (pre_proline,post_proline)
+
+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'
+ raise RuntimeError
+ return (ca_3,ca_4)
+
+
+def __CalculateBendAngle(pre_proline_axis,post_proline_axis):
+ return ost.geom.Angle(pre_proline_axis,post_proline_axis)
+
+def __CalculateWobbleAngle(pre_proline_axis,post_proline_axis,post_proline_centers,proline_pos):
+ p1=proline_pos-post_proline_centers
+ n1=p1-ost.geom.Dot(p1,post_proline_axis)*post_proline_axis
+ p2=-pre_proline_axis
+ n2=p2-ost.geom.Dot(p2,post_proline_axis)*post_proline_axis
+ sign=ost.geom.Dot(ost.geom.Cross(pre_proline_axis,n2),n2-n1)
+ sign=sign/abs(sign)
+ return sign*ost.geom.Angle(n1,n2)
+
+def __CalculateFaceShift(pre_proline_axis,post_proline_axis,pre_proline_centers,post_proline_centers,proline_pos,ca3_pos,ca4_pos,bend_angle):
+ p1=proline_pos-post_proline_centers
+ n1=p1-ost.geom.Dot(p1,post_proline_axis)*post_proline_axis
+ p2=(ca3_pos+ca4_pos)/2.0-pre_proline_centers
+ n2=p2-ost.geom.Dot(p2,pre_proline_axis)*pre_proline_axis
+ #Here we want to apply a rotation to n1, to align the post-proline axis on the pre-proline axis
+ R=ost.geom.AxisRotation(ost.geom.Cross(post_proline_axis,pre_proline_axis),bend_angle)
+ n1=R*n1
+ #We also need to determine the sign of the angle
+ sign=ost.geom.Dot(ost.geom.Cross(pre_proline_axis,n2),n2-n1)
+ sign=sign/abs(sign)
+ return sign*ost.geom.Angle(n1,n2)
+
+
+def AnalyzeHelixKink(t,sele,proline=False):
+ """
+ This function calculates the bend,wobble and face-shift angles
+ in an alpha-helix over a trajectory. The determination is more stable if
+ there are at least 4 residues on each side (8 is even better) of the prolin around which
+ the helix is kinked. The selection should contain all residues in the correct
+ order and with no gaps and no missing C-alphas.
+ Input:
+ t : The trajectory to be analyzed (CoordGroup)
+ sele : A selection containing the alpha helix to be analyzed (EntityView)
+ proline=False : An EntityView containing only the proline (or another residue) around which the
+ helix is kinked. If False, the proline will be serached for automatically
+ Output:
+ (bend_angle,face_shift,wobble_angle) : a tuple of FloatLists
+ """
+ n_frames=t.GetFrameCount()
+ (proline,proline_ca)=__FindProline(sele,proline)
+ proline_num=proline.GetNumber().num
+ (pre_proline,post_proline)=__SelectPreAndPostProline(sele,proline_num)
+ (ca_3,ca_4)=__FindCa3AndCa4(sele,proline_ca,proline_num)
+ #Here we extract the necessary information from the trajectory
+ pre_proline_axis=ost.geom.Vec3List()
+ post_proline_axis=ost.geom.Vec3List()
+ pre_proline_centers=ost.geom.Vec3List()
+ post_proline_centers=ost.geom.Vec3List()
+ ost.mol.alg.AnalyzeAlphaHelixAxis(t,pre_proline,pre_proline_axis,pre_proline_centers)
+ ost.mol.alg.AnalyzeAlphaHelixAxis(t,post_proline,post_proline_axis,post_proline_centers)
+ proline_pos=ost.mol.alg.AnalyzeAtomPos(t,proline_ca.GetHandle())
+ ca3_pos=ost.mol.alg.AnalyzeAtomPos(t,ca_3.GetHandle())
+ ca4_pos=ost.mol.alg.AnalyzeAtomPos(t,ca_4.GetHandle())
+ #Now we calculate the bend angle
+ bend_angle=[]
+ face_shift=[]
+ wobble_angle=[]
+ for i in range(n_frames):
+ bend_angle.append(__CalculateBendAngle(pre_proline_axis[i],post_proline_axis[i]))
+ face_shift.append(__CalculateFaceShift(pre_proline_axis[i],post_proline_axis[i],pre_proline_centers[i],post_proline_centers[i],proline_pos[i],ca3_pos[i],ca4_pos[i],bend_angle[i]))
+ wobble_angle.append(__CalculateWobbleAngle(pre_proline_axis[i],post_proline_axis[i],post_proline_centers[i],proline_pos[i]))
+ return (bend_angle,face_shift,wobble_angle)
+
+
+def CalculateHelixKink(sele,proline=False):
+ """
+ This function calculates the bend,wobble and face-shift angles
+ in an alpha-helix of an EntityView. The determination is more stable if
+ there are at least 4 residues on each side (8 is even better) of the prolin around which
+ the helix is kinked. The selection should contain all residues in the correct
+ order and with no gaps and no missing C-alphas.
+ Input:
+ sele : A selection containing the alpha helix to be analyzed (EntityView)
+ proline=False : An EntityView containing only the proline (or another residue) around which the
+ helix is kinked. If False, the proline will be serached for automatically
+ Output:
+ (bend_angle,face_shift,wobble_angle) : a tuple of Floats
+ """
+ (proline,proline_ca)=__FindProline(sele,proline)
+ proline_num=proline.GetNumber().num
+ (pre_proline,post_proline)=__SelectPreAndPostProline(sele,proline_num)
+ (ca_3,ca_4)=__FindCa3AndCa4(sele,proline_ca,proline_num)
+ #Here we extract the necessary information from the structure
+ pre_proline_axis=ost.mol.alg.structure_analysis.CalculateHelixAxis(pre_proline)
+ post_proline_axis=ost.mol.alg.structure_analysis.CalculateHelixAxis(post_proline)
+ prepa=pre_proline_axis.GetDirection()
+ prepc=pre_proline_axis.GetOrigin()
+ postpa=post_proline_axis.GetDirection()
+ postpc=post_proline_axis.GetOrigin()
+ #calculate the angles
+ bend=__CalculateBendAngle(prepa,postpa)
+ wobble=__CalculateWobbleAngle(prepa,postpa,postpc,proline_ca.pos)
+ shift=__CalculateFaceShift(prepa,postpa,prepc,postpc,proline_ca.pos,ca_3.pos,ca_4.pos,bend)
+ return (bend,shift,wobble)
+
+
+
+
\ No newline at end of file
diff --git a/modules/mol/alg/pymod/structure_analysis.py b/modules/mol/alg/pymod/structure_analysis.py
new file mode 100644
index 0000000000000000000000000000000000000000..7cbd0dd4b32bb7e6f4093ed23bbbb52a700fc320
--- /dev/null
+++ b/modules/mol/alg/pymod/structure_analysis.py
@@ -0,0 +1,131 @@
+"""
+Some functions for analyzing trajectories
+
+Author: Niklaus Johner
+"""
+
+import os
+import ost
+
+def GetFrameFromEntity(eh):
+ """
+ This function returns a CoordFrame from an EntityHandle
+ Input:
+ eh : EntityHandle
+ """
+ return ost.mol.CreateCoordFrame(eh.GetAtomPosList())
+
+def GetDistanceBetwCenterOfMass(sele1,sele2):
+ """
+ This function calculates the distance between the centers of mass
+ of sele1 and sele2, two selections from the same Entity.
+ Input:
+ sele1 : EntityView
+ sele2 : EntityView
+ """
+ if not sele1.IsValid() and sele2.IsValid():
+ print 'invalid view'
+ return
+ eh=sele1.GetHandle()
+ if not eh==sele2.GetHandle():
+ print 'The two views must be from the same entity'
+ return
+ f=GetFrameFromEntity(eh)
+ return f.GetDistanceBetwCenterOfMass(sele1,sele2)
+
+def GetMinDistanceBetweenViews(sele1,sele2):
+ """
+ This function calculates the minimal distance between
+ sele1 and sele2, two selections from the same Entity.
+ Input:
+ sele1 : EntityView
+ sele2 : EntityView
+ """
+ if not sele1.IsValid() and sele2.IsValid():
+ print 'invalid view'
+ return
+ eh=sele1.GetHandle()
+ if not eh==sele2.GetHandle():
+ print 'The two views must be from the same entity'
+ return
+ f=GetFrameFromEntity(eh)
+ return f.GetMinDistance(sele1,sele2)
+
+def GetMinDistBetwCenterOfMassAndView(sele1,sele2):
+ """
+ This function calculates the minimal distance between sele2 and
+ the center of mass of sele1, two selections from the same Entity.
+ Input:
+ sele1 : EntityView from which the center of mass is taken
+ sele2 : EntityView
+ """
+ if not sele1.IsValid() and sele2.IsValid():
+ print 'invalid view'
+ return
+ eh=sele1.GetHandle()
+ if not eh==sele2.GetHandle():
+ print 'The two views must be from the same entity'
+ return
+ f=GetFrameFromEntity(eh)
+ return f.GetMinDistBetwCenterOfMassAndView(sele1,sele2)
+
+
+def GetAlphaHelixContent(sele1):
+ """
+ This function calculates the content of alpha helix in a view.
+ All residues in the view have to ordered and adjacent (no gaps allowed)
+ Input:
+ sele1 : EntityView
+ """
+ if not sele1.IsValid():
+ print 'invalid view'
+ return
+ eh=sele1.GetHandle()
+ f=GetFrameFromEntity(eh)
+ return f.GetAlphaHelixContent(sele1)
+
+
+def CalculateBestFitLine(sele1):
+ """
+ This function calculates the best fit line to the atoms in sele1.
+ Input:
+ sele1 : EntityView
+ It returns a geom::Line3
+ """
+ if not sele1.IsValid():
+ print 'invalid view'
+ return
+ eh=sele1.GetHandle()
+ f=GetFrameFromEntity(eh)
+ return f.GetODRLine(sele1)
+
+def CalculateBestFitPlane(sele1):
+ """
+ This function calculates the best fit plane to the atoms in sele1.
+ Input:
+ sele1 : EntityView
+ It returns a geom::Plane
+ """
+ if not sele1.IsValid():
+ print 'invalid view'
+ return
+ eh=sele1.GetHandle()
+ f=GetFrameFromEntity(eh)
+ return f.GetODRPlane(sele1)
+
+def CalculateHelixAxis(sele1):
+ """
+ This function calculates the best fit cylinder to the CA atoms in sele1,
+ and returns its axis as a Line3. residues should be ordered correctly
+ in the EntityView.
+ Input:
+ sele1 : EntityView
+ It returns a geom::Line3
+ """
+ if not sele1.IsValid():
+ print 'invalid view'
+ return
+ eh=sele1.GetHandle()
+ f=GetFrameFromEntity(eh)
+ return f.FitCylinder(sele1)
+
diff --git a/modules/mol/alg/pymod/superpose.py b/modules/mol/alg/pymod/superpose.py
index 96ad881b0e045f8ded7af3ff745ef00a712a0ff4..76d4afe98d53178bba1cf357e2e4f827ccef7f01 100644
--- a/modules/mol/alg/pymod/superpose.py
+++ b/modules/mol/alg/pymod/superpose.py
@@ -112,10 +112,11 @@ def MatchResidueByNum(ent_a, ent_b, atoms='all'):
while True:
r_a=residues_a.next()
r_b=residues_b.next()
- while r_a.number<r_b.number:
- r_a=residues_a.next()
- while r_b.number<r_a.number:
- r_b=residues_b.next()
+ while r_a.number!=r_b.number:
+ while r_a.number<r_b.number:
+ r_a=residues_a.next()
+ while r_b.number<r_a.number:
+ r_b=residues_b.next()
assert r_a.number==r_b.number
result_a,result_b=_fetch_atoms(r_a, r_b, result_a, result_b, atmset)
except StopIteration:
diff --git a/modules/mol/alg/pymod/trajectory_analysis.py b/modules/mol/alg/pymod/trajectory_analysis.py
new file mode 100644
index 0000000000000000000000000000000000000000..b445b02351775b92ba66cf80655f63610999569f
--- /dev/null
+++ b/modules/mol/alg/pymod/trajectory_analysis.py
@@ -0,0 +1,199 @@
+"""
+Some functions for analyzing trajectories
+
+Author: Niklaus Johner
+"""
+
+import ost.mol.alg
+import ost.geom
+from ost import LogError
+import os
+
+def smooth(vec,n):
+#Function to smooth a vector or a list of floats
+#for each element it takes the average over itself and the
+#n elements on each side, so over (2n+1) elements
+ try:
+ vec2=vec.copy()
+ except:
+ vec2=vec[:]
+ for i in range(n):
+ v=0.0
+ count=1.0
+ v+=vec[i]
+ for j in range(n):
+ count+=1
+ v+=vec[i+j+1]
+ for j in range(i):
+ count+=1
+ v+=vec[i-(j+1)]
+ vec2[i]=v/float(count)
+ for i in range(1,n+1):
+ v=0.0
+ count=1.0
+ v+=vec[-i]
+ for j in range(n):
+ count+=1
+ v+=vec[-(i+j+1)]
+ for j in range(i-1):
+ count+=1
+ v+=vec[-i+j+1]
+ vec2[-i]=v/float(count)
+ for i in range(n,len(vec2)-n):
+ v=vec[i]
+ for j in range(n):
+ v+=vec[i+j+1]
+ v+=vec[i-j-1]
+ vec2[i]=v/float(2.*n+1.)
+ return vec2
+
+
+"""
+From here on the module needs numpy
+"""
+
+def RMSD_Matrix_From_Traj(t,sele,first=0,last=-1):
+ """
+ This function calculates a matrix M such that M[i,j] is the
+ RMSD of the EntityView sele between frames i and j of the trajectory t
+ aligned on sele.
+ Its inputs are:
+ t : the trajectory (CoordGroupHandle)
+ sele : the EntityView used for alignment and RMSD calculation
+ first=0 : the first frame of t to be used
+ last=-1 : the last frame of t to be used
+ Returns a numpy NxN matrix, where n is the number of frames.
+ """
+ try:
+ import numpy as npy
+ if last==-1:last=t.GetFrameCount()
+ n_frames=last-first
+ rmsd_matrix=npy.identity(n_frames)
+ for i in range(n_frames):
+ t=ost.mol.alg.SuperposeFrames(t,sele,begin=first,end=last,ref=i)
+ eh=t.GetEntity()
+ t.CopyFrame(i)
+ rmsd_matrix[i,:]=ost.mol.alg.AnalyzeRMSD(t,sele,sele)
+ if i==0:
+ last=last-first
+ first=0
+ return rmsd_matrix
+ except ImportError:
+ LogError("Function needs numpy, but I could not import it.")
+ raise
+
+
+def PairwiseDistancesFromTraj(t,sele,first=0,last=-1,seq_sep=1):
+ """
+ This function calculates the distances between any pair of atoms in the
+ EntityView sele with sequence separation larger than seq_sep from a trajectory t.
+ It return a matrix containing one line for each atom pair and N columns, where
+ N is the length of the trajectory.
+ Its inputs are:
+ t : the trajectory (CoordGroupHandle)
+ sele : the EntityView used to determine the atom pairs
+ first=0 : the first frame of t to be used
+ last=-1 : the last frame of t to be used
+ seq_sep=1 : The minimal sequence separation between
+ Returns a numpy NpairsxNframes matrix.
+ """
+ try:
+ import numpy as npy
+ if last==-1:last=t.GetFrameCount()
+ n_frames=last-first
+ n_var=0
+ for i,a1 in enumerate(sele.atoms):
+ for j,a2 in enumerate(sele.atoms):
+ if not j-i<seq_sep:n_var+=1
+ #n_var=sele.GetAtomCount()
+ #n_var=(n_var-1)*(n_var)/2.
+ dist_matrix=npy.zeros(n_frames*n_var)
+ dist_matrix=dist_matrix.reshape(n_var,n_frames)
+ k=0
+ for i,a1 in enumerate(sele.atoms):
+ for j,a2 in enumerate(sele.atoms):
+ if j-i<seq_sep:continue
+ dist_matrix[k]=ost.mol.alg.AnalyzeDistanceBetwAtoms(t,a1.GetHandle(),a2.GetHandle())[first:last]
+ k+=1
+ return dist_matrix
+ except ImportError:
+ LogError("Function needs numpy, but I could not import it.")
+ raise
+
+def DistanceMatrixFromPairwiseDistances(distances,p=2):
+ """
+ This function calculates an distance matrix M(NxN) from
+ the pairwise distances matrix D(MxN), where N is the number
+ of frames in the trajectory and M the number of atom pairs.
+ M[i,j] is the distance between frame i and frame j
+ calculated as a p-norm of the differences in distances
+ from the two frames (distance-RMSD for p=2).
+ Inputs:
+ distances : a pairwise distance matrix as obtained from PairwiseDistancesFromTraj()
+ Returns a numpy NxN matrix, where N is the number of frames.
+ """
+ try:
+ import numpy as npy
+ n1=distances.shape[0]
+ n2=distances.shape[1]
+ dist_mat=npy.identity(n2)
+ for i in range(n2):
+ for j in range(n2):
+ if j<=i:continue
+ d=(((abs(distances[:,i]-distances[:,j])**p).sum())/float(n1))**(1./p)
+ dist_mat[i,j]=d
+ dist_mat[j,i]=d
+ return dist_mat
+ except ImportError:
+ LogError("Function needs numpy, but I could not import it.")
+ raise
+
+def DistRMSDFromTraj(t,sele,ref_sele,radius=7.0,average=False,seq_sep=4,first=0,last=-1):
+ """
+ This function calculates the distance RMSD from a trajectory.
+ The distances selected for the calculation are all the distances
+ between pair of atoms that from residues that are at least seq_sep apart
+ in the sequence and that are smaller than radius in ref_sel.
+ The number and order of atoms in ref_sele and sele should be the same.
+ Its inputs are:
+ t : the trajectory (CoordGroupHandle)
+ sele : the EntityView used to determine the distances from t
+ radius=7 : the upper limit of distances in ref_sele considered for the calculation
+ seq_sep=4 : The minimal sequence separation between atom pairs considered for the calculation
+ average=false : use the average distance in the trajectory as reference instead of the distance obtained from ref_sele
+ first=0 : the first frame of t to be used
+ last=-1 : the last frame of t to be used
+ Returns a numpy vecor dist_rmsd(Nframes).
+ """
+ if not sele.GetAtomCount()==ref_sele.GetAtomCount():
+ print 'Not same number of atoms in the two views'
+ return
+ try:
+ import numpy as npy
+ if last==-1:last=t.GetFrameCount()
+ n_frames=last-first
+ dist_rmsd=npy.zeros(n_frames)
+ pair_count=0.0
+ for i,a1 in enumerate(ref_sele.atoms):
+ for j,a2 in enumerate(ref_sele.atoms):
+ if j<=i:continue
+ r1=a1.GetResidue()
+ c1=r1.GetChain()
+ r2=a2.GetResidue()
+ c2=r2.GetChain()
+ if c1==c2 and abs(r2.GetNumber().num-r1.GetNumber().num)<seq_sep:continue
+ d=ost.geom.Distance(a1.pos,a2.pos)
+ if d<radius:
+ a3=sele.atoms[i]
+ a4=sele.atoms[j]
+ d_traj=ost.mol.alg.AnalyzeDistanceBetwAtoms(t,a3.GetHandle(),a4.GetHandle())[first:last]
+ if average:d=npy.mean(d_traj)
+ for k,el in enumerate(d_traj):
+ dist_rmsd[k]+=(el-d)**2.0
+ pair_count+=1.0
+ return (dist_rmsd/float(pair_count))**0.5
+ except ImportError:
+ LogError("Function needs numpy, but I could not import it.")
+ raise
+
+
\ No newline at end of file
diff --git a/modules/mol/alg/pymod/wrap_mol_alg.cc b/modules/mol/alg/pymod/wrap_mol_alg.cc
index 4f974d940ee2f090eb4d0a5c3d90f46a06616747..c7c3e1c3b3b62e46de87b21ff5a118da5808cbcb 100644
--- a/modules/mol/alg/pymod/wrap_mol_alg.cc
+++ b/modules/mol/alg/pymod/wrap_mol_alg.cc
@@ -18,6 +18,7 @@
//------------------------------------------------------------------------------
#include <boost/python.hpp>
+#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
#include <ost/config.hh>
#include <ost/mol/alg/local_dist_test.hh>
#include <ost/mol/alg/superpose_frames.hh>
@@ -27,6 +28,7 @@ using namespace ost;
void export_svdSuperPose();
void export_TrajectoryAnalysis();
+void export_StructureAnalysis();
void export_Clash();
#if OST_IMG_ENABLED
void export_entity_to_density();
@@ -34,12 +36,39 @@ void export_entity_to_density();
namespace {
-Real (*ldt_a)(const mol::EntityView&, const mol::EntityView& ref, Real, Real, const String&)=&mol::alg::LocalDistTest;
+Real (*ldt_a)(const mol::EntityView&, const mol::alg::GlobalDistanceList& glob_dist_list, Real, const String&)=&mol::alg::LocalDistTest;
Real (*ldt_b)(const seq::AlignmentHandle&,Real, Real, int, int)=&mol::alg::LocalDistTest;
-mol::EntityView (*fc_a)(const mol::EntityView&, Real,bool)=&mol::alg::FilterClashes;
-mol::EntityView (*fc_b)(const mol::EntityHandle&, Real, bool)=&mol::alg::FilterClashes;
+mol::EntityView (*fc_a)(const mol::EntityView&, const mol::alg::ClashingDistances&,bool)=&mol::alg::FilterClashes;
+mol::EntityView (*fc_b)(const mol::EntityHandle&, const mol::alg::ClashingDistances&, bool)=&mol::alg::FilterClashes;
+mol::EntityView (*csc_a)(const mol::EntityView&, const mol::alg::StereoChemicalParams&, const mol::alg::StereoChemicalParams&, Real, Real, bool)=&mol::alg::CheckStereoChemistry;
+mol::EntityView (*csc_b)(const mol::EntityHandle&, const mol::alg::StereoChemicalParams&, const mol::alg::StereoChemicalParams&, Real, Real, bool)=&mol::alg::CheckStereoChemistry;
mol::CoordGroupHandle (*superpose_frames1)(mol::CoordGroupHandle&, mol::EntityView&, int, int, int)=&mol::alg::SuperposeFrames;
mol::CoordGroupHandle (*superpose_frames2)(mol::CoordGroupHandle&, mol::EntityView&, mol::EntityView&, int, int)=&mol::alg::SuperposeFrames;
+
+ost::mol::alg::StereoChemicalParams fill_stereochemical_params_wrapper (const String& header, const list& stereo_chemical_props_file)
+{
+ int stereo_chemical_props_file_length = boost::python::extract<int>(stereo_chemical_props_file.attr("__len__")());
+ std::vector<String> stereo_chemical_props_file_vector;
+
+ for (int i=0; i<stereo_chemical_props_file_length; i++) {
+ String extracted_string = boost::python::extract<String>(stereo_chemical_props_file[i]);
+ stereo_chemical_props_file_vector.push_back(extracted_string);
+ }
+ return ost::mol::alg::FillStereoChemicalParams(header,stereo_chemical_props_file_vector);
+}
+
+ost::mol::alg::ClashingDistances fill_clashing_distances_wrapper (const list& stereo_chemical_props_file, Real min_default_distance, Real min_distance_tolerance)
+{
+ int stereo_chemical_props_file_length = boost::python::extract<int>(stereo_chemical_props_file.attr("__len__")());
+ std::vector<String> stereo_chemical_props_file_vector(stereo_chemical_props_file_length);
+
+ for (int i=0; i<stereo_chemical_props_file_length; i++) {
+ stereo_chemical_props_file_vector[i] = boost::python::extract<char const*>(stereo_chemical_props_file[i]);
+ }
+
+ return ost::mol::alg::FillClashingDistances(stereo_chemical_props_file_vector,min_default_distance,min_distance_tolerance);
+}
+
}
@@ -48,18 +77,71 @@ BOOST_PYTHON_MODULE(_ost_mol_alg)
{
export_svdSuperPose();
export_TrajectoryAnalysis();
+ export_StructureAnalysis();
#if OST_IMG_ENABLED
export_entity_to_density();
#endif
def("LocalDistTest", ldt_a, (arg("local_ldt_property_string")=""));
def("LocalDistTest", ldt_b, (arg("ref_index")=0, arg("mdl_index")=1));
- def("FilterClashes", fc_a, (arg("ent"), arg("tolerance")=0.1, arg("always_remove_bb")=false));
- def("FilterClashes", fc_b, (arg("ent"), arg("tolerance")=0.1, arg("always_remove_bb")=false));
+ def("FilterClashes", fc_a, (arg("ent"), arg("clashing_distances"), arg("always_remove_bb")=false));
+ def("FilterClashes", fc_b, (arg("ent"), arg("clashing_distances"), arg("always_remove_bb")=false));
+ def("CheckStereoChemistry", csc_a, (arg("ent"), arg("bonds"), arg("angles"), arg("bond_tolerance"), arg("angle_tolerance"), arg("always_remove_bb")=false));
+ def("CheckStereoChemistry", csc_b, (arg("ent"), arg("bonds"), arg("angles"), arg("bond_tolerance"), arg("angle_tolerance"), arg("always_remove_bb")=false));
+ def("LDTHA",&mol::alg::LDTHA);
+ def("CreateDistanceList",&mol::alg::CreateDistanceList);
+
def("SuperposeFrames", superpose_frames1,
(arg("source"), arg("sel")=ost::mol::EntityView(), arg("begin")=0,
arg("end")=-1, arg("ref")=-1));
def("SuperposeFrames", superpose_frames2,
- (arg("source"), arg("sel")=ost::mol::EntityView(), arg("ref_view")=ost::mol::EntityView(),arg("begin")=0,
- arg("end")=-1));
+ (arg("source"), arg("sel"), arg("ref_view"),arg("begin")=0, arg("end")=-1));
+
+
+ class_<mol::alg::ClashingDistances> ("ClashingDistances" ,init<Real,Real>())
+ .def("SetClashingDistance",&mol::alg::ClashingDistances::SetClashingDistance)
+ .def("GetClashingDistance",&mol::alg::ClashingDistances::GetClashingDistance)
+ .def("GetMaxAdjustedDistance",&mol::alg::ClashingDistances::GetMaxAdjustedDistance)
+ .def("IsEmpty",&mol::alg::ClashingDistances::IsEmpty)
+
+ .def("PrintAllDistances",&mol::alg::ClashingDistances::PrintAllDistances)
+ ;
+
+ class_<mol::alg::StereoChemicalParams> ("StereoChemicalParams" ,init<>())
+ .def("SetParam",&mol::alg::StereoChemicalParams::SetParam)
+ .def("GetParam",&mol::alg::StereoChemicalParams::GetParam)
+ .def("ContainsParam",&mol::alg::StereoChemicalParams::ContainsParam)
+ .def("IsEmpty",&mol::alg::StereoChemicalParams::IsEmpty)
+
+ .def("PrintAllParameters",&mol::alg::StereoChemicalParams::PrintAllParameters)
+
+ ;
+
+ class_<mol::alg::UniqueAtomIdentifier> ("UniqueAtomIdentifier" ,init <const String&, const mol::ResNum&, const String&, const String&>())
+ .def("GetChainName",&mol::alg::UniqueAtomIdentifier::GetChainName)
+ .def("GetResNum",&mol::alg::UniqueAtomIdentifier::GetResNum)
+ .def("GetResidueName",&mol::alg::UniqueAtomIdentifier::GetResidueName)
+ .def("GetAtomName",&mol::alg::UniqueAtomIdentifier::GetAtomName)
+ ;
+
+
+ class_<mol::alg::ReferenceDistance> ("ReferenceDistance", init <const mol::alg::UniqueAtomIdentifier&,const mol::alg::UniqueAtomIdentifier&, Real, Real>())
+ .def("GetFirstAtom",&mol::alg::ReferenceDistance::GetFirstAtom)
+ .def("GetSecondAtom",&mol::alg::ReferenceDistance::GetSecondAtom)
+ .def("GetMinDistance",&mol::alg::ReferenceDistance::GetMinDistance)
+ .def("GetMaxDistance",&mol::alg::ReferenceDistance::GetMaxDistance)
+ ;
+
+ class_<std::vector<mol::alg::ReferenceDistance> >("ResidueDistanceList")
+ .def(vector_indexing_suite<std::vector<mol::alg::ReferenceDistance > >())
+ ;
+
+ class_<std::vector<mol::alg::ResidueDistanceList> >("GlobalDistanceList")
+ .def(vector_indexing_suite<std::vector<mol::alg::ResidueDistanceList > >())
+ ;
+
+ def("FillClashingDistances",&fill_clashing_distances_wrapper);
+ def("FillStereoChemicalParams",&fill_stereochemical_params_wrapper);
+ def("IsStandardResidue",&mol::alg::IsStandardResidue);
+
}
diff --git a/modules/mol/alg/src/CMakeLists.txt b/modules/mol/alg/src/CMakeLists.txt
index 47c9af142248f8a4ee18cc65bbf24fd59d7f8f92..050d4822712f8789bfac97938e18c327334f7d92 100644
--- a/modules/mol/alg/src/CMakeLists.txt
+++ b/modules/mol/alg/src/CMakeLists.txt
@@ -8,6 +8,7 @@ set(OST_MOL_ALG_HEADERS
construct_cbeta.hh
clash_score.hh
trajectory_analysis.hh
+ structure_analysis.hh
)
set(OST_MOL_ALG_SOURCES
@@ -19,6 +20,7 @@ set(OST_MOL_ALG_SOURCES
filter_clashes.cc
construct_cbeta.cc
trajectory_analysis.cc
+ structure_analysis.cc
)
set(MOL_ALG_DEPS ost_mol ost_seq)
@@ -38,7 +40,7 @@ if (ENABLE_IMG)
endif()
executable(NAME ldt SOURCES ldt.cc
- DEPENDS_ON ost_io ost_mol_alg STATIC)
+ DEPENDS_ON ost_mol ost_mol_alg ost_io STATIC)
module(NAME mol_alg SOURCES ${OST_MOL_ALG_SOURCES}
HEADERS ${OST_MOL_ALG_HEADERS}
@@ -51,3 +53,7 @@ copy_if_different("." "${STAGE_DIR}/share/openstructure"
"ost_mol_alg")
install(FILES "atom_scattering_properties.txt" DESTINATION "share/openstructure/")
+copy_if_different("." "${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/filter_clashes.cc b/modules/mol/alg/src/filter_clashes.cc
index 0fbca1696e5bc3ef1196f6d2a4863a1b0d72dcef..1b163d17616c676e0933b7ebc7bad4c6e56dea91 100644
--- a/modules/mol/alg/src/filter_clashes.cc
+++ b/modules/mol/alg/src/filter_clashes.cc
@@ -18,78 +18,479 @@
//------------------------------------------------------------------------------
#include <ost/log.hh>
#include <ost/mol/mol.hh>
+#include <sstream>
+#include <math.h>
#include "filter_clashes.hh"
+#include <ost/units.hh>
+
-namespace ost { namespace mol { namespace alg {
namespace {
-Real GetThreshold(const String& ele1, const String& ele2) {
- if (ele1.length()!=1 || ele2.length()!=1) {
- return 1.5;
+String bond_string(const ost::mol::AtomView& atom1, const ost::mol::AtomHandle& atom2) {
+ String atom1_str = atom1.GetName();
+ String atom2_str = atom2.GetName();
+ String string1,string2;
+ if (atom1_str < atom2_str) {
+ string1 = atom1_str;
+ string2 = atom2_str;
+ } else {
+ string1 = atom2_str;
+ string2 = atom1_str;
}
- switch (ele1[0]) {
- case 'C' :
- switch (ele2[0]) {
- case 'C' : return 2.10;
- case 'N' : return 2.10;
- case 'S' : return 2.45;
- case 'O' : return 2.25;
- default: return 1.5;
- }
- case 'N':
- switch (ele2[0]) {
- case 'C' : return 2.10;
- case 'N' : return 2.05;
- case 'S' : return 2.55;
- case 'O' : return 2.10;
- default: return 1.5;
+ std::stringstream stkey;
+ stkey << string1 << "-" << string2;
+ return stkey.str();
+}
+
+String angle_string(const ost::mol::AtomHandle& atom1, const ost::mol::AtomView& atom, const ost::mol::AtomHandle& atom2 ) {
+ String atom1_str = atom1.GetName();
+ String atom2_str = atom2.GetName();
+ String string1,string2;
+ if (atom1_str < atom2_str) {
+ string1 = atom1_str;
+ string2 = atom2_str;
+ } else {
+ string1 = atom2_str;
+ string2 = atom1_str;
+ }
+ std::stringstream stkey;
+ stkey << string1 << "-" << atom.GetName() << "-" << string2;
+ return stkey.str();
+}
+
+
+}
+
+
+namespace ost { namespace mol { namespace alg {
+
+void ClashingDistances::SetClashingDistance(const String& ele1,const String& ele2, Real min_distance, Real tolerance)
+{
+ std::stringstream stkey;
+ stkey << ele1 << "--" << ele2;
+ String key=stkey.str();
+ min_distance_[key]=std::make_pair<Real,Real>(min_distance,tolerance);
+}
+
+std::pair<Real,Real> ClashingDistances::GetClashingDistance(const String& ele1,const String& ele2) const
+{
+ std::stringstream stkey;
+ if (ele1<ele2) {
+ stkey << ele1 << "--" << ele2;
+ } else {
+ stkey << ele2 << "--" << ele1;
+ }
+ String key=stkey.str();
+ std::map <String,std::pair<float,float> >::const_iterator find_ci= min_distance_.find(key);
+ if (find_ci == min_distance_.end()) {
+ return std::make_pair<Real,Real> (default_min_distance_,default_min_distance_tolerance_);
+ }
+ return find_ci->second;
+}
+
+void ClashingDistances::PrintAllDistances() const
+{
+ for (std::map <String,std::pair<float,float> >::const_iterator index = min_distance_.begin();index != min_distance_.end();++index) {
+ std::cout << index->first << "\t" << index->second.first << "\t" << index->second.second << std::endl;
+ }
+}
+
+Real ClashingDistances::GetMaxAdjustedDistance() const
+{
+ Real max_adjusted_distance=0;
+ for (std::map <String,std::pair<float,float> >::const_iterator index = min_distance_.begin();index != min_distance_.end();++index) {
+ Real distance = index->second.first;
+ Real tolerance = index->second.second;
+ if ((distance-tolerance) > max_adjusted_distance) {
+ max_adjusted_distance=distance-tolerance;
+ }
+ }
+ return max_adjusted_distance;
+}
+
+bool ClashingDistances::IsEmpty() const
+{
+ if (min_distance_.size()==0) {
+ return true;
+ }
+ return false;
+}
+
+void StereoChemicalParams::SetParam(const String& param, const String& residue, Real value, Real st_dev)
+{
+ std::pair<String,String> key = std::make_pair<String,String>(param,residue);
+ params_[key]=std::make_pair<Real,Real>(value,st_dev);
+}
+
+std::pair<Real,Real> StereoChemicalParams::GetParam(const String& param,const String& residue) const
+{
+ std::pair<String,String> key = std::make_pair<String,String>(param,residue);
+ std::map<std::pair<String,String>,std::pair<float,float> >::const_iterator find_ci = params_.find(key);
+ if (find_ci == params_.end()) {
+ std::stringstream serr;
+ serr << "Entry " << param << " for residue " << residue << " not found in the parameter table";
+ throw Error(serr.str());
+ }
+ return find_ci->second;
+}
+
+bool StereoChemicalParams::ContainsParam(const String& param,const String& residue) const
+{
+ std::pair<String,String> key = std::make_pair<String,String>(param,residue);
+ std::map<std::pair<String,String>,std::pair<float,float> >::const_iterator find_ci = params_.find(key);
+ if (find_ci == params_.end()) {
+ return false;
+ }
+ return true;
+}
+
+void StereoChemicalParams::PrintAllParameters() const
+{
+ for (std::map <std::pair<String,String>,std::pair<float,float> >::const_iterator index = params_.begin();index != params_.end();++index) {
+ std::cout << index->first.first << "\t" << index->first.second << "\t" << index->second.first << "\t" << index->second.second << std::endl;
+ }
+};
+
+bool StereoChemicalParams::IsEmpty() const
+{
+ if (params_.size()==0) {
+ return true;
+ }
+ return false;
+}
+
+StereoChemicalParams FillStereoChemicalParams(const String& header, std::vector<String>& stereo_chemical_props_file)
+{
+ StereoChemicalParams table;
+ bool found=false;
+ std::vector<String>::const_iterator line_iter=stereo_chemical_props_file.begin();
+ while (line_iter!=stereo_chemical_props_file.end()) {
+ if ((*line_iter).length()!=0 && (*line_iter).length()!=1) {
+ StringRef line_string_ref(line_iter->data(),(*line_iter).length());
+ std::vector<StringRef> line_str_vec = line_string_ref.split();
+ if (line_str_vec[0].str()==header) {
+ found=true;
+ line_iter++;
+ while ((*line_iter)[0]!='-') {
+ if ((*line_iter)[0]!='#') {
+ StringRef second_line_string_ref(line_iter->data(),(*line_iter).length());
+ std::vector<StringRef> second_line_str_vec = second_line_string_ref.split();
+ if (second_line_str_vec.size()!=4) {
+ std::cout << "The number of elements in one of the lines is wrong" << std::endl;
+ return StereoChemicalParams();
+ }
+ StringRef item = second_line_str_vec[0];
+ String res = second_line_str_vec[1].str();
+ std::pair<bool,float> parse_value = second_line_str_vec[2].to_float();
+ std::pair<bool,float> parse_stddev = second_line_str_vec[3].to_float();
+ Real value,stddev;
+ if (parse_value.first==true) {
+ value=static_cast<Real>(parse_value.second);
+ } else {
+ std::cout << "One of the values in the third column is not a number" << std::endl;
+ return StereoChemicalParams();
+ };
+ if (parse_stddev.first==true) {
+ stddev=static_cast<Real>(parse_stddev.second);
+ } else {
+ std::cout << "One of the values in the fourth column is not a number" << std::endl;
+ return StereoChemicalParams();
+ };
+ std::vector<StringRef> split_item = item.split('-');
+ String rearranged_item;
+ if (split_item.size() == 2) {
+ String atom1 = split_item[0].str();
+ String atom2 = split_item[1].str();
+ if (atom2 < atom1) {
+ std::stringstream srearr;
+ srearr << atom2 << "-" << atom1;
+ rearranged_item=srearr.str();
+ } else {
+ rearranged_item = item.str();
+ }
+ } else if (split_item.size() == 3) {
+ String atom1 = split_item[0].str();
+ String atom = split_item[1].str();
+ String atom2 = split_item[2].str();
+ if (atom2 < atom1) {
+ std::stringstream srearr;
+ srearr << atom2 << "-" << atom << "-" << atom1;
+ rearranged_item=srearr.str();
+ } else {
+ rearranged_item = item.str();
+ }
+ } else {
+ std::cout << "One of the strings describing the parameter has the wrong format" << std::endl;
+ return StereoChemicalParams();
+ }
+ table.SetParam(rearranged_item,res,value,stddev);
+ line_iter++;
+ }
+ }
+ }
+ }
+ line_iter++;
+ }
+ if (found==false) {
+ std::cout << "Could not find the relevant section in the stereo-chemical parameter file" << std::endl;
+ return StereoChemicalParams();
+ };
+ return table;
+};
+
+ClashingDistances FillClashingDistances(std::vector<String>& stereo_chemical_props_file, Real min_default_distance, Real min_distance_tolerance)
+{
+ ClashingDistances table(min_default_distance,min_distance_tolerance);
+ bool found=false;
+ std::vector<String>::const_iterator line_iter=stereo_chemical_props_file.begin();
+ while (line_iter!=stereo_chemical_props_file.end()) {
+ if ((*line_iter).length()!=0 && (*line_iter).length()!=1) {
+ StringRef line_string_ref(line_iter->data(),(*line_iter).length());
+ std::vector<StringRef> line_str_vec = line_string_ref.split();
+ if (line_str_vec[0].str()=="Non-bonded") {
+ found=true;
+ line_iter++;
+ while ((*line_iter)[0]!='-') {
+ if ((*line_iter)[0]!='#') {
+ StringRef second_line_string_ref(line_iter->data(),(*line_iter).length());
+ std::vector<StringRef> second_line_str_vec = second_line_string_ref.split();
+ if (second_line_str_vec.size()!=3) {
+ std::cout << "The number of elements in one of the lines is wrong" << std::endl;
+ return ClashingDistances(min_default_distance,min_distance_tolerance);
+ }
+ String item = second_line_str_vec[0].str();
+
+ std::pair<bool,float> parse_value = second_line_str_vec[1].to_float();
+ std::pair<bool,float> parse_stddev = second_line_str_vec[2].to_float();
+ Real value,stddev;
+ if (parse_value.first==true) {
+ value=static_cast<Real>(parse_value.second);
+ } else {
+ std::cout << "One of the distance values is not a number" << std::endl;
+ return ClashingDistances(min_default_distance,min_distance_tolerance);
+ };
+ if (parse_stddev.first==true) {
+ stddev=static_cast<Real>(parse_stddev.second);
+ } else {
+ std::cout << "One of the tolerance values is not a number" << std::endl;
+ return ClashingDistances(min_default_distance,min_distance_tolerance);
+ }
+ StringRef itemsr(item.data(),item.length());
+ std::vector<StringRef> eles = itemsr.split('-');
+ if (itemsr.size() != 3) {
+ std::cout << "One of the strings describing the interacting atoms has the wrong format" << std::endl;
+ return ClashingDistances(min_default_distance,min_distance_tolerance);
+ }
+ String ele1=eles[0].str();
+ String ele2=eles[1].str();
+ if (ele2 < ele1) {
+ table.SetClashingDistance(ele2,ele1,value,stddev);
+ } else {
+ table.SetClashingDistance(ele1,ele2,value,stddev);
+ }
+ line_iter++;
+ }
+ }
+ }
+ }
+ line_iter++;
+ }
+ if (found==false) {
+ std::cout << "Could not find the relevant section in the stereo-chemical parameter file" << std::endl;
+ return ClashingDistances(min_default_distance,min_distance_tolerance);
+ }
+ return table;
+}
+
+
+EntityView CheckStereoChemistry(const EntityView& ent, const StereoChemicalParams& bond_table, const StereoChemicalParams& angle_table, Real bond_tolerance, Real angle_tolerance, bool always_remove_bb)
+{
+ Real running_sum_zscore_bonds=0.0;
+ Real running_sum_zscore_angles=0.0;
+ int bond_count = 0;
+ int bad_bond_count = 0;
+ int angle_count = 1;
+ int bad_angle_count = 0;
+ LOG_INFO("Checking stereo-chemistry")
+ EntityView filtered=ent.CreateEmptyView();
+ ResidueViewList residues=ent.GetResidueList();
+ for (ResidueViewList::iterator i=residues.begin(), e=residues.end(); i!=e; ++i) {
+ bool remove_sc=false, remove_bb=false;
+ ResidueView res=*i;
+ if (res.GetOneLetterCode()=='?') {
+ filtered.AddResidue(res, ViewAddFlag::INCLUDE_ATOMS);
+ continue;
+ }
+ String residue_str = res.GetName();
+ const AtomViewList& atoms=res.GetAtomList();
+ for (AtomViewList::const_iterator j=atoms.begin(), e2=atoms.end(); j!=e2; ++j) {
+ AtomView atom=*j;
+ String ele1=atom.GetElement();
+ if (ele1=="H" || ele1=="D") {
+ continue;
}
- case 'O':
- switch (ele2[0]) {
- case 'C' : return 2.25;
- case 'N' : return 2.10;
- case 'S' : return 2.45;
- case 'O' : return 2.05;
- default: return 1.5;
+ BondHandleList bonds = atom.GetBondList();
+
+ for (BondHandeList::const_iterator bi = bonds.begin();bi!=bonds.end();++bi) {
+ BondHandle bond = *bi;
+ AtomHandle other_atom = bond.GetOther(atom.GetHandle());
+ if (other_atom.GetResidue()!=res.GetHandle()) {
+ continue;
+ }
+ String ele2 = other_atom.GetElement();
+ if (ele2=="H" || ele2=="D") {
+ continue;
+ }
+ if (other_atom.GetHashCode() > atom.GetHandle().GetHashCode()) {
+ Real blength = bond.GetLength();
+ String bond_str = bond_string(atom,other_atom);
+ std::pair<Real,Real> length_stddev = bond_table.GetParam(bond_str,residue_str);
+ Real ref_length = length_stddev.first;
+ Real ref_stddev = length_stddev.second;
+ Real min_length = ref_length - bond_tolerance*ref_stddev;
+ Real max_length = ref_length + bond_tolerance*ref_stddev;
+ Real zscore = (blength - ref_length)/ref_stddev;
+ if (blength < min_length || blength > max_length) {
+ LOG_INFO("BOND:" << " " << res.GetChain() << " " << res.GetName() << " " << res.GetNumber() << " " << bond_str << " " << min_length << " " << max_length << " " << blength << " " << zscore << " " << "FAIL")
+ bad_bond_count++;
+ remove_sc=true;
+ if (always_remove_bb==true) {
+ remove_bb=true;
+ }
+ String name=atom.GetName();
+ if (name=="CA" || name=="N" || name=="O" || name=="C") {
+ remove_bb=true;
+ }
+ } else {
+ LOG_VERBOSE("BOND:" << " " << res.GetChain() << " " << res.GetName() << " " << res.GetNumber() << " " << bond_str << " " << min_length << " " << max_length << " " << blength << " " << zscore << " " << "PASS")
+ }
+ bond_count++;
+ running_sum_zscore_bonds+=zscore;
+ }
}
- case 'S':
- switch (ele2[0]) {
- case 'C' : return 2.45;
- case 'N' : return 2.55;
- case 'S' : return 1.80;
- case 'O' : return 2.45;
- default: return 1.5;
+
+ for (BondHandeList::const_iterator bond_iter1=bonds.begin(); bond_iter1!=bonds.end(); ++bond_iter1) {
+ BondHandle bond1=*bond_iter1;
+ AtomHandle atom1= bond1.GetOther(atom.GetHandle());
+ String ele_atom1=atom1.GetElement();
+ if (ele_atom1=="H" || ele_atom1=="D") {
+ continue;
+ }
+ if (atom1.GetResidue()!=res.GetHandle()) {
+ continue;
+ }
+ for (BondHandeList::const_iterator bond_iter2=bonds.begin(); bond_iter2!=bonds.end(); ++bond_iter2) {
+ BondHandle bond2=*bond_iter2;
+ AtomHandle atom2 = bond2.GetOther(atom.GetHandle());
+ String ele_atom2=atom2.GetElement();
+ if (ele_atom2=="H" || ele_atom2=="D") {
+ continue;
+ }
+ if (atom2.GetResidue()!=res.GetHandle()) {
+ continue;
+ }
+ if (atom1.GetHashCode() > atom2.GetHashCode()) {
+ Real awidth;
+ if (atom1.GetName()<atom2.GetName()) {
+ awidth = ent.GetAngle(atom1,atom.GetHandle(),atom2);
+ } else {
+ awidth = ent.GetAngle(atom2,atom.GetHandle(),atom1);
+ }
+ awidth/=(ost::Units::deg);
+ String angle_str = angle_string(atom1,atom,atom2);
+ std::pair<Real,Real> width_stddev = angle_table.GetParam(angle_str,residue_str);
+ Real ref_width = width_stddev.first;
+ Real ref_stddev = width_stddev.second;
+ Real min_width = ref_width - angle_tolerance*ref_stddev;
+ Real max_width = ref_width + angle_tolerance*ref_stddev;
+ Real zscore = (awidth - ref_width)/ref_stddev;
+ if (awidth < min_width || awidth > max_width) {
+ LOG_INFO("ANGLE:" << " " << res.GetChain() << " " << res.GetName() << " " << res.GetNumber() << " " << angle_str << " " << min_width << " " << max_width << " " << awidth << " " << zscore << " " << "FAIL")
+ bad_angle_count++;
+ remove_sc=true;
+ if (always_remove_bb==true) {
+ remove_bb=true;
+ }
+ String name=atom.GetName();
+ if (name=="CA" || name=="N" || name=="O" || name=="C") {
+ remove_bb=true;
+ }
+ } else {
+ LOG_VERBOSE("ANGLE:" << " " << res.GetChain() << " " << res.GetName() << " " << res.GetNumber() << " " << angle_str << " " << min_width << " " << max_width << " " << awidth << " " << zscore << " " << "PASS")
+ }
+ angle_count++;
+ running_sum_zscore_angles+=zscore;
+ }
+ }
+ }
+ }
+
+ if (remove_bb) {
+ LOG_INFO("ACTION: removing whole residue " << res);
+ continue;
+ }
+ if (remove_sc) {
+ LOG_INFO("ACTION: removing sidechain of residue " << res);
+ for (AtomViewList::const_iterator
+ j=atoms.begin(), e2=atoms.end(); j!=e2; ++j) {
+ AtomView atom=*j;
+ String name=atom.GetName();
+ if (name=="CA" || name=="N" || name=="O" || name=="C") {
+ filtered.AddAtom(atom);
+ }
}
- default:
- return 1.5;
+ continue;
+ }
+ filtered.AddResidue(res, ViewAddFlag::INCLUDE_ATOMS);
}
+ Real avg_zscore_bonds = running_sum_zscore_bonds/static_cast<float>(bond_count);
+ Real avg_zscore_angles = running_sum_zscore_angles/static_cast<float>(angle_count);
+ LOG_SCRIPT("Average Z-Score for bond lengths: " << avg_zscore_bonds);
+ LOG_SCRIPT("Bonds outside of tolerance range: " << bad_bond_count << " out of " << bond_count);
+ LOG_SCRIPT("Average Z-Score angle widths: " << avg_zscore_angles);
+ LOG_SCRIPT("Angles outside of tolerance range: " << bad_angle_count << " out of " << angle_count);
+ return filtered;
}
+EntityView CheckStereoChemistry(const EntityHandle& ent, const StereoChemicalParams& bond_table, const StereoChemicalParams& angle_table, Real bond_tolerance, Real angle_tolerance, bool always_remove_bb)
+{
+ return CheckStereoChemistry(ent.CreateFullView(), bond_table, angle_table, bond_tolerance, angle_tolerance, always_remove_bb);
}
-EntityView FilterClashes(const EntityView& ent, Real tolerance,
- bool always_remove_bb)
+
+EntityView FilterClashes(const EntityView& ent, const ClashingDistances& min_distances, bool always_remove_bb)
{
+ int distance_count = 0;
+ int bad_distance_count = 0;
+ LOG_INFO("Filtering non-bonded clashes")
EntityView filtered=ent.CreateEmptyView();
ResidueViewList residues=ent.GetResidueList();
for (ResidueViewList::iterator
i=residues.begin(), e=residues.end(); i!=e; ++i) {
bool remove_sc=false, remove_bb=false;
ResidueView res=*i;
+ if (res.GetOneLetterCode()=='?') {
+ filtered.AddResidue(res, ViewAddFlag::INCLUDE_ATOMS);
+ continue;
+ }
const AtomViewList& atoms=res.GetAtomList();
for (AtomViewList::const_iterator
j=atoms.begin(), e2=atoms.end(); j!=e2; ++j) {
AtomView atom=*j;
+
String ele1=atom.GetElement();
if (ele1=="H" || ele1=="D") {
continue;
}
- AtomViewList within=ent.FindWithin(atom.GetPos(), 2.5-tolerance);
+ AtomViewList within=ent.FindWithin(atom.GetPos(),min_distances.GetMaxAdjustedDistance());
for (AtomViewList::iterator
k=within.begin(), e3=within.end(); k!=e3; ++k) {
AtomView atom2=*k;
+
+
+
if (atom2==atom) {
continue;
}
@@ -97,33 +498,47 @@ EntityView FilterClashes(const EntityView& ent, Real tolerance,
if (ele2=="H" || ele2=="D") {
continue;
}
+
+
// In theory, this should also trigger for disulfide bonds, but
// since we don't detect disulfides correctly, we can't count on that
- // and we instead allow S-S distances down to 1.8.
+ // and we instead allow S-S distances down to 1.8.
if (atom.GetHandle().FindBondToAtom(atom2.GetHandle()).IsValid()) {
continue;
}
+
+
+
Real d=geom::Length2(atom.GetPos()-atom2.GetPos());
- Real threshold=GetThreshold(ele1, ele2)-tolerance;
+ std::pair <Real,Real> distance_tolerance=min_distances.GetClashingDistance(ele1, ele2);
+ Real distance=distance_tolerance.first;
+ Real tolerance=distance_tolerance.second;
+ Real threshold=distance-tolerance;
+
if (d<threshold*threshold) {
+ LOG_INFO(atom.GetResidue().GetChain() << " " << atom.GetResidue().GetName() << " " << atom.GetResidue().GetNumber() << " " << atom.GetName() << " " << atom2.GetResidue().GetChain() << " " << atom2.GetResidue().GetName() << " " << atom2.GetResidue().GetNumber() << " " << atom2.GetName() << " " << threshold << " " << sqrt(d) << " " << sqrt(d)-threshold << " " << "FAIL")
+ bad_distance_count++;
remove_sc=true;
if (always_remove_bb==true) {
remove_bb=true;
- continue;
}
String name=atom.GetName();
if (name=="CA" || name=="N" || name=="O" || name=="C") {
remove_bb=true;
}
+ } else {
+ LOG_VERBOSE("CLASH:" << " " << atom.GetResidue().GetChain() << " " << atom.GetResidue().GetName() << " " << atom.GetResidue().GetNumber() << " " << atom.GetName() << " " << atom2.GetResidue().GetChain() << " " << atom2.GetResidue().GetNumber() << " " << atom2.GetResidue().GetName() << " " << atom2.GetName() << " " << threshold << " " << sqrt(d) << " " << sqrt(d)-threshold << " " << "PASS")
}
+ distance_count++;
}
}
+
if (remove_bb) {
- LOG_VERBOSE("removing whole residue " << res);
+ LOG_VERBOSE("ACTION: removing whole residue " << res);
continue;
}
if (remove_sc) {
- LOG_VERBOSE("removing sidechain of residue " << res);
+ LOG_VERBOSE("ACTION: removing sidechain of residue " << res);
for (AtomViewList::const_iterator
j=atoms.begin(), e2=atoms.end(); j!=e2; ++j) {
AtomView atom=*j;
@@ -136,16 +551,16 @@ EntityView FilterClashes(const EntityView& ent, Real tolerance,
}
filtered.AddResidue(res, ViewAddFlag::INCLUDE_ATOMS);
}
+ LOG_SCRIPT(bad_distance_count << " out of " << distance_count << " non-bonded short-range distances checked shorter than tolerance distance");
return filtered;
}
-EntityView FilterClashes(const EntityHandle& ent, Real tolerance,
- bool always_remove_bb)
+EntityView FilterClashes(const EntityHandle& ent,
+ const ClashingDistances& min_distances, bool always_remove_bb)
{
- return FilterClashes(ent.CreateFullView(), tolerance, always_remove_bb);
+ return FilterClashes(ent.CreateFullView(), min_distances, always_remove_bb);
}
}}}
-
diff --git a/modules/mol/alg/src/filter_clashes.hh b/modules/mol/alg/src/filter_clashes.hh
index 052e1ce5f65efd86396de967b9ad635afee3a715..5d64fc23060cdf879c434ccf52c950444b2087d0 100644
--- a/modules/mol/alg/src/filter_clashes.hh
+++ b/modules/mol/alg/src/filter_clashes.hh
@@ -24,14 +24,70 @@
namespace ost { namespace mol { namespace alg {
+class ClashingDistances
+{
+public:
+ ClashingDistances(Real default_dist, Real tolerance): default_min_distance_(default_dist), default_min_distance_tolerance_(tolerance), valid_flag_(true) {}
+ void SetClashingDistance(const String& ele1,const String& ele2, Real min_distance, Real tolerance);
+ std::pair<Real,Real> GetClashingDistance(const String& ele1,const String& ele2) const;
+ Real GetMaxAdjustedDistance() const;
+ bool IsEmpty() const;
+
+ //DEBUG
+ void PrintAllDistances() const;
+
+private:
+
+ std::map <String,std::pair<float,float> > min_distance_;
+ Real default_min_distance_;
+ Real default_min_distance_tolerance_;
+ bool valid_flag_;
+
+};
+
+class StereoChemicalParams
+{
+
+public:
+ void SetParam(const String& param, const String& residue, Real value, Real st_dev);
+ std::pair<Real,Real> GetParam(const String& element,const String& residue) const;
+ bool ContainsParam(const String& param,const String& residue) const;
+ bool IsEmpty() const;
+
+ //DEBUG
+ void PrintAllParameters() const;
+
+private:
+
+ std::map<std::pair<String,String>,std::pair<float,float> > params_;
+
+};
+
+ClashingDistances DLLEXPORT_OST_MOL_ALG FillClashingDistances(std::vector<String>& stereo_chemical_props_file, Real min_default_distance, Real min_distance_tolerance);
+StereoChemicalParams DLLEXPORT_OST_MOL_ALG FillStereoChemicalParams(const String& header, std::vector<String>& stereo_chemical_props_file);
+
EntityView DLLEXPORT_OST_MOL_ALG FilterClashes(const EntityView& ent,
- Real tolerance=0.1,
- bool always_remove_bb=false);
+ const ClashingDistances& min_distances, bool always_remove_bb=false);
EntityView DLLEXPORT_OST_MOL_ALG FilterClashes(const EntityHandle& ent,
- Real tolerance=0.1,
- bool always_remove_bb=false);
+ const ClashingDistances& min_distances, bool always_remove_bb=false);
+
+EntityView DLLEXPORT_OST_MOL_ALG CheckStereoChemistry(const EntityView& ent,
+ const StereoChemicalParams& bond_table,
+ const StereoChemicalParams& angle_table,
+ Real bond_tolerance,
+ Real angle_tolerance,
+ bool always_remove_bb=false);
+
+EntityView DLLEXPORT_OST_MOL_ALG CheckStereoChemistry(const EntityHandle& ent,
+ const StereoChemicalParams& bond_table,
+ const StereoChemicalParams& angle_table,
+ Real bond_tolerance,
+ Real angle_tolerance,
+ bool always_remove_bb=false);
+
+
}}}
diff --git a/modules/mol/alg/src/ldt.cc b/modules/mol/alg/src/ldt.cc
index ff566e489af453c26fdc29ffacbe5c11464730eb..48dfc9a6ca3e08762a8356be905867bd3c868678 100644
--- a/modules/mol/alg/src/ldt.cc
+++ b/modules/mol/alg/src/ldt.cc
@@ -13,22 +13,32 @@
// 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.,
+// along with this library; if not, write to the Free Software Foundation, Inc.,
// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
//------------------------------------------------------------------------------
#if defined (_MSC_VER)
#define BOOST_ALL_DYN_LINK 1
#endif
#include <boost/program_options.hpp>
+#include <boost/filesystem/fstream.hpp>
+#include <boost/filesystem/convenience.hpp>
#include <ost/mol/alg/local_dist_test.hh>
#include <ost/mol/alg/filter_clashes.hh>
#include <ost/io/mol/pdb_reader.hh>
#include <ost/io/io_exception.hh>
#include <ost/conop/conop.hh>
+#include <ost/conop/amino_acids.hh>
+#include <ost/mol/iterator.hh>
+#include <ost/platform.hh>
+#include <ost/log.hh>
+
+#include <ost/conop/rule_based_builder.hh>
+#include <ost/dyn_cast.hh>
using namespace ost;
using namespace ost::io;
using namespace ost::mol;
+using namespace ost::mol::alg;
namespace po=boost::program_options;
EntityHandle load(const String& file, const IOProfile& profile)
@@ -42,7 +52,7 @@ EntityHandle load(const String& file, const IOProfile& profile)
conop_inst.ConnectAll(conop_inst.GetBuilder(), ent);
return ent;
}
- std::cerr << "ERROR: '" << file << "' does not contain any ATOM records. "
+ std::cerr << "ERROR: '" << file << "' does not contain any ATOM records. "
<< "Are you sure this is a PDB file?" << std::endl;
return EntityHandle();
} catch (io::IOException& e) {
@@ -54,25 +64,70 @@ EntityHandle load(const String& file, const IOProfile& profile)
void usage()
{
std::cerr << "usage: ldt [options] <mod1> [mod1 [mod2]] <ref>" << std::endl;
- std::cerr << " -s selection performed on ref" << std::endl;
- std::cerr << " -c use Calphas only" << std::endl;
- std::cerr << " -f filter clashes (not implemented yet)" << std::endl;
- std::cerr << " -t fault tolerant parsing" << std::endl;
+ std::cerr << " -s selection performed on ref" << std::endl;
+ std::cerr << " -c use Calphas only" << std::endl;
+ std::cerr << " -f perform structural checks and filter input data" << std::endl;
+ std::cerr << " -t fault tolerant parsing" << std::endl;
+ std::cerr << " -p <file> use specified parmeter file. Mandatory" << std::endl;
+ std::cerr << " -v <level> verbosity level (0=results only,1=problems reported, 2=full report)" << std::endl;
+ std::cerr << " -b <value> tolerance in stddevs for bonds" << std::endl;
+ std::cerr << " -a <value> tolerance in stddevs for angles" << std::endl;
+ std::cerr << " -m <value> clashing distance for unknwon atom types" << std::endl;
+ std::cerr << " -r <value> distance inclusion radius" << std::endl;
+ std::cerr << " -e print version" << std::endl;
+}
+
+std::pair<int,int> compute_coverage (const EntityView& v,const GlobalDistanceList& glob_dist_list)
+{
+ int second=0;
+ int first=0;
+ if (v.GetResidueList().size()==0) {
+ return std::make_pair<int,int>(0,1);
+ }
+ ChainView vchain=v.GetChainList()[0];
+ for (std::vector<ResidueDistanceList>::const_iterator i=glob_dist_list.begin();i!=glob_dist_list.end();++i)
+ {
+ ResNum rnum = (*i)[0].GetFirstAtom().GetResNum();
+ String rname = (*i)[0].GetFirstAtom().GetResidueName();
+ if (IsStandardResidue(rname)) {
+ second++;
+ if (vchain.FindResidue(rnum)) {
+ first++;
+ }
+ }
+ }
+ return std::make_pair<int,int>(first,second);
}
int main (int argc, char **argv)
{
+ String version = "Beta - 2012-01-17";
+ Real min_default_distance = 1.5;
+ Real min_distance_tolerance = 0.0;
+ Real bond_tolerance = 8.0;
+ Real angle_tolerance = 8.0;
+ Real radius=15.0;
+
IOProfile profile;
+ profile.bond_feasibility_check=false;
// parse options
String sel;
- bool filter_clashes=false;
+ bool structural_checks=false;
po::options_description desc("Options");
desc.add_options()
("calpha,c", "consider only calpha atoms")
- ("sel,s", po::value<String>(&sel)->default_value(""), "selection for reference")
+ ("sel,s", po::value<String>(&sel)->default_value(""), "selection performed on reference structure")
("tolerant,t", "fault tolerant mode")
- ("filter-clashes,f", "filter clashes")
- ("files", po::value< std::vector<String> >(), "input file")
+ ("structural-checks,f", "perform stereo-chemical and clash checks")
+ ("version,e", "version")
+ ("parameter-file,p", po::value<String>(), "stereo-chemical parameter file")
+ ("verbosity,v", po::value<int>(), "verbosity level")
+ ("bond_tolerance,b", po::value<Real>(), "tolerance in stddev for bonds")
+ ("angle_tolerance,a", po::value<Real>(), "tolerance in stddev for angles")
+ ("default_clash,m", po::value<Real>(), "clashing distance for unknown atom types")
+ ("inclusion_radius,r", po::value<Real>(), "distance inclusion radius")
+ ("files", po::value< std::vector<String> >(), "input file(s)")
+ ("reference",po::value<String>(),"reference(s)")
;
po::positional_options_description p;
p.add("files", -1);
@@ -81,48 +136,184 @@ int main (int argc, char **argv)
options(desc).positional(p).run(),
vm);
po::notify(vm);
+ if (vm.count("version")) {
+ std::cout << "Version: " << version << std::endl;
+ exit(0);
+ }
+ std::vector<String> files;
+ if (vm.count("files")) {
+ files=vm["files"].as<std::vector<String> >();
+ } else {
+ usage();
+ exit(-1);
+ }
if (vm.count("calpha")) {
profile.calpha_only=true;
}
- if (vm.count("filter-clashes")) {
- filter_clashes=true;
+ if (vm.count("structural-checks")) {
+ structural_checks=true;
}
if (vm.count("tolerant")) {
profile.fault_tolerant=true;
}
- std::vector<String> files;
- if (vm.count("files")) {
- files=vm["files"].as<std::vector<String> >();
- } else {
- usage();
+ String parameter_filename;
+ if (vm.count("parameter-file")) {
+ parameter_filename=vm["parameter-file"].as<String>();
+ } else if (structural_checks==true) {
+ std::cout << "Please specify a stereo-chemical parameter file" << std::endl;
exit(-1);
}
+ int verbosity_level=0;
+ int ost_verbosity_level=2;
+ if (vm.count("verbosity")) {
+ verbosity_level=vm["verbosity"].as<int>();
+ if (verbosity_level==0) {
+ ost_verbosity_level=2;
+ } else if (verbosity_level==1) {
+ ost_verbosity_level=3;
+ } else if (verbosity_level==2) {
+ ost_verbosity_level=4;
+ } else {
+ std::cout << "Verbosity level " << verbosity_level << " is not available" << std::endl;
+ exit(-1);
+ }
+ }
+
+ Logger::Instance().PushVerbosityLevel(ost_verbosity_level);
+
+ if (vm.count("bond_tolerance")) {
+ bond_tolerance=vm["bond_tolerance"].as<Real>();
+ }
+ if (vm.count("angle_tolerance")) {
+ angle_tolerance=vm["angle_tolerance"].as<Real>();
+ }
+ if (vm.count("default_clash")) {
+ min_default_distance=vm["default_clash"].as<Real>();
+ }
+ if (vm.count("inclusion_radius")) {
+ radius=vm["inclusion_radius"].as<Real>();
+ }
String ref_file=files.back();
EntityHandle ref=load(ref_file, profile);
if (!ref) {
- return -1;
+ exit(-1);
}
files.pop_back();
EntityView ref_view=ref.Select(sel);
+ GlobalDistanceList glob_dist_list = CreateDistanceList(ref_view,radius);
+ std::cout << "Verbosity level: " << verbosity_level << std::endl;
+ if (structural_checks) {
+ std::cout << "Stereo-chemical and steric clash checks: On " << std::endl;
+ } else {
+ std::cout << "Stereo-chemical and steric clash checks: Off " << std::endl;
+ }
+ std::cout << "Inclusion Radius: " << radius << std::endl;
+ if (structural_checks) {
+ std::cout << "Parameter filename: " << parameter_filename << std::endl;
+ std::cout << "Tolerance in stddevs for bonds: " << bond_tolerance << std::endl;
+ std::cout << "Tolerance in stddevs for angles: " << angle_tolerance << std::endl;
+ std::cout << "Clashing distance for unknown atom types: " << min_default_distance << std::endl;
+ LOG_INFO("Log entries format:");
+ LOG_INFO("BOND INFO FORMAT: Chain Residue ResNum Bond Min Max Observed Z-score Status");
+ LOG_INFO("ANGLE INFO FORMAT: Chain Residue ResNum Angle Min Max Observed Z-score Status");
+ LOG_INFO("CLASH INFO FORMAT: Chain1 Residue1 ResNum1 Atom1 Chain2 Residue2 ResNum2 Atom2 Observed Difference Status");
+ }
+ LOG_INFO("LDT INFO FORMAT: Chain1 Residue1 ResNum1 Atom1 Chain2 Residue2 ResNum2 Atom2 ModelDist TargetDist Difference Tolerance Status");
for (size_t i=0; i<files.size(); ++i) {
EntityHandle model=load(files[i], profile);
if (!model) {
if (!profile.fault_tolerant) {
- return -1;
+ exit(-1);
}
continue;
}
EntityView v=model.CreateFullView();
- if (filter_clashes) {
- v=alg::FilterClashes(v);
+
+
+ // The code in this following block is only used to make CASP9 models load correctly and normally commented out
+ EntityView model2=model.Select("aname!=CEN,NV,OT1,OT,CAY,CY,OXT,1OCT,NT,OT2,2OCT,OVL1,OC1,O1,OC2,O2,OVU1");
+ EntityView v1=model2.Select("not (rname==GLY and aname==CB)");
+ boost::filesystem::path pathstring(files[i]);
+
+ #if BOOST_FILESYSTEM_VERSION==3
+ String filestring=pathstring.filename().string();
+ #else
+ String filestring=pathstring.file_string();
+ #endif
+
+ if (filestring.substr(5,5)=="TS257" || filestring.substr(5,5)=="TS458" ) {
+ for (AtomHandleIter ait=v1.GetHandle().AtomsBegin();ait!=v1.GetHandle().AtomsEnd();++ait){
+ AtomHandle aitv = *ait;
+ String atomname=aitv.GetName();
+ String firstletter=atomname.substr(0,1);
+ aitv.SetElement(firstletter);
+ }
+ }
+ v=v1;
+ std::cout << "File: " << files[i] << std::endl;
+ std::pair<int,int> cov = compute_coverage(v,glob_dist_list);
+ std::cout << "Coverage: " << (float(cov.first)/float(cov.second)) << " (" << cov.first << " out of " << cov.second << " residues)" << std::endl;
+
+ if (structural_checks) {
+ boost::filesystem::path loc(parameter_filename);
+ boost::filesystem::ifstream infile(loc);
+ if (!infile) {
+ std::cout << "Could not find " << parameter_filename << std::endl;
+ exit(-1);
+ }
+ std::vector<String> stereo_chemical_props;
+ String line;
+ while (std::getline(infile, line))
+ {
+ std::stringstream line_stream(line);
+ stereo_chemical_props.push_back(line);
+ }
+ StereoChemicalParams bond_table = FillStereoChemicalParams("Bond",stereo_chemical_props);
+ if (bond_table.IsEmpty()) {
+ std::cout << "Error reading the Bond section of the stereo-chemical parameter file." << std::endl;
+ exit(-1);
+ }
+ StereoChemicalParams angle_table = FillStereoChemicalParams("Angle",stereo_chemical_props);
+ if (angle_table.IsEmpty()) {
+ std::cout << "Error reading the Angles section of the stereo-chemical parameter file." << std::endl;
+ exit(-1);
+ }
+
+ ClashingDistances nonbonded_table = FillClashingDistances(stereo_chemical_props,min_default_distance,min_distance_tolerance);
+
+ if (nonbonded_table.IsEmpty()) {
+ std::cout << "Error reading the Clashing section of the stereo-chemical parameter file." << std::endl;
+ exit(-1);
+ }
+ v=alg::CheckStereoChemistry(v,bond_table,angle_table,bond_tolerance,angle_tolerance);
+ cov = compute_coverage(v,glob_dist_list);
+ std::cout << "Coverage after stereo-chemical checks: " << (float(cov.first)/float(cov.second)) << " (" << cov.first << " out of " << cov.second << " residues)" << std::endl;
+ v=alg::FilterClashes(v,nonbonded_table);
+ cov = compute_coverage(v,glob_dist_list);
+ std::cout << "Coverage after clashing checks: " << (float(cov.first)/float(cov.second)) << " (" << cov.first << " out of " << cov.second << " residues)" << std::endl;
}
- float cutoffs[]={0.5,1,2,4};
- float ldt=0.0;
- for (int n=0; n<4; ++n) {
- ldt+=alg::LocalDistTest(v, ref_view, cutoffs[n], 8.0);
+ if (cov.first==0) {
+ std::cout << "Global LDT score: 0.0" << std::endl;
+ return 0;
}
- ldt/=4.0;
- std::cout << files[i] << " " << ldt << std::endl;
+ Real ldt=LDTHA(v, glob_dist_list);
+
+ std::cout << "Global LDT score: " << ldt << std::endl;
+ std::cout << "Local LDT Score:" << std::endl;
+ std::cout << "Chain\tResName\tResNum\tScore" << std::endl;
+ String labels[]={"localldt0.5","localldt1","localldt2","ldtlocal4"};
+ for (ResidueViewIter rit=v.ResiduesBegin();rit!=v.ResiduesEnd();++rit){
+ ResidueView ritv = *rit;
+ Real ldt_local_sum = 0;
+ if (ritv.HasProp("localldt0.5")) {
+ for (int n=0; n<4; ++n) {
+ ldt_local_sum+=ritv.GetFloatProp(labels[n]);
+ }
+ ldt_local_sum/=4.0;
+ std::cout << ritv.GetChain() << "\t" << ritv.GetName() << "\t" << ritv.GetNumber() << '\t' << ldt_local_sum << std::endl;
+ }
+ }
+ std::cout << std::endl;
}
return 0;
-}
\ No newline at end of file
+}
diff --git a/modules/mol/alg/src/local_dist_test.cc b/modules/mol/alg/src/local_dist_test.cc
index 5441f681b2349797eb6b0a38266d63285dbe7616..430dd31bebb4e5c5bea26461df9b253e8bc0d608 100644
--- a/modules/mol/alg/src/local_dist_test.cc
+++ b/modules/mol/alg/src/local_dist_test.cc
@@ -1,6 +1,7 @@
#include <ost/log.hh>
#include <ost/mol/mol.hh>
#include "local_dist_test.hh"
+#include <boost/concept_check.hpp>
namespace ost { namespace mol { namespace alg {
@@ -37,7 +38,8 @@ bool swappable(const String& rname, const String& aname)
if (rname=="ASP") {
return (aname=="OD1" || aname=="OD2");
}
- if (rname=="VAL") {
+ if (rname=="VAL") {
+
return (aname=="CG1" || aname=="CG2");
}
if (rname=="TYR" || rname=="PHE") {
@@ -49,73 +51,103 @@ bool swappable(const String& rname, const String& aname)
return false;
}
-std::pair<Real, Real> calc_overlap1(ResidueView ref_res,
- EntityView ref,
+std::pair<bool,Real> within_tolerance(Real mdl_dist, const ReferenceDistance& ref_dist, Real tol)
+{
+ Real min = ref_dist.GetMaxDistance();
+ Real max = ref_dist.GetMaxDistance();
+ bool within_tol = false;
+ Real difference = 0;
+ if (mdl_dist>=min && mdl_dist <=max) {
+ within_tol=true;
+ } else if (mdl_dist < min && std::abs(min-mdl_dist) < tol) {
+ within_tol = true;
+ } else if (mdl_dist > max && std::abs(mdl_dist-max) < tol) {
+ within_tol = true;
+ }
+ if (within_tol == false) {
+ if (mdl_dist > max) {
+ difference = mdl_dist-(max+tol);
+ } else {
+ difference = mdl_dist-(min-tol);
+ }
+ }
+ return std::make_pair<bool,Real>(within_tol,difference);
+}
+
+
+std::pair<Real, Real> calc_overlap1(const ResidueDistanceList& res_distance_list,
ChainView mdl_chain,
- Real tol, Real max_dist, bool only_fixed,
- bool swap,std::vector<std::pair<Real, Real> >& overlap_list )
+ Real tol, bool only_fixed,
+ bool swap,std::vector<std::pair<Real, Real> >& overlap_list, bool log )
{
std::pair<Real, Real> overlap(0.0, 0.0);
- AtomViewList ref_atoms=ref_res.GetAtomList();
- ResidueView mdl_res=mdl_chain.FindResidue(ref_res.GetNumber());
- AtomViewList within;
- if (max_dist<0){
- within=ref.GetAtomList();
- }
- for (AtomViewList::iterator ai=ref_atoms.begin(),
- ae=ref_atoms.end(); ai!=ae; ++ai) {
- if (ai->GetElement()=="H") { continue; }
- String name=swap ? swapped_name(ai->GetName()) : ai->GetName();
+ ResidueView mdl_res=mdl_chain.FindResidue(res_distance_list[0].GetFirstAtom().GetResNum());
+ for (ResidueDistanceList::const_iterator ai=res_distance_list.begin(),
+ ae=res_distance_list.end(); ai!=ae; ++ai) {
+ UniqueAtomIdentifier first_atom=ai->GetFirstAtom();
+ UniqueAtomIdentifier second_atom=ai->GetSecondAtom();
+ String name=swap ? swapped_name(first_atom.GetAtomName()) : first_atom.GetAtomName();
AtomView av1=mdl_res ? mdl_res.FindAtom(name) : AtomView();
- if (max_dist>=0){
- within=ref.FindWithin(ai->GetPos(), max_dist);
- }
- for (AtomViewList::iterator aj=within.begin(),
- ae2=within.end(); aj!=ae2; ++aj) {
- if (aj->GetElement()=="H") { continue; }
- if (only_fixed) {
- if (aj->GetResidue().GetNumber()==ref_res.GetNumber()) {
+
+ if (only_fixed) {
+ if (swappable(second_atom.GetResidueName(), second_atom.GetAtomName())) {
continue;
- }
- if (swappable(aj->GetResidue().GetName(), aj->GetName())) {
- continue;
- }
- AtomView av2=mdl_chain.FindAtom(aj->GetResidue().GetNumber(),
- aj->GetName());
- overlap.second+=1.0;
- if (!(av1 && av2)) {
- continue;
- }
- Real mdl_dist=geom::Length(av1.GetPos()-av2.GetPos());
- Real ref_dist=geom::Length(ai->GetPos()-aj->GetPos());
- if (std::abs(mdl_dist-ref_dist)<tol) {
- overlap.first+=1;
- }
+ }
+ AtomView av2=mdl_chain.FindAtom(second_atom.GetResNum(),second_atom.GetAtomName());
+ overlap.second+=1.0;
+ if (!(av1 && av2)) {
continue;
}
- if (aj->GetResidue().GetNumber()>ref_res.GetNumber()) {
- AtomView av2=mdl_chain.FindAtom(aj->GetResidue().GetNumber(),
- aj->GetName());
- overlap.second+=1.0;
- overlap_list[ref_res.GetIndex()].second+=1.0;
- overlap_list[aj->GetResidue().GetIndex()].second+=1.0;
- if (!(av1 && av2)) {
- continue;
- }
- Real mdl_dist=geom::Length(av1.GetPos()-av2.GetPos());
- Real ref_dist=geom::Length(ai->GetPos()-aj->GetPos());
- if (std::abs(mdl_dist-ref_dist)<tol) {
- overlap.first+=1;
- overlap_list[ref_res.GetIndex()].first+=1.0;
- overlap_list[aj->GetResidue().GetIndex()].first+=1.0;
- }
+ Real mdl_dist=geom::Length(av1.GetPos()-av2.GetPos());
+ ReferenceDistance ref_dist=*ai;
+ if (within_tolerance(mdl_dist,ref_dist,tol).first) {
+ if (log) {
+ LOG_VERBOSE("LDT:" << " " << av1.GetResidue().GetChain() << " " << av1.GetResidue().GetName() << " " << av1.GetResidue().GetNumber() << " " << av1.GetName()
+ << " " << av2.GetResidue().GetChain() << " " << av2.GetResidue().GetName() << " " << av2.GetResidue().GetNumber() << " " << av2.GetName() << " "
+ << mdl_dist << " " << ref_dist.GetMinDistance() << " " << ref_dist.GetMaxDistance() << " " << tol << " " << "PASS")
+ }
+ overlap.first+=1;
+ } else {
+ if (log) {
+ LOG_VERBOSE("LDT:" << " " << av1.GetResidue().GetChain() << " " << av1.GetResidue().GetName() << " " << av1.GetResidue().GetNumber() << " " << av1.GetName()
+ << " " << av2.GetResidue().GetChain() << " " << av2.GetResidue().GetName() << " " << av2.GetResidue().GetNumber() << " " << av2.GetName() << " "
+ << mdl_dist << " " << ref_dist.GetMinDistance() << " " << mdl_dist-ref_dist.GetMinDistance() << " " << tol << " " << "FAIL")
+ }
}
- }
- }
+ continue;
+ }
+ AtomView av2=mdl_chain.FindAtom(second_atom.GetResNum(), second_atom.GetAtomName());
+ overlap.second+=1.0;
+ if (av1) {
+ overlap_list[av1.GetResidue().GetIndex()].second+=1.0;
+ }
+ if (av2) {
+ overlap_list[av2.GetResidue().GetIndex()].second+=1.0;
+ }
+ if (!(av1 && av2)) {
+ continue;
+ }
+
+ Real mdl_dist=geom::Length(av1.GetPos()-av2.GetPos());
+ ReferenceDistance ref_dist=*ai;
+ if (within_tolerance(mdl_dist,ref_dist,tol).first) {
+ LOG_INFO("LDT:" << " " << av1.GetResidue().GetChain() << " " << av1.GetResidue().GetName() << " " << av1.GetResidue().GetNumber() << " " << av1.GetName()
+ << " " << av2.GetResidue().GetChain() << " " << av2.GetResidue().GetName() << " " << av2.GetResidue().GetNumber() << " " << av2.GetName() << " "
+ << mdl_dist << " " << ref_dist.GetMinDistance() << " " << mdl_dist-ref_dist.GetMinDistance() << " " << tol << " " << "PASS")
+ overlap.first+=1;
+ overlap_list[av1.GetResidue().GetIndex()].first+=1.0;
+ overlap_list[av2.GetResidue().GetIndex()].first+=1.0;
+ } else {
+ LOG_VERBOSE("LDT:" << " " << av1.GetResidue().GetChain() << " " << av1.GetResidue().GetName() << " " << av1.GetResidue().GetNumber() << " " << av1.GetName()
+ << " " << av2.GetResidue().GetChain() << " " << av2.GetResidue().GetName() << " " << av2.GetResidue().GetNumber() << " " << av2.GetName() << " "
+ << mdl_dist << " " << ref_dist.GetMinDistance() << " " << mdl_dist-ref_dist.GetMinDistance() << " " << tol << " " << "FAIL")
+ }
+ }
return overlap;
}
+
std::pair<Real, Real> calc_overlap2(const seq::ConstSequenceHandle& ref_seq,
const seq::ConstSequenceHandle& mdl_seq,
int pos, Real tol, Real max_dist,
@@ -143,7 +175,10 @@ std::pair<Real, Real> calc_overlap2(const seq::ConstSequenceHandle& ref_seq,
}
for (AtomViewList::iterator aj=within.begin(),
ae2=within.end(); aj!=ae2; ++aj) {
- if (aj->GetElement()=="H") { continue; }
+ if (aj->GetElement()=="H" ||
+ aj->GetResidue().GetChain()!=ai->GetResidue().GetChain()) {
+ continue;
+ }
if (only_fixed) {
if (aj->GetResidue().GetNumber()==ref_res.GetNumber()) {
continue;
@@ -172,7 +207,8 @@ std::pair<Real, Real> calc_overlap2(const seq::ConstSequenceHandle& ref_seq,
continue;
} else {
if (aj->GetResidue().GetNumber()>ref_res.GetNumber()) {
- overlap.second+=1.0;
+ overlap.second+=1.0;
+
try {
int aln_pos=ref_seq.GetPos(aj->GetResidue().GetIndex());
ResidueView r2=mdl_seq.GetResidue(aln_pos);
@@ -198,81 +234,194 @@ std::pair<Real, Real> calc_overlap2(const seq::ConstSequenceHandle& ref_seq,
}
-Real LocalDistTest(const EntityView& mdl, const EntityView& ref,
- Real cutoff, Real max_dist, const String& local_ldt_property_string)
+bool IsStandardResidue(String rn)
+{
+ String upper_rn=rn;
+ std::transform(rn.begin(),rn.end(),rn.begin(),toupper);
+ if (upper_rn == "ALA" ||
+ upper_rn == "ARG" ||
+ upper_rn == "ASN" ||
+ upper_rn == "ASP" ||
+ upper_rn == "GLN" ||
+ upper_rn == "GLU" ||
+ upper_rn == "LYS" ||
+ upper_rn == "SER" ||
+ upper_rn == "CYS" ||
+ upper_rn == "TYR" ||
+ upper_rn == "TRP" ||
+ upper_rn == "THR" ||
+ upper_rn == "VAL" ||
+ upper_rn == "ILE" ||
+ upper_rn == "MET" ||
+ upper_rn == "LEU" ||
+ upper_rn == "GLY" ||
+ upper_rn == "PRO" ||
+ upper_rn == "HIS" ||
+ upper_rn == "PHE") {
+ return true;
+ }
+ return false;
+}
+
+bool UniqueAtomIdentifier::operator==(const UniqueAtomIdentifier& rhs) const
+{
+ if (chain_ == rhs.GetChainName() &&
+ residue_ == rhs.GetResNum() &&
+ residue_name_ == rhs.GetResidueName() &&
+ atom_ == rhs.GetAtomName() ) {
+ return true;
+ }
+ return false;
+}
+
+bool ReferenceDistance::IsValid() const
+{
+ if (mind_ == -1.0 and maxd_ == -1.0) {
+ return false;
+ }
+ return true;
+}
+
+void ReferenceDistance::Print() const
+{
+ if (this->IsValid() == true) {
+ std::cout << first_atom_.GetChainName() << " " << first_atom_.GetResNum() << " " << first_atom_.GetResidueName() << " " << first_atom_.GetAtomName() << " " <<
+ second_atom_.GetChainName() << " " << second_atom_.GetResNum() << " " << second_atom_.GetResidueName() << " " << second_atom_.GetAtomName() << " " <<
+ mind_ << " " << maxd_ << std::endl;
+ } else {
+ std::cout << first_atom_.GetChainName() << " " << first_atom_.GetResNum() << " " << first_atom_.GetResidueName() << " Placeholder" << std::endl;
+ }
+}
+
+bool ReferenceDistance::operator==(const ReferenceDistance& rhs) const
+{
+ if (first_atom_ == rhs.GetFirstAtom() &&
+ second_atom_ == rhs.GetSecondAtom() &&
+ mind_ == rhs.GetMinDistance() &&
+ maxd_ == rhs.GetMaxDistance() ) {
+ return true;
+ }
+ return false;
+}
+
+
+
+
+GlobalDistanceList CreateDistanceList(const EntityView& ref,Real max_dist)
+{
+ GlobalDistanceList dist_list;
+ ResidueViewList ref_residues=ref.GetChainList()[0].GetResidueList();
+ for (ResidueViewList::iterator i=ref_residues.begin(), e=ref_residues.end(); i!=e; ++i) {
+ ResidueView rview = (*i);
+ if (IsStandardResidue(rview.GetName())) {
+ ResidueDistanceList res_dist_list;
+ AtomViewList ref_atoms=(*i).GetAtomList();
+ AtomViewList within;
+ if (max_dist<0){
+ dist_list.push_back(res_dist_list);
+ within=ref.GetAtomList();
+ }
+ for (AtomViewList::iterator ai=ref_atoms.begin(), ae=ref_atoms.end(); ai!=ae; ++ai) {
+ UniqueAtomIdentifier first_atom(ai->GetResidue().GetChain().GetName(),ai->GetResidue().GetNumber(),ai->GetResidue().GetName(),ai->GetName());
+ if (ai->GetElement()=="H") { continue; }
+ if (max_dist>=0){
+ within=ref.FindWithin(ai->GetPos(), max_dist);
+ }
+ for (AtomViewList::iterator aj=within.begin(), ae2=within.end(); aj!=ae2; ++aj) {
+ UniqueAtomIdentifier second_atom(aj->GetResidue().GetChain().GetName(),aj->GetResidue().GetNumber(),aj->GetResidue().GetName(),aj->GetName());
+ if (aj->GetElement()=="H" ||
+ aj->GetResidue().GetChain()!=ai->GetResidue().GetChain()) {
+ continue;
+ }
+ if (aj->GetResidue().GetNumber()>i->GetNumber()) {
+ Real dist=geom::Length(ai->GetPos()-aj->GetPos());
+ ReferenceDistance ref_dist(first_atom,second_atom,dist,dist);
+ res_dist_list.push_back(ref_dist);
+ }
+ }
+ }
+ if (res_dist_list.size()==0) {
+ UniqueAtomIdentifier current_residue_fake_atom(rview.GetChain().GetName(),rview.GetNumber(),rview.GetName(),"CA");
+ ReferenceDistance fake_ref_distance(current_residue_fake_atom,current_residue_fake_atom,-1.0,-1.0);
+ res_dist_list.push_back(fake_ref_distance);
+ }
+ dist_list.push_back(res_dist_list);
+ }
+ }
+ return dist_list;
+}
+
+
+Real LocalDistTest(const EntityView& mdl, const GlobalDistanceList& glob_dist_list,
+ Real cutoff, const String& local_ldt_property_string)
{
-
if (!mdl.GetResidueCount()) {
LOG_WARNING("model structures doesn't contain any residues");
return 0.0;
}
-
- if (!ref.GetResidueCount()) {
- LOG_WARNING("reference structures doesn't contain any residues");
+ if (glob_dist_list.size()==0) {
+ LOG_WARNING("global reference list is empty");
return 0.0;
}
- ResidueViewList ref_residues=ref.GetResidueList();
- std::vector<std::pair<Real, Real> > overlap_list(ref_residues.size(), std::pair<Real, Real>(0.0, 0.0));
+ std::vector<std::pair<Real, Real> > overlap_list(mdl.GetResidueCount(), std::pair<Real, Real>(0.0, 0.0));
ChainView mdl_chain=mdl.GetChainList()[0];
// Residues with symmetric side-chains require special treatment as there are
// two possible ways to name the atoms. We calculate the overlap with the
// fixed atoms and take the solution that gives bigger scores.
- XCSEditor edi=ref.GetHandle().EditXCS(BUFFERED_EDIT);
- for (ResidueViewList::iterator
- i=ref_residues.begin(), e=ref_residues.end(); i!=e; ++i) {
- const String rname=i->GetName();
- ResidueView mdl_res=mdl_chain.FindResidue(i->GetNumber());
- if (!mdl_res) {
- continue;
- }
- if (!(rname=="GLU" || rname=="ASP" || rname=="VAL" || rname=="TYR" ||
- rname=="PHE" || rname=="LYS" || rname=="ARG")) {
+ XCSEditor edi=mdl.GetHandle().EditXCS(BUFFERED_EDIT);
+ for (GlobalDistanceList::const_iterator i=glob_dist_list.begin(), e=glob_dist_list.end(); i!=e; ++i) {
+ ResidueDistanceList rdl = *i;
+ if (!rdl[0].IsValid()) {
continue;
}
-
- std::pair<Real, Real> ov1=calc_overlap1(*i, ref, mdl_chain,
- cutoff, max_dist, true,
- false, overlap_list);
- std::pair<Real, Real> ov2=calc_overlap1(*i, ref, mdl_chain,
- cutoff, max_dist, true,
- true, overlap_list);
+
+ ResNum rnum = rdl[0].GetFirstAtom().GetResNum() ;
+ String rname=rdl[0].GetFirstAtom().GetResidueName();
+ ResidueView mdl_res=mdl_chain.FindResidue(rnum);
+ if (!mdl_res) {
+ continue;
+ }
+ if (!(rname=="GLU" || rname=="ASP" || rname=="VAL" || rname=="TYR" || rname=="PHE" || rname=="LYS" || rname=="ARG")) {
+ continue;
+ }
+ std::pair<Real, Real> ov1=calc_overlap1(*i, mdl_chain,
+ cutoff, true,
+ false, overlap_list,false);
+
+ std::pair<Real, Real> ov2=calc_overlap1(*i, mdl_chain,
+ cutoff, true,
+ true, overlap_list,false);
if (ov1.first/ov1.second<ov2.first/ov2.second) {
- AtomViewList atoms=mdl_res.GetAtomList();
- for (AtomViewList::iterator j=atoms.begin(),
- e2=atoms.end(); j!=e2; ++j) {
- if (swappable(rname, j->GetName())) {
- edi.RenameAtom(j->GetHandle(), swapped_name(j->GetName()));
- }
- }
+ AtomViewList atoms=mdl_res.GetAtomList();
+ for (AtomViewList::iterator j=atoms.begin(), e2=atoms.end(); j!=e2; ++j) {
+ if (swappable(rname, j->GetName())) {
+ edi.RenameAtom(j->GetHandle(), swapped_name(j->GetName()));
+ }
+ }
}
}
+ overlap_list.clear();
std::pair<Real, Real> total_ov(0.0, 0.0);
- for (ResidueViewList::iterator
- i=ref_residues.begin(), e=ref_residues.end(); i!=e; ++i) {
- std::pair<Real, Real> ov1=calc_overlap1(*i, ref, mdl_chain, cutoff,
- max_dist, false, false, overlap_list);
- total_ov.first+=ov1.first;
- total_ov.second+=ov1.second;
- }
-
- // attach local per-residue LDT as property:
- if(local_ldt_property_string!="") {
- for (ResidueViewList::iterator
- i=ref_residues.begin(), e=ref_residues.end(); i!=e; ++i) {
- std::pair<Real, Real> ov1=calc_overlap1(*i, ref, mdl_chain, cutoff,
- max_dist, false, false, overlap_list);
- total_ov.first+=ov1.first;
- total_ov.second+=ov1.second;
- Real local_ldt=overlap_list[(*i).GetIndex()].first/(overlap_list[(*i).GetIndex()].second ? overlap_list[(*i).GetIndex()].second : 1);
- if (mdl_chain.FindResidue((*i).GetNumber()).IsValid()) {
- ResidueView mdl_res=mdl_chain.FindResidue((*i).GetNumber());
- mdl_res.SetFloatProp(local_ldt_property_string, local_ldt);
- }
+ for (GlobalDistanceList::const_iterator i=glob_dist_list.begin(), e=glob_dist_list.end(); i!=e; ++i) {
+ ResidueDistanceList rdl = *i;
+ if (rdl[0].IsValid()) {
+ std::pair<Real, Real> ov1=calc_overlap1(*i, mdl_chain, cutoff,
+ false, false, overlap_list,true);
+ total_ov.first+=ov1.first;
+ total_ov.second+=ov1.second;
}
- mdl_chain.SetFloatProp(local_ldt_property_string, total_ov.first/(total_ov.second ? total_ov.second : 1));
+ if(local_ldt_property_string!="") {
+ ResNum rn = rdl[0].GetFirstAtom().GetResNum();
+ ResidueView mdlr=mdl_chain.FindResidue(rn);
+ if (mdlr.IsValid()) {
+ int mdl_res_index =mdlr.GetIndex();
+ Real local_ldt=overlap_list[mdl_res_index].first/(overlap_list[mdl_res_index].second ? overlap_list[mdl_res_index].second : 1);
+ ResidueView res_to_wr = mdl_chain.FindResidue((*i)[0].GetFirstAtom().GetResNum());
+ res_to_wr.SetFloatProp(local_ldt_property_string, local_ldt);
+ }
+ }
}
overlap_list.clear();
-
return total_ov.first/(total_ov.second ? total_ov.second : 1);
}
@@ -327,4 +476,17 @@ Real LocalDistTest(const ost::seq::AlignmentHandle& aln,
return 0.0;
}
+Real LDTHA(EntityView& v, const GlobalDistanceList& global_dist_list)
+{
+
+ Real cutoffs[]={0.5,1,2,4};
+ String labels[]={"localldt0.5","localldt1","localldt2","ldtlocal4"};
+ Real ldt=0.0;
+ for (int n=0; n<4; ++n) {
+ ldt+=alg::LocalDistTest(v, global_dist_list, cutoffs[n], labels[n]);
+ }
+ ldt/=4.0;
+ return ldt;
+}
+
}}}
diff --git a/modules/mol/alg/src/local_dist_test.hh b/modules/mol/alg/src/local_dist_test.hh
index 76ef238034ea095ec26eebff64e08e48b60b0e8e..74e0f4f29ca00b54340a683a036904d3eb66e596 100644
--- a/modules/mol/alg/src/local_dist_test.hh
+++ b/modules/mol/alg/src/local_dist_test.hh
@@ -25,15 +25,70 @@
namespace ost { namespace mol { namespace alg {
+
+class UniqueAtomIdentifier
+{
+
+public:
+ UniqueAtomIdentifier(const String& chain,const ResNum& residue,const String& residue_name, const String& atom): chain_(chain),residue_(residue),residue_name_(residue_name),atom_(atom) {}
+
+ String GetChainName() const { return chain_; }
+ ResNum GetResNum() const { return residue_; }
+ String GetResidueName() const { return residue_name_; }
+ String GetAtomName() const { return atom_; }
+ bool operator==(const UniqueAtomIdentifier& rhs) const;
+
+private:
+
+ String chain_;
+ ResNum residue_;
+ String residue_name_;
+ String atom_;
+};
+
+class ReferenceDistance
+{
+
+public:
+
+ ReferenceDistance(const UniqueAtomIdentifier& first_atom, const UniqueAtomIdentifier& second_atom, Real mind, Real maxd):
+ first_atom_(first_atom),second_atom_(second_atom),mind_(mind),maxd_(maxd) {}
+ UniqueAtomIdentifier GetFirstAtom() const {return first_atom_;}
+ UniqueAtomIdentifier GetSecondAtom() const {return second_atom_;}
+ Real GetMinDistance() const {return mind_ ;}
+ Real GetMaxDistance() const {return maxd_ ;}
+ bool IsValid() const;
+ void Print() const;
+ bool operator==(const ReferenceDistance& rhs) const;
+
+private:
+
+ UniqueAtomIdentifier first_atom_;
+ UniqueAtomIdentifier second_atom_;
+ Real mind_;
+ Real maxd_;
+};
+
+typedef std::vector<ReferenceDistance> ResidueDistanceList;
+typedef std::vector<ResidueDistanceList> GlobalDistanceList;
+
Real DLLEXPORT_OST_MOL_ALG LocalDistTest(const EntityView& mdl,
- const EntityView& ref,
- Real cutoff, Real max_dist,
+ const GlobalDistanceList& dist_list,
+ Real cutoff,
const String& local_ldt_property_string="");
Real DLLEXPORT_OST_MOL_ALG LocalDistTest(const ost::seq::AlignmentHandle& aln,
- Real cutoff, Real max_dist,
+ Real cutoff, Real max_dist,
int ref_index=0, int mdl_index=1);
+
+Real DLLEXPORT_OST_MOL_ALG LDTHA(EntityView& v, const GlobalDistanceList& global_dist_list);
+
+GlobalDistanceList CreateDistanceList(const EntityView& ref,Real max_dist);
+bool IsStandardResidue(String rn);
+
+
+
}}}
#endif
diff --git a/modules/mol/alg/src/new_stereo_chemical_props.txt b/modules/mol/alg/src/new_stereo_chemical_props.txt
new file mode 100644
index 0000000000000000000000000000000000000000..25262efd7689fc76f4d6ea1a7c75e342e840ea1d
--- /dev/null
+++ b/modules/mol/alg/src/new_stereo_chemical_props.txt
@@ -0,0 +1,345 @@
+Bond Residue Mean StdDev
+CA-CB ALA 1.520 0.021
+N-CA ALA 1.459 0.020
+CA-C ALA 1.525 0.026
+C-O ALA 1.229 0.019
+CA-CB ARG 1.535 0.022
+CB-CG ARG 1.521 0.027
+CG-CD ARG 1.515 0.025
+CD-NE ARG 1.460 0.017
+NE-CZ ARG 1.326 0.013
+CZ-NH1 ARG 1.326 0.013
+CZ-NH2 ARG 1.326 0.013
+N-CA ARG 1.459 0.020
+CA-C ARG 1.525 0.026
+C-O ARG 1.229 0.019
+CA-CB ASN 1.527 0.026
+CB-CG ASN 1.506 0.023
+CG-OD1 ASN 1.235 0.022
+CG-ND2 ASN 1.324 0.025
+N-CA ASN 1.459 0.020
+CA-C ASN 1.525 0.026
+C-O ASN 1.229 0.019
+CA-CB ASP 1.535 0.022
+CB-CG ASP 1.513 0.021
+CG-OD1 ASP 1.249 0.023
+CG-OD2 ASP 1.249 0.023
+N-CA ASP 1.459 0.020
+CA-C ASP 1.525 0.026
+C-O ASP 1.229 0.019
+CA-CB CYS 1.526 0.013
+CB-SG CYS 1.812 0.016
+N-CA CYS 1.459 0.020
+CA-C CYS 1.525 0.026
+C-O CYS 1.229 0.019
+CA-CB GLU 1.535 0.022
+CB-CG GLU 1.517 0.019
+CG-CD GLU 1.515 0.015
+CD-OE1 GLU 1.252 0.011
+CD-OE2 GLU 1.252 0.011
+N-CA GLU 1.459 0.020
+CA-C GLU 1.525 0.026
+C-O GLU 1.229 0.019
+CA-CB GLN 1.535 0.022
+CB-CG GLN 1.521 0.027
+CG-CD GLN 1.506 0.023
+CD-OE1 GLN 1.235 0.022
+CD-NE2 GLN 1.324 0.025
+N-CA GLN 1.459 0.020
+CA-C GLN 1.525 0.026
+C-O GLN 1.229 0.019
+N-CA GLY 1.456 0.015
+CA-C GLY 1.514 0.016
+C-O GLY 1.232 0.016
+CA-CB HIS 1.535 0.022
+CB-CG HIS 1.492 0.016
+CG-ND1 HIS 1.369 0.015
+CG-CD2 HIS 1.353 0.017
+ND1-CE1 HIS 1.343 0.025
+CD2-NE2 HIS 1.415 0.021
+CE1-NE2 HIS 1.322 0.023
+N-CA HIS 1.459 0.020
+CA-C HIS 1.525 0.026
+C-O HIS 1.229 0.019
+CA-CB ILE 1.544 0.023
+CB-CG1 ILE 1.536 0.028
+CB-CG2 ILE 1.524 0.031
+CG1-CD1 ILE 1.500 0.069
+N-CA ILE 1.459 0.020
+CA-C ILE 1.525 0.026
+C-O ILE 1.229 0.019
+CA-CB LEU 1.533 0.023
+CB-CG LEU 1.521 0.029
+CG-CD1 LEU 1.514 0.037
+CG-CD2 LEU 1.514 0.037
+N-CA LEU 1.459 0.020
+CA-C LEU 1.525 0.026
+C-O LEU 1.229 0.019
+CA-CB LYS 1.535 0.022
+CB-CG LYS 1.521 0.027
+CG-CD LYS 1.520 0.034
+CD-CE LYS 1.508 0.025
+CE-NZ LYS 1.486 0.025
+N-CA LYS 1.459 0.020
+CA-C LYS 1.525 0.026
+C-O LYS 1.229 0.019
+CA-CB MET 1.535 0.022
+CB-CG MET 1.509 0.032
+CG-SD MET 1.807 0.026
+SD-CE MET 1.774 0.056
+N-CA MET 1.459 0.020
+CA-C MET 1.525 0.026
+C-O MET 1.229 0.019
+CA-CB PHE 1.535 0.022
+CB-CG PHE 1.509 0.017
+CG-CD1 PHE 1.383 0.015
+CG-CD2 PHE 1.383 0.015
+CD1-CE1 PHE 1.388 0.020
+CD2-CE2 PHE 1.388 0.020
+CE1-CZ PHE 1.369 0.019
+CE2-CZ PHE 1.369 0.019
+N-CA PHE 1.459 0.020
+CA-C PHE 1.525 0.026
+C-O PHE 1.229 0.019
+CA-CB PRO 1.531 0.020
+CB-CG PRO 1.495 0.050
+CG-CD PRO 1.502 0.033
+CD-N PRO 1.474 0.014
+N-CA PRO 1.468 0.017
+CA-C PRO 1.524 0.020
+C-O PRO 1.228 0.020
+CA-CB SER 1.525 0.015
+CB-OG SER 1.418 0.013
+N-CA SER 1.459 0.020
+CA-C SER 1.525 0.026
+C-O SER 1.229 0.019
+CA-CB THR 1.529 0.026
+CB-OG1 THR 1.428 0.020
+CB-CG2 THR 1.519 0.033
+N-CA THR 1.459 0.020
+CA-C THR 1.525 0.026
+C-O THR 1.229 0.019
+CA-CB TRP 1.535 0.022
+CB-CG TRP 1.498 0.018
+CG-CD1 TRP 1.363 0.014
+CG-CD2 TRP 1.432 0.017
+CD1-NE1 TRP 1.375 0.017
+NE1-CE2 TRP 1.371 0.013
+CD2-CE2 TRP 1.409 0.012
+CD2-CE3 TRP 1.399 0.015
+CE2-CZ2 TRP 1.393 0.017
+CE3-CZ3 TRP 1.380 0.017
+CZ2-CH2 TRP 1.369 0.019
+CZ3-CH2 TRP 1.396 0.016
+N-CA TRP 1.459 0.020
+CA-C TRP 1.525 0.026
+C-O TRP 1.229 0.019
+CA-CB TYR 1.535 0.022
+CB-CG TYR 1.512 0.015
+CG-CD1 TYR 1.387 0.013
+CG-CD2 TYR 1.387 0.013
+CD1-CE1 TYR 1.389 0.015
+CD2-CE2 TYR 1.389 0.015
+CE1-CZ TYR 1.381 0.013
+CE2-CZ TYR 1.381 0.013
+CZ-OH TYR 1.374 0.017
+N-CA TYR 1.459 0.020
+CA-C TYR 1.525 0.026
+C-O TYR 1.229 0.019
+CA-CB VAL 1.543 0.021
+CB-CG1 VAL 1.524 0.021
+CB-CG2 VAL 1.524 0.021
+N-CA VAL 1.459 0.020
+CA-C VAL 1.525 0.026
+C-O VAL 1.229 0.019
+-
+
+Angle Residue Mean StdDev
+N-CA-CB ALA 110.1 1.4
+CB-CA-C ALA 110.1 1.5
+N-CA-C ALA 111.0 2.7
+CA-C-O ALA 120.1 2.1
+N-CA-CB ARG 110.6 1.8
+CB-CA-C ARG 110.4 2.0
+CA-CB-CG ARG 113.4 2.2
+CB-CG-CD ARG 111.6 2.6
+CG-CD-NE ARG 111.8 2.1
+CD-NE-CZ ARG 123.6 1.4
+NE-CZ-NH1 ARG 120.3 0.5
+NE-CZ-NH2 ARG 120.3 0.5
+NH1-CZ-NH2 ARG 119.4 1.1
+N-CA-C ARG 111.0 2.7
+CA-C-O ARG 120.1 2.1
+N-CA-CB ASN 110.6 1.8
+CB-CA-C ASN 110.4 2.0
+CA-CB-CG ASN 113.4 2.2
+CB-CG-ND2 ASN 116.7 2.4
+CB-CG-OD1 ASN 121.6 2.0
+ND2-CG-OD1 ASN 121.9 2.3
+N-CA-C ASN 111.0 2.7
+CA-C-O ASN 120.1 2.1
+N-CA-CB ASP 110.6 1.8
+CB-CA-C ASP 110.4 2.0
+CA-CB-CG ASP 113.4 2.2
+CB-CG-OD1 ASP 118.3 0.9
+CB-CG-OD2 ASP 118.3 0.9
+OD1-CG-OD2 ASP 123.3 1.9
+N-CA-C ASP 111.0 2.7
+CA-C-O ASP 120.1 2.1
+N-CA-CB CYS 110.8 1.5
+CB-CA-C CYS 111.5 1.2
+CA-CB-SG CYS 114.2 1.1
+N-CA-C CYS 111.0 2.7
+CA-C-O CYS 120.1 2.1
+N-CA-CB GLU 110.6 1.8
+CB-CA-C GLU 110.4 2.0
+CA-CB-CG GLU 113.4 2.2
+CB-CG-CD GLU 114.2 2.7
+CG-CD-OE1 GLU 118.3 2.0
+CG-CD-OE2 GLU 118.3 2.0
+OE1-CD-OE2 GLU 123.3 1.2
+N-CA-C GLU 111.0 2.7
+CA-C-O GLU 120.1 2.1
+N-CA-CB GLN 110.6 1.8
+CB-CA-C GLN 110.4 2.0
+CA-CB-CG GLN 113.4 2.2
+CB-CG-CD GLN 111.6 2.6
+CG-CD-OE1 GLN 121.6 2.0
+CG-CD-NE2 GLN 116.7 2.4
+OE1-CD-NE2 GLN 121.9 2.3
+N-CA-C GLN 111.0 2.7
+CA-C-O GLN 120.1 2.1
+N-CA-C GLY 113.1 2.5
+CA-C-O GLY 120.6 1.8
+N-CA-CB HIS 110.6 1.8
+CB-CA-C HIS 110.4 2.0
+CA-CB-CG HIS 113.6 1.7
+CB-CG-ND1 HIS 123.2 2.5
+CB-CG-CD2 HIS 130.8 3.1
+CG-ND1-CE1 HIS 108.2 1.4
+ND1-CE1-NE2 HIS 109.9 2.2
+CE1-NE2-CD2 HIS 106.6 2.5
+NE2-CD2-CG HIS 109.2 1.9
+CD2-CG-ND1 HIS 106.0 1.4
+N-CA-C HIS 111.0 2.7
+CA-C-O HIS 120.1 2.1
+N-CA-CB ILE 110.8 2.3
+CB-CA-C ILE 111.6 2.0
+CA-CB-CG1 ILE 111.0 1.9
+CB-CG1-CD1 ILE 113.9 2.8
+CA-CB-CG2 ILE 110.9 2.0
+CG1-CB-CG2 ILE 111.4 2.2
+N-CA-C ILE 111.0 2.7
+CA-C-O ILE 120.1 2.1
+N-CA-CB LEU 110.4 2.0
+CB-CA-C LEU 110.2 1.9
+CA-CB-CG LEU 115.3 2.3
+CB-CG-CD1 LEU 111.0 1.7
+CB-CG-CD2 LEU 111.0 1.7
+CD1-CG-CD2 LEU 110.5 3.0
+N-CA-C LEU 111.0 2.7
+CA-C-O LEU 120.1 2.1
+N-CA-CB LYS 110.6 1.8
+CB-CA-C LYS 110.4 2.0
+CA-CB-CG LYS 113.4 2.2
+CB-CG-CD LYS 111.6 2.6
+CG-CD-CE LYS 111.9 3.0
+CD-CE-NZ LYS 111.7 2.3
+N-CA-C LYS 111.0 2.7
+CA-C-O LYS 120.1 2.1
+N-CA-CB MET 110.6 1.8
+CB-CA-C MET 110.4 2.0
+CA-CB-CG MET 113.3 1.7
+CB-CG-SD MET 112.4 3.0
+CG-SD-CE MET 100.2 1.6
+N-CA-C MET 111.0 2.7
+CA-C-O MET 120.1 2.1
+N-CA-CB PHE 110.6 1.8
+CB-CA-C PHE 110.4 2.0
+CA-CB-CG PHE 113.9 2.4
+CB-CG-CD1 PHE 120.8 0.7
+CB-CG-CD2 PHE 120.8 0.7
+CD1-CG-CD2 PHE 118.3 1.3
+CG-CD1-CE1 PHE 120.8 1.1
+CG-CD2-CE2 PHE 120.8 1.1
+CD1-CE1-CZ PHE 120.1 1.2
+CD2-CE2-CZ PHE 120.1 1.2
+CE1-CZ-CE2 PHE 120.0 1.8
+N-CA-C PHE 111.0 2.7
+CA-C-O PHE 120.1 2.1
+N-CA-CB PRO 103.3 1.2
+CB-CA-C PRO 111.7 2.1
+CA-CB-CG PRO 104.8 1.9
+CB-CG-CD PRO 106.5 3.9
+CG-CD-N PRO 103.2 1.5
+CA-N-CD PRO 111.7 1.4
+N-CA-C PRO 112.1 2.6
+CA-C-O PRO 120.2 2.4
+N-CA-CB SER 110.5 1.5
+CB-CA-C SER 110.1 1.9
+CA-CB-OG SER 111.2 2.7
+N-CA-C SER 111.0 2.7
+CA-C-O SER 120.1 2.1
+N-CA-CB THR 110.3 1.9
+CB-CA-C THR 111.6 2.7
+CA-CB-OG1 THR 109.0 2.1
+CA-CB-CG2 THR 112.4 1.4
+OG1-CB-CG2 THR 110.0 2.3
+N-CA-C THR 111.0 2.7
+CA-C-O THR 120.1 2.1
+N-CA-CB TRP 110.6 1.8
+CB-CA-C TRP 110.4 2.0
+CA-CB-CG TRP 113.7 1.9
+CB-CG-CD1 TRP 127.0 1.3
+CB-CG-CD2 TRP 126.6 1.3
+CD1-CG-CD2 TRP 106.3 0.8
+CG-CD1-NE1 TRP 110.1 1.0
+CD1-NE1-CE2 TRP 109.0 0.9
+NE1-CE2-CD2 TRP 107.3 1.0
+CE2-CD2-CG TRP 107.3 0.8
+CG-CD2-CE3 TRP 133.9 0.9
+NE1-CE2-CZ2 TRP 130.4 1.1
+CE3-CD2-CE2 TRP 118.7 1.2
+CD2-CE2-CZ2 TRP 122.3 1.2
+CE2-CZ2-CH2 TRP 117.4 1.0
+CZ2-CH2-CZ3 TRP 121.6 1.2
+CH2-CZ3-CE3 TRP 121.2 1.1
+CZ3-CE3-CD2 TRP 118.8 1.3
+N-CA-C TRP 111.0 2.7
+CA-C-O TRP 120.1 2.1
+N-CA-CB TYR 110.6 1.8
+CB-CA-C TYR 110.4 2.0
+CA-CB-CG TYR 113.4 1.9
+CB-CG-CD1 TYR 121.0 0.6
+CB-CG-CD2 TYR 121.0 0.6
+CD1-CG-CD2 TYR 117.9 1.1
+CG-CD1-CE1 TYR 121.3 0.8
+CG-CD2-CE2 TYR 121.3 0.8
+CD1-CE1-CZ TYR 119.8 0.9
+CD2-CE2-CZ TYR 119.8 0.9
+CE1-CZ-CE2 TYR 119.8 1.6
+CE1-CZ-OH TYR 120.1 2.7
+CE2-CZ-OH TYR 120.1 2.7
+N-CA-C TYR 111.0 2.7
+CA-C-O TYR 120.1 2.1
+N-CA-CB VAL 111.5 2.2
+CB-CA-C VAL 111.4 1.9
+CA-CB-CG1 VAL 110.9 1.5
+CA-CB-CG2 VAL 110.9 1.5
+CG1-CB-CG2 VAL 110.9 1.6
+N-CA-C VAL 111.0 2.7
+CA-C-O VAL 120.1 2.1
+-
+
+Non-bonded distance Minimum Dist Tolerance
+C-C 3.4 1.5
+C-N 3.25 1.5
+C-S 3.5 1.5
+C-O 3.22 1.5
+N-N 3.1 1.5
+N-S 3.35 1.5
+N-O 3.07 1.5
+O-S 3.32 1.5
+O-O 3.04 1.5
+S-S 2.03 1.0
+-
diff --git a/modules/mol/alg/src/stereo_chemical_props.txt b/modules/mol/alg/src/stereo_chemical_props.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f17af3cf31baf8789c648fb1d5f1eff1d882a46d
--- /dev/null
+++ b/modules/mol/alg/src/stereo_chemical_props.txt
@@ -0,0 +1,367 @@
+# This file contains stereochemical parameters used to evaluate the quality of models.
+# Bond distances and Angles come from Engh,Huber (1991). Non bonded distances come from
+
+Bond Residue Mean StdDev
+N-CA ALA 1.458 0.019
+CA-C ALA 1.525 0.021
+C-O ALA 1.231 0.02
+CA-CB ALA 1.521 0.033
+N-CA CYS 1.458 0.019
+CA-C CYS 1.525 0.021
+C-O CYS 1.231 0.02
+CA-CB CYS 1.53 0.02
+CB-SG CYS 1.808 0.033
+N-CA ASP 1.458 0.019
+CA-C ASP 1.525 0.021
+C-O ASP 1.231 0.02
+CA-CB ASP 1.53 0.02
+CB-CG ASP 1.516 0.025
+CG-OD1 ASP 1.249 0.019
+CG-OD2 ASP 1.249 0.019
+N-CA GLU 1.458 0.019
+CA-C GLU 1.525 0.021
+C-O GLU 1.231 0.02
+CA-CB GLU 1.53 0.02
+CB-CG GLU 1.52 0.03
+CG-CD GLU 1.516 0.025
+CD-OE1 GLU 1.249 0.019
+CD-OE2 GLU 1.249 0.019
+N-CA PHE 1.458 0.019
+CA-C PHE 1.525 0.021
+C-O PHE 1.231 0.02
+CA-CB PHE 1.53 0.02
+CB-CG PHE 1.502 0.023
+CG-CD1 PHE 1.384 0.021
+CG-CD2 PHE 1.384 0.021
+CD1-CE1 PHE 1.382 0.03
+CD2-CE2 PHE 1.382 0.03
+CE1-CZ PHE 1.382 0.03
+CE2-CZ PHE 1.382 0.03
+N-CA GLY 1.451 0.016
+CA-C GLY 1.516 0.018
+C-O GLY 1.231 0.02
+N-CA HIS 1.458 0.019
+CA-C HIS 1.525 0.021
+C-O HIS 1.231 0.02
+CA-CB HIS 1.53 0.02
+CB-CG HIS 1.497 0.014
+CG-ND1 HIS 1.378 0.011
+CG-CD2 HIS 1.354 0.011
+ND1-CE1 HIS 1.321 0.01
+CD2-NE2 HIS 1.374 0.011
+CE1-NE2 HIS 1.321 0.01
+N-CA ILE 1.458 0.019
+CA-C ILE 1.525 0.021
+C-O ILE 1.231 0.02
+CA-CB ILE 1.54 0.027
+CB-CG1 ILE 1.53 0.02
+CB-CG2 ILE 1.521 0.033
+CG1-CD1 ILE 1.513 0.039
+N-CA LYS 1.458 0.019
+CA-C LYS 1.525 0.021
+C-O LYS 1.231 0.02
+CA-CB LYS 1.53 0.02
+CB-CG LYS 1.52 0.03
+CG-CD LYS 1.52 0.03
+CD-CE LYS 1.52 0.03
+CE-NZ LYS 1.489 0.03
+N-CA LEU 1.458 0.019
+CA-C LEU 1.525 0.021
+C-O LEU 1.231 0.02
+CA-CB LEU 1.53 0.02
+CB-CG LEU 1.53 0.02
+CG-CD1 LEU 1.521 0.033
+CG-CD2 LEU 1.521 0.033
+N-CA MET 1.458 0.019
+CA-C MET 1.525 0.021
+C-O MET 1.231 0.02
+CA-CB MET 1.53 0.02
+CB-CG MET 1.52 0.03
+CG-SD MET 1.803 0.034
+SD-CE MET 1.791 0.059
+N-CA ASN 1.458 0.019
+CA-C ASN 1.525 0.021
+C-O ASN 1.231 0.02
+CA-CB ASN 1.53 0.02
+CB-CG ASN 1.516 0.025
+CG-OD1 ASN 1.231 0.02
+CG-ND2 ASN 1.328 0.021
+N-CA PRO 1.466 0.015
+CA-C PRO 1.525 0.021
+C-O PRO 1.231 0.02
+CA-CB PRO 1.53 0.02
+CB-CG PRO 1.492 0.05
+CG-CD PRO 1.503 0.034
+CD-N PRO 1.473 0.014
+N-CA GLN 1.458 0.019
+CA-C GLN 1.525 0.021
+C-O GLN 1.231 0.02
+CA-CB GLN 1.53 0.02
+CB-CG GLN 1.52 0.03
+CG-CD GLN 1.516 0.025
+CD-OE1 GLN 1.231 0.02
+CD-NE2 GLN 1.328 0.021
+N-CA ARG 1.458 0.019
+CA-C ARG 1.525 0.021
+C-O ARG 1.231 0.02
+CA-CB ARG 1.53 0.02
+CB-CG ARG 1.52 0.03
+CG-CD ARG 1.52 0.03
+CD-NE ARG 1.46 0.018
+NE-CZ ARG 1.329 0.014
+CZ-NH1 ARG 1.326 0.018
+CZ-NH2 ARG 1.326 0.018
+N-CA SER 1.458 0.019
+CA-C SER 1.525 0.021
+C-O SER 1.231 0.02
+CA-CB SER 1.53 0.02
+CB-OG SER 1.417 0.02
+N-CA THR 1.458 0.019
+CA-C THR 1.525 0.021
+C-O THR 1.231 0.02
+CA-CB THR 1.54 0.027
+CB-OG1 THR 1.433 0.016
+CB-CG2 THR 1.521 0.033
+N-CA VAL 1.458 0.019
+CA-C VAL 1.525 0.021
+C-O VAL 1.231 0.02
+CA-CB VAL 1.54 0.027
+CB-CG1 VAL 1.521 0.033
+CB-CG2 VAL 1.521 0.033
+N-CA TRP 1.458 0.019
+CA-C TRP 1.525 0.021
+C-O TRP 1.231 0.02
+CA-CB TRP 1.53 0.02
+CB-CG TRP 1.498 0.031
+CG-CD1 TRP 1.365 0.025
+CG-CD2 TRP 1.433 0.018
+CD1-NE1 TRP 1.374 0.021
+NE1-CE2 TRP 1.37 0.011
+CD2-CE2 TRP 1.409 0.017
+CD2-CE3 TRP 1.398 0.016
+CE2-CZ2 TRP 1.394 0.021
+CE3-CZ3 TRP 1.382 0.03
+CZ2-CH2 TRP 1.368 0.019
+CZ3-CH2 TRP 1.4 0.025
+N-CA TYR 1.458 0.019
+CA-C TYR 1.525 0.021
+C-O TYR 1.231 0.02
+CA-CB TYR 1.53 0.02
+CB-CG TYR 1.512 0.022
+CG-CD1 TYR 1.389 0.021
+CG-CD2 TYR 1.389 0.021
+CD1-CE1 TYR 1.382 0.03
+CD2-CE2 TYR 1.382 0.03
+CE1-CZ TYR 1.378 0.024
+CE2-CZ TYR 1.378 0.024
+CZ-OH TYR 1.376 0.021
+-
+
+Angle Residue Mean StdDev
+N-CA-C ALA 111.2 2.8
+CA-C-O ALA 120.8 1.7
+N-CA-CB ALA 110.4 1.5
+C-CA-CB ALA 110.5 1.5
+N-CA-C CYS 111.2 2.8
+CA-C-O CYS 120.8 1.7
+N-CA-CB CYS 110.5 1.7
+C-CA-CB CYS 110.1 1.9
+N-CA-C ASP 111.2 2.8
+CA-C-O ASP 120.8 1.7
+N-CA-CB ASP 110.5 1.7
+C-CA-CB ASP 110.1 1.9
+CA-CB-CG ASP 112.6 1.0
+CB-CG-OD2 ASP 118.4 2.3
+CB-CG-OD1 ASP 118.4 2.3
+OD2-CG-OD1 ASP 122.9 2.4
+N-CA-C GLU 111.2 2.8
+CA-C-O GLU 120.8 1.7
+N-CA-CB GLU 110.5 1.7
+C-CA-CB GLU 110.1 1.9
+CA-CB-CG GLU 114.1 2.0
+CB-CG-CD GLU 112.6 1.7
+CG-CD-OE2 GLU 118.4 2.3
+CG-CD-OE1 GLU 118.4 2.3
+OE2-CD-OE1 GLU 122.9 2.4
+N-CA-C PHE 111.2 2.8
+CA-C-O PHE 120.8 1.7
+N-CA-CB PHE 110.5 1.7
+C-CA-CB PHE 110.1 1.9
+CA-CB-CG PHE 113.8 1.0
+CB-CG-CD1 PHE 120.7 1.7
+CB-CG-CD2 PHE 120.7 1.7
+CG-CD1-CE1 PHE 120.7 1.7
+CG-CD2-CE2 PHE 120.7 1.7
+CD1-CE1-CZ PHE 120.0 1.8
+CD2-CE2-CZ PHE 120.0 1.8
+CE1-CZ-CE2 PHE 120.0 1.8
+CD1-CG-CD2 PHE 118.6 1.5
+N-CA-C GLY 112.5 2.9
+CA-C-O GLY 120.8 2.1
+N-CA-C HIS 111.2 2.8
+CA-C-O HIS 120.8 1.7
+N-CA-CB HIS 110.5 1.7
+C-CA-CB HIS 110.1 1.9
+CA-CB-CG HIS 113.8 1.0
+CB-CG-ND1 HIS 122.7 1.5
+CG-ND1-CE1 HIS 109.3 1.7
+ND1-CE1-NE2 HIS 108.4 1.0
+CE1-NE2-CD2 HIS 109.0 1.0
+NE2-CD2-CG HIS 107.2 1.0
+CD2-CG-ND1 HIS 106.1 1.0
+CB-CG-CD2 HIS 131.2 1.3
+N-CA-C ILE 111.2 2.8
+CA-C-O ILE 120.8 1.7
+N-CA-CB ILE 111.5 1.7
+C-CA-CB ILE 109.1 2.2
+CA-CB-CG2 ILE 110.5 1.7
+CA-CB-CG1 ILE 110.4 1.7
+CG2-CB-CG1 ILE 110.7 3.0
+CB-CG1-CD1 ILE 113.8 2.1
+N-CA-C LYS 111.2 2.8
+CA-C-O LYS 120.8 1.7
+N-CA-CB LYS 110.5 1.7
+C-CA-CB LYS 110.1 1.9
+CA-CB-CG LYS 114.1 2.0
+CB-CG-CD LYS 111.3 2.3
+CG-CD-CE LYS 111.3 2.3
+CD-CE-NZ LYS 111.9 3.2
+N-CA-C LEU 111.2 2.8
+CA-C-O LEU 120.8 1.7
+N-CA-CB LEU 110.5 1.7
+C-CA-CB LEU 110.1 1.9
+CA-CB-CG LEU 116.3 3.5
+CB-CG-CD1 LEU 110.7 3.0
+CB-CG-CD2 LEU 110.7 3.0
+CD1-CG-CD2 LEU 110.8 2.2
+N-CA-C MET 111.2 2.8
+CA-C-O MET 120.8 1.7
+N-CA-CB MET 110.5 1.7
+C-CA-CB MET 110.1 1.9
+CA-CB-CG MET 114.1 2.0
+CB-CG-SD MET 112.7 3.0
+CG-SD-CE MET 100.9 2.2
+N-CA-C ASN 111.2 2.8
+CA-C-O ASN 120.8 1.7
+N-CA-CB ASN 110.5 1.7
+C-CA-CB ASN 110.1 1.9
+CA-CB-CG ASN 112.6 1.0
+CB-CG-ND2 ASN 116.4 1.5
+CB-CG-OD1 ASN 120.8 2.0
+ND2-CG-OD1 ASN 122.6 1.0
+N-CA-C PRO 111.8 2.5
+CA-C-O PRO 120.8 1.7
+N-CA-CB PRO 103.0 1.1
+C-CA-CB PRO 110.1 1.9
+CA-CB-CG PRO 104.5 1.9
+CB-CG-CD PRO 106.1 3.2
+CG-CD-N PRO 103.2 1.5
+CD-N-CA PRO 112.0 1.4
+N-CA-C GLN 111.2 2.8
+CA-C-O GLN 120.8 1.7
+N-CA-CB GLN 110.5 1.7
+C-CA-CB GLN 110.1 1.9
+CA-CB-CG GLN 114.1 2.0
+CB-CG-CD GLN 112.6 1.7
+CG-CD-NE2 GLN 116.4 1.5
+CG-CD-OE1 GLN 120.8 2.0
+NE2-CD-OE1 GLN 122.6 1.0
+N-CA-C ARG 111.2 2.8
+CA-C-O ARG 120.8 1.7
+N-CA-CB ARG 110.5 1.7
+C-CA-CB ARG 110.1 1.9
+CA-CB-CG ARG 114.1 2.0
+CB-CG-CD ARG 111.3 2.3
+CG-CD-NE ARG 112.0 2.2
+CD-NE-CZ ARG 124.2 1.5
+NE-CZ-NH1 ARG 120.0 1.9
+NE-CZ-NH2 ARG 120.0 1.9
+NH1-CZ-NH2 ARG 119.7 1.8
+N-CA-C SER 111.2 2.8
+CA-C-O SER 120.8 1.7
+N-CA-CB SER 110.5 1.7
+C-CA-CB SER 110.1 1.9
+CA-CB-OG SER 111.1 2.0
+N-CA-C THR 111.2 2.8
+CA-C-O THR 120.8 1.7
+N-CA-CB THR 111.5 1.7
+C-CA-CB THR 109.1 2.2
+CA-CB-CG2 THR 110.5 1.7
+CA-CB-OG1 THR 109.6 1.5
+CG2-CB-OG1 THR 109.3 2.0
+N-CA-C VAL 111.2 2.8
+CA-C-O VAL 120.8 1.7
+N-CA-CB VAL 111.5 1.7
+C-CA-CB VAL 109.1 2.2
+CA-CB-CG1 VAL 110.5 1.7
+CA-CB-CG2 VAL 110.5 1.7
+CG1-CB-CG2 VAL 110.8 2.2
+N-CA-C TRP 111.2 2.8
+CA-C-O TRP 120.8 1.7
+N-CA-CB TRP 110.5 1.7
+C-CA-CB TRP 110.1 1.9
+CA-CB-CG TRP 113.6 1.9
+CB-CG-CD1 TRP 126.9 1.5
+CB-CG-CD2 TRP 126.8 1.4
+CD1-CG-CD2 TRP 106.3 1.6
+CG-CD1-NE1 TRP 110.2 1.3
+CD1-NE1-CE2 TRP 108.9 1.8
+NE1-CE2-CZ2 TRP 130.1 1.5
+NE1-CE2-CD2 TRP 107.4 1.3
+CZ2-CE2-CD2 TRP 122.4 1.0
+CE2-CZ2-CH2 TRP 117.5 1.3
+CZ2-CH2-CZ3 TRP 121.5 1.3
+CH2-CZ3-CE3 TRP 121.1 1.3
+CZ3-CE3-CD2 TRP 118.6 1.3
+CE3-CD2-CG TRP 133.9 1.0
+CE3-CD2-CE2 TRP 118.8 1.0
+CG-CD2-CE2 TRP 107.2 1.2
+N-CA-C TYR 111.2 2.8
+CA-C-O TYR 120.8 1.7
+N-CA-CB TYR 110.5 1.7
+C-CA-CB TYR 110.1 1.9
+CA-CB-CG TYR 113.9 1.8
+CB-CG-CD1 TYR 120.8 1.5
+CB-CG-CD2 TYR 120.8 1.5
+CG-CD1-CE1 TYR 121.2 1.5
+CG-CD2-CE2 TYR 121.2 1.5
+CD1-CE1-CZ TYR 119.6 1.8
+CD2-CE2-CZ TYR 119.6 1.8
+CE1-CZ-CE2 TYR 120.3 2.0
+CD1-CG-CD2 TYR 118.1 1.5
+CE1-CZ-OH TYR 119.9 3.0
+CE2-CZ-OH TYR 119.9 3.0
+-
+
+Non-bonded distance Minimum Dist Tolerance
+C-C 2.10 0.5
+C-N 2.10 0.5
+C-S 2.45 0.5
+C-O 2.25 0.5
+N-N 2.05 0.5
+N-S 2.55 0.5
+N-O 2.10 0.5
+O-S 2.45 0.5
+O-O 2.05 0.5
+S-S 1.80 0.5
+-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/modules/mol/alg/src/structure_analysis.cc b/modules/mol/alg/src/structure_analysis.cc
new file mode 100644
index 0000000000000000000000000000000000000000..50689dfca3a27c1a62ef999e5ce9a048baeeffda
--- /dev/null
+++ b/modules/mol/alg/src/structure_analysis.cc
@@ -0,0 +1,84 @@
+//------------------------------------------------------------------------------
+// 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
+//------------------------------------------------------------------------------
+
+/*
+ * Author Niklaus Johner
+ */
+
+#include <ost/base.hh>
+#include <ost/mol/mol.hh>
+#include "structure_analysis.hh"
+
+namespace ost { namespace mol { namespace alg {
+
+geom::Vec3List GetPosListFromView(const EntityView& view){
+ CheckHandleValidity(view);
+ geom::Vec3List vl;
+ AtomViewList atoms=view.GetAtomList();
+ vl.reserve(atoms.size());
+ for (AtomViewList::const_iterator i=atoms.begin(),
+ e=atoms.end(); i!=e; ++i) {
+ vl.push_back(i->GetPos());
+ }
+ return vl;
+}
+#if OST_IMG_ENABLED
+std::vector<Real> CalculateAgreementWithDensityMap(const geom::Vec3List& vl, img::MapHandle& density_map){
+ CheckHandleValidity(density_map);
+ std::vector<Real> v;
+ v.reserve(vl.size());
+ for (geom::Vec3List::const_iterator v1=vl.begin(),e=vl.end(); v1!=e; ++v1) {
+ img::Point p(density_map.CoordToIndex(*v1));
+ v.push_back(density_map.GetReal(p));
+ }
+ return v;
+}
+
+Real CalculateAverageAgreementWithDensityMap(const geom::Vec3List& vl, img::MapHandle& density_map){
+ CheckHandleValidity(density_map);
+ std::vector<Real> v=CalculateAgreementWithDensityMap(vl, density_map);
+ Real sum=0.0;
+ for (std::vector<Real>::const_iterator i=v.begin(),e=v.end(); i!=e; ++i) {
+ sum=sum+*i;
+ }
+ return sum/float(vl.size());
+}
+
+#endif
+void DLLEXPORT_OST_MOL_ALG WrapEntityInPeriodicCell(EntityHandle eh, const geom::Vec3 cell_center, const geom::Vec3 basis_vec){
+ mol::XCSEditor edi=eh.EditXCS(mol::BUFFERED_EDIT);
+ geom::Vec3 cm,wrapped_cm,shift;
+ edi=eh.EditXCS();
+ ResidueHandleList residues=eh.GetResidueList();
+ unsigned int n_residues=eh.GetResidueCount();
+ for (unsigned int i=0; i<n_residues; ++i) {
+ ResidueHandle r=residues[i];
+ cm=r.GetCenterOfMass();
+ wrapped_cm=geom::WrapVec3(cm,cell_center,basis_vec);
+ if (wrapped_cm==cm) continue;
+ AtomHandleList atoms=r.GetAtomList();
+ unsigned int n_atoms=r.GetAtomCount();
+ shift=wrapped_cm-cm;
+ for (unsigned int j=0; j<n_atoms; ++j) {
+ edi.SetAtomPos(atoms[j],atoms[j].GetPos()+shift);
+ }
+ }
+}
+
+}}} //ns
diff --git a/modules/mol/alg/src/structure_analysis.hh b/modules/mol/alg/src/structure_analysis.hh
new file mode 100644
index 0000000000000000000000000000000000000000..45cb601f8b32ba80656d031a211f5672202f4aed
--- /dev/null
+++ b/modules/mol/alg/src/structure_analysis.hh
@@ -0,0 +1,42 @@
+//------------------------------------------------------------------------------
+// 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
+//------------------------------------------------------------------------------
+
+/*
+ * Niklaus Johner
+ */
+#ifndef OST_STRUCTURE_ANALYSIS_HH
+#define OST_STRUCTURE_ANALYSIS_HH
+
+#include <ost/mol/alg/module_config.hh>
+
+#include <ost/mol/entity_view.hh>
+#include <ost/mol/entity_handle.hh>
+#if OST_IMG_ENABLED
+# include <ost/img/map.hh>
+#endif
+
+namespace ost { namespace mol { namespace alg {
+ geom::Vec3List DLLEXPORT_OST_MOL_ALG GetPosListFromView(const EntityView& view);
+#if OST_IMG_ENABLED
+ std::vector<Real> DLLEXPORT_OST_MOL_ALG CalculateAgreementWithDensityMap(const geom::Vec3List& vl, img::MapHandle& density_map);
+ Real DLLEXPORT_OST_MOL_ALG CalculateAverageAgreementWithDensityMap(const geom::Vec3List& vl, img::MapHandle& density_map);
+#endif
+ void DLLEXPORT_OST_MOL_ALG WrapEntityInPeriodicCell(EntityHandle eh, const geom::Vec3 cell_center, const geom::Vec3 basis_vec);
+}}}//ns
+#endif
diff --git a/modules/mol/alg/src/superpose_frames.cc b/modules/mol/alg/src/superpose_frames.cc
index 465f776e77558f14f2027d981d9c0c339a5c1e1e..85514d6d73a51ea060af6214dd9a748ca336f684 100644
--- a/modules/mol/alg/src/superpose_frames.cc
+++ b/modules/mol/alg/src/superpose_frames.cc
@@ -26,6 +26,13 @@
namespace ost { namespace mol { namespace alg {
+namespace {
+bool less_index(const mol::AtomHandle& a1, const mol::AtomHandle& a2)
+{
+ return a1.GetIndex()<a2.GetIndex();
+}
+
+}
typedef Eigen::Matrix<Real, 3, 3> EMat3;
typedef Eigen::Matrix<Real, 1, 3> ECVec3;
@@ -76,7 +83,7 @@ inline EMatX3 col_sub(const EMatX3& m, const ECVec3& s)
}
- void AddSuperposedFrame(CoordGroupHandle& superposed, EMatX3& ref_mat,EMatX3& ref_centered,ECVec3& ref_center,CoordFramePtr frame,std::vector<unsigned long>& indices)
+void AddSuperposedFrame(CoordGroupHandle& superposed, EMatX3& ref_mat,EMatX3& ref_centered,ECVec3& ref_center,CoordFramePtr frame,std::vector<unsigned long>& indices)
{
// This function superposes and then adds a CoordFrame (frame) to a CoordGroup (superposed).
// ref_mat, ref_centered and ref_center contain respectively the positions, centered positions and
@@ -144,7 +151,9 @@ CoordGroupHandle SuperposeFrames(CoordGroupHandle& cg, EntityView& sel,
indices.push_back(i->GetIndex());
}
}
- CoordGroupHandle superposed=CreateCoordGroup(cg.GetEntity().GetAtomList());
+ mol::AtomHandleList alist(cg.GetEntity().GetAtomList());
+ std::sort(alist.begin(), alist.end(),less_index);
+ CoordGroupHandle superposed=CreateCoordGroup(alist);
EMatX3 ref_mat=EMatX3::Zero(indices.size(), 3);
EMatX3 ref_centered=EMatX3::Zero(indices.size(), 3);
ECVec3 ref_center;
@@ -208,7 +217,9 @@ CoordGroupHandle SuperposeFrames(CoordGroupHandle& cg, EntityView& sel,
if (int(indices.size())!=ref_view.GetAtomCount()){
throw std::runtime_error("atom counts of the two views are not equal");
}
- CoordGroupHandle superposed=CreateCoordGroup(cg.GetEntity().GetAtomList());
+ mol::AtomHandleList alist(cg.GetEntity().GetAtomList());
+ std::sort(alist.begin(), alist.end(),less_index);
+ CoordGroupHandle superposed=CreateCoordGroup(alist);
EMatX3 ref_mat=EMatX3::Zero(indices.size(), 3);
EMatX3 ref_centered=EMatX3::Zero(indices.size(), 3);
ECVec3 ref_center;
diff --git a/modules/mol/alg/src/trajectory_analysis.cc b/modules/mol/alg/src/trajectory_analysis.cc
index 2c1225e753ba76adacfa3ccfd8dc6a2ccce18a95..4a2671c01b981c8eed22fc8ebe9c9a86a66664e7 100644
--- a/modules/mol/alg/src/trajectory_analysis.cc
+++ b/modules/mol/alg/src/trajectory_analysis.cc
@@ -25,8 +25,8 @@
#include <ost/geom/vec3.hh>
#include <ost/base.hh>
#include <ost/geom/geom.hh>
-#include <ost/mol/entity_view.hh>
-#include <ost/mol/coord_group.hh>
+#include <ost/mol/mol.hh>
+#include <ost/mol/view_op.hh>
#include "trajectory_analysis.hh"
namespace ost { namespace mol { namespace alg {
@@ -230,4 +230,173 @@ std::vector<Real> AnalyzeAromaticRingInteraction(const CoordGroupHandle& traj, c
}
return dist;
}
+
+ void AnalyzeAlphaHelixAxis(const CoordGroupHandle& traj, const EntityView& prot_seg, geom::Vec3List& directions,
+ geom::Vec3List& centers, unsigned int stride)
+ //This function calculates the best fitting cylinder to the C-alpha atoms of an EntityView and returns
+ //the geometric center as well as the axis of that cylinder. We take care to have the axis point towards
+ //the last residue of the selection, usually the direction of the alpha-helix
+ {
+ CheckHandleValidity(traj);
+ if (prot_seg.GetAtomCount()==0){
+ throw std::runtime_error("EntityView is empty");
+ }
+ std::vector<unsigned long> indices_ca;
+ geom::Line3 axis;
+ Real sign;
+ directions.reserve(ceil(traj.GetFrameCount()/float(stride)));
+ centers.reserve(ceil(traj.GetFrameCount()/float(stride)));
+ GetCaIndices(prot_seg, indices_ca);
+ unsigned int n_atoms=indices_ca.size();
+ for (size_t i=0; i<traj.GetFrameCount(); i+=stride) {
+ CoordFramePtr frame=traj.GetFrame(i);
+ axis=frame->FitCylinder(indices_ca);
+ sign=geom::Dot(axis.GetDirection(),(*frame)[indices_ca[n_atoms-1]]-axis.GetOrigin());
+ sign=sign/fabs(sign);
+ directions.push_back(sign*axis.GetDirection());
+ centers.push_back(axis.GetOrigin());
+ }
+ return;
+ }
+
+ //std::vector<geom::Line3> AnalyzeBestFitLine(const CoordGroupHandle& traj, const EntityView& prot_seg,
+ // unsigned int stride)
+ void AnalyzeBestFitLine(const CoordGroupHandle& traj, const EntityView& prot_seg, geom::Vec3List& directions,
+ geom::Vec3List& centers, unsigned int stride)
+ {
+ CheckHandleValidity(traj);
+ if (prot_seg.GetAtomCount()==0){
+ throw std::runtime_error("EntityView is empty");
+ }
+ std::vector<unsigned long> indices_ca;
+ geom::Line3 axis;
+ directions.reserve(ceil(traj.GetFrameCount()/float(stride)));
+ centers.reserve(ceil(traj.GetFrameCount()/float(stride)));
+ GetIndices(prot_seg, indices_ca);
+ for (size_t i=0; i<traj.GetFrameCount(); i+=stride) {
+ CoordFramePtr frame=traj.GetFrame(i);
+ axis=frame->GetODRLine(indices_ca);
+ directions.push_back(axis.GetDirection());
+ centers.push_back(axis.GetOrigin());
+ }
+ return;
+ }
+
+ void AnalyzeBestFitPlane(const CoordGroupHandle& traj, const EntityView& prot_seg, geom::Vec3List& normals,
+ geom::Vec3List& origins, unsigned int stride)
+ {
+ CheckHandleValidity(traj);
+ if (prot_seg.GetAtomCount()==0){
+ throw std::runtime_error("EntityView is empty");
+ }
+ std::vector<unsigned long> indices_ca;
+ geom::Plane best_plane;
+ normals.reserve(ceil(traj.GetFrameCount()/float(stride)));
+ origins.reserve(ceil(traj.GetFrameCount()/float(stride)));
+ GetIndices(prot_seg, indices_ca);
+ for (size_t i=0; i<traj.GetFrameCount(); i+=stride) {
+ CoordFramePtr frame=traj.GetFrame(i);
+ best_plane=frame->GetODRPlane(indices_ca);
+ normals.push_back(best_plane.GetNormal());
+ origins.push_back(best_plane.GetOrigin());
+ }
+ return;
+ }
+
+ std::vector<Real> AnalyzeHelicity(const CoordGroupHandle& traj, const EntityView& prot_seg,
+ unsigned int stride)
+ {
+ CheckHandleValidity(traj);
+ if (prot_seg.GetAtomCount()==0){
+ throw std::runtime_error("EntityView is empty");
+ }
+ std::vector<unsigned long> indices_c,indices_o, indices_n, indices_ca;
+ std::vector<Real> helicity;
+ helicity.reserve(ceil(traj.GetFrameCount()/float(stride)));
+ GetCaCONIndices(prot_seg, indices_ca, indices_c, indices_o, indices_n);
+ for (size_t i=0; i<traj.GetFrameCount(); i+=stride) {
+ CoordFramePtr frame=traj.GetFrame(i);
+ helicity.push_back(frame->GetAlphaHelixContent(indices_ca,indices_c,indices_o,indices_n));
+ }
+ return helicity;
+ }
+
+ //This function constructs mean structures from a trajectory
+ EntityHandle CreateMeanStructure(const CoordGroupHandle& traj, const EntityView& selection,
+ int from, int to, unsigned int stride)
+ {
+ CheckHandleValidity(traj);
+ if (to==-1)to=traj.GetFrameCount();
+ unsigned int n_atoms=selection.GetAtomCount();
+ if (to<from) {
+ throw std::runtime_error("to smaller than from");
+ }
+ unsigned int n_frames=ceil((to-from)/stride);
+ if (n_atoms==0){
+ throw std::runtime_error("EntityView is empty");
+ }
+ if (n_frames<=1) {
+ throw std::runtime_error("number of frames is too small");
+ }
+ std::vector<unsigned long> indices;
+ std::vector<geom::Vec3> mean_positions;
+ EntityHandle eh;
+ eh=CreateEntityFromView(selection,1);
+ GetIndices(selection,indices);
+ mean_positions.assign(n_atoms,geom::Vec3(0.0,0.0,0.0));
+ for (int i=from; i<to; i+=stride) {
+ CoordFramePtr frame=traj.GetFrame(i);
+ for (unsigned int j=0; j<n_atoms; ++j) {
+ mean_positions[j]+=(*frame)[indices[j]];
+ }
+ }
+ mol::XCSEditor edi=eh.EditXCS(mol::BUFFERED_EDIT);
+ AtomHandleList atoms=eh.GetAtomList();
+ for (unsigned int j=0; j<n_atoms; ++j) {
+ edi.SetAtomPos(atoms[j],mean_positions[j]/Real(n_frames));
+ }
+ return eh;
+ }
+
+ Real AnalyzeRMSF(const CoordGroupHandle& traj, const EntityView& selection, int from, int to, unsigned int stride)
+ // This function extracts the rmsf between two entity views and assigns it
+ // The views don't have to be from the same entity
+ // If you want to compare to frame i of the trajectory t, first use t.CopyFrame(i) for example:
+ // eh=io.LoadPDB(...),t=io.LoadCHARMMTraj(eh,...);Sele=eh.Select(...);t.CopyFrame(0);mol.alg.AnalyzeRMSD(t,Sele,Sele)
+ {
+ CheckHandleValidity(traj);
+ if (to==-1)to=traj.GetFrameCount();
+ unsigned int n_atoms=selection.GetAtomCount();
+ if (to<from) {
+ throw std::runtime_error("to smaller than from");
+ }
+ unsigned int n_frames=ceil((to-from)/stride);
+ if (n_atoms==0){
+ throw std::runtime_error("EntityView is empty");
+ }
+ if (n_frames<=1) {
+ throw std::runtime_error("number of frames is too small");
+ }
+ Real rmsf=0.0;
+ geom::Vec3 v;
+ std::vector<unsigned long> sele_indices;
+ std::vector<geom::Vec3> ref_pos(n_atoms,geom::Vec3(0.,0.,0.));
+ GetIndices(selection, sele_indices);
+ for (unsigned int j=0; j<n_atoms; ++j) {
+ for (int i=from; i<to; i+=stride) {
+ CoordFramePtr frame=traj.GetFrame(i);
+ ref_pos[j]+=frame->GetAtomPos(sele_indices[j]);
+ }
+ ref_pos[j]/=n_frames;
+ }
+ for (int i=from; i<to; i+=stride) {
+ CoordFramePtr frame=traj.GetFrame(i);
+ for (unsigned int j=0; j<n_atoms; ++j) {
+ v=frame->GetAtomPos(sele_indices[j])-ref_pos[j];
+ rmsf+=geom::Dot(v,v);
+ }
+ }
+ return pow(rmsf/float(n_atoms*n_frames),0.5);
+ }
+
}}} //ns
diff --git a/modules/mol/alg/src/trajectory_analysis.hh b/modules/mol/alg/src/trajectory_analysis.hh
index faa6c8ea06d657afe169ac688c8cd8e6b8148b11..f32e4a85a07538d438ca25fcfba63eb8b74b5b35 100644
--- a/modules/mol/alg/src/trajectory_analysis.hh
+++ b/modules/mol/alg/src/trajectory_analysis.hh
@@ -40,8 +40,14 @@ namespace ost { namespace mol { namespace alg {
std::vector<Real> DLLEXPORT_OST_MOL_ALG AnalyzeDistanceBetwCenterOfMass(const CoordGroupHandle& traj, const EntityView& sele1, const EntityView& sele2,unsigned int stride=1);
std::vector<Real> DLLEXPORT_OST_MOL_ALG AnalyzeDihedralAngle(const CoordGroupHandle& traj, const AtomHandle& a1, const AtomHandle& a2, const AtomHandle& a3, const AtomHandle& a4,unsigned int stride=1);
std::vector<Real> DLLEXPORT_OST_MOL_ALG AnalyzeRMSD(const CoordGroupHandle& traj, const EntityView& reference_view, const EntityView& sele,unsigned int stride=1);
+ Real DLLEXPORT_OST_MOL_ALG AnalyzeRMSF(const CoordGroupHandle& traj, const EntityView& selection,int from=0, int to=-1, unsigned int stride=1);
std::vector<Real> DLLEXPORT_OST_MOL_ALG AnalyzeMinDistance(const CoordGroupHandle& traj, const EntityView& view1, const EntityView& view2,unsigned int stride=1);
std::vector<Real> DLLEXPORT_OST_MOL_ALG AnalyzeMinDistanceBetwCenterOfMassAndView(const CoordGroupHandle& traj, const EntityView& view_cm, const EntityView& view_atoms,unsigned int stride=1);
std::vector<Real> DLLEXPORT_OST_MOL_ALG AnalyzeAromaticRingInteraction(const CoordGroupHandle& traj, const EntityView& view_ring1, const EntityView& view_ring2,unsigned int stride=1);
+ void DLLEXPORT_OST_MOL_ALG AnalyzeAlphaHelixAxis(const CoordGroupHandle& traj, const EntityView& prot_seg, geom::Vec3List& directions, geom::Vec3List& centers, unsigned int stride=1);
+ void DLLEXPORT_OST_MOL_ALG AnalyzeBestFitLine(const CoordGroupHandle& traj, const EntityView& prot_seg, geom::Vec3List& directions, geom::Vec3List& centers, unsigned int stride=1);
+ void DLLEXPORT_OST_MOL_ALG AnalyzeBestFitPlane(const CoordGroupHandle& traj, const EntityView& prot_seg, geom::Vec3List& normals, geom::Vec3List& origins, unsigned int stride=1);
+ EntityHandle DLLEXPORT_OST_MOL_ALG CreateMeanStructure(const CoordGroupHandle& traj, const EntityView& selection, int from=0, int to=-1, unsigned int stride=1);
+ std::vector<Real> DLLEXPORT_OST_MOL_ALG AnalyzeHelicity(const CoordGroupHandle& traj, const EntityView& prot_seg, unsigned int stride=1);
}}}//ns
#endif
diff --git a/modules/mol/alg/tests/test_convenient_superpose.py b/modules/mol/alg/tests/test_convenient_superpose.py
index 7e03558c06647705589200688fb313df909e5c5b..eb4331ca3e8e6b65b0201197e5755cb2e5fcab15 100644
--- a/modules/mol/alg/tests/test_convenient_superpose.py
+++ b/modules/mol/alg/tests/test_convenient_superpose.py
@@ -193,4 +193,5 @@ class TestConvenientSuperpose(unittest.TestCase):
self.assertEqualAtomOrder(view1, view2)
if __name__ == "__main__":
- unittest.main()
+ from ost import testutils
+ testutils.RunTests()
diff --git a/modules/mol/base/doc/editors.rst b/modules/mol/base/doc/editors.rst
index 574f6b18ccef97cb4922871d3942c70674f42be0..ad4d7fb07f3d0f6a135f966a7ff82ef947e2712e 100644
--- a/modules/mol/base/doc/editors.rst
+++ b/modules/mol/base/doc/editors.rst
@@ -90,6 +90,17 @@ The basic functionality of editors is implemented in the EditorBase class.
:param new_name: is the new name
:type new_name: string
+ .. method:: SetChainType(chain, type)
+
+ :param chain: Must be a valid chain
+ :param type: Must be a value of enum ChainType
+ (see :attr:`ChainHandle.type`)
+
+ .. method:: SetChainDescription(chain, description)
+
+ :param chain: Must be a valid chain
+ :param description: Description to be added
+
.. method:: InsertAtom(residue, atom_name, pos,
element="", occupancy=1.0, b_factor=0.0,
is_hetatm=False)
diff --git a/modules/mol/base/doc/entity.rst b/modules/mol/base/doc/entity.rst
index 1ee9e6bdae35cce7abfe51d84e0315a354bc25da..94b8a1b3b14bbb62f03c68a043cf270b1e827e9f 100644
--- a/modules/mol/base/doc/entity.rst
+++ b/modules/mol/base/doc/entity.rst
@@ -280,11 +280,19 @@ The Handle Classes
want to save them as PDB files
This property is read-only. To change the name, use an :class:`XCSEditor`.
-
+
Also available as :meth:`GetName`
:type: str
+ .. attribute:: type
+
+ Describes the type of the chain. See :ref:`chaintype`.
+
+ .. attribute:: description
+
+ Details about the chain. Not categorised, just text.
+
.. attribute:: residues
List of all residues of this chain. The residues are sorted from N- to
@@ -389,11 +397,18 @@ The Handle Classes
.. method:: GetAtomList()
See :attr:`atoms`
-
+
.. method:: GetName()
See :attr:`name`
+ .. method:: GetType()
+
+ See :attr:`type`
+
+ .. method:: GetDescription()
+
+ See :attr:`description`
.. class:: ResidueHandle
@@ -496,6 +511,12 @@ The Handle Classes
The chemical class of a residue is used to broadly categorize residues based
on their chemical properties. For example, peptides belong to the
`L_PEPTIDE_LINKING` or `D_PEPTIDE_LINKING` classes.
+
+ .. attribute:: chem_type
+
+ The chemical type of a residue is a classification of all compounds
+ obtained from the PDB component dictionary. For example, ions belong to the
+ class `ChemType::IONS`, amino acids to `ChemType::AMINOACIDS`.
.. attribute:: sec_structure
@@ -544,6 +565,9 @@ The Handle Classes
See :attr:`psi_torsion`
+ .. method:: GetChemType()
+
+ See :attr:`chem_type`
.. class:: AtomHandle
@@ -1513,12 +1537,84 @@ Other Entity-Related Functions
.. function:: CreateViewFromAtomList(atom_list)
- Returns a view made up of the atoms in *atom_list*. All atoms are required to
- be atoms of the same entity. Duplicate atoms are only added to the view once.
-
- :param atom_list: the atoms
- :type atom_list: :class:`AtomHandleList` or :class:`AtomViewList`
- :raises: :class:`IntegrityError` if atoms of different entities are
- encountered
+ Returns a view made up of the atoms in *atom_list*. All atoms are required to
+ be atoms of the same entity. Duplicate atoms are only added to the view once.
+
+ :param atom_list: the atoms
+ :type atom_list: :class:`AtomHandleList` or :class:`AtomViewList`
+ :raises: :class:`IntegrityError` if atoms of different entities are
+ encountered
+
+ :returns: :class:`EntityView`
+
+.. function:: CreateEntityFromView(view, include_exlusive_atoms, handle=EntityHandle())
+
+ This function behaves exactly like :meth:`EntityHandle.Copy`, except that only
+ atoms, residues, chains and bonds that are present in the view will be
+ copied.
- :returns: :class:`EntityView`
\ No newline at end of file
+ :param view: is the view to be converted to a handle
+ :param include_exlusive_atoms: if true, atoms that are part of an exclusive
+ bond (only one bond partner is included in the view) will also be included
+ in the new entity handle.
+ :param handle: If invalid a new entity will be created. If valid, the atoms,
+ residues, chains, bonds and torsions will be added to handle. This is
+ useful to combine several entities into one.
+
+ :returns :class:`EntityHandle`
+
+.. _chaintype:
+
+ChainType
+--------------------------------------------------------------------------------
+
+A ChainType fills the :attr:`ChainHandle.type` attribute. Different types are
+described in the :ref:`ChainType enum <chaintype_enum>`. Functions for setting
+a type belong to the :class:`EditorBase` class, getting is provided by the
+:class:`ChainHandle` class, further convenience functions are described here.
+
+.. _chaintype_enum:
+
+The ChainType enum
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The ChainType enum enumerates all types defined by the PDB for the MMCif file
+format. Following values are supported:
+
+ ``CHAINTYPE_POLY``, ``CHAINTYPE_NON_POLY``, ``CHAINTYPE_WATER``,
+ ``CHAINTYPE_POLY_PEPTIDE_D``, ``CHAINTYPE_POLY_PEPTIDE_L``,
+ ``CHAINTYPE_POLY_DN``, ``CHAINTYPE_POLY_RN``, ``CHAINTYPE_POLY_SAC_D``,
+ ``CHAINTYPE_POLY_SAC_L``, ``CHAINTYPE_POLY_DN_RN``,
+ ``CHAINTYPE_UNKNOWN``, ``CHAINTYPE_N_CHAINTYPES``
+
+Where ``CHAINTYPE_N_CHAINTYPES`` holds the number of different types available.
+
+Setter & Getter functions
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+:func:`EditorBase.SetChainType`, :func:`ChainHandle.GetType`
+
+
+ChainType functions
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. function:: ChainTypeFromString(identifier)
+
+ Create a ChainType item for a given string.
+
+ :param identifier: String to request a type for.
+ :type identifier: :class:`str`
+ :raises: :class:`runtime_error` if **identifier** is unrecognised.
+
+ :returns: :class:`ChainType`
+
+.. function:: StringFromChainType(type)
+
+ Return the String identifier for a given **type**.
+
+ :param type: To be translated
+ :type type: :class:`ChainType`
+ :raises: :class:`runtime_error` if **type** is unrecognised.
+
+ :returns: :class:`str`
+
diff --git a/modules/mol/base/doc/mol.rst b/modules/mol/base/doc/mol.rst
index 976c2c8aa1ced240e5c461fb7f46745c60d0b36a..a416911491999891f73e81cfa6de2c9ef085b944 100644
--- a/modules/mol/base/doc/mol.rst
+++ b/modules/mol/base/doc/mol.rst
@@ -13,4 +13,4 @@ The mol module implements data structures to work with molecular datasets. At it
editors
query
surface
- traj
\ No newline at end of file
+ traj
diff --git a/modules/mol/base/pymod/CMakeLists.txt b/modules/mol/base/pymod/CMakeLists.txt
index 87369f260e9e199fbcd107304f729f616d0d45c6..3f514b2b8afba9e8f95473898b9649da2b3afcb7 100644
--- a/modules/mol/base/pymod/CMakeLists.txt
+++ b/modules/mol/base/pymod/CMakeLists.txt
@@ -22,4 +22,6 @@ wrap_mol.cc
export_entity_property_mapper.cc
)
-pymod(NAME mol CPP ${OST_BASE_PYMOD_SOURCES} PY __init__.py)
+if (NOT ENABLE_STATIC)
+ pymod(NAME mol CPP ${OST_BASE_PYMOD_SOURCES} PY __init__.py)
+endif()
diff --git a/modules/mol/base/pymod/export_chain.cc b/modules/mol/base/pymod/export_chain.cc
index 8a4cb355258454f90c0588cba0f17cb432da9b29..36ed2b471f3a3658a9622d3fa907dc019725326f 100644
--- a/modules/mol/base/pymod/export_chain.cc
+++ b/modules/mol/base/pymod/export_chain.cc
@@ -21,6 +21,7 @@
using namespace boost::python;
#include <ost/mol/mol.hh>
+#include <ost/mol/chain_type.hh>
#include <ost/geom/export_helper/vector.hh>
using namespace ost;
using namespace ost::mol;
@@ -38,7 +39,9 @@ namespace {
typedef EntityView (ChainHandle::*QueryMethod)(const Query&, uint) const;
typedef EntityView (ChainHandle::*StringMethod)(const String&, uint) const;
QueryMethod select_query=&ChainHandle::Select;
- StringMethod select_string=&ChainHandle::Select;
+ StringMethod select_string=&ChainHandle::Select;
+ ChainType (*ChainTypeFromStringPtr)(const String& identifier) =
+ &ChainTypeFromString;
}
void export_Chain()
@@ -50,6 +53,18 @@ void export_Chain()
.def(self_ns::str(self))
.add_property("valid", &ChainBase::IsValid)
.def("IsValid", &ChainBase::IsValid)
+ .def("GetType", &ChainBase::GetType)
+ .def("GetDescription", &ChainBase::GetDescription)
+ .def("IsPolypeptide", &ChainBase::IsPolypeptide)
+ .def("IsPolynucleotide", &ChainBase::IsPolynucleotide)
+ .def("IsPolysaccharide", &ChainBase::IsPolysaccharide)
+ .def("IsPolymer", &ChainBase::IsPolymer)
+ .add_property("is_polypeptide", &ChainBase::IsPolypeptide)
+ .add_property("is_polynucleotide", &ChainBase::IsPolynucleotide)
+ .add_property("is_polysaccharide", &ChainBase::IsPolysaccharide)
+ .add_property("is_polymer", &ChainBase::IsPolymer)
+ .add_property("type", &ChainBase::GetType)
+ .add_property("description", &ChainBase::GetDescription)
;
generic_prop_def<ChainBase>(chain_base);
class_<ChainHandle, bases<ChainBase> >("ChainHandle", init<>())
@@ -78,7 +93,9 @@ void export_Chain()
.def("GetAtomCount", &ChainHandle::GetAtomCount)
.def("GetBondCount", &ChainHandle::GetBondCount)
.add_property("residue_count", &ChainHandle::GetResidueCount)
- .add_property("atom_count", &ChainHandle::GetAtomCount)
+ .add_property("atom_count", &ChainHandle::GetAtomCount)
+ .add_property("chain_type", &ChainHandle::GetType)
+ .add_property("description", &ChainHandle::GetDescription)
.def("InSequence", &ChainHandle::InSequence)
.def("Select", select_string, arg("flags")=0)
.def("Select", select_query, arg("flags")=0)
@@ -103,4 +120,25 @@ void export_Chain()
.def(vector_indexing_suite<ChainHandleList>())
.def(geom::VectorAdditions<ChainHandleList>())
;
+
+ {
+ enum_<ChainType>("ChainType")
+ .value("CHAINTYPE_POLY", CHAINTYPE_POLY)
+ .value("CHAINTYPE_NON_POLY", CHAINTYPE_NON_POLY)
+ .value("CHAINTYPE_WATER", CHAINTYPE_WATER)
+ .value("CHAINTYPE_POLY_PEPTIDE_D", CHAINTYPE_POLY_PEPTIDE_D)
+ .value("CHAINTYPE_POLY_PEPTIDE_L", CHAINTYPE_POLY_PEPTIDE_L)
+ .value("CHAINTYPE_POLY_DN", CHAINTYPE_POLY_DN)
+ .value("CHAINTYPE_POLY_RN", CHAINTYPE_POLY_RN)
+ .value("CHAINTYPE_POLY_SAC_D", CHAINTYPE_POLY_SAC_D)
+ .value("CHAINTYPE_POLY_SAC_L", CHAINTYPE_POLY_SAC_L)
+ .value("CHAINTYPE_POLY_DN_RN", CHAINTYPE_POLY_DN_RN)
+ .value("CHAINTYPE_UNKNOWN", CHAINTYPE_UNKNOWN)
+ .value("CHAINTYPE_N_CHAINTYPES", CHAINTYPE_N_CHAINTYPES)
+ .export_values()
+ ;
+ }
+
+ def("ChainTypeFromString", ChainTypeFromStringPtr);
+ def("StringFromChainType", &StringFromChainType);
}
diff --git a/modules/mol/base/pymod/export_coord_frame.cc b/modules/mol/base/pymod/export_coord_frame.cc
index fdb41fce60b8032ecb6f527256b4b9c90d7cc5e1..1f417064dd8cb2df0ee01956b1f0d0352c6c281f 100644
--- a/modules/mol/base/pymod/export_coord_frame.cc
+++ b/modules/mol/base/pymod/export_coord_frame.cc
@@ -26,26 +26,42 @@ using namespace boost::python;
using namespace ost;
using namespace ost::mol;
+geom::Vec3 (CoordFrame::*GetCellSize)() = &CoordFrame::GetCellSize;
+geom::Vec3 (CoordFrame::*GetCellAngles)() = &CoordFrame::GetCellAngles;
geom::Vec3 (CoordFrame::*get_atom_pos)(const AtomHandle& atom) = &CoordFrame::GetAtomPos;
Real (CoordFrame::*get_dist_atom)(const AtomHandle& a1, const AtomHandle& a2) = &CoordFrame::GetDistanceBetwAtoms;
Real (CoordFrame::*get_angle)(const AtomHandle& a1, const AtomHandle& a2, const AtomHandle& a3) = &CoordFrame::GetAngle;
Real (CoordFrame::*get_dihedral)(const AtomHandle& a1, const AtomHandle& a2, const AtomHandle& a3, const AtomHandle& a4) = &CoordFrame::GetDihedralAngle;
geom::Vec3 (CoordFrame::*get_cm)(const mol::EntityView& sele) = &CoordFrame::GetCenterOfMassPos;
Real (CoordFrame::*get_dist_cm)(const mol::EntityView& sele1, const mol::EntityView& sele2) = &CoordFrame::GetDistanceBetwCenterOfMass;
+Real (CoordFrame::*get_min_dist_cm_v)(const mol::EntityView& sele1, const mol::EntityView& sele2) = &CoordFrame::GetMinDistBetwCenterOfMassAndView;
Real (CoordFrame::*get_rmsd)(const mol::EntityView& Reference_View, const mol::EntityView& sele_View) = &CoordFrame::GetRMSD;
Real (CoordFrame::*get_min_dist)(const mol::EntityView& view1, const mol::EntityView& view2) = &CoordFrame::GetMinDistance;
+Real (CoordFrame::*get_alpha)(const mol::EntityView& segment) = &CoordFrame::GetAlphaHelixContent;
+geom::Line3 (CoordFrame::*get_odr_line)(const mol::EntityView& view1) = &CoordFrame::GetODRLine;
+geom::Line3 (CoordFrame::*get_odr_line2)() = &geom::Vec3List::GetODRLine;
+geom::Plane (CoordFrame::*get_odr_plane)(const mol::EntityView& view1) = &CoordFrame::GetODRPlane;
+geom::Line3 (CoordFrame::*fit_cylinder)(const mol::EntityView& view1) = &CoordFrame::FitCylinder;
void export_CoordFrame()
{
class_<CoordFrame>("CoordFrame",no_init)
+ .def("GetCellSize",GetCellSize)
+ .def("GetCellAngles",GetCellAngles)
.def("GetAtomPos", get_atom_pos)
.def("GetDistanceBetwAtoms", get_dist_atom)
.def("GetAngle", get_angle)
.def("GetDihedralAngle", get_dihedral)
.def("GetCenterOfMassPos", get_cm)
.def("GetDistanceBetwCenterOfMass", get_dist_cm)
+ .def("GetMinDistBetwCenterOfMassAndView", get_min_dist_cm_v)
.def("GetRMSD",get_rmsd)
.def("GetMinDistance",get_min_dist)
+ .def("GetODRPlane",get_odr_plane)
+ .def("GetODRLine",get_odr_line)
+ .def("GetODRLine",get_odr_line2)
+ .def("GetAlphaHelixContent",get_alpha)
+ .def("FitCylinder",fit_cylinder)
;
def("CreateCoordFrame",CreateCoordFrame);
}
diff --git a/modules/mol/base/pymod/export_coord_group.cc b/modules/mol/base/pymod/export_coord_group.cc
index 794db5363c6ae050262e51c29608977ef83d569a..6bdeb1d6958f797898aea3a2915a3063daf10dea 100644
--- a/modules/mol/base/pymod/export_coord_group.cc
+++ b/modules/mol/base/pymod/export_coord_group.cc
@@ -38,6 +38,8 @@ namespace {
void (CoordGroupHandle::*capture1)()=&CoordGroupHandle::Capture;
void (CoordGroupHandle::*capture2)(uint)=&CoordGroupHandle::Capture;
+ void (CoordGroupHandle::*add_frame1)(const geom::Vec3List&)=&CoordGroupHandle::AddFrame;
+ void (CoordGroupHandle::*add_frame2)(const geom::Vec3List&,const geom::Vec3&,const geom::Vec3&)=&CoordGroupHandle::AddFrame;
}
void export_CoordGroup()
@@ -46,8 +48,12 @@ void export_CoordGroup()
.def("IsValid",&CoordGroupHandle::IsValid)
.def("GetEntity",&CoordGroupHandle::GetEntity)
.def("GetAtomCount",&CoordGroupHandle::GetAtomCount)
+ .def("GetFrame",&CoordGroupHandle::GetFrame2)
.def("AddFrames", &CoordGroupHandle::AddFrames)
+ .def("AddFrame", add_frame1)
+ .def("AddFrame", add_frame2)
.def("GetFrameCount",&CoordGroupHandle::GetFrameCount)
+ .def("GetFramePositions",&CoordGroupHandle::GetFramePositions)
.def("SetFramePositions",&CoordGroupHandle::SetFramePositions)
.def("SetAtomPos",&CoordGroupHandle::SetAtomPos)
.def("GetAtomPos",&CoordGroupHandle::GetAtomPos)
@@ -61,7 +67,7 @@ void export_CoordGroup()
.def("GetAtomList",&CoordGroupHandle::GetAtomList)
.def("__getitem__",cg_getitem)
.def("__setitem__",cg_setitem)
- .def("Filter", &CoordGroupHandle::Filter)
+ .def("Filter", &CoordGroupHandle::Filter, (arg("selected"),arg("first")=0,arg("last")=-1))
;
def("CreateCoordGroup",CreateCoordGroup);
diff --git a/modules/mol/base/pymod/export_editors.cc b/modules/mol/base/pymod/export_editors.cc
index 34d3a7fe8960cba5019702873fca197995f22eb0..6cee09765c2ce84e7a07bbddf4d05abebdd84cf6 100644
--- a/modules/mol/base/pymod/export_editors.cc
+++ b/modules/mol/base/pymod/export_editors.cc
@@ -48,15 +48,15 @@ ResidueHandle (EditorBase::*append_a)(ChainHandle ch,
ResidueHandle (EditorBase::*append_b)(ChainHandle ch, const ResidueKey&,
const ResNum&)=&EditorBase::AppendResidue;
-void (ICSEditor::*set_torsion_a)(TorsionHandle, Real)=&ICSEditor::SetTorsionAngle;
+void (ICSEditor::*set_torsion_a)(TorsionHandle, Real, bool)=&ICSEditor::SetTorsionAngle;
void (ICSEditor::*set_torsion_b)(const AtomHandle&, const AtomHandle&,
const AtomHandle&, const AtomHandle&,
- Real)=&ICSEditor::SetTorsionAngle;
+ Real, bool)=&ICSEditor::SetTorsionAngle;
-void (ICSEditor::*rotate_torsion_a)(TorsionHandle, Real)=&ICSEditor::RotateTorsionAngle;
+void (ICSEditor::*rotate_torsion_a)(TorsionHandle, Real, bool)=&ICSEditor::RotateTorsionAngle;
void (ICSEditor::*rotate_torsion_b)(const AtomHandle&, const AtomHandle&,
const AtomHandle&, const AtomHandle&,
- Real)=&ICSEditor::RotateTorsionAngle;
+ Real, bool)=&ICSEditor::RotateTorsionAngle;
#if OST_NUMPY_SUPPORT_ENABLED
template<typename T, bool O>
@@ -212,11 +212,15 @@ void export_Editors()
.def("Connect", connect_c)
.def("Connect", connect_d)
.def("RenameChain", &EditorBase::RenameChain)
+ .def("SetChainType", &EditorBase::SetChainType)
+ .def("SetChainDescription", &EditorBase::SetChainDescription)
.def("RenameResidue", &EditorBase::RenameResidue)
+ .def("SetResidueNumber", &EditorBase::SetResidueNumber)
.def("RenameAtom", &EditorBase::RenameAtom)
.def("AddTorsion", &EditorBase::AddTorsion)
.def("ReorderResidues",&EditorBase::ReorderResidues)
.def("ReorderAllResidues",&EditorBase::ReorderAllResidues)
+ .def("RenumberAllResidues",&EditorBase::RenumberAllResidues)
;
class_<XCSEditor, bases<EditorBase> >("XCSEditor", no_init)
@@ -232,10 +236,16 @@ void export_Editors()
class_<ICSEditor, bases<EditorBase> >("ICSEditor", no_init)
.def("SetAngle", &ICSEditor::SetAngle)
.def("SetBondLength", &ICSEditor::SetBondLength)
- .def("SetTorsionAngle", set_torsion_a)
- .def("SetTorsionAngle", set_torsion_b)
- .def("RotateTorsionAngle", rotate_torsion_a)
- .def("RotateTorsionAngle", rotate_torsion_b)
+ .def("SetTorsionAngle", set_torsion_a,
+ (arg("torsion"),arg("angle"), arg("update_others")=true))
+ .def("SetTorsionAngle", set_torsion_b,
+ (arg("atom_a"), arg("atom_b"), arg("atom_c"), arg("atom_d"),
+ arg("angle"), arg("update_others")))
+ .def("RotateTorsionAngle", rotate_torsion_a,
+ (arg("torsion"),arg("angle"), arg("update_others")=true))
+ .def("RotateTorsionAngle", rotate_torsion_b,
+ (arg("atom_a"), arg("atom_b"), arg("atom_c"), arg("atom_d"),
+ arg("angle"), arg("update_others")))
.def("UpdateXCS", &ICSEditor::UpdateXCS)
.def("__exit__", &ICSEditor::UpdateXCS)
;
diff --git a/modules/mol/base/pymod/export_entity.cc b/modules/mol/base/pymod/export_entity.cc
index c46f07284aab3eec978e25d4d87c265d39133939..6fda49c793342259e0d3ab5078716d3dda8c0a5e 100644
--- a/modules/mol/base/pymod/export_entity.cc
+++ b/modules/mol/base/pymod/export_entity.cc
@@ -147,6 +147,7 @@ void export_Entity()
.def("GetMass", &EntityHandle::GetMass)
.def("GetCenterOfMass", &EntityHandle::GetCenterOfMass)
.def("GetCenterOfAtoms", &EntityHandle::GetCenterOfAtoms)
+ .def("GetAtomPosList", &EntityHandle::GetAtomPosList)
.def("GetGeometricCenter", geom_center<EntityHandle>)
.add_property("geometric_center", geom_center<EntityHandle>)
diff --git a/modules/mol/base/pymod/export_residue.cc b/modules/mol/base/pymod/export_residue.cc
index 1e1b9f74a60d94c224b9aad51153a9e873b2a4a7..284c2f0bc294825e5751a3f441e377d1d1666517 100644
--- a/modules/mol/base/pymod/export_residue.cc
+++ b/modules/mol/base/pymod/export_residue.cc
@@ -21,6 +21,7 @@
using namespace boost::python;
#include <ost/mol/chem_class.hh>
+#include <ost/mol/chem_type.hh>
#include <ost/mol/mol.hh>
#include <ost/geom/export_helper/vector.hh>
using namespace ost;
@@ -64,7 +65,40 @@ namespace {
void export_Residue()
{
+ class_<ChemClass>("ChemClass", init<char>(args("chem_class")))
+ .def(self!=self)
+ .def(self==self)
+ .def("IsPeptideLinking", &ChemClass::IsPeptideLinking)
+ .def("IsNucleotideLinking", &ChemClass::IsNucleotideLinking)
+ ;
+ implicitly_convertible<char, ChemClass>();
+ object ct_class = class_<ChemType>("ChemType", init<char>(args("chem_type")))
+ .def(self!=self)
+ .def(self==self)
+ .def(self_ns::str(self))
+ .def("IsIon", &ChemType::IsIon)
+ .def("IsNucleotide", &ChemType::IsNucleotide)
+ .def("IsSaccharide", &ChemType::IsSaccharide)
+ .def("IsAminoAcid", &ChemType::IsAminoAcid)
+ .def("IsCoenzyme", &ChemType::IsCoenzyme)
+ .def("IsDrug", &ChemType::IsDrug)
+ .def("IsNonCanonical", &ChemType::IsNonCanonical)
+ .def("IsKnown", &ChemType::IsKnown)
+ .def("IsWater", &ChemType::IsWater)
+ ;
+ implicitly_convertible<char, ChemType>();
+ ct_class.attr("IONS")=char(ChemType::IONS);
+ ct_class.attr("NONCANONICALMOLS")=char(ChemType::NONCANONICALMOLS);
+ ct_class.attr("SACCHARIDES")=char(ChemType::SACCHARIDES);
+ ct_class.attr("NUCLEOTIDES")=char(ChemType::NUCLEOTIDES);
+ ct_class.attr("AMINOACIDS")=char(ChemType::AMINOACIDS);
+ ct_class.attr("COENZYMES")=char(ChemType::COENZYMES);
+ ct_class.attr("WATERCOORDIONS")=char(ChemType::WATERCOORDIONS);
+ ct_class.attr("DRUGS")=char(ChemType::DRUGS);
+ ct_class.attr("WATERS")=char(ChemType::WATERS);
+ ct_class.attr("UNKNOWN")=char(ChemType::UNKNOWN);
+
class_<ResNum>("ResNum", init<int>(args("num")))
.def(init<int,char>(args("num", "ins_code")))
.def("GetNum", &ResNum::GetNum)
@@ -79,6 +113,10 @@ void export_Residue()
.def(self<=self)
.def(self==self)
.def(self!=self)
+ .def(self+=self)
+ .def(self-=self)
+ .def(self+self)
+ .def(self-self)
.def(self+=int())
.def(self-=int())
.def(self+int())
@@ -133,7 +171,8 @@ void export_Residue()
.def("SetOneLetterCode", &ResidueBase::SetOneLetterCode)
.add_property("one_letter_code", &ResidueBase::GetOneLetterCode,
&ResidueBase::SetOneLetterCode)
- .def("GetQualifedName", &ResidueBase::GetQualifiedName)
+ .def("GetQualifiedName", &ResidueBase::GetQualifiedName)
+ .add_property("qualified_name", &ResidueBase::GetQualifiedName)
.def("IsPeptideLinking", &ResidueBase::IsPeptideLinking)
.add_property("peptide_linking", &ResidueBase::IsPeptideLinking)
@@ -144,13 +183,15 @@ void export_Residue()
.def("GetKey", &ResidueBase::GetKey,
return_value_policy<copy_const_reference>())
- .def("GetName", &ResidueBase::GetName,
+ .def("GetName", &ResidueBase::GetName,
return_value_policy<copy_const_reference>())
.def("GetNumber", &ResidueBase::GetNumber,
return_value_policy<copy_const_reference>())
.def("GetChemClass", &ResidueBase::GetChemClass)
+ .add_property("chem_class", &ResidueBase::GetChemClass, set_chemclass)
.def("SetChemClass", set_chemclass)
- .add_property("chem_class",&ResidueBase::GetChemClass,set_chemclass)
+ .def("GetChemType", &ResidueBase::GetChemType)
+ .add_property("chem_type", &ResidueBase::GetChemType)
.add_property("is_ligand", &ResidueBase::IsLigand, &ResidueBase::SetIsLigand)
.def("IsLigand", &ResidueBase::IsLigand)
.def("SetIsLigand", &ResidueBase::SetIsLigand)
@@ -165,7 +206,6 @@ void export_Residue()
.add_property("name",
make_function(&ResidueBase::GetName,
return_value_policy<copy_const_reference>()))
- .add_property("qualified_name", &ResidueBase::GetQualifiedName)
.def("IsValid", &ResidueBase::IsValid)
.add_property("valid", &ResidueBase::IsValid)
;
diff --git a/modules/mol/base/pymod/export_torsion.cc b/modules/mol/base/pymod/export_torsion.cc
index e7b45e0fd4c3afb385410f688267e05406351250..fbf9e2b726880b9e56a430e3def0aa50f0c1fd7b 100644
--- a/modules/mol/base/pymod/export_torsion.cc
+++ b/modules/mol/base/pymod/export_torsion.cc
@@ -49,14 +49,8 @@ void export_Torsion()
.add_property("third", &TorsionHandle::GetThird)
.add_property("fourth", &TorsionHandle::GetFourth)
.def("IsValid", &TorsionHandle::IsValid)
- .def("SetAngle", &TorsionHandle::SetAngle)
.def("GetAngle", &TorsionHandle::GetAngle)
- .def("RotateAngle", &TorsionHandle::RotateAngle,
- X_rotate_angle_overloads(args("angle", "up")))
- .add_property("angle", &TorsionHandle::GetAngle,
- &TorsionHandle::SetAngle)
- .def("SetAngle", &TorsionHandle::SetAngle,
- X_set_angle_overloads(args("angle", "up")))
+ .add_property("angle", &TorsionHandle::GetAngle)
.def(self_ns::str(self))
;
diff --git a/modules/mol/base/pymod/export_visitor.cc b/modules/mol/base/pymod/export_visitor.cc
index 0def51e95380ce057536b3de2395474f2cc84bb8..3a6d1e3285153e2bc71ff09f562d4e2e18b3645e 100644
--- a/modules/mol/base/pymod/export_visitor.cc
+++ b/modules/mol/base/pymod/export_visitor.cc
@@ -23,8 +23,6 @@ using namespace boost::python;
using namespace ost;
using namespace ost::mol;
-namespace {
-
struct WrappedVisitor : EntityVisitor
{
WrappedVisitor(PyObject *p)
@@ -63,7 +61,6 @@ struct WrappedVisitor : EntityVisitor
PyObject* self;
};
-}
void export_Visitor()
{
class_<EntityVisitor, WrappedVisitor>("EntityVisitor", init<>())
diff --git a/modules/mol/base/pymod/wrap_mol.cc b/modules/mol/base/pymod/wrap_mol.cc
index f29d1377f4bc0ccf14289b50df67e994208e99e5..33b09e2f20b4c1126f05cf501c04a599663048f9 100644
--- a/modules/mol/base/pymod/wrap_mol.cc
+++ b/modules/mol/base/pymod/wrap_mol.cc
@@ -19,7 +19,9 @@
#include <boost/python.hpp>
#include <ost/mol/transform.hh>
#include <ost/mol/editor_base.hh>
+#if(OST_INFO_ENABLED)
#include <ost/info/info.hh>
+#endif
using namespace boost::python;
using namespace ost::mol;
@@ -95,7 +97,9 @@ BOOST_PYTHON_MODULE(_ost_mol)
.def("ApplyZAxisTranslation",&Transform::ApplyZAxisTranslation)
.def("ApplyAxisRotation",&Transform::ApplyAxisRotation)
;
+#if(OST_INFO_ENABLED)
def("TransformToInfo", &TransformToInfo);
def("TransformFromInfo", &TransformFromInfo);
-
+#endif
+
}
diff --git a/modules/mol/base/src/CMakeLists.txt b/modules/mol/base/src/CMakeLists.txt
index b11b6e54c28389f77a429affc569470c14499ae4..134eb4e25691507a50039077bdf58099b57ae9ea 100644
--- a/modules/mol/base/src/CMakeLists.txt
+++ b/modules/mol/base/src/CMakeLists.txt
@@ -8,6 +8,7 @@ bond_handle.cc
chain_base.cc
chain_handle.cc
chain_view.cc
+chain_type.cc
coord_frame.cc
coord_group.cc
editor_base.cc
@@ -47,7 +48,9 @@ bond_table.hh
chain_base.hh
chain_handle.hh
chain_view.hh
+chain_type.hh
chem_class.hh
+chem_type.hh
coord_group.hh
coord_source.hh
in_mem_coord_source.hh
@@ -97,7 +100,13 @@ foreach(_impl_src ${OST_MOL_IMPL_SOURCES})
list(APPEND OST_MOL_SOURCES impl/${_impl_src})
endforeach()
+if(ENABLE_INFO)
+ set (INFO_DEPS ost_info)
+else()
+ list(APPEND LINK ${Boost_REGEX_LIBRARY})
+endif()
+
module(NAME mol SOURCES ${OST_MOL_SOURCES}
HEADERS ${OST_MOL_IMPL_HEADERS} IN_DIR impl
${OST_MOL_HEADERS} HEADER_OUTPUT_DIR ost/mol
- DEPENDS_ON ost_geom ost_base ost_info)
+ DEPENDS_ON ost_geom ost_base ${INFO_DEPS})
diff --git a/modules/mol/base/src/atom_base.cc b/modules/mol/base/src/atom_base.cc
index 642ea5aa93baad015633ab13caedbb2f7e3f704d..c818fbc1cec5ee0c0fa1be6fbb51eb59750133f0 100644
--- a/modules/mol/base/src/atom_base.cc
+++ b/modules/mol/base/src/atom_base.cc
@@ -69,6 +69,17 @@ geom::Vec3 AtomBase::GetAltPos(const String& alt_group) const
return impl_->GetResidue()->GetAltAtomPos(Impl(), alt_group);
}
+Real AtomBase::GetAltBFactor(const String& alt_group) const
+{
+ this->CheckValidity();
+ return impl_->GetResidue()->GetAltAtomBFactor(Impl(), alt_group);
+}
+Real AtomBase::GetAltOcc(const String& alt_group) const
+{
+ this->CheckValidity();
+ return impl_->GetResidue()->GetAltAtomOcc(Impl(), alt_group);
+}
+
std::vector<String> AtomBase::GetAltGroupNames() const
{
this->CheckValidity();
diff --git a/modules/mol/base/src/atom_base.hh b/modules/mol/base/src/atom_base.hh
index 8d19514af07c9e58536cf505ee7f51f11098dd52..13795311560e4c81d46063156c75aa6459359131 100644
--- a/modules/mol/base/src/atom_base.hh
+++ b/modules/mol/base/src/atom_base.hh
@@ -87,6 +87,8 @@ public:
const geom::Vec3& GetOriginalPos() const;
/// \brief get alternative atom position
geom::Vec3 GetAltPos(const String& alt_group) const;
+ Real GetAltBFactor(const String& alt_group) const;
+ Real GetAltOcc(const String& alt_group) const;
std::vector<String> GetAltGroupNames() const;
diff --git a/modules/mol/base/src/chain_base.cc b/modules/mol/base/src/chain_base.cc
index a82f8c05b92d0028396375c087176bc4571e3cda..bbf0cfdad68397971844ba49fb5e2ba4b378d953 100644
--- a/modules/mol/base/src/chain_base.cc
+++ b/modules/mol/base/src/chain_base.cc
@@ -44,6 +44,14 @@ String ChainBase::GetName() const {
return impl_->GetName();
}
+ChainType ChainBase::GetType() const {
+ return impl_->GetType();
+}
+
+String ChainBase::GetDescription() const {
+ return impl_->GetDescription();
+}
+
void ChainBase::CheckValidity() const {
if (!impl_)
throw InvalidHandle();
@@ -59,5 +67,32 @@ std::ostream& operator<<(std::ostream& os, const ChainBase& chain)
return os;
}
+bool ChainBase::IsPolymer() const
+{
+ this->CheckValidity();
+ return impl_->IsPolymer();
+
+}
+
+bool ChainBase::IsPolysaccharide() const
+{
+ this->CheckValidity();
+ return impl_->IsPolysaccharide();
+
+}
+
+bool ChainBase::IsPolypeptide() const
+{
+ this->CheckValidity();
+ return impl_->IsPolypeptide();
+
+}
+
+bool ChainBase::IsPolynucleotide() const
+{
+ this->CheckValidity();
+ return impl_->IsPolynucleotide();
+}
+
}} // ns
diff --git a/modules/mol/base/src/chain_base.hh b/modules/mol/base/src/chain_base.hh
index 4a904a2a87e67e72b015deb7d643ebe8df5f8804..984c948fd94b934656f4920baf3e1da739efd89a 100644
--- a/modules/mol/base/src/chain_base.hh
+++ b/modules/mol/base/src/chain_base.hh
@@ -22,6 +22,7 @@
#include <ost/mol/module_config.hh>
#include <ost/mol/impl/chain_impl_fw.hh>
+#include <ost/mol/chain_type.hh>
#include <ost/generic_property.hh>
namespace ost { namespace mol {
@@ -59,10 +60,35 @@ public:
friend class ConstGenericPropContainer<ChainBase>;
String GetName() const;
+ /// \brief Get the type of a chain.
+ ///
+ /// \return chain type of ChainType
+ ChainType GetType() const;
+
+ /// \brief Get information about a chain.
+ ///
+ /// \return description
+ String GetDescription() const;
+
const impl::ChainImplPtr& Impl() const {
return impl_;
}
+ /// \brief whether the chain is a polymer
+ ///
+ /// True if one of IsPolysaccharide(), IsPolynucleotide(), IsPolypeptide() is
+ /// true or the chain is of type CHAINTYPE_POLYMER.
+ bool IsPolymer() const;
+
+ /// \brief whether the chain is a polysaccharide
+ bool IsPolysaccharide() const;
+
+ /// \brief whether the chain is a polypeptide
+ bool IsPolypeptide() const;
+
+ /// \brief whether the chain is a polynucleotide
+ bool IsPolynucleotide() const;
+
impl::ChainImplPtr& Impl() {
return impl_;
}
diff --git a/modules/mol/base/src/chain_handle.cc b/modules/mol/base/src/chain_handle.cc
index 9ff209e3571e80fc5c653af540ce5027cabc6ff2..c1e745f2c2c4456fb765782d17caf13630d32d07 100644
--- a/modules/mol/base/src/chain_handle.cc
+++ b/modules/mol/base/src/chain_handle.cc
@@ -251,5 +251,11 @@ EntityView ChainHandle::Select(const String& q, QueryFlags flags) const {
else return this->GetEntity().Select(Query("cname='"+Impl()->GetName()+"'"), flags);
}
+void ChainHandle::SetInSequence(const int index)
+{
+ this->CheckValidity();
+ Impl()->SetInSequence(index);
+}
+
}}
diff --git a/modules/mol/base/src/chain_handle.hh b/modules/mol/base/src/chain_handle.hh
index 576c4b6715a6b0a796abe6e1b78fc4bd41da11d5..8f88c6e3757473acd558c0d0b830e56f46235a29 100644
--- a/modules/mol/base/src/chain_handle.hh
+++ b/modules/mol/base/src/chain_handle.hh
@@ -193,7 +193,9 @@ public:
bool operator==(const ChainHandle& ref) const;
bool operator!=(const ChainHandle& ref) const;
-
+ /// \brief checks whether res breaks the in sequence property
+ /// and updates it accordingly
+ void SetInSequence(const int index);
};
}} // ns
diff --git a/modules/mol/base/src/chain_type.cc b/modules/mol/base/src/chain_type.cc
new file mode 100644
index 0000000000000000000000000000000000000000..6b3841d8909e4378db492db306efe86ece0bba44
--- /dev/null
+++ b/modules/mol/base/src/chain_type.cc
@@ -0,0 +1,98 @@
+//------------------------------------------------------------------------------
+// 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
+//------------------------------------------------------------------------------
+
+#include <stdexcept>
+#include "chain_type.hh"
+
+namespace ost { namespace mol {
+
+ChainType ChainTypeFromString(StringRef identifier)
+{
+
+ // chain types as found in the entity category of a mmcif file
+ if(StringRef("polymer", 7) == identifier) {
+ return CHAINTYPE_POLY;
+ }else if(StringRef("non-polymer", 11) == identifier) {
+ return CHAINTYPE_NON_POLY;
+ }else if(StringRef("water", 5) == identifier) {
+ return CHAINTYPE_WATER;
+ // chain types as found in the entity_poly category of a mmcif file
+ } else if(StringRef("polypeptide(D)", 14) == identifier) {
+ return CHAINTYPE_POLY_PEPTIDE_D;
+ } else if(StringRef("polypeptide(L)", 14) == identifier) {
+ return CHAINTYPE_POLY_PEPTIDE_L;
+ } else if(StringRef("polydeoxyribonucleotide", 23) == identifier) {
+ return CHAINTYPE_POLY_DN;
+ } else if(StringRef("polyribonucleotide", 18) == identifier) {
+ return CHAINTYPE_POLY_RN;
+ } else if(StringRef("polysaccharide(D)", 17) == identifier) {
+ return CHAINTYPE_POLY_SAC_D;
+ } else if(StringRef("polysaccharide(L)", 17) == identifier) {
+ return CHAINTYPE_POLY_SAC_L;
+ } else if(StringRef("polydeoxyribonucleotide/polyribonucleotide hybrid",
+ 49) == identifier) {
+ return CHAINTYPE_POLY_DN_RN;
+ } else if(StringRef("other", 5) == identifier) {
+ return CHAINTYPE_UNKNOWN;
+ }
+
+ throw std::runtime_error("Unrecognised chain type descriptor found: '" +
+ identifier.str() +"'!");
+}
+
+ChainType ChainTypeFromString(const String& identifier)
+{
+ return ChainTypeFromString(StringRef(identifier.c_str(),
+ identifier.length()));
+}
+
+String StringFromChainType(ChainType type)
+{
+ // chain types as found in the entity category of a mmcif file
+ if (CHAINTYPE_POLY == type) {
+ return "polymer";
+ } else if (CHAINTYPE_NON_POLY == type) {
+ return "non-polymer";
+ } else if (CHAINTYPE_WATER == type) {
+ return "water";
+ // chain types as found in the entity_poly category of a mmcif file
+ } else if (CHAINTYPE_POLY_PEPTIDE_D == type) {
+ return "polypeptide(D)";
+ } else if (CHAINTYPE_POLY_PEPTIDE_L == type) {
+ return "polypeptide(L)";
+ } else if (CHAINTYPE_POLY_DN == type) {
+ return "polydeoxyribonucleotide";
+ } else if (CHAINTYPE_POLY_RN == type) {
+ return "polyribonucleotide";
+ } else if (CHAINTYPE_POLY_SAC_D == type) {
+ return "polysaccharide(D)";
+ } else if (CHAINTYPE_POLY_SAC_L == type) {
+ return "polysaccharide(L)";
+ } else if (CHAINTYPE_POLY_DN_RN == type) {
+ return "polydeoxyribonucleotide/polyribonucleotide hybrid";
+ } else if (CHAINTYPE_UNKNOWN == type) {
+ return "other";
+ }
+
+ std::stringstream ss("Unknonw ChainType item found: '");
+ ss << type << "'!";
+ throw std::runtime_error(ss.str());
+}
+
+}} //ns
diff --git a/modules/mol/base/src/chain_type.hh b/modules/mol/base/src/chain_type.hh
new file mode 100644
index 0000000000000000000000000000000000000000..18a00fb457cd4f49ba261aab3f2f74c11cb91508
--- /dev/null
+++ b/modules/mol/base/src/chain_type.hh
@@ -0,0 +1,69 @@
+//------------------------------------------------------------------------------
+// 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_CHAIN_TYPE_HH
+#define OST_CHAIN_TYPE_HH
+
+#include <ost/base.hh>
+#include <ost/string_ref.hh>
+
+namespace ost { namespace mol {
+
+/// \enum different kinds of chains
+typedef enum {
+ CHAINTYPE_POLY, ///< polymer
+ CHAINTYPE_NON_POLY, ///< non-polymer
+ CHAINTYPE_WATER, ///< water
+ CHAINTYPE_POLY_PEPTIDE_D, ///< (D) amino acid sequence
+ CHAINTYPE_POLY_PEPTIDE_L, ///< (L) amino acid sequence
+ CHAINTYPE_POLY_DN, ///< polydeoxyribonucleotide
+ CHAINTYPE_POLY_RN, ///< polyribonucleotide
+ CHAINTYPE_POLY_SAC_D, ///< polysaccharide(D)
+ CHAINTYPE_POLY_SAC_L, ///< polysaccharide(L)
+ CHAINTYPE_POLY_DN_RN, ///<polydeoxyribonucleotide/ -ribonucleotide hybrid
+ CHAINTYPE_UNKNOWN, ///< guess what
+ CHAINTYPE_N_CHAINTYPES ///< no. of chain types
+} ChainType;
+
+/// \brief Create a ChainType item for a given string
+///
+/// \param identifier StringRef to be translated
+///
+/// \return The ChainType corresponding to the input, throws a
+/// std::runtime_error on unknown type
+ChainType ChainTypeFromString(const StringRef identifier);
+
+/// \brief Create a ChainType item for a given string
+///
+/// \param identifier String to be translated
+///
+/// \return The ChainType corresponding to the input, throws a
+/// std::runtime_error on unknown type
+ChainType ChainTypeFromString(const String& identifier);
+
+/// \brief Return the String identifier for a given type
+///
+/// \param type ChainType to be translated
+///
+/// \return String corresponding to the input, throws a std::runtime_error on
+/// unknown type
+String StringFromChainType(ChainType type);
+
+}} //ns
+
+#endif
diff --git a/modules/mol/base/src/chain_view.cc b/modules/mol/base/src/chain_view.cc
index b940a37ee37dd8f82c302ba4b5a51119169cb6f6..4727e31ddce6764bcdfc0e78bb5e7c3c31e0d83f 100644
--- a/modules/mol/base/src/chain_view.cc
+++ b/modules/mol/base/src/chain_view.cc
@@ -334,14 +334,10 @@ bool ChainView::operator!=(const ChainView& rhs) const
Real ChainView::GetMass() const {
this->CheckValidity();
- Real mass = 0;
+ double mass = 0;
ResidueViewList::const_iterator i;
for (i=data_->residues.begin(); i!=data_->residues.end(); ++i) {
- ResidueView r=*i;
- for (AtomViewList::const_iterator j=r.GetAtomList().begin(),
- e2=r.GetAtomList().end(); j!=e2; ++j) {
- mass+=j->GetMass();
- }
+ mass+=i->GetMass();
}
return mass;
}
diff --git a/modules/mol/base/src/chem_type.hh b/modules/mol/base/src/chem_type.hh
new file mode 100644
index 0000000000000000000000000000000000000000..eac806433400daeb1ead20ecf88ddff558b64fc7
--- /dev/null
+++ b/modules/mol/base/src/chem_type.hh
@@ -0,0 +1,104 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2010 by the OpenStructure authors
+//
+// This library is free 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_BASE_CHEM_TYPE_HI
+#define OST_BASE_CHEM_TYPE_HI
+#include <vector>
+
+#include <boost/shared_ptr.hpp>
+
+#include <ost/mol/module_config.hh>
+
+
+namespace ost { namespace mol {
+
+struct ChemType {
+ const static char IONS ='I';
+ const static char NONCANONICALMOLS ='M';
+ const static char SACCHARIDES ='S';
+ const static char NUCLEOTIDES ='N';
+ const static char AMINOACIDS ='A';
+ const static char COENZYMES ='E';
+ const static char WATERCOORDIONS ='C';
+ const static char DRUGS ='D';
+ const static char WATERS ='W';
+ const static char UNKNOWN ='U';
+
+ explicit ChemType(char chem_type)
+ : chem_type_(chem_type) {
+ }
+
+ ChemType()
+ : chem_type_(UNKNOWN) {
+ }
+
+ bool operator==(const ChemType& cc) const {
+ return cc.chem_type_==chem_type_;
+ }
+
+ bool operator!=(const ChemType& cc) const {
+ return this->operator!=(cc);
+ }
+
+ bool IsIon() const {
+ return (chem_type_==ChemType::IONS ||
+ chem_type_==ChemType::WATERCOORDIONS);
+ }
+
+ bool IsNucleotide() const {
+ return (chem_type_==ChemType::NUCLEOTIDES);
+ }
+
+ bool IsSaccharide() const {
+ return (chem_type_==ChemType::SACCHARIDES);
+ }
+
+ bool IsAminoAcid() const {
+ return (chem_type_==ChemType::AMINOACIDS);
+ }
+
+ bool IsCoenzyme() const {
+ return (chem_type_==ChemType::COENZYMES);
+ }
+
+ bool IsDrug() const {
+ return (chem_type_==ChemType::DRUGS);
+ }
+
+ bool IsWater() const {
+ return (chem_type_==ChemType::WATERS);
+ }
+
+ bool IsNonCanonical() const {
+ return (chem_type_==ChemType::NONCANONICALMOLS);
+ }
+
+ bool IsKnown() const {
+ return (chem_type_!=ChemType::UNKNOWN);
+ }
+
+ operator char() const {
+ return chem_type_;
+ }
+
+private:
+ char chem_type_;
+};
+
+}} // ns
+#endif
diff --git a/modules/mol/base/src/coord_frame.cc b/modules/mol/base/src/coord_frame.cc
index 80ef4f58f3ea3aed2b1ae691b6cc35c70107faf0..71b9ed9a64d4f21eeed7630e886f47c02ee96d8e 100644
--- a/modules/mol/base/src/coord_frame.cc
+++ b/modules/mol/base/src/coord_frame.cc
@@ -28,6 +28,7 @@
#include <ost/mol/view_op.hh>
#include <ost/mol/mol.hh>
#include "coord_frame.hh"
+#include <ost/base.hh>
namespace ost { namespace mol {
@@ -84,7 +85,52 @@ namespace ost { namespace mol {
indices.push_back(i->GetIndex());
}
}
+
+ void GetCaIndices(const EntityView& segment, std::vector<unsigned long>& indices_ca){
+ mol::AtomView ca;
+ ResidueViewList residues=segment.GetResidueList();
+ indices_ca.reserve(residues.size());
+ //for (ResidueViewList::const_iterator res=residues.begin()+1,
+ // e=residues.end(); res!=e-1; ++res){
+ // if (!InSequence((*res).GetHandle(),(*(res+1)).GetHandle())) throw std::runtime_error("Residues are not in a continuous sequence");
+ //}
+ for (ResidueViewList::const_iterator res=residues.begin(),
+ e=residues.end(); res!=e; ++res) {
+ ca=res->FindAtom("CA");
+ CheckHandleValidity(ca);
+ indices_ca.push_back(ca.GetIndex());
+ }
+ }
+ void GetCaCONIndices(const EntityView& segment, std::vector<unsigned long>& indices_ca,
+ std::vector<unsigned long>& indices_c, std::vector<unsigned long>& indices_o, std::vector<unsigned long>& indices_n){
+ mol::AtomView a,n,c,o;
+ ResidueViewList residues=segment.GetResidueList();
+ indices_ca.reserve(residues.size());
+ indices_n.reserve(residues.size());
+ indices_c.reserve(residues.size());
+ indices_o.reserve(residues.size());
+ for (ResidueViewList::const_iterator res=residues.begin()+1,
+ e=residues.end(); res!=e-1; ++res){
+ if (!InSequence((*res).GetHandle(),(*(res+1)).GetHandle())) throw std::runtime_error("Residues are not in a continuous sequence");
+ }
+ for (ResidueViewList::const_iterator res=residues.begin(),
+ e=residues.end(); res!=e; ++res) {
+ a=res->FindAtom("CA");
+ CheckHandleValidity(a);
+ indices_ca.push_back(a.GetIndex());
+ c=res->FindAtom("C");
+ CheckHandleValidity(c);
+ indices_c.push_back(c.GetIndex());
+ o=res->FindAtom("O");
+ CheckHandleValidity(o);
+ indices_o.push_back(o.GetIndex());
+ n=res->FindAtom("N");
+ CheckHandleValidity(n);
+ indices_n.push_back(n.GetIndex());
+ }
+ }
+
void GetMasses(const EntityView& sele, std::vector<Real>& masses){
// This function returns a vector containing the atom masses of the atoms in an EntityView
// It is used together with GetIndices to accelerate the extraction of RMSD from a trajectory
@@ -218,5 +264,161 @@ namespace ost { namespace mol {
GetIndicesAndMasses(view_cm,indices_cm,masses_cm);
return this->GetMinDistBetwCenterOfMassAndView(indices_cm,masses_cm,indices_atoms);
}
+
+ geom::Line3 CoordFrame::GetODRLine(std::vector<unsigned long>& indices_ca){
+ //Returns the best fit line to atoms with indices in indices_ca
+ geom::Vec3List atoms_pos_list;
+ atoms_pos_list.reserve(indices_ca.size());
+ for (std::vector<unsigned long>::const_iterator i1=indices_ca.begin(),e=indices_ca.end(); i1!=e; ++i1) {
+ atoms_pos_list.push_back((*this)[*i1]);
+ }
+ return atoms_pos_list.GetODRLine();
+ }
+
+ geom::Line3 CoordFrame::GetODRLine(const mol::EntityView& view1){
+ //Returns the best fit line to atoms in the EntityView view1
+ std::vector<unsigned long> indices;
+ GetIndices(view1,indices);
+ return this->GetODRLine(indices);
+ }
+
+ geom::Plane CoordFrame::GetODRPlane(std::vector<unsigned long>& indices_ca){
+ //Returns the normal to the best fit plane to atoms with indices in indices_ca
+ geom::Vec3List atoms_pos_list;
+ atoms_pos_list.reserve(indices_ca.size());
+ for (std::vector<unsigned long>::const_iterator i1=indices_ca.begin(),e=indices_ca.end(); i1!=e; ++i1) {
+ atoms_pos_list.push_back((*this)[*i1]);
+ }
+ return atoms_pos_list.GetODRPlane();
+ }
+
+ geom::Plane CoordFrame::GetODRPlane(const mol::EntityView& view1){
+ //Returns the best fit plane to atoms in the EntityView view1
+ std::vector<unsigned long> indices;
+ GetIndices(view1,indices);
+ return this->GetODRPlane(indices);
+ }
+
+ geom::Line3 CoordFrame::FitCylinder(std::vector<unsigned long>& indices_ca){
+ //Returns a line which is the axis of a fitted cylinder to the atoms with indices given in indices_ca
+ //It is assumed that we fit an alpha-helix and that the CA atoms are oredered sequentially
+ //This is used for the initial guess of the helix axis
+ geom::Vec3List atoms_pos_list;
+ int n_atoms=indices_ca.size();
+ atoms_pos_list.reserve(n_atoms);
+ for (std::vector<unsigned long>::const_iterator i1=indices_ca.begin(),e=indices_ca.end(); i1!=e; ++i1) {
+ atoms_pos_list.push_back((*this)[*i1]);
+ }
+ //Initial guess
+ geom::Vec3 initial_axis=geom::Vec3(0.0,0.0,0.0),center=geom::Vec3(0.0,0.0,0.0);
+ if (n_atoms<5) {
+ initial_axis=atoms_pos_list[n_atoms-1]-atoms_pos_list[0];
+ }
+ else {
+ for (geom::Vec3List::const_iterator i=atoms_pos_list.begin(),e=atoms_pos_list.end()-4; i!=e; ++i) {
+ initial_axis+=(*(i+4))-(*i);
+ }
+ }
+ for (geom::Vec3List::const_iterator i=atoms_pos_list.begin(),e=atoms_pos_list.end(); i!=e; ++i) {
+ center+=(*i);
+ }
+ center/=atoms_pos_list.size();
+ return atoms_pos_list.FitCylinder(initial_axis,center);
+ }
+
+ geom::Line3 CoordFrame::FitCylinder(const mol::EntityView& view1){
+ // Return a lin which is the axis of the best fit cylinder to the CA atoms
+ // of the EntityView.
+ // It is assumed that we fit an alpha-helix and that the CA atoms are oredered sequentially
+ CheckHandleValidity(view1);
+ std::vector<unsigned long> indices_ca;
+ GetCaIndices(view1, indices_ca);
+ return CoordFrame::FitCylinder(indices_ca);
+ }
+
+ Real CoordFrame::GetAlphaHelixContent(const mol::EntityView& segment){
+ //Returns the percentage of residues in the EntityView (segment) that are in an alpha-helix
+ //Each residue is assigned as being in an alpha-helix or not, based on and backbone torsion angles
+ //and the hydrogen bonding (O-N) (this term is used only if the segment contains at least 8 residues
+ //The entity view should be a single segment with no gaps and no missing N,CA,C,O backbone atoms
+ //the first and last residues will not be asessed for helicity
+ CheckHandleValidity(segment);
+ std::vector<unsigned long> indices_c, indices_n, indices_ca, indices_o;
+ GetCaCONIndices(segment, indices_ca, indices_c, indices_o, indices_n);
+ return CoordFrame::GetAlphaHelixContent(indices_ca,indices_c,indices_o,indices_n);
+ }
+
+ Real Eval2AngleDist(Real phi, Real phi0, Real psi, Real psi0, Real delta){
+ //Returns a score between 0 and 1 measuring the distance between
+ //a pair of angles and a pair of reference angles
+ Real d1,d2,d;
+ d1=abs(phi-phi0);
+ d2=abs(psi-psi0);
+ if (d1>M_PI) d1=abs(d1-2.*M_PI);
+ if (d2>M_PI) d1=abs(d2-2.*M_PI);
+ d=(pow(d1,2.)+pow(d2,2.))/pow(delta,2.);
+ return 1./(1+d);
+ }
+
+ Real CoordFrame::GetAlphaHelixContent(std::vector<unsigned long>& indices_ca, std::vector<unsigned long>& indices_c,
+ std::vector<unsigned long>& indices_o, std::vector<unsigned long>& indices_n){
+ //See CoordFrame::GetAlphaHelixContent(const mol::EntityView) above.
+ unsigned long n_atoms=indices_ca.size();
+ geom::Vec3 c_previous,n,ca,c,n_next;
+ Real phi,psi,phi_0=-1.2,psi_0=-0.785,delta=0.8,d_0=3.3;
+ unsigned long n_helical_res=0;
+ std::vector<Real> score,dist,score2,dist2;
+ score.reserve(n_atoms-2);
+ score2.reserve(n_atoms-2);
+ dist.reserve(n_atoms-2);
+ dist2.reserve(n_atoms-2);
+ if (n_atoms!=indices_n.size()||n_atoms!=indices_c.size()||n_atoms!=indices_o.size()){
+ throw std::runtime_error("not same numbers of CA, C, O and N atoms in the selection");
+ }
+ if (n_atoms<=5){
+ throw std::runtime_error("At least five residues are needed to calulate an alpha helix similarity");
+ }
+ c=(*this)[indices_c[0]];
+ n_next=(*this)[indices_n[1]];
+ for (unsigned long i=1; i!=n_atoms-1; ++i){
+ c_previous=c;
+ n=n_next;
+ ca=(*this)[indices_ca[i]];
+ c=(*this)[indices_c[i]];
+ n_next=(*this)[indices_n[i+1]];
+ phi=geom::DihedralAngle(c_previous,n,ca,c);
+ psi=geom::DihedralAngle(n,ca,c,n_next);
+ score.push_back(Eval2AngleDist(phi,phi_0,psi,psi_0,delta));
+ }
+ score2[0]=pow(score[0]*score[1],3./2.);
+ score2[n_atoms-3]=pow(score[n_atoms-3]*score[n_atoms-4],3./2.);
+ for (unsigned long i=1; i!=n_atoms-3; ++i){
+ score2[i]=score[i-1]*score[i]*score[i+1];
+ }
+ if (n_atoms>=8){
+ for (unsigned long i=1; i!=n_atoms-1; ++i){
+ if (i<n_atoms-4){
+ dist.push_back(geom::Distance((*this)[indices_o[i]],(*this)[indices_n[i+4]]));
+ if (i>=5) {
+ dist2.push_back(std::min(dist[i-1],dist[i-5]));
+ }
+ else dist2.push_back(dist[i-1]);
+ }
+ else dist2.push_back(geom::Distance((*this)[indices_n[i]],(*this)[indices_o[i-4]]));
+ }
+ for (unsigned long i=0; i!=n_atoms-2; ++i){
+ if (dist2[i]<=d_0 || score2[i]>=0.3)n_helical_res+=1;
+ }
+ }
+ else {
+ for (unsigned long i=0; i!=n_atoms-2; ++i){
+ if (score2[i]>=0.3)n_helical_res+=1;
+ }
+ }
+ return Real(n_helical_res)/Real(n_atoms-2);
+ }
+
+
+
}}//ns
diff --git a/modules/mol/base/src/coord_frame.hh b/modules/mol/base/src/coord_frame.hh
index 8b34cc52acb31086b8ee02d074fe0aac526e22f8..98eb0c25c5560dbce0ad43e8450e79b8994b46df 100644
--- a/modules/mol/base/src/coord_frame.hh
+++ b/modules/mol/base/src/coord_frame.hh
@@ -31,15 +31,28 @@
namespace ost { namespace mol {
class DLLEXPORT_OST_MOL CoordFrame : public geom::Vec3List{
+private:
+ geom::Vec3 periodic_cell_sizes_;
+ geom::Vec3 periodic_cell_angles_;
public:
typedef geom::Vec3List base_type;
- CoordFrame() : base_type() {}
+ CoordFrame() : base_type() {}
CoordFrame(size_t size, const geom::Vec3& value=geom::Vec3()) : base_type(size, value) {}
CoordFrame(base_type::iterator b, base_type::iterator e): base_type(b, e) { }
CoordFrame(const base_type& rhs) : base_type(rhs) { }
CoordFrame(const std::vector<geom::Vec3>& rhs) : base_type(rhs) { }
+ CoordFrame(const std::vector<geom::Vec3>& rhs,const geom::Vec3 box_size, const geom::Vec3 box_angles) : base_type(rhs) {
+ this->periodic_cell_sizes_=box_size;
+ this->periodic_cell_angles_=box_angles;
+ }
+ geom::Vec3 GetCellSize() {
+ return this->periodic_cell_sizes_;
+ }
+ geom::Vec3 GetCellAngles() {
+ return this->periodic_cell_angles_;
+ }
geom::Vec3 GetAtomPos(const AtomHandle& atom);
geom::Vec3 GetAtomPos(int atom_index);
Real GetDistanceBetwAtoms(const AtomHandle& a1, const AtomHandle& a2);
@@ -60,13 +73,25 @@ public:
Real GetMinDistBetwCenterOfMassAndView(std::vector<unsigned long>& indices_cm, std::vector<Real>& masses_cm,
std::vector<unsigned long>& indices_atoms);
Real GetMinDistBetwCenterOfMassAndView(const mol::EntityView& view_cm, const mol::EntityView& view_atoms);
+ geom::Line3 GetODRLine(std::vector<unsigned long>& indices_ca);
+ geom::Plane GetODRPlane(std::vector<unsigned long>& indices_ca);
+ geom::Line3 GetODRLine(const mol::EntityView& view1);
+ geom::Plane GetODRPlane(const mol::EntityView& view1);
+ geom::Line3 FitCylinder(std::vector<unsigned long>& indices_ca);
+ geom::Line3 FitCylinder(const mol::EntityView& view1);
+ Real GetAlphaHelixContent(std::vector<unsigned long>& indices_ca, std::vector<unsigned long>& indices_c,
+ std::vector<unsigned long>& indices_o, std::vector<unsigned long>& indices_n);
+ Real GetAlphaHelixContent(const mol::EntityView& segment);
};
void GetIndices(const EntityView& sele, std::vector<unsigned long>& indices);
void GetMasses(const EntityView& sele, std::vector<Real>& masses);
void GetIndicesAndMasses(const EntityView& sele, std::vector<unsigned long>& indices,std::vector<Real>& masses);
void GetPositions(const EntityView& sele, std::vector<geom::Vec3>& ref_pos);
-
+ void GetCaIndices(const EntityView& segment, std::vector<unsigned long>& indices_ca);
+ void GetCaCONIndices(const EntityView& segment, std::vector<unsigned long>& indices_ca, std::vector<unsigned long>& indices_c,
+ std::vector<unsigned long>& indices_o, std::vector<unsigned long>& indices_n);
+
typedef boost::shared_ptr<CoordFrame> CoordFramePtr;
typedef std::vector<CoordFramePtr> CoordFrameList;
diff --git a/modules/mol/base/src/coord_group.cc b/modules/mol/base/src/coord_group.cc
index f92c58e22b44f9dc4cd81753e288acefd164be9a..db3fd341ce04a76c6e928ca1e0fd93e869b583c7 100644
--- a/modules/mol/base/src/coord_group.cc
+++ b/modules/mol/base/src/coord_group.cc
@@ -73,6 +73,14 @@ void CoordGroupHandle::SetFramePositions(uint frame,
//source_->SetFramePositions(frame, clist);
}
+
+geom::Vec3List CoordGroupHandle::GetFramePositions(uint frame)
+ {
+ this->CheckValidity();
+ return *(this->GetFrame(frame));
+ }
+
+
void CoordGroupHandle::CopyFrame(uint frame)
{
this->CheckValidity();
@@ -95,6 +103,16 @@ CoordGroupHandle::operator bool() const
}
}
+ void CoordGroupHandle::AddFrame(const geom::Vec3List& clist, const geom::Vec3& cell_size, const geom::Vec3& cell_angles)
+{
+ this->CheckValidity();
+ if (source_->IsMutable()) {
+ source_->AddFrame(clist,cell_size,cell_angles);
+ } else {
+ throw IntegrityError("Can't add frame to immutable CoordGroup");
+ }
+}
+
void CoordGroupHandle::AddFrames(const CoordGroupHandle& cg)
{
this->CheckValidity();
@@ -135,6 +153,12 @@ CoordFramePtr CoordGroupHandle::GetFrame(uint frame) const
return source_->GetFrame(frame);
}
+CoordFrame CoordGroupHandle::GetFrame2(uint frame)
+{
+ this->CheckValidity();
+ return *(source_->GetFrame(frame));
+}
+
AtomHandleList CoordGroupHandle::GetAtomList() const
{
this->CheckValidity();
@@ -171,7 +195,7 @@ void CoordGroupHandle::Capture(uint frame)
}
}
-CoordGroupHandle CoordGroupHandle::Filter(const EntityView& selected) const
+CoordGroupHandle CoordGroupHandle::Filter(const EntityView& selected, int first, int last) const
{
this->CheckValidity();
std::vector<unsigned long> indices;
@@ -194,8 +218,9 @@ CoordGroupHandle CoordGroupHandle::Filter(const EntityView& selected) const
CoordGroupHandle filtered_cg=CreateCoordGroup(new_ent.GetAtomList());
std::vector<geom::Vec3> vecs(indices.size());
- for (size_t i=0; i<this->GetFrameCount(); ++i) {
- LOG_INFO("Filtering frame " << i << "/" << this->GetFrameCount());
+ if (last==-1) last=this->GetFrameCount();
+ for (int i=first; i<last; ++i) {
+ LOG_INFO("Filtering frame " << i << "/" << last);
CoordFramePtr frame=this->GetFrame(i);
for (std::vector<unsigned long>::const_iterator
j=indices.begin(), e2=indices.end(); j!=e2; ++j) {
diff --git a/modules/mol/base/src/coord_group.hh b/modules/mol/base/src/coord_group.hh
index 2b6d6fe7f4c40a68e323151f299ffeb184943e45..652fe34636d3dc11c7fa5168c83c05d906b6524a 100644
--- a/modules/mol/base/src/coord_group.hh
+++ b/modules/mol/base/src/coord_group.hh
@@ -52,6 +52,9 @@ public:
/// initial atomlist
void SetFramePositions(uint frame, const std::vector<geom::Vec3>& clist);
+ /// \brief get the positions of all the atoms in the given frame
+ geom::Vec3List GetFramePositions(uint frame);
+
/// \brief copy atom positions of given frame to stored atoms in entity
void CopyFrame(uint frame);
@@ -66,7 +69,8 @@ public:
/// \brief add frame
//void AddFrame(const std::vector<geom::Vec3>& clist);
void AddFrame(const geom::Vec3List& clist);
-
+ void AddFrame(const geom::Vec3List& clist,const geom::Vec3& cell_size,const geom::Vec3& cell_angles);
+
void AddFrames(const CoordGroupHandle& cg);
/// \brief set an indidivial atom position in the given frame
void SetAtomPos(uint frame, AtomHandle atom, const geom::Vec3& pos);
@@ -82,10 +86,11 @@ public:
AtomHandleList GetAtomList() const;
CoordFramePtr GetFrame(uint frame) const;
+ CoordFrame GetFrame2(uint frame);
/// \brief return a filtered coord group, containing only the atoms in the
/// view
- CoordGroupHandle Filter(const EntityView& selected) const;
+ CoordGroupHandle Filter(const EntityView& selected,int first=0,int last=-1) const;
CoordGroupHandle(CoordSourcePtr source);
diff --git a/modules/mol/base/src/coord_source.hh b/modules/mol/base/src/coord_source.hh
index 604817535d9bc2fc0bd12c20739135e287642862..fec0d9946cb2ecd275abb23d5ebb58b080422734 100644
--- a/modules/mol/base/src/coord_source.hh
+++ b/modules/mol/base/src/coord_source.hh
@@ -70,6 +70,7 @@ public:
void Capture(uint f);
virtual void AddFrame(const std::vector<geom::Vec3>& coords) = 0;
+ 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;
protected:
void SetMutable(bool flag);
diff --git a/modules/mol/base/src/editor_base.cc b/modules/mol/base/src/editor_base.cc
index 7718234673d7e35c33aee25b113a33e1c2dc2d54..d75827806359c8dc5036fa7cf819abb0ce7ffcc6 100644
--- a/modules/mol/base/src/editor_base.cc
+++ b/modules/mol/base/src/editor_base.cc
@@ -76,12 +76,31 @@ void EditorBase::RenameResidue(ResidueHandle res, const String& new_name)
res.Impl()->SetKey(new_name);
}
+void EditorBase::SetResidueNumber(ResidueHandle res, const ResNum& new_num)
+{
+ CheckHandleValidity(res);
+ int index=res.GetIndex();
+ res.Impl()->SetNumber(new_num);
+ res.GetChain().SetInSequence(index);
+}
+
void EditorBase::RenameChain(ChainHandle chain, const String& new_name)
{
CheckHandleValidity(chain);
ent_.Impl()->RenameChain(chain.Impl(), new_name);
}
+void EditorBase::SetChainType(ChainHandle chain, const ChainType type)
+{
+ CheckHandleValidity(chain);
+ chain.Impl()->SetType(type);
+}
+
+void EditorBase::SetChainDescription(ChainHandle chain, const String desc)
+{
+ CheckHandleValidity(chain);
+ chain.Impl()->SetDescription(desc);
+}
AtomHandle EditorBase::InsertAtom(ResidueHandle res, const String& name,
const geom::Vec3& pos, const String& ele,
@@ -100,21 +119,26 @@ AtomHandle EditorBase::InsertAtom(ResidueHandle res, const String& name,
AtomHandle EditorBase::InsertAltAtom(ResidueHandle res, const String& name,
const String& alt_group,
const geom::Vec3& pos,
- const String& ele)
+ const String& ele, Real occ,
+ Real b_factor)
{
CheckHandleValidity(res);
ent_.Impl()->MarkTraceDirty();
- AtomHandle atom(res.Impl()->InsertAltAtom(name, alt_group, pos, ele));
+ AtomHandle atom(res.Impl()->InsertAltAtom(name, alt_group, pos,
+ ele, occ, b_factor));
this->UpdateTrace();
return atom;
}
void EditorBase::AddAltAtomPos(const String& group,
const AtomHandle& atom,
- const geom::Vec3& position)
+ const geom::Vec3& position, Real occ,
+ Real b_factor)
{
CheckHandleValidity(atom);
- atom.GetResidue().Impl()->AddAltAtomPos(group, atom.Impl(), position);
+ atom.GetResidue().Impl()->AddAltAtomPos(group, atom.Impl(),
+ position, occ, b_factor);
+
}
void EditorBase::DeleteChain(const ChainHandle& chain)
@@ -146,6 +170,11 @@ void EditorBase::ReorderAllResidues()
ent_.Impl()->ReorderAllResidues();
}
+void EditorBase::RenumberAllResidues(int start, bool keep_spacing)
+{
+ ent_.Impl()->RenumberAllResidues(start, keep_spacing);
+}
+
void EditorBase::RenameAtom(AtomHandle atom, const String& new_name)
{
CheckHandleValidity(atom);
@@ -206,6 +235,7 @@ void EditorBase::UpdateTrace()
{
if (mode_==UNBUFFERED_EDIT) {
ent_.Impl()->TraceDirectionality();
+ ent_.Impl()->UpdateICSIfNeeded();
}
}
diff --git a/modules/mol/base/src/editor_base.hh b/modules/mol/base/src/editor_base.hh
index 48bf067bd19ea8c1957d60fe3ba3c439f86b4917..504311d547cf00f43e11fb5b1c49925a16564e34 100644
--- a/modules/mol/base/src/editor_base.hh
+++ b/modules/mol/base/src/editor_base.hh
@@ -124,7 +124,8 @@ public:
/// \sa EditorBase::AddAltAtomPos(), ResidueHandle
AtomHandle InsertAltAtom(ResidueHandle residue, const String& name,
const String& alt_group, const geom::Vec3& pos,
- const String& ele="");
+ const String& ele="", Real occ=1.0,
+ Real b_factor=0.0);
/// \brief Add alternative atom position
/// \param group is the name of the alternative atom position group. If no
/// group of that name exists, it will be created.
@@ -136,7 +137,8 @@ public:
/// is the alternative position
/// \sa EditorBase::InsertAltAtom(), ResidueHandle
void AddAltAtomPos(const String& group, const AtomHandle& atom,
- const geom::Vec3& position);
+ const geom::Vec3& position, Real occ=1.0,
+ Real b_factor=0.0);
//\}
/// \brief connect two atoms with bond
@@ -153,8 +155,23 @@ public:
unsigned char bond_order);
void RenameResidue(ResidueHandle res, const String& new_name);
-
+
+ void SetResidueNumber(ResidueHandle res, const ResNum& num);
+
void RenameChain(ChainHandle chain, const String& new_name);
+
+ /// \brief Assign type of chain according to ChainType.
+ ///
+ /// \param chain chain to assign to
+ /// \param type type of the chain
+ void SetChainType(ChainHandle chain, const ChainType type);
+
+ /// \brief Assign a description to a chain.
+ ///
+ /// \param chain chain to assign to
+ /// \param desc description
+ void SetChainDescription(ChainHandle chain, const String desc);
+
/// \brief Delete all atoms of residue
///
/// All associated torsions and bonds will also be removed
@@ -190,6 +207,17 @@ public:
/// \brief reorder residues of all chains based on their residue number
void ReorderAllResidues();
+
+ /// \brief renumber residues of all chains
+ ///
+ /// \param start
+ /// Residues of every chain will be renumbered, whereas the first
+ /// residue gets the residue number start.
+ ///
+ /// \param keep_spacing
+ /// If set to false, residues will continously be renumbered ongoing from start.
+ /// Otherwise the spacings between the residues are kept.
+ void RenumberAllResidues(int start, bool keep_spacing);
/// \brief Get edit mode of editor
EditMode GetMode() const {return mode_;}
diff --git a/modules/mol/base/src/entity_handle.cc b/modules/mol/base/src/entity_handle.cc
index e975132ea84a50c5ea7fb76026cff894645b6920..0abad5ede1b3241f05300b5768cf0b7c332f4c12 100644
--- a/modules/mol/base/src/entity_handle.cc
+++ b/modules/mol/base/src/entity_handle.cc
@@ -362,6 +362,18 @@ AtomHandleList EntityHandle::GetAtomList() const
return atoms;
}
+geom::Vec3List EntityHandle::GetAtomPosList() const {
+ this->CheckValidity();
+ geom::Vec3List atom_pos_list;
+ atom_pos_list.reserve(this->GetAtomCount());
+ AtomHandleList atom_list=this->GetAtomList();
+ for (AtomHandleList::const_iterator a=atom_list.begin(), e=atom_list.end(); a!=e; ++a) {
+ atom_pos_list.push_back(a->GetPos());
+ }
+ return atom_pos_list;
+ //return Impl()->GetAtomPosList();
+}
+
EntityHandle EntityHandle::GetHandle() const
{
return *this;
diff --git a/modules/mol/base/src/entity_handle.hh b/modules/mol/base/src/entity_handle.hh
index 0fcadee77d9e68b69048b7c346d3d3c266919fd0..67b2a847e4ab4050d9dfd9043e9fa3ab46ae0bd6 100644
--- a/modules/mol/base/src/entity_handle.hh
+++ b/modules/mol/base/src/entity_handle.hh
@@ -280,6 +280,9 @@ public:
/// \sa #AtomsBegin, #AtomsEnd
AtomHandleList GetAtomList() const;
+ /// \brief get complete list of atom positions
+ geom::Vec3List GetAtomPosList() const;
+
/// \brief Get editor for external coordinate system to manipulate atom
/// positions
/// \sa editors
diff --git a/modules/mol/base/src/entity_view.cc b/modules/mol/base/src/entity_view.cc
index 3e5445b56a8936c7562c5e0d830ad0785c1b1ccb..a88f0b39553a438c0d51359fee91cacf9d85a7a1 100644
--- a/modules/mol/base/src/entity_view.cc
+++ b/modules/mol/base/src/entity_view.cc
@@ -187,10 +187,10 @@ geom::Vec3 EntityView::GetCenterOfMass() const
Real EntityView::GetMass() const
{
- Real mass = 0;
- AtomViewIter it=this->AtomsBegin();
- for(; it!=this->AtomsEnd(); ++it) {
- mass+=(*it).GetMass();
+ this->CheckValidity();
+ double mass = 0;
+ for (ChainViewList::iterator i=data_->chains.begin();i!=data_->chains.end(); ++i) {
+ mass+=i->GetMass();
}
return mass;
}
diff --git a/modules/mol/base/src/ics_editor.cc b/modules/mol/base/src/ics_editor.cc
index c374a0f09697accb0f56fee925200d3b03df4879..910c7fd85365f747e12eed613147bde49b2a4fdb 100644
--- a/modules/mol/base/src/ics_editor.cc
+++ b/modules/mol/base/src/ics_editor.cc
@@ -23,6 +23,7 @@
#include "impl/torsion_impl.hh"
#include "impl/entity_impl.hh"
#include "impl/connector_impl.hh"
+#include "impl/atom_impl.hh"
/*
Author: Marco Biasini
*/
@@ -96,18 +97,20 @@ bool ICSEditor::SetAngle(const AtomHandle& atom_a, const AtomHandle& atom_b,
return return_value;
}
-void ICSEditor::SetTorsionAngle(TorsionHandle torsion, Real angle)
+void ICSEditor::SetTorsionAngle(TorsionHandle torsion, Real angle,
+ bool update_others)
{
CheckHandleValidity(torsion);
- torsion.Impl()->SetAngle(angle, false);
+ torsion.Impl()->SetAngle(angle, update_others);
ent_.Impl()->MarkXCSDirty();
this->Update();
}
-void ICSEditor::RotateTorsionAngle(TorsionHandle torsion, Real angle)
+void ICSEditor::RotateTorsionAngle(TorsionHandle torsion, Real angle,
+ bool update_others)
{
CheckHandleValidity(torsion);
- torsion.Impl()->RotateAngle(angle, false);
+ torsion.Impl()->RotateAngle(angle, update_others);
ent_.Impl()->MarkXCSDirty();
this->Update();
}
@@ -116,7 +119,9 @@ void ICSEditor::RotateTorsionAngle(TorsionHandle torsion, Real angle)
void ICSEditor::RotateTorsionAngle(const AtomHandle& atom_a,
const AtomHandle& atom_b,
const AtomHandle& atom_c,
- const AtomHandle& atom_d, Real angle)
+ const AtomHandle& atom_d,
+ Real angle,
+ bool update_others)
{
CheckHandleValidity(atom_a);
CheckHandleValidity(atom_b);
@@ -124,7 +129,7 @@ void ICSEditor::RotateTorsionAngle(const AtomHandle& atom_a,
CheckHandleValidity(atom_d);
impl::Dihedral d(atom_a.Impl(), atom_b.Impl(), atom_c.Impl(), atom_d.Impl());
Real cur_angle=d.GetAngleICS();
- d.SetAngleICS(cur_angle+angle);
+ d.SetAngleICS(cur_angle+angle, update_others);
ent_.Impl()->MarkXCSDirty();
this->Update();
}
@@ -133,16 +138,19 @@ void ICSEditor::RotateTorsionAngle(const AtomHandle& atom_a,
void ICSEditor::SetTorsionAngle(const AtomHandle& atom_a,
const AtomHandle& atom_b,
const AtomHandle& atom_c,
- const AtomHandle& atom_d, Real angle)
+ const AtomHandle& atom_d,
+ Real angle,
+ bool update_others)
{
CheckHandleValidity(atom_a);
CheckHandleValidity(atom_b);
CheckHandleValidity(atom_c);
CheckHandleValidity(atom_d);
impl::Dihedral d(atom_a.Impl(), atom_b.Impl(), atom_c.Impl(), atom_d.Impl());
- d.SetAngleICS(angle, false);
+ d.SetAngleICS(angle, update_others);
ent_.Impl()->MarkXCSDirty();
this->Update();
}
+
}} // ns
diff --git a/modules/mol/base/src/ics_editor.hh b/modules/mol/base/src/ics_editor.hh
index 9643336949dbf2fe700187feee372f5baca235cc..eb51807432d2a9aa3f2ddeb08b48c5a8ea88d073 100644
--- a/modules/mol/base/src/ics_editor.hh
+++ b/modules/mol/base/src/ics_editor.hh
@@ -74,19 +74,22 @@ public:
/// bonds untouched, use the SetDihedralAngle() function
///
/// \sa RotateTorsionAngle
- void SetTorsionAngle(TorsionHandle torsion, Real angle);
+ void SetTorsionAngle(TorsionHandle torsion, Real angle,
+ bool update_others=true);
/// \brief rotate torsion angle
- void RotateTorsionAngle(TorsionHandle torsion, Real delta);
+ void RotateTorsionAngle(TorsionHandle torsion, Real delta,
+ bool update_others=true);
void RotateTorsionAngle(const AtomHandle& atom_a,
const AtomHandle& atom_b,
const AtomHandle& atom_c,
const AtomHandle& atom_d,
- Real angle);
+ Real angle,
+ bool update_others=true);
void SetTorsionAngle(const AtomHandle& atom_a, const AtomHandle& atom_b,
const AtomHandle& atom_c, const AtomHandle& atom_d,
- Real angle);
+ Real angle, bool update_others=true);
/// \brief immediately update external coordinate system
void UpdateXCS();
diff --git a/modules/mol/base/src/impl/atom_group.hh b/modules/mol/base/src/impl/atom_group.hh
index 934fda241c3c614185a2fe32a77ccdad6b0582e3..50a7c6338972313b36f41bed8072f60d42cdf21a 100644
--- a/modules/mol/base/src/impl/atom_group.hh
+++ b/modules/mol/base/src/impl/atom_group.hh
@@ -29,10 +29,13 @@ namespace ost { namespace mol {namespace impl {
struct AtomGroupEntry {
AtomGroupEntry() {}
- AtomGroupEntry(const AtomImplPtr& a, const geom::Vec3& p)
- : atom(a), pos(p) {}
+ AtomGroupEntry(const AtomImplPtr& a, const geom::Vec3& p,
+ Real o, Real b)
+ : atom(a), pos(p), occ(o), b_factor(b) {}
impl::AtomImplW atom;
geom::Vec3 pos;
+ Real occ;
+ Real b_factor;
};
typedef std::vector<AtomGroupEntry> AtomGroupEntryList;
diff --git a/modules/mol/base/src/impl/chain_impl.cc b/modules/mol/base/src/impl/chain_impl.cc
index 421f98dd4a43bafb12537e1649b51aba49abb9d3..009f436a5406a42caeda27605574587d48decbe3 100644
--- a/modules/mol/base/src/impl/chain_impl.cc
+++ b/modules/mol/base/src/impl/chain_impl.cc
@@ -36,7 +36,9 @@ ChainImpl::ChainImpl(const EntityImplPtr& e, const String& name):
ent_(e),
name_(name),
residue_list_(),
- in_sequence_(true)
+ in_sequence_(true),
+ type_(CHAINTYPE_UNKNOWN),
+ description_()
{}
String ChainImpl::GetName() const
@@ -398,14 +400,11 @@ void ChainImpl::AssignSecondaryStructure(SecStructure ss,
Real ChainImpl::GetMass() const
{
- Real mass = 0;
+ double mass = 0;
for (ResidueImplList::const_iterator i=residue_list_.begin();
i!=residue_list_.end(); ++i) {
ResidueImplPtr r=*i;
- for (AtomImplList::iterator j=r->GetAtomList().begin();
- j!=r->GetAtomList().end(); ++j) {
- mass+=(*j)->GetMass();
- }
+ mass+=r->GetMass();
}
return mass;
}
@@ -485,4 +484,41 @@ void ChainImpl::ReorderResidues()
UpdateShifts();
}
+void ChainImpl::RenumberAllResidues(int start, bool keep_spacing)
+{
+ ResNum actual_num=ResNum(start);
+ ResNum original_start_num=residue_list_[0]->GetNumber();
+ ResNum start_diff=ResNum(start)-original_start_num;
+
+
+ for (ResidueImplList::const_iterator i=residue_list_.begin();
+ i!=residue_list_.end(); ++i) {
+
+ if(keep_spacing){
+ ResNum temp=(*i)->GetNumber();
+ (*i)->SetNumber(temp+start_diff);
+ continue;
+ }
+
+ (*i)->SetNumber(actual_num);
+ actual_num++;
+ }
+ UpdateShifts();
+}
+
+void ChainImpl::SetInSequence(const int index)
+{
+ ResNum num=residue_list_[index]->GetNumber();
+ //Check if rp is in sequence
+ if (in_sequence_) {
+ if (index>0 && residue_list_[index-1]->GetNumber()>=num)
+ in_sequence_=false;
+ if (index<static_cast<int>(residue_list_.size())-1 && residue_list_[index+1]->GetNumber()<=num)
+ in_sequence_=false;
+ }
+ if (in_sequence_) {
+ this->UpdateShifts();
+ }
+}
+
}}} // ns
diff --git a/modules/mol/base/src/impl/chain_impl.hh b/modules/mol/base/src/impl/chain_impl.hh
index d7d2ca64beeb0f464263c8ddedd9f3da8be5a2ae..bcb3436e2bc463dadcfe1ca6af4e1bbac48af24b 100644
--- a/modules/mol/base/src/impl/chain_impl.hh
+++ b/modules/mol/base/src/impl/chain_impl.hh
@@ -25,6 +25,7 @@
#include <ost/geom/geom.hh>
#include <ost/mol/residue_prop.hh>
+#include <ost/mol/chain_type.hh>
#include <ost/mol/impl/chain_impl_fw.hh>
#include <ost/mol/impl/residue_impl_fw.hh>
#include <ost/mol/impl/entity_impl_fw.hh>
@@ -46,7 +47,62 @@ public:
void SetName(const String& new_name);
String GetName() const;
+
+ /// \brief Assign a type to a chain.
+ ///
+ /// \param type chain type of ChainType
+ void SetType(const ChainType type)
+ {
+ type_ = type;
+ }
+
+ /// \brief Get the type of a chain.
+ ///
+ /// \return chain type of ChainType
+ ChainType GetType() const
+ {
+ return type_;
+ }
+ /// \brief whether the chain is a polymer
+ bool IsPolymer() const
+ {
+ return type_==CHAINTYPE_POLY || this->IsPolypeptide() ||
+ this->IsPolynucleotide() || this->IsPolysaccharide();
+ }
+ /// \brief whether the chain is a polysaccharide
+ bool IsPolysaccharide() const
+ {
+ return type_==CHAINTYPE_POLY_SAC_D || type_==CHAINTYPE_POLY_SAC_L;
+ }
+ /// \brief whether the chain is a polypeptide
+ bool IsPolypeptide() const
+ {
+ return type_==CHAINTYPE_POLY_PEPTIDE_D || type_==CHAINTYPE_POLY_PEPTIDE_L;
+ }
+ /// \brief whether the chain is a polynucleotide
+ bool IsPolynucleotide() const
+ {
+ return type_==CHAINTYPE_POLY_DN || type_==CHAINTYPE_POLY_RN ||
+ type_==CHAINTYPE_POLY_DN_RN;
+ }
+
+ /// \brief Assign a description to a chain.
+ ///
+ /// \param desc description
+ void SetDescription(const String desc)
+ {
+ description_ = desc;
+ }
+
+ /// \brief Get information about a chain
+ ///
+ /// \return description
+ String GetDescription() const
+ {
+ return description_;
+ }
+
/// \brief append new residue with exactly the same parameters as res, but
/// no atoms and bonds
ResidueImplPtr AppendResidue(const ResidueImplPtr& res);
@@ -113,13 +169,18 @@ public:
void DeleteAllResidues();
void ReorderResidues();
+
+ void RenumberAllResidues(int start, bool keep_spacing);
int GetIndex(const ResidueImplPtr& res) const;
void AssignSecondaryStructure(SecStructure ss,
const ResNum& start,
const ResNum& end);
int GetIndexForResNum(const ResNum& number) const;
-
+ ///\brief checks if the residue with that index breaks the in_sequence
+ /// property and updates it accordingly
+ void SetInSequence(int index);
+
private:
int GetIndexForResNumInSequence(const ResNum& number) const;
void UpdateShifts();
@@ -134,6 +195,8 @@ private:
/// \brief whether the residue numbers are in ascending order or not. Used
/// to optimize residue by number lookup.
bool in_sequence_;
+ ChainType type_;
+ String description_; ///< special aspects of the chain
};
}}} // ns
diff --git a/modules/mol/base/src/impl/connector_impl.cc b/modules/mol/base/src/impl/connector_impl.cc
index 8bafe009b6a110edecd96cadc3492ed348dc1f19..3a5a61532b5e6f61c58b960c3b0ba0b3f41789c9 100644
--- a/modules/mol/base/src/impl/connector_impl.cc
+++ b/modules/mol/base/src/impl/connector_impl.cc
@@ -92,14 +92,22 @@ Real ConnectorImpl::GetLength() const
}
void ConnectorImpl::SetDir(const geom::Vec3& dir) {
- geom::Vec3 v=Normalize(dir);
- local_rot_=find_rotation(v);
+ if(Length(dir)==0) {
+ local_rot_=geom::Mat3(1,0,0,0,1,0,0,0,1);
+ } else {
+ geom::Vec3 v=Normalize(dir);
+ local_rot_=find_rotation(v);
+ }
}
void ConnectorImpl::SetDirAndLength(const geom::Vec3& dir) {
len_=Length(dir);
- geom::Vec3 v=dir/len_;
- local_rot_=find_rotation(v);
+ if(len_==0) {
+ local_rot_=geom::Mat3(1,0,0,0,1,0,0,0,1);
+ } else {
+ geom::Vec3 v=dir/len_;
+ local_rot_=find_rotation(v);
+ }
}
bool ConnectorImpl::IsConnectorOf(const AtomImplPtr& a,
diff --git a/modules/mol/base/src/impl/dihedral.hh b/modules/mol/base/src/impl/dihedral.hh
index 2996205ba7e06cfd53c2a45829335c365a034d28..a722c93e60ff4b8d015d5f5bb97bc7d1b3a9709c 100644
--- a/modules/mol/base/src/impl/dihedral.hh
+++ b/modules/mol/base/src/impl/dihedral.hh
@@ -52,7 +52,7 @@ public:
/// \param update_other
/// If true, connectors of atom3 are updated accordingly, otherwise
/// they will be left untouched
- void SetAngleICS(Real angle, bool update_other=false);
+ void SetAngleICS(Real angle, bool update_other);
geom::Vec3 GetPos() const;
geom::Vec3 GetOriginalPos() const;
diff --git a/modules/mol/base/src/impl/entity_impl.cc b/modules/mol/base/src/impl/entity_impl.cc
index 305e3423041abfb58252cf417a861ada5d77967b..6942ce00fee8b3a93f45e31c083b90c51c80bdd3 100644
--- a/modules/mol/base/src/impl/entity_impl.cc
+++ b/modules/mol/base/src/impl/entity_impl.cc
@@ -307,11 +307,13 @@ geom::Vec3 EntityImpl::GetCenterOfMass() const {
return center;
}
+
Real EntityImpl::GetMass() const {
- Real mass=0.0;
- for (AtomImplMap::const_iterator it = atom_map_.begin();
- it!=atom_map_.end();++it) {
- mass+=it->second->GetMass();
+ double mass=0.0;
+ for (ChainImplList::const_iterator i=chain_list_.begin(),
+ e=chain_list_.end(); i!=e; ++i) {
+ ChainImplPtr chain=*i;
+ mass+=chain->GetMass();
}
return mass;
}
@@ -1209,4 +1211,12 @@ void EntityImpl::ReorderAllResidues()
}
}
+void EntityImpl::RenumberAllResidues(int start, bool keep_spacing)
+{
+ for(ChainImplList::iterator cit=chain_list_.begin();cit!=chain_list_.end();++cit) {
+ (*cit)->RenumberAllResidues(start, keep_spacing);
+ }
+
+}
+
}}} // ns
diff --git a/modules/mol/base/src/impl/entity_impl.hh b/modules/mol/base/src/impl/entity_impl.hh
index 3c5000920c23a959ab631e62874d54df6cce6878..d1d1ca050f30a7fdee8d7ab5d64bf417ee183dc8 100644
--- a/modules/mol/base/src/impl/entity_impl.hh
+++ b/modules/mol/base/src/impl/entity_impl.hh
@@ -93,7 +93,6 @@ public:
Real GetMass() const;
geom::Vec3 GetCenterOfMass() const;
geom::Vec3 GetCenterOfAtoms() const;
-
/// \brief returns the axis-aligned bounding box of the entity
geom::AlignedCuboid GetBounds() const;
@@ -254,6 +253,8 @@ public:
void ReorderAllResidues();
+ void RenumberAllResidues(int start, bool keep_spacing);
+
private:
void DoCopy(EntityImplPtr dest);
diff --git a/modules/mol/base/src/impl/query_impl.cc b/modules/mol/base/src/impl/query_impl.cc
index a70cfa813b39d63d9337cfb6135846d63796f8fb..965f1dbe418ce9bf391449d0bc1f46a215874c7b 100644
--- a/modules/mol/base/src/impl/query_impl.cc
+++ b/modules/mol/base/src/impl/query_impl.cc
@@ -283,12 +283,7 @@ bool QueryImpl::IsAlwaysUndef(const Node* ast,
if (lop_node) {
bool lhs = this->IsAlwaysUndef(lop_node->GetLHS(), target_level);
bool rhs = this->IsAlwaysUndef(lop_node->GetRHS(), target_level);
- switch (lop_node->GetOP()) {
- case LOP_AND:
- return lhs || rhs;
- case LOP_OR:
- return lhs && rhs;
- }
+ return lhs && rhs;
}
else {
const SelNode* sel_node = dynamic_cast<const SelNode*>(ast);
diff --git a/modules/mol/base/src/impl/residue_impl.cc b/modules/mol/base/src/impl/residue_impl.cc
index 28f0cc6f9047616848e8d0a334da946a6fdfea9f..1e0fa1d461662e1895f6d8dd5bbeb7d8a58479f6 100644
--- a/modules/mol/base/src/impl/residue_impl.cc
+++ b/modules/mol/base/src/impl/residue_impl.cc
@@ -91,7 +91,8 @@ Real ResidueImpl::GetAverageBFactor() const
}
void ResidueImpl::AddAltAtom(const String& group, const AtomImplPtr& atom,
- const geom::Vec3& position) {
+ const geom::Vec3& position,
+ Real occ, Real b_factor) {
if (group.length()==0)
throw Error("alt atom group name can't be empty String");
@@ -106,7 +107,7 @@ void ResidueImpl::AddAltAtom(const String& group, const AtomImplPtr& atom,
curr_group_=group;
}
}
- i->second.atoms.push_back(AtomGroupEntry(atom, position));
+ i->second.atoms.push_back(AtomGroupEntry(atom, position, occ, b_factor));
}
geom::Vec3 ResidueImpl::GetAltAtomPos(const AtomImplPtr& atom,
@@ -127,12 +128,47 @@ geom::Vec3 ResidueImpl::GetAltAtomPos(const AtomImplPtr& atom,
" does not have alternative atom position '"+group+"'");
}
+Real ResidueImpl::GetAltAtomOcc(const AtomImplPtr& atom,
+ const String& group) const
+{
+ AtomEntryGroups::const_iterator i=alt_groups_.find(group);
+ if (i==alt_groups_.end()) {
+ throw Error("No alt atom group '"+group+"'");
+ }
+ const AtomGroup& g=i->second;
+ for (AtomGroupEntryList::const_iterator j=g.atoms.begin(),
+ e=g.atoms.end(); j!=e; ++j) {
+ if (atom==j->atom.lock()) {
+ return j->occ;
+ }
+ }
+ throw Error(atom->GetQualifiedName()+
+ " does not have alternative atom position '"+group+"'");
+}
+Real ResidueImpl::GetAltAtomBFactor(const AtomImplPtr& atom,
+ const String& group) const
+{
+ AtomEntryGroups::const_iterator i=alt_groups_.find(group);
+ if (i==alt_groups_.end()) {
+ throw Error("No alt atom group '"+group+"'");
+ }
+ const AtomGroup& g=i->second;
+ for (AtomGroupEntryList::const_iterator j=g.atoms.begin(),
+ e=g.atoms.end(); j!=e; ++j) {
+ if (atom==j->atom.lock()) {
+ return j->b_factor;
+ }
+ }
+ throw Error(atom->GetQualifiedName()+
+ " does not have alternative atom position '"+group+"'");
+}
AtomImplPtr ResidueImpl::InsertAltAtom(const String& name,
const String& alt_group,
const geom::Vec3& pos,
- const String& ele) {
+ const String& ele,
+ Real occupancy, Real b_factor) {
AtomImplPtr atom=this->InsertAtom(name, pos, ele);
- this->AddAltAtom(alt_group, atom, pos);
+ this->AddAltAtom(alt_group, atom, pos, occupancy, b_factor);
return atom;
}
@@ -451,7 +487,7 @@ void ResidueImpl::RemoveAltPositionsForAtom(const AtomImplPtr& atom) {
Real ResidueImpl::GetMass() const
{
- Real mass = 0;
+ double mass = 0;
for (AtomImplList::const_iterator i=atom_list_.begin();
i!=atom_list_.end(); ++i) {
mass+=(*i)->GetMass();
@@ -506,7 +542,8 @@ geom::Vec3 ResidueImpl::GetCenterOfMass() const
void ResidueImpl::AddAltAtomPos(const String& group,
const AtomImplPtr& atom,
- const geom::Vec3& position) {
+ const geom::Vec3& position,
+ Real occ, Real b_factor) {
// Make sure atom is already registered for having an alternative position.
// Bail out, if this is not the case.
AtomEntryGroups::iterator i=alt_groups_.begin();
@@ -522,7 +559,7 @@ void ResidueImpl::AddAltAtomPos(const String& group,
}
}
if (found)
- this->AddAltAtom(group, atom, position);
+ this->AddAltAtom(group, atom, position, occ, b_factor);
else {
String m="Definition of alternative position without prior call to "
"InsertAltAtom is not allowed";
@@ -582,6 +619,8 @@ bool ResidueImpl::SwitchAtomPos(const String& group) {
AtomGroupEntry& entry=*k;
assert(!entry.atom.expired());
entry.pos=entry.atom.lock()->OriginalPos();
+ entry.occ=entry.atom.lock()->GetOccupancy();
+ entry.b_factor=entry.atom.lock()->GetBFactor();
}
}
AtomGroup& agr=i->second;
@@ -595,6 +634,8 @@ bool ResidueImpl::SwitchAtomPos(const String& group) {
geom::Mat4 transf_matrix = ent.GetTransformationMatrix();
geom::Vec3 transf_pos = geom::Vec3(transf_matrix*geom::Vec4(entry.pos));
entry.atom.lock()->TransformedPos()=transf_pos;
+ entry.atom.lock()->SetBFactor(j->b_factor);
+ entry.atom.lock()->SetOccupancy(j->occ);
}
curr_group_=group;
return true;
diff --git a/modules/mol/base/src/impl/residue_impl.hh b/modules/mol/base/src/impl/residue_impl.hh
index 8b01d32d2f3d8873f8098805dbe62028334dc2ec..24f829c6922bdbfdcc0ee8645cbec80e4ff49f88 100644
--- a/modules/mol/base/src/impl/residue_impl.hh
+++ b/modules/mol/base/src/impl/residue_impl.hh
@@ -34,6 +34,7 @@
#include <ost/mol/impl/torsion_impl_fw.hh>
#include <ost/mol/impl/atom_group.hh>
#include <ost/mol/chem_class.hh>
+#include <ost/mol/chem_type.hh>
#include <ost/generic_property.hh>
#include <ost/mol/property_id.hh>
@@ -57,7 +58,8 @@ public:
/// no bonds
AtomImplPtr InsertAtom(const AtomImplPtr& atom);
AtomImplPtr InsertAltAtom(const String& name, const String& alt_group,
- const geom::Vec3& pos, const String& ele);
+ const geom::Vec3& pos, const String& ele,
+ Real occ, Real b_factor);
const ResNum& GetNumber() const {return num_;}
void SetNumber(const ResNum& num) {num_=num;}
@@ -166,8 +168,11 @@ public:
void AddAltAtomPos(const String& group,
const AtomImplPtr& atom,
- const geom::Vec3& position);
+ const geom::Vec3& position,
+ Real occ, Real b_factor);
geom::Vec3 GetAltAtomPos(const AtomImplPtr& atom, const String& group) const;
+ Real GetAltAtomOcc(const AtomImplPtr& atom, const String& group) const;
+ Real GetAltAtomBFactor(const AtomImplPtr& atom, const String& group) const;
const String& GetCurrentAltGroupName() const {
@@ -196,6 +201,12 @@ public:
ChemClass GetChemClass() const {
return chem_class_;
}
+ ChemType GetChemType() const {
+ return chem_type_;
+ }
+ void SetChemType(ChemType ct) {
+ chem_type_=ct;
+ }
TorsionImplP FindTorsion(const String& torsion_name) const;
@@ -214,7 +225,7 @@ public:
void SetIsLigand(bool flag) { ligand_=flag; }
private:
void AddAltAtom(const String& group, const AtomImplPtr& atom,
- const geom::Vec3& position);
+ const geom::Vec3& position, Real occ, Real b_factor);
void RemoveAltPositionsForAtom(const AtomImplPtr& atom);
String curr_group_;
@@ -227,6 +238,7 @@ private:
TorsionImplList torsion_list_;
SecStructure sec_structure_;
ChemClass chem_class_;
+ ChemType chem_type_;
char olc_;
// whether the residue is part of the protein.
// TODO: this should be fixed to be a enum'ed type aka
diff --git a/modules/mol/base/src/impl/torsion_impl.cc b/modules/mol/base/src/impl/torsion_impl.cc
index 744d648f33f3139d1bb03c7327f8ef0a9a77b7f1..9f9ffcdd9b74fa46969ed70f934b1c0a434e4602 100644
--- a/modules/mol/base/src/impl/torsion_impl.cc
+++ b/modules/mol/base/src/impl/torsion_impl.cc
@@ -48,8 +48,8 @@ Real TorsionImpl::GetAngle() const {
}
}
-void TorsionImpl::SetAngle(Real angle, bool up) {
- this->SetAngleICS(angle, true);
+void TorsionImpl::SetAngle(Real angle, bool update_others) {
+ this->SetAngleICS(angle, update_others);
}
void TorsionImpl::Apply(EntityVisitor& v) {
@@ -57,8 +57,8 @@ void TorsionImpl::Apply(EntityVisitor& v) {
v.VisitTorsion(TorsionHandle(shared_from_this()));
}
-void TorsionImpl::RotateAngle(Real angle, bool up) {
- this->SetAngle(this->GetAngleICS()+angle, up);
+void TorsionImpl::RotateAngle(Real angle, bool update_others) {
+ this->SetAngle(this->GetAngleICS()+angle, update_others);
}
}}} // ns
diff --git a/modules/mol/base/src/in_mem_coord_source.cc b/modules/mol/base/src/in_mem_coord_source.cc
index 1690c11048713795f5bf3d86bbef29b9fb82702f..ea01db894a69efa04189e126b3f2d6429df46f12 100644
--- a/modules/mol/base/src/in_mem_coord_source.cc
+++ b/modules/mol/base/src/in_mem_coord_source.cc
@@ -30,6 +30,12 @@ void InMemCoordSource::AddFrame(const std::vector<geom::Vec3>& coords)
frames_.push_back(fp);
}
+void InMemCoordSource::AddFrame(const std::vector<geom::Vec3>& coords,const geom::Vec3& cell_size,const geom::Vec3& cell_angles)
+{
+ CoordFramePtr fp(new CoordFrame(coords,cell_size,cell_angles));
+ frames_.push_back(fp);
+}
+
void InMemCoordSource::InsertFrame(int pos, const std::vector<geom::Vec3>& coords)
{
CoordFrameList::iterator it = frames_.begin();
diff --git a/modules/mol/base/src/in_mem_coord_source.hh b/modules/mol/base/src/in_mem_coord_source.hh
index dc032ebbea294fdc6b4bb7ba86d79847b5e818ca..0984791aae634bcf315efe08f55f10850ef77c5f 100644
--- a/modules/mol/base/src/in_mem_coord_source.hh
+++ b/modules/mol/base/src/in_mem_coord_source.hh
@@ -44,6 +44,7 @@ public:
void AddFrame(const CoordFramePtr& frame);
virtual void AddFrame(const std::vector<geom::Vec3>& coords);
+ virtual void AddFrame(const std::vector<geom::Vec3>& coords,const geom::Vec3& cell_size,const geom::Vec3& cell_angles);
virtual void InsertFrame(int pos, const std::vector<geom::Vec3>& coords);
private:
diff --git a/modules/mol/base/src/query_state.cc b/modules/mol/base/src/query_state.cc
index d8d4da028c2f727bde33cb8305a7bf8ae09a0b08..63a4be69387dd7a3e6aaf3865b8737fe8a5b58d6 100644
--- a/modules/mol/base/src/query_state.cc
+++ b/modules/mol/base/src/query_state.cc
@@ -321,7 +321,7 @@ boost::logic::tribool QueryState::EvalAtom(const AtomImplPtr& a) {
case Prop::ANAME:
str_value = a->Name();
s_[*i] = cmp_string(ss.comp_op,str_value,
- boost::get<StringOrRegexParam>(ss.param));
+ boost::get<StringOrRegexParam>(ss.param));
break;
case Prop::AINDEX:
int_value=(a->GetIndex());
@@ -330,27 +330,27 @@ boost::logic::tribool QueryState::EvalAtom(const AtomImplPtr& a) {
case Prop::AX:
float_value=(a->TransformedPos())[0];
s_[*i]=cmp_num<Real>(ss.comp_op, float_value,
- boost::get<float>(ss.param));
+ boost::get<float>(ss.param));
break;
case Prop::AY:
float_value=(a->TransformedPos())[1];
s_[*i]=cmp_num<Real>(ss.comp_op, float_value,
- boost::get<float>(ss.param));
+ boost::get<float>(ss.param));
break;
case Prop::AZ:
float_value=(a->TransformedPos())[2];
s_[*i]=cmp_num<Real>(ss.comp_op, float_value,
- boost::get<float>(ss.param));
+ boost::get<float>(ss.param));
break;
case Prop::OCC:
float_value=a->GetOccupancy();
s_[*i]=cmp_num<Real>(ss.comp_op, float_value,
- boost::get<float>(ss.param));
+ boost::get<float>(ss.param));
break;
case Prop::ELE:
str_value = a->GetElement();
s_[*i] = cmp_string(ss.comp_op,str_value,
- boost::get<StringOrRegexParam>(ss.param));
+ boost::get<StringOrRegexParam>(ss.param));
break;
case Prop::ABFAC:
float_value=a->GetBFactor();
diff --git a/modules/mol/base/src/residue_base.cc b/modules/mol/base/src/residue_base.cc
index 7d15ad5f6fff00b62a223b8f41417f25d0703d8d..07950307d012a33735f6630a5d171d8e8ad8c7ce 100644
--- a/modules/mol/base/src/residue_base.cc
+++ b/modules/mol/base/src/residue_base.cc
@@ -104,6 +104,18 @@ void ResidueBase::SetChemClass(ChemClass cc)
Impl()->SetChemClass(cc);
}
+void ResidueBase::SetChemType(ChemType ct)
+{
+ this->CheckValidity();
+ Impl()->SetChemType(ct);
+}
+
+ChemType ResidueBase::GetChemType() const
+{
+ this->CheckValidity();
+ return Impl()->GetChemType();
+};
+
SecStructure ResidueBase::GetSecStructure() const
{
this->CheckValidity();
diff --git a/modules/mol/base/src/residue_base.hh b/modules/mol/base/src/residue_base.hh
index c994b9a3098b48479300c811d55583cc213ad16c..993683cb223aaf661704ce0c08c81d16f55f1bbf 100644
--- a/modules/mol/base/src/residue_base.hh
+++ b/modules/mol/base/src/residue_base.hh
@@ -27,6 +27,7 @@
#include <ost/mol/sec_structure.hh>
#include <ost/mol/handle_type_fw.hh>
#include <ost/mol/chem_class.hh>
+#include <ost/mol/chem_type.hh>
#include <ost/generic_property.hh>
#include "property_id.hh"
@@ -55,7 +56,12 @@ namespace ost { namespace mol {
/// participate in a peptide bond. For nucleotides, the chemical class is either
/// ChemClass::RNA_LINKING or ChemClass::DNA_LINKING. For unknown compounds the
/// chemical class is ChemClass::UNKNOWN.
-///
+///
+/// In addition, residues have a ChemType. A classification of all components into
+/// nine categories (ions, non-canonical molecules, saccharised, nucleotides,
+/// amino acids, co-enzymes, water coordinated ions, drugs, solvents) as obtained
+/// from the PDB.
+///
/// When loading an entity from file, the one-letter and chemical class of a
/// residue are assigned by the \ref conop::Builder "default builder".
class DLLEXPORT_OST_MOL ResidueBase:
@@ -116,7 +122,12 @@ public:
ChemClass GetChemClass() const;
void SetChemClass(ChemClass cc);
-
+
+ /// \brief PDB ligand classification from component dictionary
+ ChemType GetChemType() const;
+
+ void SetChemType(ChemType ct);
+
/// \brief Get secondary structure type. By default, the residue is in COIL
/// conformation.
SecStructure GetSecStructure() const;
diff --git a/modules/mol/base/src/residue_prop.hh b/modules/mol/base/src/residue_prop.hh
index 19bccc98e7e39e4f27c2001feb7efe58ceaf3fbe..e86eef5f11b16ba4eed55153e0cb38901faedd1e 100644
--- a/modules/mol/base/src/residue_prop.hh
+++ b/modules/mol/base/src/residue_prop.hh
@@ -28,9 +28,10 @@ namespace ost { namespace mol {
class DLLEXPORT ResNum: private
boost::additive<ResNum, int,
+ boost::additive<ResNum,
boost::totally_ordered<ResNum,
boost::totally_ordered<ResNum, int,
- boost::unit_steppable<ResNum> > > >
+ boost::unit_steppable<ResNum> > > > >
{
public:
ResNum(int n):
@@ -74,7 +75,7 @@ public:
num_-=r.num_;
return num_;
}
-
+
ResNum& operator++()
{
++num_;
diff --git a/modules/mol/base/src/torsion_handle.cc b/modules/mol/base/src/torsion_handle.cc
index c4bac5ff1455e70cf4ba5f3ba51c650d9cea3334..2830bc8211ef30477693f3610b76b46fdf79d27e 100644
--- a/modules/mol/base/src/torsion_handle.cc
+++ b/modules/mol/base/src/torsion_handle.cc
@@ -95,18 +95,6 @@ Real TorsionHandle::GetAngle() const
this->CheckValidity();
return impl_->GetAngle();
}
-
-void TorsionHandle::SetAngle(Real a, bool up)
-{
- this->CheckValidity();
- impl_->SetAngle(a, up);
-}
-
-void TorsionHandle::RotateAngle(Real angle, bool up)
-{
- this->CheckValidity();
- impl_->RotateAngle(angle, up);
-}
void TorsionHandle::CheckValidity() const {
if (!impl_)
diff --git a/modules/mol/base/src/torsion_handle.hh b/modules/mol/base/src/torsion_handle.hh
index 856cd67e731983ee898213101d52764b214ddb07..06f7e7bf0eb7283318617f8fd0a4f222718f87ad 100644
--- a/modules/mol/base/src/torsion_handle.hh
+++ b/modules/mol/base/src/torsion_handle.hh
@@ -87,18 +87,6 @@ public:
/// \brief get position, i.e midpoint between the second and third atom (original coordinates)
geom::Vec3 GetOriginalPos() const;
- /// \brief set absolute torsion angle
- ///
- /// All connectors at the third atom (A3) will be adjusted accordingly. If
- /// you only want to adjust the bond between A3 and A4, and leave the other
- /// bonds untouched, use the ost::SetDihedralAngle() function
- ///
- /// \sa RotateAngle
- void SetAngle(Real a, bool up=true);
-
- /// relative rotation, either upstream or downstream
- void RotateAngle(Real angle, bool up=true);
-
impl::TorsionImplP& Impl() {
return impl_;
}
diff --git a/modules/mol/base/src/transform.cc b/modules/mol/base/src/transform.cc
index ffee262dec1767ac26e6645ead08fb3d8bd3acf6..c1ffbff6b8a34bf6016d01fba72deeba8a2f4fdb 100644
--- a/modules/mol/base/src/transform.cc
+++ b/modules/mol/base/src/transform.cc
@@ -16,9 +16,12 @@
// along with this library; if not, write to the Free Software Foundation, Inc.,
// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
//------------------------------------------------------------------------------
+
+#include <ost/config.hh>
+#if(OST_INFO_ENABLED)
#include <ost/info/info.hh>
#include <ost/info/geom_info_conversion.hh>
-
+#endif
#include "transform.hh"
namespace ost {
@@ -193,6 +196,7 @@ void Transform::update_tm()
ttm_ = Transpose(tm_);
}
+#if(OST_INFO_ENABLED)
Transform TransformFromInfo(const info::InfoGroup& group)
{
if (!group.HasItem("center")) {
@@ -222,5 +226,6 @@ void TransformToInfo(const Transform& transform, info::InfoGroup& group)
info::InfoGroup rot=group.CreateGroup("rotation");
info::Mat3ToInfo(transform.GetRot(), rot);
}
+#endif
}} // ns
diff --git a/modules/mol/base/src/transform.hh b/modules/mol/base/src/transform.hh
index 5c9acd27605bbff805b40eaac297c83219cd5582..1ed33135e1ca1287f0e2c9debc151aeacca069cc 100644
--- a/modules/mol/base/src/transform.hh
+++ b/modules/mol/base/src/transform.hh
@@ -23,8 +23,11 @@
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>
namespace ost { namespace mol {
@@ -81,6 +84,7 @@ private:
void update_tm();
};
+#if(OST_INFO_ENABLED)
/// \brief read transformation from info group
/// \relates Transform
Transform DLLEXPORT_OST_MOL TransformFromInfo(const info::InfoGroup& group);
@@ -88,6 +92,7 @@ Transform DLLEXPORT_OST_MOL TransformFromInfo(const info::InfoGroup& group);
/// \relates Transform
void DLLEXPORT_OST_MOL TransformToInfo(const Transform& transform,
info::InfoGroup& group);
+#endif
}} // ns
#endif
diff --git a/modules/mol/base/src/view_op.hh b/modules/mol/base/src/view_op.hh
index b673f160c30ef63e0c9ea46ce3f78b3bce160262..1774b289dc7689166f075500f2ee3c96026e3a35 100644
--- a/modules/mol/base/src/view_op.hh
+++ b/modules/mol/base/src/view_op.hh
@@ -86,7 +86,8 @@ CompareViews(const EntityView& view1, const EntityView& view2);
///
/// \param view is the view to be converted to a handle
/// \param include_exlusive_atoms if true, atoms that are part of an exclusive
-/// bond will also be included in the new entity handle.
+/// bond (only one bond partner is included in the view) will also be included
+/// in the new entity handle.
/// \param handle If invalid a new entity will be created. If valid, the atoms,
/// residues, chains, bonds and torsions will be added to handle. This is
/// useful to combine several entities into one.
diff --git a/modules/mol/base/tests/test_chain.cc b/modules/mol/base/tests/test_chain.cc
index a2bdda81f87a8fb3b703a5489b232e8bd0ae00eb..3b7bbd85b15bee45ec61832548dfc97541893257 100644
--- a/modules/mol/base/tests/test_chain.cc
+++ b/modules/mol/base/tests/test_chain.cc
@@ -202,4 +202,136 @@ BOOST_AUTO_TEST_CASE(rename_chain)
BOOST_CHECK_EQUAL(eh.GetChainCount(), 2);
}
+BOOST_AUTO_TEST_CASE(chain_type)
+{
+ EntityHandle eh = CreateEntity();
+ XCSEditor e = eh.EditXCS();
+ ChainHandle ch1 = e.InsertChain("A");
+
+ // setting/ getting
+ BOOST_CHECK(ch1.GetType() == CHAINTYPE_UNKNOWN);
+ BOOST_CHECK(!ch1.IsPolymer());
+ BOOST_CHECK(!ch1.IsPolysaccharide());
+ BOOST_CHECK(!ch1.IsPolypeptide());
+ BOOST_CHECK(!ch1.IsPolynucleotide());
+ e.SetChainType(ch1, CHAINTYPE_POLY);
+ BOOST_CHECK(ch1.GetType() == CHAINTYPE_POLY);
+ BOOST_CHECK(ch1.IsPolymer());
+ BOOST_CHECK(!ch1.IsPolysaccharide());
+ BOOST_CHECK(!ch1.IsPolypeptide());
+ BOOST_CHECK(!ch1.IsPolynucleotide());
+ e.SetChainType(ch1, CHAINTYPE_NON_POLY);
+ BOOST_CHECK(ch1.GetType() == CHAINTYPE_NON_POLY);
+ BOOST_CHECK(!ch1.IsPolymer());
+ BOOST_CHECK(!ch1.IsPolysaccharide());
+ BOOST_CHECK(!ch1.IsPolypeptide());
+ BOOST_CHECK(!ch1.IsPolynucleotide());
+ e.SetChainType(ch1, CHAINTYPE_WATER);
+ BOOST_CHECK(ch1.GetType() == CHAINTYPE_WATER);
+ BOOST_CHECK(!ch1.IsPolymer());
+ BOOST_CHECK(!ch1.IsPolysaccharide());
+ BOOST_CHECK(!ch1.IsPolypeptide());
+ BOOST_CHECK(!ch1.IsPolynucleotide());
+ e.SetChainType(ch1, CHAINTYPE_POLY_PEPTIDE_D);
+ BOOST_CHECK(ch1.IsPolymer());
+ BOOST_CHECK(!ch1.IsPolysaccharide());
+ BOOST_CHECK(ch1.IsPolypeptide());
+ BOOST_CHECK(!ch1.IsPolynucleotide());
+ BOOST_CHECK(ch1.GetType() == CHAINTYPE_POLY_PEPTIDE_D);
+ e.SetChainType(ch1, CHAINTYPE_POLY_PEPTIDE_L);
+ BOOST_CHECK(ch1.IsPolymer());
+ BOOST_CHECK(!ch1.IsPolysaccharide());
+ BOOST_CHECK(ch1.IsPolypeptide());
+ BOOST_CHECK(!ch1.IsPolynucleotide());
+ BOOST_CHECK(ch1.GetType() == CHAINTYPE_POLY_PEPTIDE_L);
+ e.SetChainType(ch1, CHAINTYPE_POLY_DN);
+ BOOST_CHECK(ch1.IsPolymer());
+ BOOST_CHECK(!ch1.IsPolysaccharide());
+ BOOST_CHECK(!ch1.IsPolypeptide());
+ BOOST_CHECK(ch1.IsPolynucleotide());
+ BOOST_CHECK(ch1.GetType() == CHAINTYPE_POLY_DN);
+ e.SetChainType(ch1, CHAINTYPE_POLY_RN);
+ BOOST_CHECK(ch1.IsPolymer());
+ BOOST_CHECK(!ch1.IsPolysaccharide());
+ BOOST_CHECK(!ch1.IsPolypeptide());
+ BOOST_CHECK(ch1.IsPolynucleotide());
+ BOOST_CHECK(ch1.GetType() == CHAINTYPE_POLY_RN);
+ e.SetChainType(ch1, CHAINTYPE_POLY_SAC_D);
+ BOOST_CHECK(ch1.IsPolymer());
+ BOOST_CHECK(ch1.IsPolysaccharide());
+ BOOST_CHECK(!ch1.IsPolypeptide());
+ BOOST_CHECK(!ch1.IsPolynucleotide());
+ BOOST_CHECK(ch1.GetType() == CHAINTYPE_POLY_SAC_D);
+ e.SetChainType(ch1, CHAINTYPE_POLY_SAC_L);
+ BOOST_CHECK(ch1.IsPolymer());
+ BOOST_CHECK(ch1.IsPolysaccharide());
+ BOOST_CHECK(!ch1.IsPolypeptide());
+ BOOST_CHECK(!ch1.IsPolynucleotide());
+ BOOST_CHECK(ch1.GetType() == CHAINTYPE_POLY_SAC_L);
+ e.SetChainType(ch1, CHAINTYPE_POLY_DN_RN);
+ BOOST_CHECK(ch1.GetType() == CHAINTYPE_POLY_DN_RN);
+ BOOST_CHECK(ch1.IsPolymer());
+ BOOST_CHECK(!ch1.IsPolysaccharide());
+ BOOST_CHECK(!ch1.IsPolypeptide());
+ BOOST_CHECK(ch1.IsPolynucleotide());
+ e.SetChainType(ch1, CHAINTYPE_N_CHAINTYPES);
+ BOOST_CHECK(ch1.GetType() == CHAINTYPE_N_CHAINTYPES);
+ e.SetChainType(ch1, CHAINTYPE_UNKNOWN);
+ BOOST_CHECK(ch1.GetType() == CHAINTYPE_UNKNOWN);
+
+ // string -> chain type
+ BOOST_CHECK(ChainTypeFromString("polymer") == CHAINTYPE_POLY);
+ BOOST_CHECK(ChainTypeFromString("non-polymer") == CHAINTYPE_NON_POLY);
+ BOOST_CHECK(ChainTypeFromString("water") == CHAINTYPE_WATER);
+ BOOST_CHECK(ChainTypeFromString("polypeptide(D)") ==
+ CHAINTYPE_POLY_PEPTIDE_D);
+ BOOST_CHECK(ChainTypeFromString("polypeptide(L)") ==
+ CHAINTYPE_POLY_PEPTIDE_L);
+ BOOST_CHECK(ChainTypeFromString("polydeoxyribonucleotide") ==
+ CHAINTYPE_POLY_DN);
+ BOOST_CHECK(ChainTypeFromString("polyribonucleotide") ==
+ CHAINTYPE_POLY_RN);
+ BOOST_CHECK(ChainTypeFromString("polysaccharide(D)") ==
+ CHAINTYPE_POLY_SAC_D);
+ BOOST_CHECK(ChainTypeFromString("polysaccharide(L)") ==
+ CHAINTYPE_POLY_SAC_L);
+ BOOST_CHECK(ChainTypeFromString(
+ "polydeoxyribonucleotide/polyribonucleotide hybrid") ==
+ CHAINTYPE_POLY_DN_RN);
+ BOOST_CHECK(ChainTypeFromString("other") == CHAINTYPE_UNKNOWN);
+ BOOST_CHECK_THROW(ChainTypeFromString("supposed to fail"),
+ std::runtime_error);
+
+ // chain type -> string
+ BOOST_CHECK(StringFromChainType(CHAINTYPE_POLY) == "polymer");
+ BOOST_CHECK(StringFromChainType(CHAINTYPE_NON_POLY) == "non-polymer");
+ BOOST_CHECK(StringFromChainType(CHAINTYPE_WATER) == "water");
+ BOOST_CHECK(StringFromChainType(CHAINTYPE_POLY_PEPTIDE_D) ==
+ "polypeptide(D)");
+ BOOST_CHECK(StringFromChainType(CHAINTYPE_POLY_PEPTIDE_L) ==
+ "polypeptide(L)");
+ BOOST_CHECK(StringFromChainType(CHAINTYPE_POLY_DN) ==
+ "polydeoxyribonucleotide");
+ BOOST_CHECK(StringFromChainType(CHAINTYPE_POLY_RN) == "polyribonucleotide");
+ BOOST_CHECK(StringFromChainType(CHAINTYPE_POLY_SAC_D) ==
+ "polysaccharide(D)");
+ BOOST_CHECK(StringFromChainType(CHAINTYPE_POLY_SAC_L) ==
+ "polysaccharide(L)");
+ BOOST_CHECK(StringFromChainType(CHAINTYPE_POLY_DN_RN) ==
+ "polydeoxyribonucleotide/polyribonucleotide hybrid");
+ BOOST_CHECK(StringFromChainType(CHAINTYPE_UNKNOWN) == "other");
+ BOOST_CHECK_THROW(StringFromChainType(CHAINTYPE_N_CHAINTYPES),
+ std::runtime_error);
+}
+
+BOOST_AUTO_TEST_CASE(chain_description)
+{
+ EntityHandle eh=CreateEntity();
+ XCSEditor e = eh.EditXCS();
+ ChainHandle ch1 = e.InsertChain("A");
+ String description = "Very important information";
+ e.SetChainDescription(ch1, description);
+ BOOST_CHECK(ch1.GetDescription() == description);
+}
+
BOOST_AUTO_TEST_SUITE_END()
diff --git a/modules/mol/base/tests/test_ics.cc b/modules/mol/base/tests/test_ics.cc
index 8c26db5d96c1738e8454487366989ca1041255c1..4f84f6a78bf0882302f9d5edce87ed13656b6064 100644
--- a/modules/mol/base/tests/test_ics.cc
+++ b/modules/mol/base/tests/test_ics.cc
@@ -59,6 +59,37 @@ struct Structure {
AtomHandle a5;
};
+struct TorsionStructure {
+ TorsionStructure()
+ {
+ e=CreateEntity();
+ ICSEditor editor=e.EditICS();
+ c=editor.InsertChain("A");
+ r=editor.AppendResidue(c, "TORSTIN");
+ a1=editor.InsertAtom(r, "X1", geom::Vec3( 0.0, -1.0, 0.0));
+ a2=editor.InsertAtom(r, "X2", geom::Vec3( 1.0, 0.0, 0.0));
+ a3=editor.InsertAtom(r, "X3", geom::Vec3( 2.0, 0.0, 0.0));
+ a4=editor.InsertAtom(r, "X4", geom::Vec3( 3.0, 1.0, 0.0));
+ a5=editor.InsertAtom(r, "X5", geom::Vec3( 3.0, -1.0, 0.0));
+ editor.Connect(a1, a2);
+ editor.Connect(a2, a3);
+ editor.Connect(a3, a4);
+ editor.Connect(a3, a5);
+ t1 = editor.AddTorsion("T1", a1, a2, a3, a4);
+ t2 = editor.AddTorsion("T2", a1, a2, a3, a5);
+ }
+ EntityHandle e;
+ ChainHandle c;
+ ResidueHandle r;
+ AtomHandle a1;
+ AtomHandle a2;
+ AtomHandle a3;
+ AtomHandle a4;
+ AtomHandle a5;
+ TorsionHandle t1;
+ TorsionHandle t2;
+};
+
const static Real EPSILON=0.000001;
Real angle_xcs(AtomHandle a1, AtomHandle a2, AtomHandle a3) {
@@ -72,6 +103,118 @@ bool test_angle(Real a, Real e) {
BOOST_AUTO_TEST_SUITE( mol_base )
+BOOST_AUTO_TEST_CASE(ics_update_icsbondlength)
+{
+ TorsionStructure s;
+ mol::BondHandle bond = s.a2.FindBondToAtom(s.a3);
+ BOOST_CHECK_CLOSE(bond.GetLength(), Real(1.0), Real(EPSILON));
+}
+
+BOOST_AUTO_TEST_CASE(ics_settorsion_unbuffered)
+{
+ Real eps = 0.0001;
+ TorsionStructure s;
+ ICSEditor e = s.e.EditICS(mol::UNBUFFERED_EDIT);
+ BOOST_CHECK_CLOSE(s.t1.GetAngle(), Real(M_PI), Real(eps));
+ BOOST_CHECK_SMALL(s.t2.GetAngle(), eps);
+ e.SetTorsionAngle(s.t1,0);
+ BOOST_CHECK_SMALL(s.t1.GetAngle(), eps);
+ BOOST_CHECK_CLOSE(s.t2.GetAngle(), Real(M_PI), Real(eps));
+ e.SetTorsionAngle(s.t2,M_PI/4);
+ BOOST_CHECK_CLOSE(s.t2.GetAngle(), Real(M_PI/4), Real(eps));
+ BOOST_CHECK_CLOSE(s.t1.GetAngle(), Real(-M_PI+M_PI/4), Real(eps));
+ e.SetTorsionAngle(s.t1,-M_PI/4);
+ BOOST_CHECK_CLOSE(s.t1.GetAngle(), Real(-M_PI/4), Real(eps));
+ BOOST_CHECK_CLOSE(s.t2.GetAngle(), Real(3/4.*M_PI), Real(eps));
+ e.RotateTorsionAngle(s.t1, M_PI/4);
+ BOOST_CHECK_SMALL(s.t1.GetAngle(), eps);
+ BOOST_CHECK_CLOSE(std::abs(s.t2.GetAngle()), Real(M_PI), Real(eps));
+}
+
+BOOST_AUTO_TEST_CASE(ics_settorsion_buffered)
+{
+ Real eps = 0.0001;
+ TorsionStructure s;
+ ICSEditor e = s.e.EditICS(mol::BUFFERED_EDIT);
+ BOOST_CHECK_CLOSE(s.t1.GetAngle(), Real(M_PI), Real(eps));
+ BOOST_CHECK_SMALL(s.t2.GetAngle(), eps);
+ e.SetTorsionAngle(s.t1,0);
+ BOOST_CHECK_SMALL(s.t1.GetAngle(), eps);
+ BOOST_CHECK_CLOSE(s.t2.GetAngle(), Real(M_PI), Real(eps));
+ e.SetTorsionAngle(s.t2,M_PI/4);
+ BOOST_CHECK_CLOSE(s.t2.GetAngle(), Real(M_PI/4), Real(eps));
+ BOOST_CHECK_CLOSE(s.t1.GetAngle(), Real(-M_PI+M_PI/4), Real(eps));
+ e.SetTorsionAngle(s.t1,-M_PI/4);
+ BOOST_CHECK_CLOSE(s.t1.GetAngle(), Real(-M_PI/4), Real(eps));
+ BOOST_CHECK_CLOSE(s.t2.GetAngle(), Real(3/4.*M_PI), Real(eps));
+ e.RotateTorsionAngle(s.t1, M_PI/4);
+ BOOST_CHECK_SMALL(s.t1.GetAngle(), eps);
+ BOOST_CHECK_CLOSE(std::abs(s.t2.GetAngle()), Real(M_PI), Real(eps));
+}
+
+BOOST_AUTO_TEST_CASE(ics_settorsion_unbuffered_update_others)
+{
+ Real eps = 0.0001;
+ TorsionStructure s;
+ ICSEditor e = s.e.EditICS(mol::UNBUFFERED_EDIT);
+ BOOST_CHECK_CLOSE(s.t1.GetAngle(), Real(M_PI), Real(eps));
+ BOOST_CHECK_SMALL(s.t2.GetAngle(), eps);
+ e.SetTorsionAngle(s.t1,0,false);
+ BOOST_CHECK_SMALL(s.t1.GetAngle(), eps);
+ BOOST_CHECK_SMALL(s.t2.GetAngle(), eps);
+ e.SetTorsionAngle(s.t2,M_PI/4,false);
+ BOOST_CHECK_CLOSE(s.t2.GetAngle(), Real(M_PI/4), Real(eps));
+ BOOST_CHECK_SMALL(s.t1.GetAngle(), eps);
+ e.SetTorsionAngle(s.t1,-M_PI/4,false);
+ BOOST_CHECK_CLOSE(s.t1.GetAngle(), Real(-M_PI/4), Real(eps));
+ BOOST_CHECK_CLOSE(s.t2.GetAngle(), Real(M_PI/4), Real(eps));
+ e.RotateTorsionAngle(s.t1, M_PI/4,false);
+ BOOST_CHECK_SMALL(s.t1.GetAngle(), eps);
+ BOOST_CHECK_CLOSE(s.t2.GetAngle(), Real(M_PI/4), Real(eps));
+}
+
+BOOST_AUTO_TEST_CASE(ics_settorsion_buffered_update_others)
+{
+ Real eps = 0.0001;
+ TorsionStructure s;
+ ICSEditor e = s.e.EditICS(mol::BUFFERED_EDIT);
+ BOOST_CHECK_CLOSE(s.t1.GetAngle(), Real(M_PI), Real(eps));
+ BOOST_CHECK_SMALL(s.t2.GetAngle(), eps);
+ e.SetTorsionAngle(s.t1,0,false);
+ BOOST_CHECK_SMALL(s.t1.GetAngle(), eps);
+ BOOST_CHECK_SMALL(s.t2.GetAngle(), eps);
+ e.SetTorsionAngle(s.t2,M_PI/4,false);
+ BOOST_CHECK_CLOSE(s.t2.GetAngle(), Real(M_PI/4), Real(eps));
+ BOOST_CHECK_SMALL(s.t1.GetAngle(), eps);
+ e.SetTorsionAngle(s.t1,-M_PI/4,false);
+ BOOST_CHECK_CLOSE(s.t1.GetAngle(), Real(-M_PI/4), Real(eps));
+ BOOST_CHECK_CLOSE(s.t2.GetAngle(), Real(M_PI/4), Real(eps));
+ e.RotateTorsionAngle(s.t1, M_PI/4,false);
+ BOOST_CHECK_SMALL(s.t1.GetAngle(), eps);
+ BOOST_CHECK_CLOSE(s.t2.GetAngle(), Real(M_PI/4), Real(eps));
+}
+
+BOOST_AUTO_TEST_CASE(ics_settorsion_linear_unbuffered)
+{
+ Real eps = 0.0001;
+ TorsionStructure s;
+ ICSEditor e = s.e.EditICS(mol::UNBUFFERED_EDIT);
+ e.SetAngle(s.a2,s.a3,s.a4,M_PI);
+ BOOST_CHECK_SMALL(s.t1.GetAngle(), eps);
+ BOOST_CHECK_SMALL(s.t2.GetAngle(), eps);
+ e.SetTorsionAngle(s.t1,0);
+ BOOST_CHECK_SMALL(s.t1.GetAngle(), eps);
+ BOOST_CHECK_SMALL(s.t2.GetAngle(), eps);
+ e.SetTorsionAngle(s.t2,M_PI/4);
+ BOOST_CHECK_SMALL(s.t1.GetAngle(), eps);
+ BOOST_CHECK_CLOSE(s.t2.GetAngle(), Real(M_PI/4), Real(eps));
+ e.SetTorsionAngle(s.t1,-M_PI/4);
+ BOOST_CHECK_SMALL(s.t1.GetAngle(), eps);
+ BOOST_CHECK_SMALL(s.t2.GetAngle(), eps);
+ e.RotateTorsionAngle(s.t1, M_PI/4);
+ BOOST_CHECK_SMALL(s.t1.GetAngle(), eps);
+ BOOST_CHECK_CLOSE(s.t2.GetAngle(), Real(M_PI/4), Real(eps));
+}
BOOST_AUTO_TEST_CASE(ics_angle_trivia)
{
@@ -147,4 +290,4 @@ BOOST_AUTO_TEST_CASE(ics_get_angle)
<< " found");
}
-BOOST_AUTO_TEST_SUITE_END()
\ No newline at end of file
+BOOST_AUTO_TEST_SUITE_END()
diff --git a/modules/mol/base/tests/test_numpy.py b/modules/mol/base/tests/test_numpy.py
index 14496c0c0ef2d3cb3632ebbb620890d4a9e126a0..217ed89dd7adb6380b6fea22719e49f310b2c2cb 100644
--- a/modules/mol/base/tests/test_numpy.py
+++ b/modules/mol/base/tests/test_numpy.py
@@ -1,17 +1,25 @@
import unittest
-from ost import *
+if __name__== '__main__':
+ import sys
+ sys.path.insert(0,"../../../../stage/lib64/openstructure/")
+ sys.path.insert(0,"../../../../stage/lib/openstructure/")
+
+import ost
-has_numpy=True
-try:
- import numpy
-except ImportError:
+if ost.WITH_NUMPY:
+ has_numpy=True
+ try:
+ import numpy
+ except ImportError, e:
+ has_numpy=False
+else:
has_numpy=False
def v2v(v):
- return geom.Vec3(float(v[0]),float(v[1]),float(v[2]))
+ return ost.geom.Vec3(float(v[0]),float(v[1]),float(v[2]))
def dd(v1,v2):
- return geom.Distance(v1,v2)<1e-8
+ return ost.geom.Distance(v1,v2)<1e-8
class TestNumpy(unittest.TestCase):
def setUp(self):
@@ -20,46 +28,46 @@ class TestNumpy(unittest.TestCase):
def test_(self):
if not has_numpy:
return
- entity=mol.CreateEntity()
+ entity=ost.mol.CreateEntity()
ed=entity.EditXCS()
ch=ed.InsertChain("X")
re=ed.AppendResidue(ch,"ALA")
- a0=ed.InsertAtom(re,"A",geom.Vec3(0,0,0))
+ a0=ed.InsertAtom(re,"A",ost.geom.Vec3(0,0,0))
self.assertEqual(a0.GetIndex(),0)
- a1=ed.InsertAtom(re,"B",geom.Vec3(1,0,0))
+ a1=ed.InsertAtom(re,"B",ost.geom.Vec3(1,0,0))
self.assertEqual(a1.GetIndex(),1)
- a2=ed.InsertAtom(re,"C",geom.Vec3(2,0,0))
+ a2=ed.InsertAtom(re,"C",ost.geom.Vec3(2,0,0))
self.assertEqual(a2.GetIndex(),2)
- a3=ed.InsertAtom(re,"D",geom.Vec3(3,0,0))
+ a3=ed.InsertAtom(re,"D",ost.geom.Vec3(3,0,0))
self.assertEqual(a3.GetIndex(),3)
- self.assertTrue(dd(a0.pos,geom.Vec3(0,0,0)))
- self.assertTrue(dd(a1.pos,geom.Vec3(1,0,0)))
- self.assertTrue(dd(a2.pos,geom.Vec3(2,0,0)))
- self.assertTrue(dd(a3.pos,geom.Vec3(3,0,0)))
+ self.assertTrue(dd(a0.pos,ost.geom.Vec3(0,0,0)))
+ self.assertTrue(dd(a1.pos,ost.geom.Vec3(1,0,0)))
+ self.assertTrue(dd(a2.pos,ost.geom.Vec3(2,0,0)))
+ self.assertTrue(dd(a3.pos,ost.geom.Vec3(3,0,0)))
ed.SetAtomTransformedPos(entity.GetAtomList(),
numpy.array([[0,1,0],[0,2,0],[0,3,0],[0,4,0]], dtype=numpy.float32))
- self.assertTrue(dd(a0.pos,geom.Vec3(0,1,0)))
- self.assertTrue(dd(a1.pos,geom.Vec3(0,2,0)))
- self.assertTrue(dd(a2.pos,geom.Vec3(0,3,0)))
- self.assertTrue(dd(a3.pos,geom.Vec3(0,4,0)))
+ self.assertTrue(dd(a0.pos,ost.geom.Vec3(0,1,0)))
+ self.assertTrue(dd(a1.pos,ost.geom.Vec3(0,2,0)))
+ self.assertTrue(dd(a2.pos,ost.geom.Vec3(0,3,0)))
+ self.assertTrue(dd(a3.pos,ost.geom.Vec3(0,4,0)))
na=entity.positions
- self.assertTrue(dd(v2v(na[0]),geom.Vec3(0,1,0)))
- self.assertTrue(dd(v2v(na[1]),geom.Vec3(0,2,0)))
- self.assertTrue(dd(v2v(na[2]),geom.Vec3(0,3,0)))
- self.assertTrue(dd(v2v(na[3]),geom.Vec3(0,4,0)))
+ self.assertTrue(dd(v2v(na[0]),ost.geom.Vec3(0,1,0)))
+ self.assertTrue(dd(v2v(na[1]),ost.geom.Vec3(0,2,0)))
+ self.assertTrue(dd(v2v(na[2]),ost.geom.Vec3(0,3,0)))
+ self.assertTrue(dd(v2v(na[3]),ost.geom.Vec3(0,4,0)))
ed.SetAtomTransformedPos([3,99,2],
numpy.array([[0,0,-3],[-1,-1,-1],[0,0,-2]], dtype=numpy.float32))
- self.assertTrue(dd(a0.pos,geom.Vec3(0,1,0)))
- self.assertTrue(dd(a1.pos,geom.Vec3(0,2,0)))
- self.assertTrue(dd(a2.pos,geom.Vec3(0,0,-2)))
- self.assertTrue(dd(a3.pos,geom.Vec3(0,0,-3)))
+ self.assertTrue(dd(a0.pos,ost.geom.Vec3(0,1,0)))
+ self.assertTrue(dd(a1.pos,ost.geom.Vec3(0,2,0)))
+ self.assertTrue(dd(a2.pos,ost.geom.Vec3(0,0,-2)))
+ self.assertTrue(dd(a3.pos,ost.geom.Vec3(0,0,-3)))
if __name__== '__main__':
unittest.main()
diff --git a/modules/seq/alg/doc/seqalg.rst b/modules/seq/alg/doc/seqalg.rst
index 79e6ca62bb3d97082b37fcbb9afee719e12b276f..02f74c4f78015926f5faae38c54d5a4c72f24218 100644
--- a/modules/seq/alg/doc/seqalg.rst
+++ b/modules/seq/alg/doc/seqalg.rst
@@ -35,11 +35,32 @@
considered as aligned. There is no information in the pairwise alignment to
guide the merging, the result is undefined.
+.. autofunction:: ValidateSEQRESAlignment
+
.. autofunction:: AlignToSEQRES
.. autofunction:: AlignmentFromChainView
+.. function:: Conservation(aln, assign=true, prop_name="cons", ignore_gap=false)
+ Calculates conservation scores for each column in the alignment, according to
+ the ConSurf method (Armon et al., J. Mol. Biol. (2001) 307, 447-463).
+
+ The conservation score is a value between 0 and 1. The bigger the number
+ the more conserved the aligned residues are.
+
+ :param aln: An alignment handle
+ :type aln: :class:`~ost.seq.AlignmentHandle`
+ :param assign: If true, the conservation scores are assigned to attached
+ residues. The name of the property can be changed with the prop_name
+ parameter. Useful when coloring entities based on sequence conservation.
+ :param prop_name: The property name for assigning the conservation to
+ attached residues. Defaults to 'cons'.
+ :param ignore_gap: If true, the dissimilarity between two gaps is increased to
+ 6.0 instead of 0.5 as defined in the original version. Without this, a
+ stretch where in the alignment there is only one sequence which is
+ aligned to only gaps, is considered highly conserved (depending on the
+ number of gap sequences).
.. function:: LocalAlign(seq1, seq2, subst_weight, gap_open=-5, gap_ext=-2)
diff --git a/modules/seq/alg/pymod/CMakeLists.txt b/modules/seq/alg/pymod/CMakeLists.txt
index dfe07488ea145a451a10f6bb6a47facbc9b3cf40..0821b510a21cb8ad806b21a958a3592f24f6679f 100644
--- a/modules/seq/alg/pymod/CMakeLists.txt
+++ b/modules/seq/alg/pymod/CMakeLists.txt
@@ -1,7 +1,8 @@
set(OST_SEQ_ALG_PYMOD_SOURCES
wrap_seq_alg.cc
)
-
-pymod(NAME seq_alg OUTPUT_DIR ost/seq/alg
- CPP ${OST_SEQ_ALG_PYMOD_SOURCES}
- PY __init__.py mat.py renumber.py)
+if (NOT ENABLE_STATIC)
+ pymod(NAME seq_alg OUTPUT_DIR ost/seq/alg
+ CPP ${OST_SEQ_ALG_PYMOD_SOURCES}
+ PY __init__.py mat.py renumber.py)
+endif()
diff --git a/modules/seq/alg/pymod/__init__.py b/modules/seq/alg/pymod/__init__.py
index 24e79daac0e896b25b08b92caf51c3a0a9c46c6f..63157ea31e84892007da778d3ac09c00c51c52df 100644
--- a/modules/seq/alg/pymod/__init__.py
+++ b/modules/seq/alg/pymod/__init__.py
@@ -1,7 +1,61 @@
from _ost_seq_alg import *
from ost.seq.alg.mat import *
-def AlignToSEQRES(chain, seqres):
+def ValidateSEQRESAlignment(aln, chain=None):
+ """
+ Checks a sequence aligned to a SEQRES sequence to be free of strand breaks.
+ Residues divided by gaps are not considered as breakage but may also not be
+ connected.
+
+ :param aln: Alignment
+ :type aln: :class:`~ost.seq.AlignmentHandle`
+ :param chain: Source of the sequence
+ :type chain: :class:`~ost.mol.ChainHandle`
+
+ :returns: True if all residues (beside gaped ones) are connected, False
+ otherwise.
+ """
+ from ost import LogWarning
+ from ost import seq
+ from ost import mol
+ if aln.GetCount() != 2:
+ raise ValueError('Alignment contains more than 2 sequences!')
+ sequence = aln.GetSequence(1)
+ if len(sequence) == 0:
+ return True
+ if chain == None:
+ if sequence.HasAttachedView() == False:
+ raise ValueError("Alignment is missing an attached chain view.")
+ chain = sequence.GetAttachedView()
+ residues = chain.residues
+ # eat up all beginning gaps
+ j = 1
+ for s in sequence:
+ if s != '-':
+ break
+ j += 1;
+ l = sequence[j-1]
+ i = 0
+ # run over sequence & alignment
+ for s in sequence[j:]:
+ if s != '-':
+ i += 1
+ r1 = residues[i-1]
+ r2 = residues[i]
+ if r1.one_letter_code=='?' or r2.one_letter_code=='?':
+ continue
+ if l != '-':
+ if not mol.InSequence(r1.handle, r2.handle):
+ LogWarning('%s and %s are not connected by peptide bond' % (str(r1), str(r2)))
+ return False
+ else:
+ if mol.InSequence(r1.handle, r2.handle):
+ LogWarning('%s and %s are connected by peptide bond' % (str(r1), str(r2)))
+ return False
+ l = s
+ return True
+
+def AlignToSEQRES(chain, seqres, try_resnum_first=False, validate=True):
"""
Aligns the residues of chain to the SEQRES sequence, inserting gaps where
needed. The function uses the connectivity of the protein backbone to find
@@ -9,35 +63,73 @@ def AlignToSEQRES(chain, seqres):
sequence.
All the non-ligand, peptide-linking residues of the chain must be listed in
- SEQRES. If there are any additional residues in the chain, the function raises
- a ValueError.
-
+ SEQRES. If there are any additional residues in the chain, the function
+ raises a ValueError.
+
+ If 'try_resnum_first' is set, building the alignment following residue numbers
+ is tried first.
+
+ If 'validate' is set (default), the alignment is checked using
+ :func:`~ost.seq.alg.ValidateSEQRESAlignment`.
+
+ :param chain: Source of the sequence
+ :type chain: :class:`~ost.mol.ChainHandle`
+ :param seqres: SEQRES sequence
+ :type seqres: :class:`str`
+ :param try_resnum_first: Try to align by residue number
+ :type try_resnum_first: :class:`bool`
+ :param validate: Validate alignment by
+ :func:`~ost.seq.alg.ValidateSEQRESAlignment`
+ :type validate: :class:`bool`
+
:returns: The alignment of the residues in the chain and the SEQRES entries.
:rtype: :class:`~ost.seq.AlignmentHandle`
"""
+
+ def IsEqual(olc1, olc2):
+ return olc1 in ('X', '?') or olc2 in ('X', '?') or olc1 == olc2
+
from ost import seq
from ost import mol
- view=chain.Select('ligand=false and peptide=true')
+ from ost import LogWarning
+ view=chain
residues=view.residues
if len(residues)==0:
return seq.CreateAlignment()
- fragments=[residues[0].one_letter_code]
- for r1, r2 in zip(residues[:-2], residues[1:]):
- if not mol.InSequence(r1.handle, r2.handle):
- fragments.append('')
- fragments[-1]+=r2.one_letter_code
- ss=str(seqres)
- pos=0
- aln_seq=''
- for frag in fragments:
- new_pos=ss.find(frag, pos)
- if new_pos==-1:
- raise ValueError('"%s" is not a substring of "%s"' % (frag, ss))
- aln_seq+='-'*(new_pos-pos)+frag
- pos=new_pos+len(frag)
- aln_seq+='-'*(len(seqres)-len(aln_seq))
- return seq.CreateAlignment(seq.CreateSequence('SEQRES', str(seqres)),
- seq.CreateSequence('atoms', aln_seq))
+ if try_resnum_first:
+ aln_seq = seq.CreateSequence('atoms', '-'*len(seqres))
+ for r1 in residues:
+ if r1.number.num <= len(seqres) and r1.number.num > 0:
+ if IsEqual(seqres[r1.number.num - 1], r1.one_letter_code):
+ aln_seq[r1.number.num - 1] = r1.one_letter_code
+ else:
+ LogWarning('Sequence mismatch: chain has "' + r1.one_letter_code +
+ '", while SEQRES is "' + seqres[r1.number.num - 1] +
+ '" at the corresponding position.')
+ try_resnum_first = False
+ break
+ if not try_resnum_first:
+ fragments=[residues[0].one_letter_code]
+ for r1, r2 in zip(residues[:-1], residues[1:]):
+ if not mol.InSequence(r1.handle, r2.handle):
+ fragments.append('')
+ fragments[-1]+=r2.one_letter_code
+ ss=str(seqres)
+ pos=0
+ aln_seq=''
+ for frag in fragments:
+ new_pos=ss.find(frag, pos)
+ if new_pos==-1:
+ raise ValueError('"%s" is not a substring of "%s"' % (frag, ss))
+ aln_seq+='-'*(new_pos-pos)+frag
+ pos=new_pos+len(frag)
+ aln_seq = seq.CreateSequence('atoms',
+ aln_seq+('-'*(len(seqres)-len(aln_seq))))
+ alignment = seq.CreateAlignment(seq.CreateSequence('SEQRES', str(seqres)),
+ aln_seq)
+ if validate and not ValidateSEQRESAlignment(alignment, view):
+ raise ValueError("SEQRES cannot be aligned with its corresponding chain.")
+ return alignment
def AlignmentFromChainView(chain, handle_seq_name='handle',
diff --git a/modules/seq/alg/pymod/wrap_seq_alg.cc b/modules/seq/alg/pymod/wrap_seq_alg.cc
index 5c1fba67787786393921b1c5710be59ba6079381..9239d1ec3d2e759729cfb1bcde0fb9005e52ded1 100644
--- a/modules/seq/alg/pymod/wrap_seq_alg.cc
+++ b/modules/seq/alg/pymod/wrap_seq_alg.cc
@@ -53,7 +53,7 @@ BOOST_PYTHON_MODULE(_ost_seq_alg)
.def("SetWeight", &SubstWeightMatrix::SetWeight)
;
def("MergePairwiseAlignments", &MergePairwiseAlignments);
- def("Conservation", &Conservation, (arg("assign")=true, arg("prop_name")="cons"));
+ def("Conservation", &Conservation, (arg("assign")=true, arg("prop_name")="cons", arg("ignore_gap")=false));
def("LocalAlign", &LocalAlign, (arg("seq1"), arg("seq2"),arg("subst_weight"),
arg("gap_open")=-5, arg("gap_ext")=-2));
def("GlobalAlign", &GlobalAlign,(arg("seq1"),arg("seq2"),arg("subst_weight"),
diff --git a/modules/seq/alg/src/CMakeLists.txt b/modules/seq/alg/src/CMakeLists.txt
index fe23aa52cce246216e0aeb8b10c578f795e27881..ccffcacf464cc22d85f62a6d5190067b76622cb7 100644
--- a/modules/seq/alg/src/CMakeLists.txt
+++ b/modules/seq/alg/src/CMakeLists.txt
@@ -16,10 +16,13 @@ local_align.cc
global_align.cc
sequence_identity.cc
ins_del.cc
-subst_weight_matrix.cc
conservation.cc
)
+if (ENABLE_INFO)
+ list (APPEND OST_SEQ_ALG_SOURCES subst_weight_matrix.cc)
+endif()
+
module(NAME seq_alg HEADER_OUTPUT_DIR ost/seq/alg SOURCES ${OST_SEQ_ALG_SOURCES}
HEADERS ${OST_SEQ_ALG_HEADERS} DEPENDS_ON ost_seq)
diff --git a/modules/seq/alg/src/conservation.cc b/modules/seq/alg/src/conservation.cc
index 2b5bf3481c22a5801176b1aa1f8ff227df1f7dc4..e80077efd254deead27d156cd556d0da2f90721f 100644
--- a/modules/seq/alg/src/conservation.cc
+++ b/modules/seq/alg/src/conservation.cc
@@ -75,7 +75,7 @@ static float CHEM_DISSIM[][24]={
-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00}
};
-float PhysicoChemicalDissim(char c1, char c2)
+float PhysicoChemicalDissim(char c1, char c2, bool ignore_gap)
{
static int indices[]={2, 23, 0, 9, 7, 17, 3, 10, 15, -1,
11, 14, 16, 8, -1, 1, 6, 12, 4, 5,
@@ -94,12 +94,15 @@ float PhysicoChemicalDissim(char c1, char c2)
s=CHEM_DISSIM[idx_b][idx_a-idx_b];
else
s=CHEM_DISSIM[idx_a][idx_b-idx_a];
+ if (ignore_gap && idx_a==20 && idx_b==20) {
+ s=6.0;
+ }
assert(s>=0.0);
return s;
}
std::vector<Real> Conservation(const AlignmentHandle& aln, bool assign,
- const String& prop)
+ const String& prop, bool ignore_gap)
{
std::vector<Real> cons(aln.GetLength(), 0.0);
int comb=(aln.GetCount()*(aln.GetCount()-1))/2;
@@ -108,7 +111,7 @@ std::vector<Real> Conservation(const AlignmentHandle& aln, bool assign,
AlignedColumn c=aln[col];
for (int i=0; i<aln.GetCount(); ++i) {
for (int j=i+1; j<aln.GetCount(); ++j) {
- score+=PhysicoChemicalDissim(c[i], c[j]);
+ score+=PhysicoChemicalDissim(c[i], c[j], ignore_gap);
}
}
score=1.0-score/(6.0*comb);
diff --git a/modules/seq/alg/src/conservation.hh b/modules/seq/alg/src/conservation.hh
index 8e4146ee790f68056ad55e1b6efa62466c5e3135..651b5bdd150348ef812bf839e37e458e2fc2eb86 100644
--- a/modules/seq/alg/src/conservation.hh
+++ b/modules/seq/alg/src/conservation.hh
@@ -35,9 +35,15 @@ namespace ost { namespace seq { namespace alg {
/// parameter. Useful when coloring entities based on sequence conservation.
/// \p prop_name The property name for assigning the conservation to
/// attached residues. Defaults to 'cons'.
+/// \p ignore_gap If true, the dissimilarity between two gaps is increased to
+/// 6.0 instead of 0.5 as defined in the original version. Without this, a
+/// stretch where in the alignment there is only one sequence which is
+/// aligned to only gaps, is considered highly conserved (depending on the
+/// number of gap sequences).
///
std::vector<Real> DLLEXPORT_OST_SEQ_ALG Conservation(const AlignmentHandle& aln,
bool assign=true,
- const String& prop_name="cons");
+ const String& prop_name="cons",
+ bool ignore_gap=false);
}}}
diff --git a/modules/seq/alg/src/merge_pairwise_alignments.cc b/modules/seq/alg/src/merge_pairwise_alignments.cc
index 9d60859a07b99b7dda1724f54306f91a7605690b..c522869cfa50c64a6609d59fb856b733aa6288cf 100644
--- a/modules/seq/alg/src/merge_pairwise_alignments.cc
+++ b/modules/seq/alg/src/merge_pairwise_alignments.cc
@@ -87,7 +87,8 @@ SequenceHandle shift_reference(const ConstSequenceHandle& ref_seq,
}
new_sequence << ref_str.substr(last);
SequenceHandle s=CreateSequence(ref_seq.GetName(),
- new_sequence.str());
+ new_sequence.str(),
+ ref_seq.GetRole());
if (ref_seq.HasAttachedView())
s.AttachView(ref_seq.GetAttachedView());
s.SetOffset(ref_seq.GetOffset());
@@ -122,7 +123,8 @@ SequenceHandle realign_sequence(const AlignmentHandle& aln,
}
new_sequence << s2.GetOneLetterCode(i);
}
- SequenceHandle s=CreateSequence(s2.GetName(), new_sequence.str());
+ SequenceHandle s=CreateSequence(s2.GetName(), new_sequence.str(),
+ s2.GetRole());
if (s2.HasAttachedView())
s.AttachView(s2.GetAttachedView());
s.SetOffset(s2.GetOffset());
diff --git a/modules/seq/alg/src/subst_weight_matrix.hh b/modules/seq/alg/src/subst_weight_matrix.hh
index f310893ab6a002a830d432a0b07d0547fbb3943d..97f0ef825cb45dda7e2572558b2917498e87a353 100644
--- a/modules/seq/alg/src/subst_weight_matrix.hh
+++ b/modules/seq/alg/src/subst_weight_matrix.hh
@@ -21,7 +21,11 @@
#include <ctype.h>
#include <string.h>
+#include <boost/shared_ptr.hpp>
+#include <ost/config.hh>
+#if(OST_INFO_ENABLED)
#include <ost/info/info_fw.hh>
+#endif
#include <ost/seq/alg/module_config.hh>
/*
@@ -86,12 +90,14 @@ private:
WeightType weights_[ALPHABET_SIZE*ALPHABET_SIZE];
};
+#if(OST_INFO_ENABLED)
SubstWeightMatrixPtr DLLEXPORT_OST_SEQ_ALG
SubstWeightMatrixFromInfo(const info::InfoGroup& group);
void DLLEXPORT_OST_SEQ_ALG
SubstWeightMatrixToInfo(const SubstWeightMatrixPtr& subst_mat,
info::InfoGroup& group);
+#endif
}}}
diff --git a/modules/seq/alg/tests/CMakeLists.txt b/modules/seq/alg/tests/CMakeLists.txt
index 3a26d1d67c0f00c64b810a752eb38f7cfd174723..76b599790fd34347fcff9b518c3c72b8fb85811e 100644
--- a/modules/seq/alg/tests/CMakeLists.txt
+++ b/modules/seq/alg/tests/CMakeLists.txt
@@ -6,6 +6,7 @@ set(OST_SEQ_ALG_UNIT_TESTS
test_local_align.py
test_global_align.py
test_weight_matrix.py
+ test_aligntoseqres.py
)
ost_unittest(MODULE seq_alg SOURCES "${OST_SEQ_ALG_UNIT_TESTS}")
diff --git a/modules/seq/alg/tests/test_aligntoseqres.py b/modules/seq/alg/tests/test_aligntoseqres.py
new file mode 100644
index 0000000000000000000000000000000000000000..0f4b8ceaa9bdbdf61bec7a390127b6ebc6687f89
--- /dev/null
+++ b/modules/seq/alg/tests/test_aligntoseqres.py
@@ -0,0 +1,72 @@
+import unittest
+from ost import *
+from ost import settings
+from ost import seq
+from ost import io
+
+class TestAlignToSeqRes(unittest.TestCase):
+ def testAlignWorking(self):
+ ent, seqres = io.LoadMMCIF("testfiles/align_to_seqres.mmcif", seqres = True)
+ chain = ent.FindChain("A")
+ sequence = seqres.FindSequence(chain.GetName());
+ seqres_aln = seq.alg.AlignToSEQRES(chain, sequence, try_resnum_first=False)
+ self.assertEqual(str(sequence), "MYTNSDFVVIKALEDGVNVIGLTRGADTRFHHSEKLDKGEV"+
+ "LIAQFTEHTSAIKVRGKAYIQTRHGVIESEGKK")
+ self.assertEqual(str(seqres_aln.sequences[1]), "----SDFVVIKALEDGVNVIGLTR--"+
+ "-TRFHHSEKLDKGEVLIAQFTEHTSAIKVRGKAYIQTRHGVIESEGK-")
+
+ seqres_aln = seq.alg.AlignToSEQRES(chain, sequence, try_resnum_first=True)
+ self.assertEqual(str(seqres_aln.sequences[1]), "----SDFVVIKALEDGVNVIGLTR--"+
+ "-TRFHHSEKLDKGEVLIAQFTEHTSAIKVRGKAYIQTRHGVIESEGK-")
+
+ def testAlignFail(self):
+ ent, seqres = io.LoadMMCIF("testfiles/align_to_seqres_valueerror.mmcif",
+ seqres = True)
+ chain = ent.FindChain("A")
+ sequence = seqres.FindSequence(chain.GetName());
+ ost.PushVerbosityLevel(0)
+ self.assertRaises(ValueError, seq.alg.AlignToSEQRES, chain, sequence, True)
+ ost.PopVerbosityLevel()
+
+ def testValidateWorking(self):
+ ent, seqres = io.LoadMMCIF("testfiles/align_to_seqres.mmcif", seqres = True)
+ chain = ent.FindChain("A")
+ sequence = seqres.FindSequence(chain.GetName());
+ seqres_aln = seq.alg.AlignToSEQRES(chain, sequence, try_resnum_first=False)
+ self.assertEqual(seq.alg.ValidateSEQRESAlignment(seqres_aln, chain), True)
+
+ def testValidateWorkingOnAttachedView(self):
+ ent, seqres = io.LoadMMCIF("testfiles/align_to_seqres.mmcif", seqres = True)
+ chain = ent.FindChain("A")
+ sequence = seqres.FindSequence(chain.GetName());
+ seqres_aln = seq.alg.AlignToSEQRES(chain, sequence, try_resnum_first=False)
+ seqres_aln.AttachView(1, chain.Select(''))
+ self.assertEqual(seq.alg.ValidateSEQRESAlignment(seqres_aln), True)
+
+ def testValidateEmptySequenceWorking(self):
+ alignment = seq.CreateAlignment(seq.CreateSequence('SEQRES', ''),
+ seq.CreateSequence('atoms', ''))
+ chain = mol.ChainHandle()
+ self.assertEqual(seq.alg.ValidateSEQRESAlignment(alignment, chain), True)
+
+ def testValidateStrandBreakageFail(self):
+ ent, seqres = io.LoadMMCIF("testfiles/validate_segres_aln_breakage.mmcif",
+ seqres = True)
+ chain = ent.FindChain("A")
+ sequence = seqres.FindSequence(chain.GetName());
+ seqres_aln = seq.alg.AlignToSEQRES(chain, sequence, try_resnum_first = True,
+ validate = False)
+ self.assertEqual(seq.alg.ValidateSEQRESAlignment(seqres_aln, chain), False)
+
+ def testValidateGapConnectedFail(self):
+ ent, seqres = io.LoadMMCIF("testfiles/validate_seqres_aln_connected.mmcif",
+ seqres = True,)
+ chain = ent.FindChain("A")
+ sequence = seqres.FindSequence(chain.GetName());
+ seqres_aln = seq.alg.AlignToSEQRES(chain, sequence, try_resnum_first = True,
+ validate = False)
+ self.assertEqual(seq.alg.ValidateSEQRESAlignment(seqres_aln, chain), False)
+
+if __name__ == "__main__":
+ from ost import testutils
+ testutils.RunTests()
diff --git a/modules/seq/alg/tests/test_global_align.py b/modules/seq/alg/tests/test_global_align.py
index aed51741b8ef35f0afdbd02b250cc93ea1c05f23..b23503cd02c2fbd9684a4355cbb14e7e53120a02 100644
--- a/modules/seq/alg/tests/test_global_align.py
+++ b/modules/seq/alg/tests/test_global_align.py
@@ -44,7 +44,5 @@ class TestGlobalAlign(unittest.TestCase):
self.assertEqual(alns[0].sequences[1].offset, 0)
if __name__ == "__main__":
- try:
- unittest.main()
- except Exception, e:
- print e
+ from ost import testutils
+ testutils.RunTests()
diff --git a/modules/seq/alg/tests/test_local_align.py b/modules/seq/alg/tests/test_local_align.py
index ff6872f9df22b261947e9abdbda12319e22a6d5a..47f78f68668e17e7413cbd18bbf09f9dd94b0b46 100644
--- a/modules/seq/alg/tests/test_local_align.py
+++ b/modules/seq/alg/tests/test_local_align.py
@@ -43,7 +43,5 @@ class TestLocalAlign(unittest.TestCase):
self.assertEqual(alns[0].sequences[1].offset, 2)
if __name__ == "__main__":
- try:
- unittest.main()
- except Exception, e:
- print e
+ from ost import testutils
+ testutils.RunTests()
diff --git a/modules/seq/alg/tests/test_merge_pairwise_alignments.cc b/modules/seq/alg/tests/test_merge_pairwise_alignments.cc
index 851f5c9f163911f1166492a25fd94ebcf4c5ea5a..25f9b836bd361560531922e2215bd3001cc909f0 100644
--- a/modules/seq/alg/tests/test_merge_pairwise_alignments.cc
+++ b/modules/seq/alg/tests/test_merge_pairwise_alignments.cc
@@ -34,15 +34,15 @@ BOOST_AUTO_TEST_SUITE(ost_seq_alg)
BOOST_AUTO_TEST_CASE(merge_pairwise_alignments_one)
{
- SequenceHandle ref=CreateSequence("REF", "abcdefghijklmn");
+ SequenceHandle ref=CreateSequence("REF", "abcdefghijklmn", "R");
SequenceHandle s1=CreateSequence("S1", "abcd---efghijklmn");
- SequenceHandle s2=CreateSequence("S2", "abcdxyzefghijklmn");
+ SequenceHandle s2=CreateSequence("S2", "abcdxyzefghijklmn", "X");
AlignmentHandle aln1=CreateAlignment();
aln1.AddSequence(s1);
aln1.AddSequence(s2);
SequenceHandle s3=CreateSequence("S1", "abcdefghij---klmn");
- SequenceHandle s4=CreateSequence("S2", "abcdefghijxyzklmn");
+ SequenceHandle s4=CreateSequence("S2", "abcdefghijxyzklmn", "Y");
AlignmentHandle aln2=CreateAlignment();
aln2.AddSequence(s3);
@@ -55,6 +55,9 @@ BOOST_AUTO_TEST_CASE(merge_pairwise_alignments_one)
BOOST_CHECK_EQUAL(seqs[0].GetString(), "abcd---efghij---klmn");
BOOST_CHECK_EQUAL(seqs[1].GetString(), "abcdxyzefghij---klmn");
BOOST_CHECK_EQUAL(seqs[2].GetString(), "abcd---efghijxyzklmn");
+ BOOST_CHECK_EQUAL(seqs[0].GetRole(), "R");
+ BOOST_CHECK_EQUAL(seqs[1].GetRole(), "X");
+ BOOST_CHECK_EQUAL(seqs[2].GetRole(), "Y");
}
BOOST_AUTO_TEST_CASE(merge_pairwise_alignments_two)
diff --git a/modules/seq/alg/tests/test_renumber.py b/modules/seq/alg/tests/test_renumber.py
index 76a9bf1d1d37284914ff7f23f2d32923c451d4f4..51e4727d3cfb7b3f87fea3517f9664fe7c896b16 100644
--- a/modules/seq/alg/tests/test_renumber.py
+++ b/modules/seq/alg/tests/test_renumber.py
@@ -118,7 +118,5 @@ if __name__ == "__main__":
except(settings.FileNotFound):
print "Could not find clustalw executable: ignoring unit tests"
sys.exit(0)
- try:
- unittest.main()
- except Exception, e:
- print e
+ from ost import testutils
+ testutils.RunTests()
diff --git a/modules/seq/alg/tests/test_weight_matrix.py b/modules/seq/alg/tests/test_weight_matrix.py
index 7d85996fb3e74d0aa3ee87eace30a04881b0918a..91cf830379b7e7a3dccb5de3694267497f4d480f 100644
--- a/modules/seq/alg/tests/test_weight_matrix.py
+++ b/modules/seq/alg/tests/test_weight_matrix.py
@@ -39,7 +39,5 @@ class TestWeightMatrix(unittest.TestCase):
self.assertEqual(mat.GetWeight('?', 'E'), 0)
if __name__ == "__main__":
- try:
- unittest.main()
- except Exception, e:
- print e
+ from ost import testutils
+ testutils.RunTests()
diff --git a/modules/seq/alg/tests/testfiles/align_to_seqres.mmcif b/modules/seq/alg/tests/testfiles/align_to_seqres.mmcif
new file mode 100644
index 0000000000000000000000000000000000000000..177b53a64ae4319b48350ac7e132badbbf20e2d4
--- /dev/null
+++ b/modules/seq/alg/tests/testfiles/align_to_seqres.mmcif
@@ -0,0 +1,564 @@
+data_3BAR
+# based on 3AQD
+_entry.id 3BAR
+#
+loop_
+_entity.id
+_entity.type
+_entity.src_method
+_entity.pdbx_description
+_entity.formula_weight
+_entity.pdbx_number_of_molecules
+_entity.details
+1 polymer man 'Transcription attenuation protein mtrB' 8257.458 22 ?
+2 water nat water 18.015 7 ?
+#
+_entity_poly.entity_id 1
+_entity_poly.type 'polypeptide(L)'
+_entity_poly.nstd_linkage no
+_entity_poly.nstd_monomer no
+_entity_poly.pdbx_seq_one_letter_code MYTNSDFVVIKALEDGVNVIGLTRGADTRFHHSEKLDKGEVLIAQFTEHTSAIKVRGKAYIQTRHGVIESEGKK
+_entity_poly.pdbx_seq_one_letter_code_can MYTNSDFVVIKALEDGVNVIGLTRGADTRFHHSEKLDKGEVLIAQFTEHTSAIKVRGKAYIQTRHGVIESEGKK
+_entity_poly.pdbx_strand_id A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V
+#
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_entity_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.B_iso_or_equiv
+_atom_site.Cartn_x_esd
+_atom_site.Cartn_y_esd
+_atom_site.Cartn_z_esd
+_atom_site.occupancy_esd
+_atom_site.B_iso_or_equiv_esd
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_comp_id
+_atom_site.auth_asym_id
+_atom_site.auth_atom_id
+_atom_site.pdbx_PDB_model_num
+ATOM 1 N N . SER A 1 5 ? 8.892 13.236 -28.550 1.00 81.62 ? ? ? ? ? ? 7 SER A N 1
+ATOM 2 C CA . SER A 1 5 ? 8.449 14.550 -29.128 1.00 80.98 ? ? ? ? ? ? 7 SER A CA 1
+ATOM 3 C C . SER A 1 5 ? 7.181 15.159 -28.476 1.00 77.44 ? ? ? ? ? ? 7 SER A C 1
+ATOM 4 O O . SER A 1 5 ? 6.463 15.940 -29.117 1.00 76.80 ? ? ? ? ? ? 7 SER A O 1
+ATOM 5 C CB . SER A 1 5 ? 8.239 14.416 -30.651 1.00 81.96 ? ? ? ? ? ? 7 SER A CB 1
+ATOM 6 O OG . SER A 1 5 ? 9.441 14.629 -31.378 1.00 87.04 ? ? ? ? ? ? 7 SER A OG 1
+ATOM 7 N N . ASP A 1 6 ? 6.910 14.822 -27.217 1.00 73.87 ? ? ? ? ? ? 8 ASP A N 1
+ATOM 8 C CA . ASP A 1 6 ? 5.670 15.258 -26.582 1.00 69.40 ? ? ? ? ? ? 8 ASP A CA 1
+ATOM 9 C C . ASP A 1 6 ? 5.834 16.550 -25.785 1.00 68.43 ? ? ? ? ? ? 8 ASP A C 1
+ATOM 10 O O . ASP A 1 6 ? 6.944 16.907 -25.403 1.00 70.90 ? ? ? ? ? ? 8 ASP A O 1
+ATOM 11 C CB . ASP A 1 6 ? 5.104 14.146 -25.703 1.00 67.64 ? ? ? ? ? ? 8 ASP A CB 1
+ATOM 12 C CG . ASP A 1 6 ? 3.570 14.083 -25.751 1.00 64.57 ? ? ? ? ? ? 8 ASP A CG 1
+ATOM 13 O OD1 . ASP A 1 6 ? 2.949 15.085 -26.195 1.00 63.11 ? ? ? ? ? ? 8 ASP A OD1 1
+ATOM 14 O OD2 . ASP A 1 6 ? 2.984 13.032 -25.353 1.00 62.17 ? ? ? ? ? ? 8 ASP A OD2 1
+ATOM 15 N N . PHE A 1 7 ? 4.726 17.246 -25.545 1.00 64.53 ? ? ? ? ? ? 9 PHE A N 1
+ATOM 16 C CA . PHE A 1 7 ? 4.750 18.548 -24.879 1.00 61.94 ? ? ? ? ? ? 9 PHE A CA 1
+ATOM 17 C C . PHE A 1 7 ? 3.673 18.732 -23.796 1.00 57.92 ? ? ? ? ? ? 9 PHE A C 1
+ATOM 18 O O . PHE A 1 7 ? 2.693 17.987 -23.744 1.00 55.70 ? ? ? ? ? ? 9 PHE A O 1
+ATOM 19 C CB . PHE A 1 7 ? 4.618 19.664 -25.915 1.00 63.43 ? ? ? ? ? ? 9 PHE A CB 1
+ATOM 20 C CG . PHE A 1 7 ? 3.282 19.718 -26.567 1.00 62.41 ? ? ? ? ? ? 9 PHE A CG 1
+ATOM 21 C CD1 . PHE A 1 7 ? 2.231 20.382 -25.970 1.00 61.82 ? ? ? ? ? ? 9 PHE A CD1 1
+ATOM 22 C CD2 . PHE A 1 7 ? 3.075 19.105 -27.775 1.00 64.02 ? ? ? ? ? ? 9 PHE A CD2 1
+ATOM 23 C CE1 . PHE A 1 7 ? 0.988 20.428 -26.567 1.00 60.16 ? ? ? ? ? ? 9 PHE A CE1 1
+ATOM 24 C CE2 . PHE A 1 7 ? 1.832 19.145 -28.383 1.00 62.57 ? ? ? ? ? ? 9 PHE A CE2 1
+ATOM 25 C CZ . PHE A 1 7 ? 0.783 19.808 -27.775 1.00 60.25 ? ? ? ? ? ? 9 PHE A CZ 1
+ATOM 26 N N . VAL A 1 8 ? 3.861 19.735 -22.938 1.00 55.04 ? ? ? ? ? ? 10 VAL A N 1
+ATOM 27 C CA . VAL A 1 8 ? 2.861 20.095 -21.949 1.00 50.88 ? ? ? ? ? ? 10 VAL A CA 1
+ATOM 28 C C . VAL A 1 8 ? 2.487 21.551 -22.098 1.00 49.54 ? ? ? ? ? ? 10 VAL A C 1
+ATOM 29 O O . VAL A 1 8 ? 3.323 22.385 -22.446 1.00 50.85 ? ? ? ? ? ? 10 VAL A O 1
+ATOM 30 C CB . VAL A 1 8 ? 3.326 19.851 -20.511 1.00 51.03 ? ? ? ? ? ? 10 VAL A CB 1
+ATOM 31 C CG1 . VAL A 1 8 ? 3.832 18.442 -20.371 1.00 50.13 ? ? ? ? ? ? 10 VAL A CG1 1
+ATOM 32 C CG2 . VAL A 1 8 ? 4.402 20.826 -20.090 1.00 53.19 ? ? ? ? ? ? 10 VAL A CG2 1
+ATOM 33 N N . VAL A 1 9 ? 1.215 21.844 -21.842 1.00 46.06 ? ? ? ? ? ? 11 VAL A N 1
+ATOM 34 C CA . VAL A 1 9 ? 0.687 23.206 -21.880 1.00 44.00 ? ? ? ? ? ? 11 VAL A CA 1
+ATOM 35 C C . VAL A 1 9 ? 0.489 23.603 -20.434 1.00 44.21 ? ? ? ? ? ? 11 VAL A C 1
+ATOM 36 O O . VAL A 1 9 ? -0.170 22.877 -19.678 1.00 42.41 ? ? ? ? ? ? 11 VAL A O 1
+ATOM 37 C CB . VAL A 1 9 ? -0.661 23.252 -22.624 1.00 42.00 ? ? ? ? ? ? 11 VAL A CB 1
+ATOM 38 C CG1 . VAL A 1 9 ? -1.295 24.607 -22.528 1.00 40.79 ? ? ? ? ? ? 11 VAL A CG1 1
+ATOM 39 C CG2 . VAL A 1 9 ? -0.455 22.906 -24.078 1.00 40.13 ? ? ? ? ? ? 11 VAL A CG2 1
+ATOM 40 N N . ILE A 1 10 ? 1.076 24.738 -20.056 1.00 46.10 ? ? ? ? ? ? 12 ILE A N 1
+ATOM 41 C CA . ILE A 1 10 ? 1.003 25.240 -18.696 1.00 47.51 ? ? ? ? ? ? 12 ILE A CA 1
+ATOM 42 C C . ILE A 1 10 ? 0.516 26.657 -18.743 1.00 48.05 ? ? ? ? ? ? 12 ILE A C 1
+ATOM 43 O O . ILE A 1 10 ? 1.137 27.508 -19.380 1.00 49.65 ? ? ? ? ? ? 12 ILE A O 1
+ATOM 44 C CB . ILE A 1 10 ? 2.374 25.247 -18.012 1.00 49.28 ? ? ? ? ? ? 12 ILE A CB 1
+ATOM 45 C CG1 . ILE A 1 10 ? 2.981 23.848 -18.003 1.00 49.95 ? ? ? ? ? ? 12 ILE A CG1 1
+ATOM 46 C CG2 . ILE A 1 10 ? 2.247 25.753 -16.603 1.00 50.91 ? ? ? ? ? ? 12 ILE A CG2 1
+ATOM 47 C CD1 . ILE A 1 10 ? 4.435 23.827 -17.677 1.00 54.16 ? ? ? ? ? ? 12 ILE A CD1 1
+ATOM 48 N N . LYS A 1 11 ? -0.606 26.901 -18.076 1.00 47.39 ? ? ? ? ? ? 13 LYS A N 1
+ATOM 49 C CA . LYS A 1 11 ? -1.139 28.252 -17.917 1.00 48.23 ? ? ? ? ? ? 13 LYS A CA 1
+ATOM 50 C C . LYS A 1 11 ? -0.998 28.660 -16.473 1.00 50.10 ? ? ? ? ? ? 13 LYS A C 1
+ATOM 51 O O . LYS A 1 11 ? -1.441 27.931 -15.579 1.00 49.40 ? ? ? ? ? ? 13 LYS A O 1
+ATOM 52 C CB . LYS A 1 11 ? -2.609 28.311 -18.304 1.00 46.00 ? ? ? ? ? ? 13 LYS A CB 1
+ATOM 53 C CG . LYS A 1 11 ? -3.144 29.706 -18.267 1.00 45.91 ? ? ? ? ? ? 13 LYS A CG 1
+ATOM 54 C CD . LYS A 1 11 ? -4.640 29.741 -18.402 1.00 43.12 ? ? ? ? ? ? 13 LYS A CD 1
+ATOM 55 C CE . LYS A 1 11 ? -5.103 31.182 -18.619 1.00 44.02 ? ? ? ? ? ? 13 LYS A CE 1
+ATOM 56 N NZ . LYS A 1 11 ? -6.563 31.312 -18.363 1.00 43.35 ? ? ? ? ? ? 13 LYS A NZ 1
+ATOM 57 N N . ALA A 1 12 ? -0.379 29.818 -16.242 1.00 53.49 ? ? ? ? ? ? 14 ALA A N 1
+ATOM 58 C CA . ALA A 1 12 ? -0.115 30.296 -14.876 1.00 55.56 ? ? ? ? ? ? 14 ALA A CA 1
+ATOM 59 C C . ALA A 1 12 ? -1.354 30.960 -14.272 1.00 55.44 ? ? ? ? ? ? 14 ALA A C 1
+ATOM 60 O O . ALA A 1 12 ? -1.938 31.848 -14.881 1.00 55.76 ? ? ? ? ? ? 14 ALA A O 1
+ATOM 61 C CB . ALA A 1 12 ? 1.042 31.240 -14.890 1.00 58.43 ? ? ? ? ? ? 14 ALA A CB 1
+ATOM 62 N N . LEU A 1 13 ? -1.767 30.514 -13.093 1.00 55.02 ? ? ? ? ? ? 15 LEU A N 1
+ATOM 63 C CA . LEU A 1 13 ? -2.966 31.063 -12.438 1.00 55.23 ? ? ? ? ? ? 15 LEU A CA 1
+ATOM 64 C C . LEU A 1 13 ? -2.665 32.145 -11.380 1.00 58.70 ? ? ? ? ? ? 15 LEU A C 1
+ATOM 65 O O . LEU A 1 13 ? -3.574 32.758 -10.809 1.00 58.84 ? ? ? ? ? ? 15 LEU A O 1
+ATOM 66 C CB . LEU A 1 13 ? -3.811 29.932 -11.832 1.00 52.50 ? ? ? ? ? ? 15 LEU A CB 1
+ATOM 67 C CG . LEU A 1 13 ? -4.415 28.951 -12.839 1.00 47.91 ? ? ? ? ? ? 15 LEU A CG 1
+ATOM 68 C CD1 . LEU A 1 13 ? -4.953 27.698 -12.151 1.00 44.21 ? ? ? ? ? ? 15 LEU A CD1 1
+ATOM 69 C CD2 . LEU A 1 13 ? -5.494 29.672 -13.668 1.00 46.05 ? ? ? ? ? ? 15 LEU A CD2 1
+ATOM 70 N N . GLU A 1 14 ? -1.379 32.359 -11.120 1.00 62.66 ? ? ? ? ? ? 16 GLU A N 1
+ATOM 71 C CA . GLU A 1 14 ? -0.899 33.425 -10.252 1.00 67.00 ? ? ? ? ? ? 16 GLU A CA 1
+ATOM 72 C C . GLU A 1 14 ? 0.409 33.922 -10.836 1.00 70.32 ? ? ? ? ? ? 16 GLU A C 1
+ATOM 73 O O . GLU A 1 14 ? 0.914 33.339 -11.785 1.00 70.03 ? ? ? ? ? ? 16 GLU A O 1
+ATOM 74 C CB . GLU A 1 14 ? -0.696 32.923 -8.819 1.00 67.19 ? ? ? ? ? ? 16 GLU A CB 1
+ATOM 75 C CG . GLU A 1 14 ? 0.432 31.895 -8.625 1.00 68.58 ? ? ? ? ? ? 16 GLU A CG 1
+ATOM 76 C CD . GLU A 1 14 ? 0.454 31.270 -7.222 1.00 70.39 ? ? ? ? ? ? 16 GLU A CD 1
+ATOM 77 O OE1 . GLU A 1 14 ? -0.457 31.541 -6.412 1.00 71.02 ? ? ? ? ? ? 16 GLU A OE1 1
+ATOM 78 O OE2 . GLU A 1 14 ? 1.387 30.491 -6.926 1.00 71.29 ? ? ? ? ? ? 16 GLU A OE2 1
+ATOM 79 N N . ASP A 1 15 ? 0.955 35.001 -10.285 1.00 74.75 ? ? ? ? ? ? 17 ASP A N 1
+ATOM 80 C CA . ASP A 1 15 ? 2.250 35.491 -10.740 1.00 78.78 ? ? ? ? ? ? 17 ASP A CA 1
+ATOM 81 C C . ASP A 1 15 ? 3.325 34.615 -10.138 1.00 79.87 ? ? ? ? ? ? 17 ASP A C 1
+ATOM 82 O O . ASP A 1 15 ? 3.099 33.950 -9.124 1.00 79.33 ? ? ? ? ? ? 17 ASP A O 1
+ATOM 83 C CB . ASP A 1 15 ? 2.475 36.953 -10.336 1.00 81.65 ? ? ? ? ? ? 17 ASP A CB 1
+ATOM 84 C CG . ASP A 1 15 ? 1.621 37.937 -11.140 1.00 83.16 ? ? ? ? ? ? 17 ASP A CG 1
+ATOM 85 O OD1 . ASP A 1 15 ? 1.344 37.691 -12.326 1.00 82.40 ? ? ? ? ? ? 17 ASP A OD1 1
+ATOM 86 O OD2 . ASP A 1 15 ? 1.231 38.982 -10.589 1.00 86.46 ? ? ? ? ? ? 17 ASP A OD2 1
+ATOM 87 N N . GLY A 1 16 ? 4.489 34.606 -10.778 1.00 81.58 ? ? ? ? ? ? 18 GLY A N 1
+ATOM 88 C CA . GLY A 1 16 ? 5.660 33.903 -10.248 1.00 82.57 ? ? ? ? ? ? 18 GLY A CA 1
+ATOM 89 C C . GLY A 1 16 ? 5.555 32.392 -10.154 1.00 80.35 ? ? ? ? ? ? 18 GLY A C 1
+ATOM 90 O O . GLY A 1 16 ? 6.059 31.793 -9.215 1.00 81.29 ? ? ? ? ? ? 18 GLY A O 1
+ATOM 91 N N . VAL A 1 17 ? 4.892 31.781 -11.128 1.00 77.56 ? ? ? ? ? ? 19 VAL A N 1
+ATOM 92 C CA . VAL A 1 17 ? 4.885 30.336 -11.259 1.00 74.50 ? ? ? ? ? ? 19 VAL A CA 1
+ATOM 93 C C . VAL A 1 17 ? 6.239 29.942 -11.826 1.00 76.68 ? ? ? ? ? ? 19 VAL A C 1
+ATOM 94 O O . VAL A 1 17 ? 6.799 30.655 -12.655 1.00 78.24 ? ? ? ? ? ? 19 VAL A O 1
+ATOM 95 C CB . VAL A 1 17 ? 3.755 29.861 -12.187 1.00 71.56 ? ? ? ? ? ? 19 VAL A CB 1
+ATOM 96 C CG1 . VAL A 1 17 ? 3.820 28.364 -12.384 1.00 67.63 ? ? ? ? ? ? 19 VAL A CG1 1
+ATOM 97 C CG2 . VAL A 1 17 ? 2.409 30.247 -11.611 1.00 67.92 ? ? ? ? ? ? 19 VAL A CG2 1
+ATOM 98 N N . ASN A 1 18 ? 6.764 28.812 -11.381 1.00 77.33 ? ? ? ? ? ? 20 ASN A N 1
+ATOM 99 C CA . ASN A 1 18 ? 8.086 28.396 -11.775 1.00 79.46 ? ? ? ? ? ? 20 ASN A CA 1
+ATOM 100 C C . ASN A 1 18 ? 8.067 27.069 -12.528 1.00 77.29 ? ? ? ? ? ? 20 ASN A C 1
+ATOM 101 O O . ASN A 1 18 ? 7.635 26.058 -11.989 1.00 75.60 ? ? ? ? ? ? 20 ASN A O 1
+ATOM 102 C CB . ASN A 1 18 ? 8.941 28.291 -10.526 1.00 82.30 ? ? ? ? ? ? 20 ASN A CB 1
+ATOM 103 C CG . ASN A 1 18 ? 10.360 28.739 -10.753 1.00 89.13 ? ? ? ? ? ? 20 ASN A CG 1
+ATOM 104 O OD1 . ASN A 1 18 ? 10.690 29.305 -11.791 1.00 92.93 ? ? ? ? ? ? 20 ASN A OD1 1
+ATOM 105 N ND2 . ASN A 1 18 ? 11.217 28.488 -9.773 1.00 94.39 ? ? ? ? ? ? 20 ASN A ND2 1
+ATOM 106 N N . VAL A 1 19 ? 8.521 27.077 -13.779 1.00 76.88 ? ? ? ? ? ? 21 VAL A N 1
+ATOM 107 C CA . VAL A 1 19 ? 8.542 25.871 -14.600 1.00 75.28 ? ? ? ? ? ? 21 VAL A CA 1
+ATOM 108 C C . VAL A 1 19 ? 9.970 25.398 -14.720 1.00 78.52 ? ? ? ? ? ? 21 VAL A C 1
+ATOM 109 O O . VAL A 1 19 ? 10.747 25.948 -15.489 1.00 80.53 ? ? ? ? ? ? 21 VAL A O 1
+ATOM 110 C CB . VAL A 1 19 ? 7.946 26.104 -16.005 1.00 73.54 ? ? ? ? ? ? 21 VAL A CB 1
+ATOM 111 C CG1 . VAL A 1 19 ? 7.966 24.838 -16.807 1.00 70.33 ? ? ? ? ? ? 21 VAL A CG1 1
+ATOM 112 C CG2 . VAL A 1 19 ? 6.528 26.602 -15.913 1.00 69.44 ? ? ? ? ? ? 21 VAL A CG2 1
+ATOM 113 N N . ILE A 1 20 ? 10.305 24.368 -13.960 1.00 80.07 ? ? ? ? ? ? 22 ILE A N 1
+ATOM 114 C CA . ILE A 1 20 ? 11.683 23.949 -13.817 1.00 83.77 ? ? ? ? ? ? 22 ILE A CA 1
+ATOM 115 C C . ILE A 1 20 ? 12.004 22.729 -14.664 1.00 83.74 ? ? ? ? ? ? 22 ILE A C 1
+ATOM 116 O O . ILE A 1 20 ? 11.349 21.705 -14.536 1.00 81.42 ? ? ? ? ? ? 22 ILE A O 1
+ATOM 117 C CB . ILE A 1 20 ? 12.014 23.661 -12.348 1.00 84.59 ? ? ? ? ? ? 22 ILE A CB 1
+ATOM 118 C CG1 . ILE A 1 20 ? 11.522 24.802 -11.467 1.00 85.96 ? ? ? ? ? ? 22 ILE A CG1 1
+ATOM 119 C CG2 . ILE A 1 20 ? 13.511 23.484 -12.166 1.00 89.81 ? ? ? ? ? ? 22 ILE A CG2 1
+ATOM 120 C CD1 . ILE A 1 20 ? 11.484 24.464 -9.998 1.00 87.43 ? ? ? ? ? ? 22 ILE A CD1 1
+ATOM 121 N N . GLY A 1 21 ? 13.019 22.862 -15.520 1.00 86.57 ? ? ? ? ? ? 23 GLY A N 1
+ATOM 122 C CA . GLY A 1 21 ? 13.522 21.775 -16.358 1.00 88.60 ? ? ? ? ? ? 23 GLY A CA 1
+ATOM 123 C C . GLY A 1 21 ? 14.674 21.070 -15.675 1.00 91.29 ? ? ? ? ? ? 23 GLY A C 1
+ATOM 124 O O . GLY A 1 21 ? 15.573 21.716 -15.154 1.00 94.14 ? ? ? ? ? ? 23 GLY A O 1
+ATOM 125 N N . LEU A 1 22 ? 14.642 19.743 -15.672 1.00 91.36 ? ? ? ? ? ? 24 LEU A N 1
+ATOM 126 C CA . LEU A 1 22 ? 15.603 18.932 -14.926 1.00 92.96 ? ? ? ? ? ? 24 LEU A CA 1
+ATOM 127 C C . LEU A 1 22 ? 16.447 18.089 -15.876 1.00 94.68 ? ? ? ? ? ? 24 LEU A C 1
+ATOM 128 O O . LEU A 1 22 ? 15.939 17.601 -16.885 1.00 94.04 ? ? ? ? ? ? 24 LEU A O 1
+ATOM 129 C CB . LEU A 1 22 ? 14.860 18.047 -13.924 1.00 91.08 ? ? ? ? ? ? 24 LEU A CB 1
+ATOM 130 C CG . LEU A 1 22 ? 14.551 18.518 -12.493 1.00 90.38 ? ? ? ? ? ? 24 LEU A CG 1
+ATOM 131 C CD1 . LEU A 1 22 ? 14.342 20.009 -12.384 1.00 91.01 ? ? ? ? ? ? 24 LEU A CD1 1
+ATOM 132 C CD2 . LEU A 1 22 ? 13.342 17.791 -11.921 1.00 85.41 ? ? ? ? ? ? 24 LEU A CD2 1
+ATOM 133 N N . THR A 1 23 ? 17.733 17.926 -15.565 1.00 96.47 ? ? ? ? ? ? 25 THR A N 1
+ATOM 134 C CA . THR A 1 23 ? 18.688 17.343 -16.531 1.00 98.30 ? ? ? ? ? ? 25 THR A CA 1
+ATOM 135 C C . THR A 1 23 ? 19.007 15.862 -16.352 1.00 98.49 ? ? ? ? ? ? 25 THR A C 1
+ATOM 136 O O . THR A 1 23 ? 18.826 15.304 -15.266 1.00 98.19 ? ? ? ? ? ? 25 THR A O 1
+ATOM 137 C CB . THR A 1 23 ? 20.028 18.102 -16.553 1.00 100.21 ? ? ? ? ? ? 25 THR A CB 1
+ATOM 138 O OG1 . THR A 1 23 ? 20.490 18.282 -15.208 1.00 101.37 ? ? ? ? ? ? 25 THR A OG1 1
+ATOM 139 C CG2 . THR A 1 23 ? 19.883 19.457 -17.252 1.00 100.72 ? ? ? ? ? ? 25 THR A CG2 1
+ATOM 140 N N . ARG A 1 24 ? 19.501 15.246 -17.430 1.00 99.49 ? ? ? ? ? ? 26 ARG A N 1
+ATOM 141 C CA . ARG A 1 24 ? 19.857 13.819 -17.452 1.00 99.94 ? ? ? ? ? ? 26 ARG A CA 1
+ATOM 142 C C . ARG A 1 24 ? 21.154 13.541 -16.693 1.00 101.44 ? ? ? ? ? ? 26 ARG A C 1
+ATOM 143 O O . ARG A 1 24 ? 22.240 13.904 -17.147 1.00 103.26 ? ? ? ? ? ? 26 ARG A O 1
+ATOM 144 C CB . ARG A 1 24 ? 19.955 13.281 -18.893 1.00 100.14 ? ? ? ? ? ? 26 ARG A CB 1
+ATOM 145 C CG . ARG A 1 24 ? 18.620 13.217 -19.642 1.00 99.36 ? ? ? ? ? ? 26 ARG A CG 1
+ATOM 146 C CD . ARG A 1 24 ? 18.634 12.164 -20.759 1.00 100.98 ? ? ? ? ? ? 26 ARG A CD 1
+ATOM 147 N NE . ARG A 1 24 ? 17.552 12.352 -21.740 1.00 100.55 ? ? ? ? ? ? 26 ARG A NE 1
+ATOM 148 C CZ . ARG A 1 24 ? 17.231 11.494 -22.716 1.00 99.98 ? ? ? ? ? ? 26 ARG A CZ 1
+ATOM 149 N NH1 . ARG A 1 24 ? 17.891 10.344 -22.876 1.00 99.60 ? ? ? ? ? ? 26 ARG A NH1 1
+ATOM 150 N NH2 . ARG A 1 24 ? 16.229 11.791 -23.537 1.00 99.33 ? ? ? ? ? ? 26 ARG A NH2 1
+ATOM 151 N N . THR A 1 28 ? 22.527 16.428 -12.721 1.00 120.13 ? ? ? ? ? ? 30 THR A N 1
+ATOM 152 C CA . THR A 1 28 ? 21.235 15.835 -13.090 1.00 118.47 ? ? ? ? ? ? 30 THR A CA 1
+ATOM 153 C C . THR A 1 28 ? 20.021 16.467 -12.351 1.00 117.17 ? ? ? ? ? ? 30 THR A C 1
+ATOM 154 O O . THR A 1 28 ? 18.867 16.073 -12.593 1.00 115.70 ? ? ? ? ? ? 30 THR A O 1
+ATOM 155 C CB . THR A 1 28 ? 21.259 14.241 -13.007 1.00 118.06 ? ? ? ? ? ? 30 THR A CB 1
+ATOM 156 O OG1 . THR A 1 28 ? 19.946 13.697 -13.234 1.00 116.11 ? ? ? ? ? ? 30 THR A OG1 1
+ATOM 157 C CG2 . THR A 1 28 ? 21.822 13.727 -11.660 1.00 118.37 ? ? ? ? ? ? 30 THR A CG2 1
+ATOM 158 N N . ARG A 1 29 ? 20.289 17.464 -11.492 1.00 117.71 ? ? ? ? ? ? 31 ARG A N 1
+ATOM 159 C CA . ARG A 1 29 ? 19.261 18.091 -10.604 1.00 116.35 ? ? ? ? ? ? 31 ARG A CA 1
+ATOM 160 C C . ARG A 1 29 ? 18.477 19.294 -11.195 1.00 115.56 ? ? ? ? ? ? 31 ARG A C 1
+ATOM 161 O O . ARG A 1 29 ? 18.271 19.360 -12.420 1.00 115.47 ? ? ? ? ? ? 31 ARG A O 1
+ATOM 162 C CB . ARG A 1 29 ? 19.840 18.428 -9.204 1.00 117.16 ? ? ? ? ? ? 31 ARG A CB 1
+ATOM 163 C CG . ARG A 1 29 ? 21.320 18.904 -9.113 1.00 119.11 ? ? ? ? ? ? 31 ARG A CG 1
+ATOM 164 C CD . ARG A 1 29 ? 21.638 20.210 -9.857 1.00 119.60 ? ? ? ? ? ? 31 ARG A CD 1
+ATOM 165 N NE . ARG A 1 29 ? 22.419 19.952 -11.068 1.00 120.44 ? ? ? ? ? ? 31 ARG A NE 1
+ATOM 166 C CZ . ARG A 1 29 ? 21.980 20.123 -12.315 1.00 119.80 ? ? ? ? ? ? 31 ARG A CZ 1
+ATOM 167 N NH1 . ARG A 1 29 ? 22.780 19.853 -13.337 1.00 121.30 ? ? ? ? ? ? 31 ARG A NH1 1
+ATOM 168 N NH2 . ARG A 1 29 ? 20.756 20.576 -12.552 1.00 117.87 ? ? ? ? ? ? 31 ARG A NH2 1
+ATOM 169 N N . PHE A 1 30 ? 18.052 20.228 -10.323 1.00 114.83 ? ? ? ? ? ? 32 PHE A N 1
+ATOM 170 C CA . PHE A 1 30 ? 17.248 21.413 -10.728 1.00 113.80 ? ? ? ? ? ? 32 PHE A CA 1
+ATOM 171 C C . PHE A 1 30 ? 18.047 22.475 -11.541 1.00 114.52 ? ? ? ? ? ? 32 PHE A C 1
+ATOM 172 O O . PHE A 1 30 ? 18.937 23.145 -11.001 1.00 115.82 ? ? ? ? ? ? 32 PHE A O 1
+ATOM 173 C CB . PHE A 1 30 ? 16.487 22.093 -9.541 1.00 113.41 ? ? ? ? ? ? 32 PHE A CB 1
+ATOM 174 C CG . PHE A 1 30 ? 16.144 21.179 -8.346 1.00 112.64 ? ? ? ? ? ? 32 PHE A CG 1
+ATOM 175 C CD1 . PHE A 1 30 ? 15.540 21.740 -7.207 1.00 112.23 ? ? ? ? ? ? 32 PHE A CD1 1
+ATOM 176 C CD2 . PHE A 1 30 ? 16.423 19.805 -8.338 1.00 111.84 ? ? ? ? ? ? 32 PHE A CD2 1
+ATOM 177 C CE1 . PHE A 1 30 ? 15.212 20.957 -6.091 1.00 111.54 ? ? ? ? ? ? 32 PHE A CE1 1
+ATOM 178 C CE2 . PHE A 1 30 ? 16.110 19.015 -7.218 1.00 111.19 ? ? ? ? ? ? 32 PHE A CE2 1
+ATOM 179 C CZ . PHE A 1 30 ? 15.497 19.590 -6.097 1.00 111.08 ? ? ? ? ? ? 32 PHE A CZ 1
+ATOM 180 N N . HIS A 1 31 ? 17.677 22.645 -12.817 1.00 113.18 ? ? ? ? ? ? 33 HIS A N 1
+ATOM 181 C CA . HIS A 1 31 ? 18.505 23.317 -13.836 1.00 113.51 ? ? ? ? ? ? 33 HIS A CA 1
+ATOM 182 C C . HIS A 1 31 ? 17.843 24.573 -14.459 1.00 112.40 ? ? ? ? ? ? 33 HIS A C 1
+ATOM 183 O O . HIS A 1 31 ? 17.840 25.650 -13.849 1.00 112.91 ? ? ? ? ? ? 33 HIS A O 1
+ATOM 184 C CB . HIS A 1 31 ? 18.897 22.274 -14.908 1.00 113.74 ? ? ? ? ? ? 33 HIS A CB 1
+ATOM 185 C CG . HIS A 1 31 ? 19.881 22.761 -15.933 1.00 116.22 ? ? ? ? ? ? 33 HIS A CG 1
+ATOM 186 N ND1 . HIS A 1 31 ? 21.201 23.036 -15.635 1.00 118.98 ? ? ? ? ? ? 33 HIS A ND1 1
+ATOM 187 C CD2 . HIS A 1 31 ? 19.743 22.976 -17.264 1.00 116.72 ? ? ? ? ? ? 33 HIS A CD2 1
+ATOM 188 C CE1 . HIS A 1 31 ? 21.826 23.425 -16.734 1.00 120.25 ? ? ? ? ? ? 33 HIS A CE1 1
+ATOM 189 N NE2 . HIS A 1 31 ? 20.964 23.395 -17.736 1.00 119.10 ? ? ? ? ? ? 33 HIS A NE2 1
+ATOM 190 N N . HIS A 1 32 ? 17.298 24.431 -15.670 1.00 110.63 ? ? ? ? ? ? 34 HIS A N 1
+ATOM 191 C CA . HIS A 1 32 ? 16.630 25.529 -16.377 1.00 108.57 ? ? ? ? ? ? 34 HIS A CA 1
+ATOM 192 C C . HIS A 1 32 ? 15.315 25.908 -15.701 1.00 105.41 ? ? ? ? ? ? 34 HIS A C 1
+ATOM 193 O O . HIS A 1 32 ? 14.336 25.165 -15.760 1.00 102.47 ? ? ? ? ? ? 34 HIS A O 1
+ATOM 194 C CB . HIS A 1 32 ? 16.384 25.161 -17.858 1.00 108.29 ? ? ? ? ? ? 34 HIS A CB 1
+ATOM 195 C CG . HIS A 1 32 ? 15.859 26.296 -18.697 1.00 108.03 ? ? ? ? ? ? 34 HIS A CG 1
+ATOM 196 N ND1 . HIS A 1 32 ? 16.492 27.522 -18.778 1.00 111.34 ? ? ? ? ? ? 34 HIS A ND1 1
+ATOM 197 C CD2 . HIS A 1 32 ? 14.778 26.380 -19.511 1.00 103.90 ? ? ? ? ? ? 34 HIS A CD2 1
+ATOM 198 C CE1 . HIS A 1 32 ? 15.812 28.317 -19.586 1.00 109.77 ? ? ? ? ? ? 34 HIS A CE1 1
+ATOM 199 N NE2 . HIS A 1 32 ? 14.772 27.647 -20.051 1.00 105.66 ? ? ? ? ? ? 34 HIS A NE2 1
+ATOM 200 N N . SER A 1 33 ? 15.303 27.064 -15.056 1.00 104.75 ? ? ? ? ? ? 35 SER A N 1
+ATOM 201 C CA . SER A 1 33 ? 14.079 27.599 -14.485 1.00 101.92 ? ? ? ? ? ? 35 SER A CA 1
+ATOM 202 C C . SER A 1 33 ? 13.450 28.601 -15.456 1.00 99.94 ? ? ? ? ? ? 35 SER A C 1
+ATOM 203 O O . SER A 1 33 ? 14.146 29.196 -16.272 1.00 101.93 ? ? ? ? ? ? 35 SER A O 1
+ATOM 204 C CB . SER A 1 33 ? 14.372 28.236 -13.124 1.00 103.64 ? ? ? ? ? ? 35 SER A CB 1
+ATOM 205 O OG . SER A 1 33 ? 13.401 29.202 -12.771 1.00 103.74 ? ? ? ? ? ? 35 SER A OG 1
+ATOM 206 N N . GLU A 1 34 ? 12.136 28.778 -15.372 1.00 95.30 ? ? ? ? ? ? 36 GLU A N 1
+ATOM 207 C CA . GLU A 1 34 ? 11.425 29.699 -16.249 1.00 92.35 ? ? ? ? ? ? 36 GLU A CA 1
+ATOM 208 C C . GLU A 1 34 ? 10.221 30.272 -15.520 1.00 90.03 ? ? ? ? ? ? 36 GLU A C 1
+ATOM 209 O O . GLU A 1 34 ? 9.296 29.543 -15.201 1.00 87.29 ? ? ? ? ? ? 36 GLU A O 1
+ATOM 210 C CB . GLU A 1 34 ? 10.977 28.964 -17.511 1.00 90.67 ? ? ? ? ? ? 36 GLU A CB 1
+ATOM 211 C CG . GLU A 1 34 ? 10.555 29.867 -18.650 1.00 90.72 ? ? ? ? ? ? 36 GLU A CG 1
+ATOM 212 C CD . GLU A 1 34 ? 11.736 30.565 -19.310 1.00 96.24 ? ? ? ? ? ? 36 GLU A CD 1
+ATOM 213 O OE1 . GLU A 1 34 ? 12.815 29.937 -19.462 1.00 99.38 ? ? ? ? ? ? 36 GLU A OE1 1
+ATOM 214 O OE2 . GLU A 1 34 ? 11.578 31.748 -19.685 1.00 98.37 ? ? ? ? ? ? 36 GLU A OE2 1
+ATOM 215 N N . LYS A 1 35 ? 10.235 31.569 -15.239 1.00 90.36 ? ? ? ? ? ? 37 LYS A N 1
+ATOM 216 C CA . LYS A 1 35 ? 9.139 32.178 -14.506 1.00 88.38 ? ? ? ? ? ? 37 LYS A CA 1
+ATOM 217 C C . LYS A 1 35 ? 7.977 32.484 -15.433 1.00 85.67 ? ? ? ? ? ? 37 LYS A C 1
+ATOM 218 O O . LYS A 1 35 ? 8.172 32.833 -16.592 1.00 86.06 ? ? ? ? ? ? 37 LYS A O 1
+ATOM 219 C CB . LYS A 1 35 ? 9.601 33.433 -13.768 1.00 91.44 ? ? ? ? ? ? 37 LYS A CB 1
+ATOM 220 N N . LEU A 1 36 ? 6.766 32.325 -14.915 1.00 81.92 ? ? ? ? ? ? 38 LEU A N 1
+ATOM 221 C CA . LEU A 1 36 ? 5.539 32.641 -15.640 1.00 78.89 ? ? ? ? ? ? 38 LEU A CA 1
+ATOM 222 C C . LEU A 1 36 ? 4.640 33.528 -14.797 1.00 78.12 ? ? ? ? ? ? 38 LEU A C 1
+ATOM 223 O O . LEU A 1 36 ? 4.498 33.299 -13.601 1.00 77.83 ? ? ? ? ? ? 38 LEU A O 1
+ATOM 224 C CB . LEU A 1 36 ? 4.770 31.368 -15.979 1.00 77.62 ? ? ? ? ? ? 38 LEU A CB 1
+ATOM 225 C CG . LEU A 1 36 ? 4.861 30.675 -17.336 1.00 76.31 ? ? ? ? ? ? 38 LEU A CG 1
+ATOM 226 C CD1 . LEU A 1 36 ? 3.481 30.149 -17.653 1.00 74.28 ? ? ? ? ? ? 38 LEU A CD1 1
+ATOM 227 C CD2 . LEU A 1 36 ? 5.328 31.599 -18.436 1.00 76.23 ? ? ? ? ? ? 38 LEU A CD2 1
+ATOM 228 N N . ASP A 1 37 ? 4.015 34.523 -15.417 1.00 77.70 ? ? ? ? ? ? 39 ASP A N 1
+ATOM 229 C CA . ASP A 1 37 ? 3.127 35.429 -14.691 1.00 77.42 ? ? ? ? ? ? 39 ASP A CA 1
+ATOM 230 C C . ASP A 1 37 ? 1.666 35.169 -15.004 1.00 73.58 ? ? ? ? ? ? 39 ASP A C 1
+ATOM 231 O O . ASP A 1 37 ? 1.352 34.676 -16.075 1.00 72.04 ? ? ? ? ? ? 39 ASP A O 1
+ATOM 232 C CB . ASP A 1 37 ? 3.473 36.886 -14.995 1.00 80.86 ? ? ? ? ? ? 39 ASP A CB 1
+ATOM 233 C CG . ASP A 1 37 ? 4.632 37.408 -14.159 1.00 86.94 ? ? ? ? ? ? 39 ASP A CG 1
+ATOM 234 O OD1 . ASP A 1 37 ? 4.986 36.781 -13.125 1.00 88.70 ? ? ? ? ? ? 39 ASP A OD1 1
+ATOM 235 O OD2 . ASP A 1 37 ? 5.178 38.463 -14.548 1.00 92.58 ? ? ? ? ? ? 39 ASP A OD2 1
+ATOM 236 N N . LYS A 1 38 ? 0.788 35.520 -14.065 1.00 71.09 ? ? ? ? ? ? 40 LYS A N 1
+ATOM 237 C CA . LYS A 1 38 ? -0.646 35.219 -14.127 1.00 67.44 ? ? ? ? ? ? 40 LYS A CA 1
+ATOM 238 C C . LYS A 1 38 ? -1.246 35.395 -15.514 1.00 65.75 ? ? ? ? ? ? 40 LYS A C 1
+ATOM 239 O O . LYS A 1 38 ? -1.274 36.506 -16.038 1.00 66.82 ? ? ? ? ? ? 40 LYS A O 1
+ATOM 240 C CB . LYS A 1 38 ? -1.408 36.092 -13.130 1.00 67.43 ? ? ? ? ? ? 40 LYS A CB 1
+ATOM 241 C CG . LYS A 1 38 ? -2.847 35.692 -12.912 1.00 65.33 ? ? ? ? ? ? 40 LYS A CG 1
+ATOM 242 C CD . LYS A 1 38 ? -3.496 36.530 -11.819 1.00 65.17 ? ? ? ? ? ? 40 LYS A CD 1
+ATOM 243 C CE . LYS A 1 38 ? -4.727 35.828 -11.238 1.00 64.58 ? ? ? ? ? ? 40 LYS A CE 1
+ATOM 244 N NZ . LYS A 1 38 ? -5.911 36.738 -11.093 1.00 64.29 ? ? ? ? ? ? 40 LYS A NZ 1
+ATOM 245 N N . GLY A 1 39 ? -1.710 34.288 -16.097 1.00 62.75 ? ? ? ? ? ? 41 GLY A N 1
+ATOM 246 C CA . GLY A 1 39 ? -2.358 34.280 -17.410 1.00 60.49 ? ? ? ? ? ? 41 GLY A CA 1
+ATOM 247 C C . GLY A 1 39 ? -1.471 33.947 -18.599 1.00 60.30 ? ? ? ? ? ? 41 GLY A C 1
+ATOM 248 O O . GLY A 1 39 ? -1.957 33.805 -19.718 1.00 58.95 ? ? ? ? ? ? 41 GLY A O 1
+ATOM 249 N N . GLU A 1 40 ? -0.167 33.843 -18.366 1.00 61.59 ? ? ? ? ? ? 42 GLU A N 1
+ATOM 250 C CA . GLU A 1 40 ? 0.777 33.499 -19.424 1.00 62.43 ? ? ? ? ? ? 42 GLU A CA 1
+ATOM 251 C C . GLU A 1 40 ? 0.720 32.015 -19.667 1.00 59.62 ? ? ? ? ? ? 42 GLU A C 1
+ATOM 252 O O . GLU A 1 40 ? 0.425 31.239 -18.761 1.00 58.37 ? ? ? ? ? ? 42 GLU A O 1
+ATOM 253 C CB . GLU A 1 40 ? 2.200 33.917 -19.056 1.00 65.52 ? ? ? ? ? ? 42 GLU A CB 1
+ATOM 254 C CG . GLU A 1 40 ? 2.523 35.352 -19.404 1.00 71.75 ? ? ? ? ? ? 42 GLU A CG 1
+ATOM 255 C CD . GLU A 1 40 ? 3.754 35.879 -18.701 1.00 79.02 ? ? ? ? ? ? 42 GLU A CD 1
+ATOM 256 O OE1 . GLU A 1 40 ? 4.375 35.124 -17.926 1.00 79.96 ? ? ? ? ? ? 42 GLU A OE1 1
+ATOM 257 O OE2 . GLU A 1 40 ? 4.097 37.059 -18.923 1.00 83.29 ? ? ? ? ? ? 42 GLU A OE2 1
+ATOM 258 N N . VAL A 1 41 ? 1.004 31.619 -20.895 1.00 58.12 ? ? ? ? ? ? 43 VAL A N 1
+ATOM 259 C CA . VAL A 1 41 ? 0.931 30.221 -21.282 1.00 55.42 ? ? ? ? ? ? 43 VAL A CA 1
+ATOM 260 C C . VAL A 1 41 ? 2.254 29.747 -21.855 1.00 57.22 ? ? ? ? ? ? 43 VAL A C 1
+ATOM 261 O O . VAL A 1 41 ? 2.823 30.381 -22.755 1.00 58.88 ? ? ? ? ? ? 43 VAL A O 1
+ATOM 262 C CB . VAL A 1 41 ? -0.180 29.994 -22.309 1.00 53.28 ? ? ? ? ? ? 43 VAL A CB 1
+ATOM 263 C CG1 . VAL A 1 41 ? -0.060 28.645 -22.920 1.00 50.49 ? ? ? ? ? ? 43 VAL A CG1 1
+ATOM 264 C CG2 . VAL A 1 41 ? -1.523 30.132 -21.664 1.00 49.78 ? ? ? ? ? ? 43 VAL A CG2 1
+ATOM 265 N N . LEU A 1 42 ? 2.738 28.629 -21.323 1.00 57.21 ? ? ? ? ? ? 44 LEU A N 1
+ATOM 266 C CA . LEU A 1 42 ? 3.960 28.037 -21.813 1.00 58.54 ? ? ? ? ? ? 44 LEU A CA 1
+ATOM 267 C C . LEU A 1 42 ? 3.633 26.718 -22.458 1.00 56.54 ? ? ? ? ? ? 44 LEU A C 1
+ATOM 268 O O . LEU A 1 42 ? 2.882 25.928 -21.899 1.00 54.68 ? ? ? ? ? ? 44 LEU A O 1
+ATOM 269 C CB . LEU A 1 42 ? 4.954 27.852 -20.680 1.00 60.35 ? ? ? ? ? ? 44 LEU A CB 1
+ATOM 270 C CG . LEU A 1 42 ? 6.378 27.476 -21.074 1.00 64.66 ? ? ? ? ? ? 44 LEU A CG 1
+ATOM 271 C CD1 . LEU A 1 42 ? 7.071 28.595 -21.816 1.00 69.92 ? ? ? ? ? ? 44 LEU A CD1 1
+ATOM 272 C CD2 . LEU A 1 42 ? 7.171 27.112 -19.839 1.00 67.81 ? ? ? ? ? ? 44 LEU A CD2 1
+ATOM 273 N N . ILE A 1 43 ? 4.162 26.504 -23.657 1.00 56.61 ? ? ? ? ? ? 45 ILE A N 1
+ATOM 274 C CA . ILE A 1 43 ? 4.086 25.207 -24.298 1.00 55.49 ? ? ? ? ? ? 45 ILE A CA 1
+ATOM 275 C C . ILE A 1 43 ? 5.487 24.630 -24.267 1.00 57.96 ? ? ? ? ? ? 45 ILE A C 1
+ATOM 276 O O . ILE A 1 43 ? 6.345 25.038 -25.046 1.00 60.01 ? ? ? ? ? ? 45 ILE A O 1
+ATOM 277 C CB . ILE A 1 43 ? 3.621 25.276 -25.757 1.00 54.45 ? ? ? ? ? ? 45 ILE A CB 1
+ATOM 278 C CG1 . ILE A 1 43 ? 2.749 26.525 -26.016 1.00 53.11 ? ? ? ? ? ? 45 ILE A CG1 1
+ATOM 279 C CG2 . ILE A 1 43 ? 2.966 23.955 -26.167 1.00 50.96 ? ? ? ? ? ? 45 ILE A CG2 1
+ATOM 280 C CD1 . ILE A 1 43 ? 1.330 26.489 -25.511 1.00 48.47 ? ? ? ? ? ? 45 ILE A CD1 1
+ATOM 281 N N . ALA A 1 44 ? 5.708 23.687 -23.351 1.00 58.61 ? ? ? ? ? ? 46 ALA A N 1
+ATOM 282 C CA . ALA A 1 44 ? 7.019 23.104 -23.115 1.00 60.53 ? ? ? ? ? ? 46 ALA A CA 1
+ATOM 283 C C . ALA A 1 44 ? 7.098 21.728 -23.724 1.00 60.54 ? ? ? ? ? ? 46 ALA A C 1
+ATOM 284 O O . ALA A 1 44 ? 6.238 20.893 -23.489 1.00 58.05 ? ? ? ? ? ? 46 ALA A O 1
+ATOM 285 C CB . ALA A 1 44 ? 7.298 23.026 -21.643 1.00 61.04 ? ? ? ? ? ? 46 ALA A CB 1
+ATOM 286 N N . GLN A 1 45 ? 8.142 21.522 -24.518 1.00 63.39 ? ? ? ? ? ? 47 GLN A N 1
+ATOM 287 C CA . GLN A 1 45 ? 8.433 20.236 -25.131 1.00 64.77 ? ? ? ? ? ? 47 GLN A CA 1
+ATOM 288 C C . GLN A 1 45 ? 9.599 19.592 -24.406 1.00 67.08 ? ? ? ? ? ? 47 GLN A C 1
+ATOM 289 O O . GLN A 1 45 ? 10.492 20.287 -23.920 1.00 69.41 ? ? ? ? ? ? 47 GLN A O 1
+ATOM 290 C CB . GLN A 1 45 ? 8.791 20.423 -26.602 1.00 65.44 ? ? ? ? ? ? 47 GLN A CB 1
+ATOM 291 C CG . GLN A 1 45 ? 8.796 19.131 -27.399 1.00 65.31 ? ? ? ? ? ? 47 GLN A CG 1
+ATOM 292 C CD . GLN A 1 45 ? 9.318 19.305 -28.829 1.00 68.03 ? ? ? ? ? ? 47 GLN A CD 1
+ATOM 293 O OE1 . GLN A 1 45 ? 10.214 20.129 -29.090 1.00 70.64 ? ? ? ? ? ? 47 GLN A OE1 1
+ATOM 294 N NE2 . GLN A 1 45 ? 8.757 18.518 -29.767 1.00 65.95 ? ? ? ? ? ? 47 GLN A NE2 1
+ATOM 295 N N . PHE A 1 46 ? 9.590 18.266 -24.339 1.00 67.71 ? ? ? ? ? ? 48 PHE A N 1
+ATOM 296 C CA . PHE A 1 46 ? 10.706 17.526 -23.777 1.00 70.43 ? ? ? ? ? ? 48 PHE A CA 1
+ATOM 297 C C . PHE A 1 46 ? 11.857 17.437 -24.766 1.00 74.96 ? ? ? ? ? ? 48 PHE A C 1
+ATOM 298 O O . PHE A 1 46 ? 11.675 16.991 -25.907 1.00 74.94 ? ? ? ? ? ? 48 PHE A O 1
+ATOM 299 C CB . PHE A 1 46 ? 10.269 16.127 -23.384 1.00 67.85 ? ? ? ? ? ? 48 PHE A CB 1
+ATOM 300 C CG . PHE A 1 46 ? 9.527 16.081 -22.099 1.00 64.51 ? ? ? ? ? ? 48 PHE A CG 1
+ATOM 301 C CD1 . PHE A 1 46 ? 10.218 16.130 -20.894 1.00 65.87 ? ? ? ? ? ? 48 PHE A CD1 1
+ATOM 302 C CD2 . PHE A 1 46 ? 8.130 15.992 -22.085 1.00 59.45 ? ? ? ? ? ? 48 PHE A CD2 1
+ATOM 303 C CE1 . PHE A 1 46 ? 9.533 16.094 -19.687 1.00 63.95 ? ? ? ? ? ? 48 PHE A CE1 1
+ATOM 304 C CE2 . PHE A 1 46 ? 7.427 15.953 -20.885 1.00 57.67 ? ? ? ? ? ? 48 PHE A CE2 1
+ATOM 305 C CZ . PHE A 1 46 ? 8.130 16.002 -19.680 1.00 60.02 ? ? ? ? ? ? 48 PHE A CZ 1
+ATOM 306 N N . THR A 1 47 ? 13.038 17.869 -24.334 1.00 80.48 ? ? ? ? ? ? 49 THR A N 1
+ATOM 307 C CA . THR A 1 47 ? 14.238 17.712 -25.140 1.00 86.44 ? ? ? ? ? ? 49 THR A CA 1
+ATOM 308 C C . THR A 1 47 ? 14.993 16.474 -24.653 1.00 88.73 ? ? ? ? ? ? 49 THR A C 1
+ATOM 309 O O . THR A 1 47 ? 14.523 15.780 -23.752 1.00 86.98 ? ? ? ? ? ? 49 THR A O 1
+ATOM 310 C CB . THR A 1 47 ? 15.135 18.969 -25.068 1.00 89.11 ? ? ? ? ? ? 49 THR A CB 1
+ATOM 311 O OG1 . THR A 1 47 ? 15.953 18.934 -23.892 1.00 92.76 ? ? ? ? ? ? 49 THR A OG1 1
+ATOM 312 C CG2 . THR A 1 47 ? 14.285 20.230 -25.055 1.00 88.83 ? ? ? ? ? ? 49 THR A CG2 1
+ATOM 313 N N . GLU A 1 48 ? 16.145 16.187 -25.257 1.00 93.73 ? ? ? ? ? ? 50 GLU A N 1
+ATOM 314 C CA . GLU A 1 48 ? 17.052 15.170 -24.714 1.00 98.04 ? ? ? ? ? ? 50 GLU A CA 1
+ATOM 315 C C . GLU A 1 48 ? 17.700 15.685 -23.409 1.00 99.89 ? ? ? ? ? ? 50 GLU A C 1
+ATOM 316 O O . GLU A 1 48 ? 17.792 14.952 -22.420 1.00 99.46 ? ? ? ? ? ? 50 GLU A O 1
+ATOM 317 C CB . GLU A 1 48 ? 18.103 14.731 -25.754 1.00 100.79 ? ? ? ? ? ? 50 GLU A CB 1
+ATOM 318 C CG . GLU A 1 48 ? 19.096 15.818 -26.196 0.50 107.62 ? ? ? ? ? ? 50 GLU A CG 1
+ATOM 319 C CD . GLU A 1 48 ? 20.357 15.251 -26.838 0.50 115.10 ? ? ? ? ? ? 50 GLU A CD 1
+ATOM 320 O OE1 . GLU A 1 48 ? 21.467 15.702 -26.482 0.50 120.30 ? ? ? ? ? ? 50 GLU A OE1 1
+ATOM 321 O OE2 . GLU A 1 48 ? 20.241 14.354 -27.697 0.50 115.44 ? ? ? ? ? ? 50 GLU A OE2 1
+ATOM 322 N N . HIS A 1 49 ? 18.108 16.957 -23.422 1.00 102.54 ? ? ? ? ? ? 51 HIS A N 1
+ATOM 323 C CA . HIS A 1 49 ? 18.615 17.674 -22.247 1.00 104.56 ? ? ? ? ? ? 51 HIS A CA 1
+ATOM 324 C C . HIS A 1 49 ? 17.684 17.578 -21.032 1.00 100.90 ? ? ? ? ? ? 51 HIS A C 1
+ATOM 325 O O . HIS A 1 49 ? 18.145 17.604 -19.888 1.00 102.24 ? ? ? ? ? ? 51 HIS A O 1
+ATOM 326 C CB . HIS A 1 49 ? 18.790 19.162 -22.576 1.00 107.45 ? ? ? ? ? ? 51 HIS A CB 1
+ATOM 327 C CG . HIS A 1 49 ? 19.959 19.466 -23.458 1.00 115.35 ? ? ? ? ? ? 51 HIS A CG 1
+ATOM 328 N ND1 . HIS A 1 49 ? 19.964 19.199 -24.811 1.00 117.92 ? ? ? ? ? ? 51 HIS A ND1 1
+ATOM 329 C CD2 . HIS A 1 49 ? 21.153 20.047 -23.185 1.00 122.56 ? ? ? ? ? ? 51 HIS A CD2 1
+ATOM 330 C CE1 . HIS A 1 49 ? 21.117 19.586 -25.330 1.00 123.61 ? ? ? ? ? ? 51 HIS A CE1 1
+ATOM 331 N NE2 . HIS A 1 49 ? 21.855 20.106 -24.366 1.00 126.48 ? ? ? ? ? ? 51 HIS A NE2 1
+ATOM 332 N N . THR A 1 50 ? 16.377 17.481 -21.294 1.00 95.68 ? ? ? ? ? ? 52 THR A N 1
+ATOM 333 C CA . THR A 1 50 ? 15.340 17.640 -20.268 1.00 90.19 ? ? ? ? ? ? 52 THR A CA 1
+ATOM 334 C C . THR A 1 50 ? 14.528 16.370 -20.027 1.00 86.57 ? ? ? ? ? ? 52 THR A C 1
+ATOM 335 O O . THR A 1 50 ? 13.629 16.031 -20.795 1.00 83.93 ? ? ? ? ? ? 52 THR A O 1
+ATOM 336 C CB . THR A 1 50 ? 14.419 18.847 -20.596 1.00 89.09 ? ? ? ? ? ? 52 THR A CB 1
+ATOM 337 O OG1 . THR A 1 50 ? 15.128 20.061 -20.323 1.00 91.82 ? ? ? ? ? ? 52 THR A OG1 1
+ATOM 338 C CG2 . THR A 1 50 ? 13.158 18.832 -19.761 1.00 84.32 ? ? ? ? ? ? 52 THR A CG2 1
+ATOM 339 N N . SER A 1 51 ? 14.863 15.686 -18.938 1.00 85.07 ? ? ? ? ? ? 53 SER A N 1
+ATOM 340 C CA . SER A 1 51 ? 14.183 14.465 -18.518 1.00 82.20 ? ? ? ? ? ? 53 SER A CA 1
+ATOM 341 C C . SER A 1 51 ? 12.860 14.724 -17.792 1.00 78.23 ? ? ? ? ? ? 53 SER A C 1
+ATOM 342 O O . SER A 1 51 ? 11.863 14.057 -18.069 1.00 75.30 ? ? ? ? ? ? 53 SER A O 1
+ATOM 343 C CB . SER A 1 51 ? 15.103 13.617 -17.631 1.00 84.25 ? ? ? ? ? ? 53 SER A CB 1
+ATOM 344 O OG . SER A 1 51 ? 15.508 14.324 -16.475 1.00 87.22 ? ? ? ? ? ? 53 SER A OG 1
+ATOM 345 N N . ALA A 1 52 ? 12.855 15.681 -16.867 1.00 76.66 ? ? ? ? ? ? 54 ALA A N 1
+ATOM 346 C CA . ALA A 1 52 ? 11.660 15.983 -16.082 1.00 73.63 ? ? ? ? ? ? 54 ALA A CA 1
+ATOM 347 C C . ALA A 1 52 ? 11.347 17.470 -16.020 1.00 72.67 ? ? ? ? ? ? 54 ALA A C 1
+ATOM 348 O O . ALA A 1 52 ? 12.231 18.295 -16.168 1.00 74.97 ? ? ? ? ? ? 54 ALA A O 1
+ATOM 349 C CB . ALA A 1 52 ? 11.807 15.427 -14.697 1.00 73.72 ? ? ? ? ? ? 54 ALA A CB 1
+ATOM 350 N N . ILE A 1 53 ? 10.078 17.799 -15.808 1.00 69.28 ? ? ? ? ? ? 55 ILE A N 1
+ATOM 351 C CA . ILE A 1 53 ? 9.644 19.182 -15.648 1.00 67.60 ? ? ? ? ? ? 55 ILE A CA 1
+ATOM 352 C C . ILE A 1 53 ? 8.807 19.315 -14.386 1.00 66.31 ? ? ? ? ? ? 55 ILE A C 1
+ATOM 353 O O . ILE A 1 53 ? 7.813 18.615 -14.234 1.00 63.74 ? ? ? ? ? ? 55 ILE A O 1
+ATOM 354 C CB . ILE A 1 53 ? 8.816 19.679 -16.852 1.00 66.27 ? ? ? ? ? ? 55 ILE A CB 1
+ATOM 355 C CG1 . ILE A 1 53 ? 9.678 19.756 -18.104 1.00 67.47 ? ? ? ? ? ? 55 ILE A CG1 1
+ATOM 356 C CG2 . ILE A 1 53 ? 8.217 21.057 -16.579 1.00 65.21 ? ? ? ? ? ? 55 ILE A CG2 1
+ATOM 357 C CD1 . ILE A 1 53 ? 8.873 19.776 -19.383 1.00 65.20 ? ? ? ? ? ? 55 ILE A CD1 1
+ATOM 358 N N . LYS A 1 54 ? 9.212 20.225 -13.498 1.00 67.56 ? ? ? ? ? ? 56 LYS A N 1
+ATOM 359 C CA . LYS A 1 54 ? 8.518 20.471 -12.242 1.00 66.86 ? ? ? ? ? ? 56 LYS A CA 1
+ATOM 360 C C . LYS A 1 54 ? 7.790 21.787 -12.345 1.00 66.25 ? ? ? ? ? ? 56 LYS A C 1
+ATOM 361 O O . LYS A 1 54 ? 8.325 22.736 -12.899 1.00 67.88 ? ? ? ? ? ? 56 LYS A O 1
+ATOM 362 C CB . LYS A 1 54 ? 9.524 20.526 -11.091 1.00 69.15 ? ? ? ? ? ? 56 LYS A CB 1
+ATOM 363 C CG . LYS A 1 54 ? 8.919 20.527 -9.688 1.00 66.38 ? ? ? ? ? ? 56 LYS A CG 1
+ATOM 364 C CD . LYS A 1 54 ? 9.898 21.069 -8.644 1.00 66.41 ? ? ? ? ? ? 56 LYS A CD 1
+ATOM 365 C CE . LYS A 1 54 ? 10.805 19.996 -8.061 1.00 66.08 ? ? ? ? ? ? 56 LYS A CE 1
+ATOM 366 N NZ . LYS A 1 54 ? 11.738 20.531 -7.020 1.00 66.38 ? ? ? ? ? ? 56 LYS A NZ 1
+ATOM 367 N N . VAL A 1 55 ? 6.569 21.843 -11.826 1.00 63.79 ? ? ? ? ? ? 57 VAL A N 1
+ATOM 368 C CA . VAL A 1 55 ? 5.805 23.088 -11.783 1.00 62.60 ? ? ? ? ? ? 57 VAL A CA 1
+ATOM 369 C C . VAL A 1 55 ? 5.508 23.478 -10.335 1.00 63.99 ? ? ? ? ? ? 57 VAL A C 1
+ATOM 370 O O . VAL A 1 55 ? 4.827 22.751 -9.607 1.00 62.58 ? ? ? ? ? ? 57 VAL A O 1
+ATOM 371 C CB . VAL A 1 55 ? 4.491 22.999 -12.582 1.00 60.05 ? ? ? ? ? ? 57 VAL A CB 1
+ATOM 372 C CG1 . VAL A 1 55 ? 3.777 24.330 -12.592 1.00 58.65 ? ? ? ? ? ? 57 VAL A CG1 1
+ATOM 373 C CG2 . VAL A 1 55 ? 4.759 22.561 -14.001 1.00 57.89 ? ? ? ? ? ? 57 VAL A CG2 1
+ATOM 374 N N . ARG A 1 56 ? 6.046 24.625 -9.926 1.00 67.06 ? ? ? ? ? ? 58 ARG A N 1
+ATOM 375 C CA . ARG A 1 56 ? 5.822 25.201 -8.602 1.00 68.68 ? ? ? ? ? ? 58 ARG A CA 1
+ATOM 376 C C . ARG A 1 56 ? 4.944 26.430 -8.775 1.00 68.31 ? ? ? ? ? ? 58 ARG A C 1
+ATOM 377 O O . ARG A 1 56 ? 5.295 27.346 -9.516 1.00 69.78 ? ? ? ? ? ? 58 ARG A O 1
+ATOM 378 C CB . ARG A 1 56 ? 7.149 25.622 -7.961 1.00 71.82 ? ? ? ? ? ? 58 ARG A CB 1
+ATOM 379 C CG . ARG A 1 56 ? 7.919 24.540 -7.264 1.00 71.32 ? ? ? ? ? ? 58 ARG A CG 1
+ATOM 380 C CD . ARG A 1 56 ? 8.899 25.124 -6.251 1.00 74.34 ? ? ? ? ? ? 58 ARG A CD 1
+ATOM 381 N NE . ARG A 1 56 ? 10.303 24.967 -6.641 1.00 76.63 ? ? ? ? ? ? 58 ARG A NE 1
+ATOM 382 C CZ . ARG A 1 56 ? 11.114 24.011 -6.180 1.00 77.74 ? ? ? ? ? ? 58 ARG A CZ 1
+ATOM 383 N NH1 . ARG A 1 56 ? 10.668 23.111 -5.308 1.00 77.26 ? ? ? ? ? ? 58 ARG A NH1 1
+ATOM 384 N NH2 . ARG A 1 56 ? 12.380 23.947 -6.590 1.00 79.00 ? ? ? ? ? ? 58 ARG A NH2 1
+ATOM 385 N N . GLY A 1 57 ? 3.795 26.450 -8.116 1.00 66.23 ? ? ? ? ? ? 59 GLY A N 1
+ATOM 386 C CA . GLY A 1 57 ? 2.891 27.591 -8.224 1.00 64.54 ? ? ? ? ? ? 59 GLY A CA 1
+ATOM 387 C C . GLY A 1 57 ? 1.515 27.161 -8.671 1.00 61.40 ? ? ? ? ? ? 59 GLY A C 1
+ATOM 388 O O . GLY A 1 57 ? 1.324 26.011 -9.023 1.00 60.50 ? ? ? ? ? ? 59 GLY A O 1
+ATOM 389 N N . LYS A 1 58 ? 0.553 28.077 -8.652 1.00 59.63 ? ? ? ? ? ? 60 LYS A N 1
+ATOM 390 C CA . LYS A 1 58 ? -0.823 27.767 -9.030 1.00 56.33 ? ? ? ? ? ? 60 LYS A CA 1
+ATOM 391 C C . LYS A 1 58 ? -0.937 27.782 -10.560 1.00 54.36 ? ? ? ? ? ? 60 LYS A C 1
+ATOM 392 O O . LYS A 1 58 ? -0.806 28.840 -11.173 1.00 55.40 ? ? ? ? ? ? 60 LYS A O 1
+ATOM 393 C CB . LYS A 1 58 ? -1.776 28.800 -8.402 1.00 56.75 ? ? ? ? ? ? 60 LYS A CB 1
+ATOM 394 C CG . LYS A 1 58 ? -3.130 28.251 -7.937 1.00 56.71 ? ? ? ? ? ? 60 LYS A CG 1
+ATOM 395 C CD . LYS A 1 58 ? -3.097 27.743 -6.485 1.00 57.00 ? ? ? ? ? ? 60 LYS A CD 1
+ATOM 396 C CE . LYS A 1 58 ? -4.401 27.012 -6.119 1.00 56.07 ? ? ? ? ? ? 60 LYS A CE 1
+ATOM 397 N N . ALA A 1 59 ? -1.157 26.623 -11.185 1.00 50.90 ? ? ? ? ? ? 61 ALA A N 1
+ATOM 398 C CA . ALA A 1 59 ? -1.229 26.563 -12.652 1.00 48.01 ? ? ? ? ? ? 61 ALA A CA 1
+ATOM 399 C C . ALA A 1 59 ? -2.205 25.512 -13.166 1.00 44.63 ? ? ? ? ? ? 61 ALA A C 1
+ATOM 400 O O . ALA A 1 59 ? -2.516 24.556 -12.458 1.00 43.62 ? ? ? ? ? ? 61 ALA A O 1
+ATOM 401 C CB . ALA A 1 59 ? 0.153 26.320 -13.244 1.00 49.49 ? ? ? ? ? ? 61 ALA A CB 1
+ATOM 402 N N . TYR A 1 60 ? -2.667 25.686 -14.404 1.00 41.70 ? ? ? ? ? ? 62 TYR A N 1
+ATOM 403 C CA . TYR A 1 60 ? -3.493 24.707 -15.082 1.00 38.07 ? ? ? ? ? ? 62 TYR A CA 1
+ATOM 404 C C . TYR A 1 60 ? -2.627 24.044 -16.134 1.00 37.82 ? ? ? ? ? ? 62 TYR A C 1
+ATOM 405 O O . TYR A 1 60 ? -1.998 24.722 -16.954 1.00 38.91 ? ? ? ? ? ? 62 TYR A O 1
+ATOM 406 C CB . TYR A 1 60 ? -4.671 25.417 -15.716 1.00 36.81 ? ? ? ? ? ? 62 TYR A CB 1
+ATOM 407 C CG . TYR A 1 60 ? -5.719 24.566 -16.417 1.00 33.24 ? ? ? ? ? ? 62 TYR A CG 1
+ATOM 408 C CD1 . TYR A 1 60 ? -6.553 23.709 -15.702 1.00 30.81 ? ? ? ? ? ? 62 TYR A CD1 1
+ATOM 409 C CD2 . TYR A 1 60 ? -5.925 24.669 -17.795 1.00 32.16 ? ? ? ? ? ? 62 TYR A CD2 1
+ATOM 410 C CE1 . TYR A 1 60 ? -7.554 22.938 -16.349 1.00 26.98 ? ? ? ? ? ? 62 TYR A CE1 1
+ATOM 411 C CE2 . TYR A 1 60 ? -6.915 23.914 -18.446 1.00 29.38 ? ? ? ? ? ? 62 TYR A CE2 1
+ATOM 412 C CZ . TYR A 1 60 ? -7.728 23.053 -17.716 1.00 26.79 ? ? ? ? ? ? 62 TYR A CZ 1
+ATOM 413 O OH . TYR A 1 60 ? -8.701 22.329 -18.381 1.00 24.12 ? ? ? ? ? ? 62 TYR A OH 1
+ATOM 414 N N . ILE A 1 61 ? -2.579 22.717 -16.097 1.00 36.07 ? ? ? ? ? ? 63 ILE A N 1
+ATOM 415 C CA . ILE A 1 61 ? -1.662 21.980 -16.938 1.00 35.83 ? ? ? ? ? ? 63 ILE A CA 1
+ATOM 416 C C . ILE A 1 61 ? -2.384 20.971 -17.798 1.00 33.41 ? ? ? ? ? ? 63 ILE A C 1
+ATOM 417 O O . ILE A 1 61 ? -3.202 20.217 -17.298 1.00 31.94 ? ? ? ? ? ? 63 ILE A O 1
+ATOM 418 C CB . ILE A 1 61 ? -0.610 21.239 -16.097 1.00 37.09 ? ? ? ? ? ? 63 ILE A CB 1
+ATOM 419 C CG1 . ILE A 1 61 ? 0.153 22.208 -15.183 1.00 40.08 ? ? ? ? ? ? 63 ILE A CG1 1
+ATOM 420 C CG2 . ILE A 1 61 ? 0.358 20.461 -17.018 1.00 38.40 ? ? ? ? ? ? 63 ILE A CG2 1
+ATOM 421 C CD1 . ILE A 1 61 ? 0.912 21.521 -14.083 1.00 42.02 ? ? ? ? ? ? 63 ILE A CD1 1
+ATOM 422 N N . GLN A 1 62 ? -2.075 20.961 -19.094 1.00 32.65 ? ? ? ? ? ? 64 GLN A N 1
+ATOM 423 C CA . GLN A 1 62 ? -2.645 19.966 -20.035 1.00 31.02 ? ? ? ? ? ? 64 GLN A CA 1
+ATOM 424 C C . GLN A 1 62 ? -1.536 19.076 -20.577 1.00 31.29 ? ? ? ? ? ? 64 GLN A C 1
+ATOM 425 O O . GLN A 1 62 ? -0.503 19.573 -21.072 1.00 33.32 ? ? ? ? ? ? 64 GLN A O 1
+ATOM 426 C CB . GLN A 1 62 ? -3.321 20.649 -21.251 1.00 30.42 ? ? ? ? ? ? 64 GLN A CB 1
+ATOM 427 C CG . GLN A 1 62 ? -4.366 21.714 -20.928 1.00 29.89 ? ? ? ? ? ? 64 GLN A CG 1
+ATOM 428 C CD . GLN A 1 62 ? -5.024 22.308 -22.172 1.00 30.22 ? ? ? ? ? ? 64 GLN A CD 1
+ATOM 429 O OE1 . GLN A 1 62 ? -4.345 22.746 -23.129 1.00 31.89 ? ? ? ? ? ? 64 GLN A OE1 1
+ATOM 430 N NE2 . GLN A 1 62 ? -6.362 22.351 -22.155 1.00 28.53 ? ? ? ? ? ? 64 GLN A NE2 1
+ATOM 431 N N . THR A 1 63 ? -1.751 17.773 -20.518 1.00 29.70 ? ? ? ? ? ? 65 THR A N 1
+ATOM 432 C CA . THR A 1 63 ? -0.825 16.842 -21.142 1.00 29.95 ? ? ? ? ? ? 65 THR A CA 1
+ATOM 433 C C . THR A 1 63 ? -1.610 15.830 -21.967 1.00 28.22 ? ? ? ? ? ? 65 THR A C 1
+ATOM 434 O O . THR A 1 63 ? -2.852 15.745 -21.879 1.00 26.39 ? ? ? ? ? ? 65 THR A O 1
+ATOM 435 C CB . THR A 1 63 ? -0.010 16.071 -20.095 1.00 30.81 ? ? ? ? ? ? 65 THR A CB 1
+ATOM 436 O OG1 . THR A 1 63 ? -0.897 15.297 -19.248 1.00 30.42 ? ? ? ? ? ? 65 THR A OG1 1
+ATOM 437 C CG2 . THR A 1 63 ? 0.824 17.023 -19.275 1.00 33.74 ? ? ? ? ? ? 65 THR A CG2 1
+ATOM 438 N N . ARG A 1 64 ? -0.886 15.027 -22.737 1.00 28.10 ? ? ? ? ? ? 66 ARG A N 1
+ATOM 439 C CA . ARG A 1 64 ? -1.516 13.903 -23.389 1.00 26.73 ? ? ? ? ? ? 66 ARG A CA 1
+ATOM 440 C C . ARG A 1 64 ? -2.410 13.108 -22.409 1.00 25.08 ? ? ? ? ? ? 66 ARG A C 1
+ATOM 441 O O . ARG A 1 64 ? -3.376 12.454 -22.828 1.00 23.73 ? ? ? ? ? ? 66 ARG A O 1
+ATOM 442 C CB . ARG A 1 64 ? -0.460 13.014 -24.044 1.00 27.91 ? ? ? ? ? ? 66 ARG A CB 1
+ATOM 443 C CG . ARG A 1 64 ? -1.032 11.692 -24.648 1.00 29.01 ? ? ? ? ? ? 66 ARG A CG 1
+ATOM 444 C CD . ARG A 1 64 ? -0.213 11.224 -25.909 1.00 33.87 ? ? ? ? ? ? 66 ARG A CD 1
+ATOM 445 N NE . ARG A 1 64 ? 1.113 10.719 -25.542 1.00 39.87 ? ? ? ? ? ? 66 ARG A NE 1
+ATOM 446 C CZ . ARG A 1 64 ? 1.273 9.451 -25.149 1.00 45.46 ? ? ? ? ? ? 66 ARG A CZ 1
+ATOM 447 N NH1 . ARG A 1 64 ? 2.466 9.006 -24.775 1.00 48.49 ? ? ? ? ? ? 66 ARG A NH1 1
+ATOM 448 N NH2 . ARG A 1 64 ? 0.208 8.625 -25.112 1.00 45.95 ? ? ? ? ? ? 66 ARG A NH2 1
+ATOM 449 N N . HIS A 1 65 ? -2.111 13.173 -21.107 1.00 24.86 ? ? ? ? ? ? 67 HIS A N 1
+ATOM 450 C CA . HIS A 1 65 ? -2.841 12.331 -20.131 1.00 24.10 ? ? ? ? ? ? 67 HIS A CA 1
+ATOM 451 C C . HIS A 1 65 ? -4.020 13.013 -19.469 1.00 23.34 ? ? ? ? ? ? 67 HIS A C 1
+ATOM 452 O O . HIS A 1 65 ? -4.610 12.431 -18.508 1.00 22.91 ? ? ? ? ? ? 67 HIS A O 1
+ATOM 453 C CB . HIS A 1 65 ? -1.918 11.730 -19.064 1.00 24.80 ? ? ? ? ? ? 67 HIS A CB 1
+ATOM 454 C CG . HIS A 1 65 ? -0.816 10.907 -19.640 1.00 27.48 ? ? ? ? ? ? 67 HIS A CG 1
+ATOM 455 N ND1 . HIS A 1 65 ? -0.956 10.191 -20.818 1.00 28.09 ? ? ? ? ? ? 67 HIS A ND1 1
+ATOM 456 C CD2 . HIS A 1 65 ? 0.447 10.682 -19.209 1.00 30.60 ? ? ? ? ? ? 67 HIS A CD2 1
+ATOM 457 C CE1 . HIS A 1 65 ? 0.181 9.571 -21.091 1.00 30.69 ? ? ? ? ? ? 67 HIS A CE1 1
+ATOM 458 N NE2 . HIS A 1 65 ? 1.041 9.835 -20.121 1.00 32.56 ? ? ? ? ? ? 67 HIS A NE2 1
+ATOM 459 N N . GLY A 1 66 ? -4.357 14.217 -19.977 1.00 23.45 ? ? ? ? ? ? 68 GLY A N 1
+ATOM 460 C CA . GLY A 1 66 ? -5.543 14.957 -19.528 1.00 23.05 ? ? ? ? ? ? 68 GLY A CA 1
+ATOM 461 C C . GLY A 1 66 ? -5.125 16.212 -18.813 1.00 23.58 ? ? ? ? ? ? 68 GLY A C 1
+ATOM 462 O O . GLY A 1 66 ? -3.974 16.630 -18.952 1.00 24.68 ? ? ? ? ? ? 68 GLY A O 1
+ATOM 463 N N . VAL A 1 67 ? -6.046 16.822 -18.054 1.00 23.73 ? ? ? ? ? ? 69 VAL A N 1
+ATOM 464 C CA . VAL A 1 67 ? -5.685 18.035 -17.310 1.00 25.29 ? ? ? ? ? ? 69 VAL A CA 1
+ATOM 465 C C . VAL A 1 67 ? -5.378 17.774 -15.842 1.00 27.38 ? ? ? ? ? ? 69 VAL A C 1
+ATOM 466 O O . VAL A 1 67 ? -5.799 16.787 -15.265 1.00 26.03 ? ? ? ? ? ? 69 VAL A O 1
+ATOM 467 C CB . VAL A 1 67 ? -6.706 19.173 -17.463 1.00 24.18 ? ? ? ? ? ? 69 VAL A CB 1
+ATOM 468 C CG1 . VAL A 1 67 ? -7.328 19.087 -18.796 1.00 23.47 ? ? ? ? ? ? 69 VAL A CG1 1
+ATOM 469 C CG2 . VAL A 1 67 ? -7.792 19.078 -16.407 1.00 23.38 ? ? ? ? ? ? 69 VAL A CG2 1
+ATOM 470 N N . ILE A 1 68 ? -4.609 18.685 -15.274 1.00 31.58 ? ? ? ? ? ? 70 ILE A N 1
+ATOM 471 C CA . ILE A 1 68 ? -4.257 18.667 -13.875 1.00 35.85 ? ? ? ? ? ? 70 ILE A CA 1
+ATOM 472 C C . ILE A 1 68 ? -3.894 20.103 -13.437 1.00 40.48 ? ? ? ? ? ? 70 ILE A C 1
+ATOM 473 O O . ILE A 1 68 ? -3.442 20.943 -14.252 1.00 41.26 ? ? ? ? ? ? 70 ILE A O 1
+ATOM 474 C CB . ILE A 1 68 ? -3.137 17.660 -13.591 1.00 35.31 ? ? ? ? ? ? 70 ILE A CB 1
+ATOM 475 C CG1 . ILE A 1 68 ? -3.062 17.400 -12.099 1.00 34.94 ? ? ? ? ? ? 70 ILE A CG1 1
+ATOM 476 C CG2 . ILE A 1 68 ? -1.813 18.148 -14.144 1.00 36.89 ? ? ? ? ? ? 70 ILE A CG2 1
+ATOM 477 C CD1 . ILE A 1 68 ? -2.514 16.052 -11.774 1.00 34.03 ? ? ? ? ? ? 70 ILE A CD1 1
+ATOM 478 N N . GLU A 1 69 ? -4.123 20.367 -12.150 1.00 45.39 ? ? ? ? ? ? 71 GLU A N 1
+ATOM 479 C CA . GLU A 1 69 ? -3.959 21.684 -11.556 1.00 51.34 ? ? ? ? ? ? 71 GLU A CA 1
+ATOM 480 C C . GLU A 1 69 ? -2.832 21.594 -10.527 1.00 55.11 ? ? ? ? ? ? 71 GLU A C 1
+ATOM 481 O O . GLU A 1 69 ? -2.859 20.721 -9.664 1.00 55.41 ? ? ? ? ? ? 71 GLU A O 1
+ATOM 482 C CB . GLU A 1 69 ? -5.285 22.073 -10.896 1.00 50.78 ? ? ? ? ? ? 71 GLU A CB 1
+ATOM 483 C CG . GLU A 1 69 ? -5.358 23.453 -10.275 1.00 56.29 ? ? ? ? ? ? 71 GLU A CG 1
+ATOM 484 C CD . GLU A 1 69 ? -6.733 23.756 -9.687 1.00 59.81 ? ? ? ? ? ? 71 GLU A CD 1
+ATOM 485 O OE1 . GLU A 1 69 ? -6.805 24.062 -8.476 1.00 61.66 ? ? ? ? ? ? 71 GLU A OE1 1
+ATOM 486 O OE2 . GLU A 1 69 ? -7.742 23.685 -10.439 1.00 59.40 ? ? ? ? ? ? 71 GLU A OE2 1
+ATOM 487 N N . SER A 1 70 ? -1.830 22.463 -10.633 1.00 60.26 ? ? ? ? ? ? 72 SER A N 1
+ATOM 488 C CA . SER A 1 70 ? -0.785 22.528 -9.618 1.00 65.19 ? ? ? ? ? ? 72 SER A CA 1
+ATOM 489 C C . SER A 1 70 ? -1.191 23.554 -8.582 1.00 67.72 ? ? ? ? ? ? 72 SER A C 1
+ATOM 490 O O . SER A 1 70 ? -1.586 24.664 -8.933 1.00 68.67 ? ? ? ? ? ? 72 SER A O 1
+ATOM 491 C CB . SER A 1 70 ? 0.566 22.885 -10.232 1.00 66.81 ? ? ? ? ? ? 72 SER A CB 1
+ATOM 492 O OG . SER A 1 70 ? 0.520 24.141 -10.869 1.00 69.19 ? ? ? ? ? ? 72 SER A OG 1
+ATOM 493 N N . GLU A 1 71 ? -1.109 23.173 -7.312 1.00 70.07 ? ? ? ? ? ? 73 GLU A N 1
+ATOM 494 C CA . GLU A 1 71 ? -1.494 24.038 -6.212 1.00 72.36 ? ? ? ? ? ? 73 GLU A CA 1
+ATOM 495 C C . GLU A 1 71 ? -0.236 24.266 -5.347 1.00 75.16 ? ? ? ? ? ? 73 GLU A C 1
+ATOM 496 O O . GLU A 1 71 ? -0.249 24.010 -4.173 1.00 77.08 ? ? ? ? ? ? 73 GLU A O 1
+ATOM 497 C CB . GLU A 1 71 ? -2.606 23.360 -5.394 1.00 71.07 ? ? ? ? ? ? 73 GLU A CB 1
+ATOM 498 C CG . GLU A 1 71 ? -3.410 22.310 -6.167 1.00 69.29 ? ? ? ? ? ? 73 GLU A CG 1
+ATOM 499 C CD . GLU A 1 71 ? -4.836 22.110 -5.652 1.00 67.49 ? ? ? ? ? ? 73 GLU A CD 1
+ATOM 500 O OE1 . GLU A 1 71 ? -5.627 23.072 -5.780 1.00 67.26 ? ? ? ? ? ? 73 GLU A OE1 1
+ATOM 501 O OE2 . GLU A 1 71 ? -5.169 20.998 -5.157 1.00 64.72 ? ? ? ? ? ? 73 GLU A OE2 1
+ATOM 502 N N . GLY A 1 72 ? 0.917 24.600 -5.926 1.00 75.64 ? ? ? ? ? ? 74 GLY A N 1
+ATOM 503 C CA . GLY A 1 72 ? 2.179 24.627 -5.145 1.00 76.28 ? ? ? ? ? ? 74 GLY A CA 1
+ATOM 504 C C . GLY A 1 72 ? 2.532 25.958 -4.485 1.00 77.39 ? ? ? ? ? ? 74 GLY A C 1
+ATOM 505 O O . GLY A 1 72 ? 1.761 26.914 -4.592 1.00 77.60 ? ? ? ? ? ? 74 GLY A O 1
+ATOM 506 N N . LYS A 1 73 ? 3.692 26.048 -3.818 1.00 78.11 ? ? ? ? ? ? 75 LYS A N 1
+ATOM 507 C CA . LYS A 1 73 ? 4.129 27.336 -3.223 1.00 79.14 ? ? ? ? ? ? 75 LYS A CA 1
+ATOM 508 C C . LYS A 1 73 ? 4.479 28.474 -4.244 1.00 79.69 ? ? ? ? ? ? 75 LYS A C 1
+ATOM 509 O O . LYS A 1 73 ? 5.535 28.516 -4.903 1.00 79.72 ? ? ? ? ? ? 75 LYS A O 1
+ATOM 510 C CB . LYS A 1 73 ? 5.211 27.143 -2.149 1.00 79.82 ? ? ? ? ? ? 75 LYS A CB 1
+ATOM 511 C CG . LYS A 1 73 ? 6.646 27.001 -2.680 1.00 82.03 ? ? ? ? ? ? 75 LYS A CG 1
+ATOM 512 C CD . LYS A 1 73 ? 7.702 26.968 -1.556 1.00 83.81 ? ? ? ? ? ? 75 LYS A CD 1
+ATOM 513 C CE . LYS A 1 73 ? 9.130 26.847 -2.110 1.00 84.65 ? ? ? ? ? ? 75 LYS A CE 1
+ATOM 514 N NZ . LYS A 1 73 ? 10.106 26.489 -1.037 1.00 84.64 ? ? ? ? ? ? 75 LYS A NZ 1
diff --git a/modules/seq/alg/tests/testfiles/align_to_seqres_valueerror.mmcif b/modules/seq/alg/tests/testfiles/align_to_seqres_valueerror.mmcif
new file mode 100644
index 0000000000000000000000000000000000000000..fd150386f4a9ee2b5b37be54323e96830d2ccd14
--- /dev/null
+++ b/modules/seq/alg/tests/testfiles/align_to_seqres_valueerror.mmcif
@@ -0,0 +1,564 @@
+data_3BAR
+# based on 3AQD
+_entry.id 3BAR
+#
+loop_
+_entity.id
+_entity.type
+_entity.src_method
+_entity.pdbx_description
+_entity.formula_weight
+_entity.pdbx_number_of_molecules
+_entity.details
+1 polymer man 'Transcription attenuation protein mtrB' 8257.458 22 ?
+2 water nat water 18.015 7 ?
+#
+_entity_poly.entity_id 1
+_entity_poly.type 'polypeptide(L)'
+_entity_poly.nstd_linkage no
+_entity_poly.nstd_monomer no
+_entity_poly.pdbx_seq_one_letter_code MYTNSDFVVIKALEDWVNVIGLTRGADTRFHHSEKLDKGEVLIAQFTEHTSAIKVRGKAYIQTRHGVIESEGKK
+_entity_poly.pdbx_seq_one_letter_code_can MYTNSDFVVIKALEDWVNVIGLTRGADTRFHHSEKLDKGEVLIAQFTEHTSAIKVRGKAYIQTRHGVIESEGKK
+_entity_poly.pdbx_strand_id A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V
+#
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_entity_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.B_iso_or_equiv
+_atom_site.Cartn_x_esd
+_atom_site.Cartn_y_esd
+_atom_site.Cartn_z_esd
+_atom_site.occupancy_esd
+_atom_site.B_iso_or_equiv_esd
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_comp_id
+_atom_site.auth_asym_id
+_atom_site.auth_atom_id
+_atom_site.pdbx_PDB_model_num
+ATOM 1 N N . SER A 1 5 ? 8.892 13.236 -28.550 1.00 81.62 ? ? ? ? ? ? 7 SER A N 1
+ATOM 2 C CA . SER A 1 5 ? 8.449 14.550 -29.128 1.00 80.98 ? ? ? ? ? ? 7 SER A CA 1
+ATOM 3 C C . SER A 1 5 ? 7.181 15.159 -28.476 1.00 77.44 ? ? ? ? ? ? 7 SER A C 1
+ATOM 4 O O . SER A 1 5 ? 6.463 15.940 -29.117 1.00 76.80 ? ? ? ? ? ? 7 SER A O 1
+ATOM 5 C CB . SER A 1 5 ? 8.239 14.416 -30.651 1.00 81.96 ? ? ? ? ? ? 7 SER A CB 1
+ATOM 6 O OG . SER A 1 5 ? 9.441 14.629 -31.378 1.00 87.04 ? ? ? ? ? ? 7 SER A OG 1
+ATOM 7 N N . ASP A 1 6 ? 6.910 14.822 -27.217 1.00 73.87 ? ? ? ? ? ? 8 ASP A N 1
+ATOM 8 C CA . ASP A 1 6 ? 5.670 15.258 -26.582 1.00 69.40 ? ? ? ? ? ? 8 ASP A CA 1
+ATOM 9 C C . ASP A 1 6 ? 5.834 16.550 -25.785 1.00 68.43 ? ? ? ? ? ? 8 ASP A C 1
+ATOM 10 O O . ASP A 1 6 ? 6.944 16.907 -25.403 1.00 70.90 ? ? ? ? ? ? 8 ASP A O 1
+ATOM 11 C CB . ASP A 1 6 ? 5.104 14.146 -25.703 1.00 67.64 ? ? ? ? ? ? 8 ASP A CB 1
+ATOM 12 C CG . ASP A 1 6 ? 3.570 14.083 -25.751 1.00 64.57 ? ? ? ? ? ? 8 ASP A CG 1
+ATOM 13 O OD1 . ASP A 1 6 ? 2.949 15.085 -26.195 1.00 63.11 ? ? ? ? ? ? 8 ASP A OD1 1
+ATOM 14 O OD2 . ASP A 1 6 ? 2.984 13.032 -25.353 1.00 62.17 ? ? ? ? ? ? 8 ASP A OD2 1
+ATOM 15 N N . PHE A 1 7 ? 4.726 17.246 -25.545 1.00 64.53 ? ? ? ? ? ? 9 PHE A N 1
+ATOM 16 C CA . PHE A 1 7 ? 4.750 18.548 -24.879 1.00 61.94 ? ? ? ? ? ? 9 PHE A CA 1
+ATOM 17 C C . PHE A 1 7 ? 3.673 18.732 -23.796 1.00 57.92 ? ? ? ? ? ? 9 PHE A C 1
+ATOM 18 O O . PHE A 1 7 ? 2.693 17.987 -23.744 1.00 55.70 ? ? ? ? ? ? 9 PHE A O 1
+ATOM 19 C CB . PHE A 1 7 ? 4.618 19.664 -25.915 1.00 63.43 ? ? ? ? ? ? 9 PHE A CB 1
+ATOM 20 C CG . PHE A 1 7 ? 3.282 19.718 -26.567 1.00 62.41 ? ? ? ? ? ? 9 PHE A CG 1
+ATOM 21 C CD1 . PHE A 1 7 ? 2.231 20.382 -25.970 1.00 61.82 ? ? ? ? ? ? 9 PHE A CD1 1
+ATOM 22 C CD2 . PHE A 1 7 ? 3.075 19.105 -27.775 1.00 64.02 ? ? ? ? ? ? 9 PHE A CD2 1
+ATOM 23 C CE1 . PHE A 1 7 ? 0.988 20.428 -26.567 1.00 60.16 ? ? ? ? ? ? 9 PHE A CE1 1
+ATOM 24 C CE2 . PHE A 1 7 ? 1.832 19.145 -28.383 1.00 62.57 ? ? ? ? ? ? 9 PHE A CE2 1
+ATOM 25 C CZ . PHE A 1 7 ? 0.783 19.808 -27.775 1.00 60.25 ? ? ? ? ? ? 9 PHE A CZ 1
+ATOM 26 N N . VAL A 1 8 ? 3.861 19.735 -22.938 1.00 55.04 ? ? ? ? ? ? 10 VAL A N 1
+ATOM 27 C CA . VAL A 1 8 ? 2.861 20.095 -21.949 1.00 50.88 ? ? ? ? ? ? 10 VAL A CA 1
+ATOM 28 C C . VAL A 1 8 ? 2.487 21.551 -22.098 1.00 49.54 ? ? ? ? ? ? 10 VAL A C 1
+ATOM 29 O O . VAL A 1 8 ? 3.323 22.385 -22.446 1.00 50.85 ? ? ? ? ? ? 10 VAL A O 1
+ATOM 30 C CB . VAL A 1 8 ? 3.326 19.851 -20.511 1.00 51.03 ? ? ? ? ? ? 10 VAL A CB 1
+ATOM 31 C CG1 . VAL A 1 8 ? 3.832 18.442 -20.371 1.00 50.13 ? ? ? ? ? ? 10 VAL A CG1 1
+ATOM 32 C CG2 . VAL A 1 8 ? 4.402 20.826 -20.090 1.00 53.19 ? ? ? ? ? ? 10 VAL A CG2 1
+ATOM 33 N N . VAL A 1 9 ? 1.215 21.844 -21.842 1.00 46.06 ? ? ? ? ? ? 11 VAL A N 1
+ATOM 34 C CA . VAL A 1 9 ? 0.687 23.206 -21.880 1.00 44.00 ? ? ? ? ? ? 11 VAL A CA 1
+ATOM 35 C C . VAL A 1 9 ? 0.489 23.603 -20.434 1.00 44.21 ? ? ? ? ? ? 11 VAL A C 1
+ATOM 36 O O . VAL A 1 9 ? -0.170 22.877 -19.678 1.00 42.41 ? ? ? ? ? ? 11 VAL A O 1
+ATOM 37 C CB . VAL A 1 9 ? -0.661 23.252 -22.624 1.00 42.00 ? ? ? ? ? ? 11 VAL A CB 1
+ATOM 38 C CG1 . VAL A 1 9 ? -1.295 24.607 -22.528 1.00 40.79 ? ? ? ? ? ? 11 VAL A CG1 1
+ATOM 39 C CG2 . VAL A 1 9 ? -0.455 22.906 -24.078 1.00 40.13 ? ? ? ? ? ? 11 VAL A CG2 1
+ATOM 40 N N . ILE A 1 10 ? 1.076 24.738 -20.056 1.00 46.10 ? ? ? ? ? ? 12 ILE A N 1
+ATOM 41 C CA . ILE A 1 10 ? 1.003 25.240 -18.696 1.00 47.51 ? ? ? ? ? ? 12 ILE A CA 1
+ATOM 42 C C . ILE A 1 10 ? 0.516 26.657 -18.743 1.00 48.05 ? ? ? ? ? ? 12 ILE A C 1
+ATOM 43 O O . ILE A 1 10 ? 1.137 27.508 -19.380 1.00 49.65 ? ? ? ? ? ? 12 ILE A O 1
+ATOM 44 C CB . ILE A 1 10 ? 2.374 25.247 -18.012 1.00 49.28 ? ? ? ? ? ? 12 ILE A CB 1
+ATOM 45 C CG1 . ILE A 1 10 ? 2.981 23.848 -18.003 1.00 49.95 ? ? ? ? ? ? 12 ILE A CG1 1
+ATOM 46 C CG2 . ILE A 1 10 ? 2.247 25.753 -16.603 1.00 50.91 ? ? ? ? ? ? 12 ILE A CG2 1
+ATOM 47 C CD1 . ILE A 1 10 ? 4.435 23.827 -17.677 1.00 54.16 ? ? ? ? ? ? 12 ILE A CD1 1
+ATOM 48 N N . LYS A 1 11 ? -0.606 26.901 -18.076 1.00 47.39 ? ? ? ? ? ? 13 LYS A N 1
+ATOM 49 C CA . LYS A 1 11 ? -1.139 28.252 -17.917 1.00 48.23 ? ? ? ? ? ? 13 LYS A CA 1
+ATOM 50 C C . LYS A 1 11 ? -0.998 28.660 -16.473 1.00 50.10 ? ? ? ? ? ? 13 LYS A C 1
+ATOM 51 O O . LYS A 1 11 ? -1.441 27.931 -15.579 1.00 49.40 ? ? ? ? ? ? 13 LYS A O 1
+ATOM 52 C CB . LYS A 1 11 ? -2.609 28.311 -18.304 1.00 46.00 ? ? ? ? ? ? 13 LYS A CB 1
+ATOM 53 C CG . LYS A 1 11 ? -3.144 29.706 -18.267 1.00 45.91 ? ? ? ? ? ? 13 LYS A CG 1
+ATOM 54 C CD . LYS A 1 11 ? -4.640 29.741 -18.402 1.00 43.12 ? ? ? ? ? ? 13 LYS A CD 1
+ATOM 55 C CE . LYS A 1 11 ? -5.103 31.182 -18.619 1.00 44.02 ? ? ? ? ? ? 13 LYS A CE 1
+ATOM 56 N NZ . LYS A 1 11 ? -6.563 31.312 -18.363 1.00 43.35 ? ? ? ? ? ? 13 LYS A NZ 1
+ATOM 57 N N . ALA A 1 12 ? -0.379 29.818 -16.242 1.00 53.49 ? ? ? ? ? ? 14 ALA A N 1
+ATOM 58 C CA . ALA A 1 12 ? -0.115 30.296 -14.876 1.00 55.56 ? ? ? ? ? ? 14 ALA A CA 1
+ATOM 59 C C . ALA A 1 12 ? -1.354 30.960 -14.272 1.00 55.44 ? ? ? ? ? ? 14 ALA A C 1
+ATOM 60 O O . ALA A 1 12 ? -1.938 31.848 -14.881 1.00 55.76 ? ? ? ? ? ? 14 ALA A O 1
+ATOM 61 C CB . ALA A 1 12 ? 1.042 31.240 -14.890 1.00 58.43 ? ? ? ? ? ? 14 ALA A CB 1
+ATOM 62 N N . LEU A 1 13 ? -1.767 30.514 -13.093 1.00 55.02 ? ? ? ? ? ? 15 LEU A N 1
+ATOM 63 C CA . LEU A 1 13 ? -2.966 31.063 -12.438 1.00 55.23 ? ? ? ? ? ? 15 LEU A CA 1
+ATOM 64 C C . LEU A 1 13 ? -2.665 32.145 -11.380 1.00 58.70 ? ? ? ? ? ? 15 LEU A C 1
+ATOM 65 O O . LEU A 1 13 ? -3.574 32.758 -10.809 1.00 58.84 ? ? ? ? ? ? 15 LEU A O 1
+ATOM 66 C CB . LEU A 1 13 ? -3.811 29.932 -11.832 1.00 52.50 ? ? ? ? ? ? 15 LEU A CB 1
+ATOM 67 C CG . LEU A 1 13 ? -4.415 28.951 -12.839 1.00 47.91 ? ? ? ? ? ? 15 LEU A CG 1
+ATOM 68 C CD1 . LEU A 1 13 ? -4.953 27.698 -12.151 1.00 44.21 ? ? ? ? ? ? 15 LEU A CD1 1
+ATOM 69 C CD2 . LEU A 1 13 ? -5.494 29.672 -13.668 1.00 46.05 ? ? ? ? ? ? 15 LEU A CD2 1
+ATOM 70 N N . GLU A 1 14 ? -1.379 32.359 -11.120 1.00 62.66 ? ? ? ? ? ? 16 GLU A N 1
+ATOM 71 C CA . GLU A 1 14 ? -0.899 33.425 -10.252 1.00 67.00 ? ? ? ? ? ? 16 GLU A CA 1
+ATOM 72 C C . GLU A 1 14 ? 0.409 33.922 -10.836 1.00 70.32 ? ? ? ? ? ? 16 GLU A C 1
+ATOM 73 O O . GLU A 1 14 ? 0.914 33.339 -11.785 1.00 70.03 ? ? ? ? ? ? 16 GLU A O 1
+ATOM 74 C CB . GLU A 1 14 ? -0.696 32.923 -8.819 1.00 67.19 ? ? ? ? ? ? 16 GLU A CB 1
+ATOM 75 C CG . GLU A 1 14 ? 0.432 31.895 -8.625 1.00 68.58 ? ? ? ? ? ? 16 GLU A CG 1
+ATOM 76 C CD . GLU A 1 14 ? 0.454 31.270 -7.222 1.00 70.39 ? ? ? ? ? ? 16 GLU A CD 1
+ATOM 77 O OE1 . GLU A 1 14 ? -0.457 31.541 -6.412 1.00 71.02 ? ? ? ? ? ? 16 GLU A OE1 1
+ATOM 78 O OE2 . GLU A 1 14 ? 1.387 30.491 -6.926 1.00 71.29 ? ? ? ? ? ? 16 GLU A OE2 1
+ATOM 79 N N . ASP A 1 15 ? 0.955 35.001 -10.285 1.00 74.75 ? ? ? ? ? ? 17 ASP A N 1
+ATOM 80 C CA . ASP A 1 15 ? 2.250 35.491 -10.740 1.00 78.78 ? ? ? ? ? ? 17 ASP A CA 1
+ATOM 81 C C . ASP A 1 15 ? 3.325 34.615 -10.138 1.00 79.87 ? ? ? ? ? ? 17 ASP A C 1
+ATOM 82 O O . ASP A 1 15 ? 3.099 33.950 -9.124 1.00 79.33 ? ? ? ? ? ? 17 ASP A O 1
+ATOM 83 C CB . ASP A 1 15 ? 2.475 36.953 -10.336 1.00 81.65 ? ? ? ? ? ? 17 ASP A CB 1
+ATOM 84 C CG . ASP A 1 15 ? 1.621 37.937 -11.140 1.00 83.16 ? ? ? ? ? ? 17 ASP A CG 1
+ATOM 85 O OD1 . ASP A 1 15 ? 1.344 37.691 -12.326 1.00 82.40 ? ? ? ? ? ? 17 ASP A OD1 1
+ATOM 86 O OD2 . ASP A 1 15 ? 1.231 38.982 -10.589 1.00 86.46 ? ? ? ? ? ? 17 ASP A OD2 1
+ATOM 87 N N . GLY A 1 16 ? 4.489 34.606 -10.778 1.00 81.58 ? ? ? ? ? ? 18 GLY A N 1
+ATOM 88 C CA . GLY A 1 16 ? 5.660 33.903 -10.248 1.00 82.57 ? ? ? ? ? ? 18 GLY A CA 1
+ATOM 89 C C . GLY A 1 16 ? 5.555 32.392 -10.154 1.00 80.35 ? ? ? ? ? ? 18 GLY A C 1
+ATOM 90 O O . GLY A 1 16 ? 6.059 31.793 -9.215 1.00 81.29 ? ? ? ? ? ? 18 GLY A O 1
+ATOM 91 N N . VAL A 1 17 ? 4.892 31.781 -11.128 1.00 77.56 ? ? ? ? ? ? 19 VAL A N 1
+ATOM 92 C CA . VAL A 1 17 ? 4.885 30.336 -11.259 1.00 74.50 ? ? ? ? ? ? 19 VAL A CA 1
+ATOM 93 C C . VAL A 1 17 ? 6.239 29.942 -11.826 1.00 76.68 ? ? ? ? ? ? 19 VAL A C 1
+ATOM 94 O O . VAL A 1 17 ? 6.799 30.655 -12.655 1.00 78.24 ? ? ? ? ? ? 19 VAL A O 1
+ATOM 95 C CB . VAL A 1 17 ? 3.755 29.861 -12.187 1.00 71.56 ? ? ? ? ? ? 19 VAL A CB 1
+ATOM 96 C CG1 . VAL A 1 17 ? 3.820 28.364 -12.384 1.00 67.63 ? ? ? ? ? ? 19 VAL A CG1 1
+ATOM 97 C CG2 . VAL A 1 17 ? 2.409 30.247 -11.611 1.00 67.92 ? ? ? ? ? ? 19 VAL A CG2 1
+ATOM 98 N N . ASN A 1 18 ? 6.764 28.812 -11.381 1.00 77.33 ? ? ? ? ? ? 20 ASN A N 1
+ATOM 99 C CA . ASN A 1 18 ? 8.086 28.396 -11.775 1.00 79.46 ? ? ? ? ? ? 20 ASN A CA 1
+ATOM 100 C C . ASN A 1 18 ? 8.067 27.069 -12.528 1.00 77.29 ? ? ? ? ? ? 20 ASN A C 1
+ATOM 101 O O . ASN A 1 18 ? 7.635 26.058 -11.989 1.00 75.60 ? ? ? ? ? ? 20 ASN A O 1
+ATOM 102 C CB . ASN A 1 18 ? 8.941 28.291 -10.526 1.00 82.30 ? ? ? ? ? ? 20 ASN A CB 1
+ATOM 103 C CG . ASN A 1 18 ? 10.360 28.739 -10.753 1.00 89.13 ? ? ? ? ? ? 20 ASN A CG 1
+ATOM 104 O OD1 . ASN A 1 18 ? 10.690 29.305 -11.791 1.00 92.93 ? ? ? ? ? ? 20 ASN A OD1 1
+ATOM 105 N ND2 . ASN A 1 18 ? 11.217 28.488 -9.773 1.00 94.39 ? ? ? ? ? ? 20 ASN A ND2 1
+ATOM 106 N N . VAL A 1 19 ? 8.521 27.077 -13.779 1.00 76.88 ? ? ? ? ? ? 21 VAL A N 1
+ATOM 107 C CA . VAL A 1 19 ? 8.542 25.871 -14.600 1.00 75.28 ? ? ? ? ? ? 21 VAL A CA 1
+ATOM 108 C C . VAL A 1 19 ? 9.970 25.398 -14.720 1.00 78.52 ? ? ? ? ? ? 21 VAL A C 1
+ATOM 109 O O . VAL A 1 19 ? 10.747 25.948 -15.489 1.00 80.53 ? ? ? ? ? ? 21 VAL A O 1
+ATOM 110 C CB . VAL A 1 19 ? 7.946 26.104 -16.005 1.00 73.54 ? ? ? ? ? ? 21 VAL A CB 1
+ATOM 111 C CG1 . VAL A 1 19 ? 7.966 24.838 -16.807 1.00 70.33 ? ? ? ? ? ? 21 VAL A CG1 1
+ATOM 112 C CG2 . VAL A 1 19 ? 6.528 26.602 -15.913 1.00 69.44 ? ? ? ? ? ? 21 VAL A CG2 1
+ATOM 113 N N . ILE A 1 20 ? 10.305 24.368 -13.960 1.00 80.07 ? ? ? ? ? ? 22 ILE A N 1
+ATOM 114 C CA . ILE A 1 20 ? 11.683 23.949 -13.817 1.00 83.77 ? ? ? ? ? ? 22 ILE A CA 1
+ATOM 115 C C . ILE A 1 20 ? 12.004 22.729 -14.664 1.00 83.74 ? ? ? ? ? ? 22 ILE A C 1
+ATOM 116 O O . ILE A 1 20 ? 11.349 21.705 -14.536 1.00 81.42 ? ? ? ? ? ? 22 ILE A O 1
+ATOM 117 C CB . ILE A 1 20 ? 12.014 23.661 -12.348 1.00 84.59 ? ? ? ? ? ? 22 ILE A CB 1
+ATOM 118 C CG1 . ILE A 1 20 ? 11.522 24.802 -11.467 1.00 85.96 ? ? ? ? ? ? 22 ILE A CG1 1
+ATOM 119 C CG2 . ILE A 1 20 ? 13.511 23.484 -12.166 1.00 89.81 ? ? ? ? ? ? 22 ILE A CG2 1
+ATOM 120 C CD1 . ILE A 1 20 ? 11.484 24.464 -9.998 1.00 87.43 ? ? ? ? ? ? 22 ILE A CD1 1
+ATOM 121 N N . GLY A 1 21 ? 13.019 22.862 -15.520 1.00 86.57 ? ? ? ? ? ? 23 GLY A N 1
+ATOM 122 C CA . GLY A 1 21 ? 13.522 21.775 -16.358 1.00 88.60 ? ? ? ? ? ? 23 GLY A CA 1
+ATOM 123 C C . GLY A 1 21 ? 14.674 21.070 -15.675 1.00 91.29 ? ? ? ? ? ? 23 GLY A C 1
+ATOM 124 O O . GLY A 1 21 ? 15.573 21.716 -15.154 1.00 94.14 ? ? ? ? ? ? 23 GLY A O 1
+ATOM 125 N N . LEU A 1 22 ? 14.642 19.743 -15.672 1.00 91.36 ? ? ? ? ? ? 24 LEU A N 1
+ATOM 126 C CA . LEU A 1 22 ? 15.603 18.932 -14.926 1.00 92.96 ? ? ? ? ? ? 24 LEU A CA 1
+ATOM 127 C C . LEU A 1 22 ? 16.447 18.089 -15.876 1.00 94.68 ? ? ? ? ? ? 24 LEU A C 1
+ATOM 128 O O . LEU A 1 22 ? 15.939 17.601 -16.885 1.00 94.04 ? ? ? ? ? ? 24 LEU A O 1
+ATOM 129 C CB . LEU A 1 22 ? 14.860 18.047 -13.924 1.00 91.08 ? ? ? ? ? ? 24 LEU A CB 1
+ATOM 130 C CG . LEU A 1 22 ? 14.551 18.518 -12.493 1.00 90.38 ? ? ? ? ? ? 24 LEU A CG 1
+ATOM 131 C CD1 . LEU A 1 22 ? 14.342 20.009 -12.384 1.00 91.01 ? ? ? ? ? ? 24 LEU A CD1 1
+ATOM 132 C CD2 . LEU A 1 22 ? 13.342 17.791 -11.921 1.00 85.41 ? ? ? ? ? ? 24 LEU A CD2 1
+ATOM 133 N N . THR A 1 23 ? 17.733 17.926 -15.565 1.00 96.47 ? ? ? ? ? ? 25 THR A N 1
+ATOM 134 C CA . THR A 1 23 ? 18.688 17.343 -16.531 1.00 98.30 ? ? ? ? ? ? 25 THR A CA 1
+ATOM 135 C C . THR A 1 23 ? 19.007 15.862 -16.352 1.00 98.49 ? ? ? ? ? ? 25 THR A C 1
+ATOM 136 O O . THR A 1 23 ? 18.826 15.304 -15.266 1.00 98.19 ? ? ? ? ? ? 25 THR A O 1
+ATOM 137 C CB . THR A 1 23 ? 20.028 18.102 -16.553 1.00 100.21 ? ? ? ? ? ? 25 THR A CB 1
+ATOM 138 O OG1 . THR A 1 23 ? 20.490 18.282 -15.208 1.00 101.37 ? ? ? ? ? ? 25 THR A OG1 1
+ATOM 139 C CG2 . THR A 1 23 ? 19.883 19.457 -17.252 1.00 100.72 ? ? ? ? ? ? 25 THR A CG2 1
+ATOM 140 N N . ARG A 1 24 ? 19.501 15.246 -17.430 1.00 99.49 ? ? ? ? ? ? 26 ARG A N 1
+ATOM 141 C CA . ARG A 1 24 ? 19.857 13.819 -17.452 1.00 99.94 ? ? ? ? ? ? 26 ARG A CA 1
+ATOM 142 C C . ARG A 1 24 ? 21.154 13.541 -16.693 1.00 101.44 ? ? ? ? ? ? 26 ARG A C 1
+ATOM 143 O O . ARG A 1 24 ? 22.240 13.904 -17.147 1.00 103.26 ? ? ? ? ? ? 26 ARG A O 1
+ATOM 144 C CB . ARG A 1 24 ? 19.955 13.281 -18.893 1.00 100.14 ? ? ? ? ? ? 26 ARG A CB 1
+ATOM 145 C CG . ARG A 1 24 ? 18.620 13.217 -19.642 1.00 99.36 ? ? ? ? ? ? 26 ARG A CG 1
+ATOM 146 C CD . ARG A 1 24 ? 18.634 12.164 -20.759 1.00 100.98 ? ? ? ? ? ? 26 ARG A CD 1
+ATOM 147 N NE . ARG A 1 24 ? 17.552 12.352 -21.740 1.00 100.55 ? ? ? ? ? ? 26 ARG A NE 1
+ATOM 148 C CZ . ARG A 1 24 ? 17.231 11.494 -22.716 1.00 99.98 ? ? ? ? ? ? 26 ARG A CZ 1
+ATOM 149 N NH1 . ARG A 1 24 ? 17.891 10.344 -22.876 1.00 99.60 ? ? ? ? ? ? 26 ARG A NH1 1
+ATOM 150 N NH2 . ARG A 1 24 ? 16.229 11.791 -23.537 1.00 99.33 ? ? ? ? ? ? 26 ARG A NH2 1
+ATOM 151 N N . THR A 1 28 ? 22.527 16.428 -12.721 1.00 120.13 ? ? ? ? ? ? 30 THR A N 1
+ATOM 152 C CA . THR A 1 28 ? 21.235 15.835 -13.090 1.00 118.47 ? ? ? ? ? ? 30 THR A CA 1
+ATOM 153 C C . THR A 1 28 ? 20.021 16.467 -12.351 1.00 117.17 ? ? ? ? ? ? 30 THR A C 1
+ATOM 154 O O . THR A 1 28 ? 18.867 16.073 -12.593 1.00 115.70 ? ? ? ? ? ? 30 THR A O 1
+ATOM 155 C CB . THR A 1 28 ? 21.259 14.241 -13.007 1.00 118.06 ? ? ? ? ? ? 30 THR A CB 1
+ATOM 156 O OG1 . THR A 1 28 ? 19.946 13.697 -13.234 1.00 116.11 ? ? ? ? ? ? 30 THR A OG1 1
+ATOM 157 C CG2 . THR A 1 28 ? 21.822 13.727 -11.660 1.00 118.37 ? ? ? ? ? ? 30 THR A CG2 1
+ATOM 158 N N . ARG A 1 29 ? 20.289 17.464 -11.492 1.00 117.71 ? ? ? ? ? ? 31 ARG A N 1
+ATOM 159 C CA . ARG A 1 29 ? 19.261 18.091 -10.604 1.00 116.35 ? ? ? ? ? ? 31 ARG A CA 1
+ATOM 160 C C . ARG A 1 29 ? 18.477 19.294 -11.195 1.00 115.56 ? ? ? ? ? ? 31 ARG A C 1
+ATOM 161 O O . ARG A 1 29 ? 18.271 19.360 -12.420 1.00 115.47 ? ? ? ? ? ? 31 ARG A O 1
+ATOM 162 C CB . ARG A 1 29 ? 19.840 18.428 -9.204 1.00 117.16 ? ? ? ? ? ? 31 ARG A CB 1
+ATOM 163 C CG . ARG A 1 29 ? 21.320 18.904 -9.113 1.00 119.11 ? ? ? ? ? ? 31 ARG A CG 1
+ATOM 164 C CD . ARG A 1 29 ? 21.638 20.210 -9.857 1.00 119.60 ? ? ? ? ? ? 31 ARG A CD 1
+ATOM 165 N NE . ARG A 1 29 ? 22.419 19.952 -11.068 1.00 120.44 ? ? ? ? ? ? 31 ARG A NE 1
+ATOM 166 C CZ . ARG A 1 29 ? 21.980 20.123 -12.315 1.00 119.80 ? ? ? ? ? ? 31 ARG A CZ 1
+ATOM 167 N NH1 . ARG A 1 29 ? 22.780 19.853 -13.337 1.00 121.30 ? ? ? ? ? ? 31 ARG A NH1 1
+ATOM 168 N NH2 . ARG A 1 29 ? 20.756 20.576 -12.552 1.00 117.87 ? ? ? ? ? ? 31 ARG A NH2 1
+ATOM 169 N N . PHE A 1 30 ? 18.052 20.228 -10.323 1.00 114.83 ? ? ? ? ? ? 32 PHE A N 1
+ATOM 170 C CA . PHE A 1 30 ? 17.248 21.413 -10.728 1.00 113.80 ? ? ? ? ? ? 32 PHE A CA 1
+ATOM 171 C C . PHE A 1 30 ? 18.047 22.475 -11.541 1.00 114.52 ? ? ? ? ? ? 32 PHE A C 1
+ATOM 172 O O . PHE A 1 30 ? 18.937 23.145 -11.001 1.00 115.82 ? ? ? ? ? ? 32 PHE A O 1
+ATOM 173 C CB . PHE A 1 30 ? 16.487 22.093 -9.541 1.00 113.41 ? ? ? ? ? ? 32 PHE A CB 1
+ATOM 174 C CG . PHE A 1 30 ? 16.144 21.179 -8.346 1.00 112.64 ? ? ? ? ? ? 32 PHE A CG 1
+ATOM 175 C CD1 . PHE A 1 30 ? 15.540 21.740 -7.207 1.00 112.23 ? ? ? ? ? ? 32 PHE A CD1 1
+ATOM 176 C CD2 . PHE A 1 30 ? 16.423 19.805 -8.338 1.00 111.84 ? ? ? ? ? ? 32 PHE A CD2 1
+ATOM 177 C CE1 . PHE A 1 30 ? 15.212 20.957 -6.091 1.00 111.54 ? ? ? ? ? ? 32 PHE A CE1 1
+ATOM 178 C CE2 . PHE A 1 30 ? 16.110 19.015 -7.218 1.00 111.19 ? ? ? ? ? ? 32 PHE A CE2 1
+ATOM 179 C CZ . PHE A 1 30 ? 15.497 19.590 -6.097 1.00 111.08 ? ? ? ? ? ? 32 PHE A CZ 1
+ATOM 180 N N . HIS A 1 31 ? 17.677 22.645 -12.817 1.00 113.18 ? ? ? ? ? ? 33 HIS A N 1
+ATOM 181 C CA . HIS A 1 31 ? 18.505 23.317 -13.836 1.00 113.51 ? ? ? ? ? ? 33 HIS A CA 1
+ATOM 182 C C . HIS A 1 31 ? 17.843 24.573 -14.459 1.00 112.40 ? ? ? ? ? ? 33 HIS A C 1
+ATOM 183 O O . HIS A 1 31 ? 17.840 25.650 -13.849 1.00 112.91 ? ? ? ? ? ? 33 HIS A O 1
+ATOM 184 C CB . HIS A 1 31 ? 18.897 22.274 -14.908 1.00 113.74 ? ? ? ? ? ? 33 HIS A CB 1
+ATOM 185 C CG . HIS A 1 31 ? 19.881 22.761 -15.933 1.00 116.22 ? ? ? ? ? ? 33 HIS A CG 1
+ATOM 186 N ND1 . HIS A 1 31 ? 21.201 23.036 -15.635 1.00 118.98 ? ? ? ? ? ? 33 HIS A ND1 1
+ATOM 187 C CD2 . HIS A 1 31 ? 19.743 22.976 -17.264 1.00 116.72 ? ? ? ? ? ? 33 HIS A CD2 1
+ATOM 188 C CE1 . HIS A 1 31 ? 21.826 23.425 -16.734 1.00 120.25 ? ? ? ? ? ? 33 HIS A CE1 1
+ATOM 189 N NE2 . HIS A 1 31 ? 20.964 23.395 -17.736 1.00 119.10 ? ? ? ? ? ? 33 HIS A NE2 1
+ATOM 190 N N . HIS A 1 32 ? 17.298 24.431 -15.670 1.00 110.63 ? ? ? ? ? ? 34 HIS A N 1
+ATOM 191 C CA . HIS A 1 32 ? 16.630 25.529 -16.377 1.00 108.57 ? ? ? ? ? ? 34 HIS A CA 1
+ATOM 192 C C . HIS A 1 32 ? 15.315 25.908 -15.701 1.00 105.41 ? ? ? ? ? ? 34 HIS A C 1
+ATOM 193 O O . HIS A 1 32 ? 14.336 25.165 -15.760 1.00 102.47 ? ? ? ? ? ? 34 HIS A O 1
+ATOM 194 C CB . HIS A 1 32 ? 16.384 25.161 -17.858 1.00 108.29 ? ? ? ? ? ? 34 HIS A CB 1
+ATOM 195 C CG . HIS A 1 32 ? 15.859 26.296 -18.697 1.00 108.03 ? ? ? ? ? ? 34 HIS A CG 1
+ATOM 196 N ND1 . HIS A 1 32 ? 16.492 27.522 -18.778 1.00 111.34 ? ? ? ? ? ? 34 HIS A ND1 1
+ATOM 197 C CD2 . HIS A 1 32 ? 14.778 26.380 -19.511 1.00 103.90 ? ? ? ? ? ? 34 HIS A CD2 1
+ATOM 198 C CE1 . HIS A 1 32 ? 15.812 28.317 -19.586 1.00 109.77 ? ? ? ? ? ? 34 HIS A CE1 1
+ATOM 199 N NE2 . HIS A 1 32 ? 14.772 27.647 -20.051 1.00 105.66 ? ? ? ? ? ? 34 HIS A NE2 1
+ATOM 200 N N . SER A 1 33 ? 15.303 27.064 -15.056 1.00 104.75 ? ? ? ? ? ? 35 SER A N 1
+ATOM 201 C CA . SER A 1 33 ? 14.079 27.599 -14.485 1.00 101.92 ? ? ? ? ? ? 35 SER A CA 1
+ATOM 202 C C . SER A 1 33 ? 13.450 28.601 -15.456 1.00 99.94 ? ? ? ? ? ? 35 SER A C 1
+ATOM 203 O O . SER A 1 33 ? 14.146 29.196 -16.272 1.00 101.93 ? ? ? ? ? ? 35 SER A O 1
+ATOM 204 C CB . SER A 1 33 ? 14.372 28.236 -13.124 1.00 103.64 ? ? ? ? ? ? 35 SER A CB 1
+ATOM 205 O OG . SER A 1 33 ? 13.401 29.202 -12.771 1.00 103.74 ? ? ? ? ? ? 35 SER A OG 1
+ATOM 206 N N . GLU A 1 34 ? 12.136 28.778 -15.372 1.00 95.30 ? ? ? ? ? ? 36 GLU A N 1
+ATOM 207 C CA . GLU A 1 34 ? 11.425 29.699 -16.249 1.00 92.35 ? ? ? ? ? ? 36 GLU A CA 1
+ATOM 208 C C . GLU A 1 34 ? 10.221 30.272 -15.520 1.00 90.03 ? ? ? ? ? ? 36 GLU A C 1
+ATOM 209 O O . GLU A 1 34 ? 9.296 29.543 -15.201 1.00 87.29 ? ? ? ? ? ? 36 GLU A O 1
+ATOM 210 C CB . GLU A 1 34 ? 10.977 28.964 -17.511 1.00 90.67 ? ? ? ? ? ? 36 GLU A CB 1
+ATOM 211 C CG . GLU A 1 34 ? 10.555 29.867 -18.650 1.00 90.72 ? ? ? ? ? ? 36 GLU A CG 1
+ATOM 212 C CD . GLU A 1 34 ? 11.736 30.565 -19.310 1.00 96.24 ? ? ? ? ? ? 36 GLU A CD 1
+ATOM 213 O OE1 . GLU A 1 34 ? 12.815 29.937 -19.462 1.00 99.38 ? ? ? ? ? ? 36 GLU A OE1 1
+ATOM 214 O OE2 . GLU A 1 34 ? 11.578 31.748 -19.685 1.00 98.37 ? ? ? ? ? ? 36 GLU A OE2 1
+ATOM 215 N N . LYS A 1 35 ? 10.235 31.569 -15.239 1.00 90.36 ? ? ? ? ? ? 37 LYS A N 1
+ATOM 216 C CA . LYS A 1 35 ? 9.139 32.178 -14.506 1.00 88.38 ? ? ? ? ? ? 37 LYS A CA 1
+ATOM 217 C C . LYS A 1 35 ? 7.977 32.484 -15.433 1.00 85.67 ? ? ? ? ? ? 37 LYS A C 1
+ATOM 218 O O . LYS A 1 35 ? 8.172 32.833 -16.592 1.00 86.06 ? ? ? ? ? ? 37 LYS A O 1
+ATOM 219 C CB . LYS A 1 35 ? 9.601 33.433 -13.768 1.00 91.44 ? ? ? ? ? ? 37 LYS A CB 1
+ATOM 220 N N . LEU A 1 36 ? 6.766 32.325 -14.915 1.00 81.92 ? ? ? ? ? ? 38 LEU A N 1
+ATOM 221 C CA . LEU A 1 36 ? 5.539 32.641 -15.640 1.00 78.89 ? ? ? ? ? ? 38 LEU A CA 1
+ATOM 222 C C . LEU A 1 36 ? 4.640 33.528 -14.797 1.00 78.12 ? ? ? ? ? ? 38 LEU A C 1
+ATOM 223 O O . LEU A 1 36 ? 4.498 33.299 -13.601 1.00 77.83 ? ? ? ? ? ? 38 LEU A O 1
+ATOM 224 C CB . LEU A 1 36 ? 4.770 31.368 -15.979 1.00 77.62 ? ? ? ? ? ? 38 LEU A CB 1
+ATOM 225 C CG . LEU A 1 36 ? 4.861 30.675 -17.336 1.00 76.31 ? ? ? ? ? ? 38 LEU A CG 1
+ATOM 226 C CD1 . LEU A 1 36 ? 3.481 30.149 -17.653 1.00 74.28 ? ? ? ? ? ? 38 LEU A CD1 1
+ATOM 227 C CD2 . LEU A 1 36 ? 5.328 31.599 -18.436 1.00 76.23 ? ? ? ? ? ? 38 LEU A CD2 1
+ATOM 228 N N . ASP A 1 37 ? 4.015 34.523 -15.417 1.00 77.70 ? ? ? ? ? ? 39 ASP A N 1
+ATOM 229 C CA . ASP A 1 37 ? 3.127 35.429 -14.691 1.00 77.42 ? ? ? ? ? ? 39 ASP A CA 1
+ATOM 230 C C . ASP A 1 37 ? 1.666 35.169 -15.004 1.00 73.58 ? ? ? ? ? ? 39 ASP A C 1
+ATOM 231 O O . ASP A 1 37 ? 1.352 34.676 -16.075 1.00 72.04 ? ? ? ? ? ? 39 ASP A O 1
+ATOM 232 C CB . ASP A 1 37 ? 3.473 36.886 -14.995 1.00 80.86 ? ? ? ? ? ? 39 ASP A CB 1
+ATOM 233 C CG . ASP A 1 37 ? 4.632 37.408 -14.159 1.00 86.94 ? ? ? ? ? ? 39 ASP A CG 1
+ATOM 234 O OD1 . ASP A 1 37 ? 4.986 36.781 -13.125 1.00 88.70 ? ? ? ? ? ? 39 ASP A OD1 1
+ATOM 235 O OD2 . ASP A 1 37 ? 5.178 38.463 -14.548 1.00 92.58 ? ? ? ? ? ? 39 ASP A OD2 1
+ATOM 236 N N . LYS A 1 38 ? 0.788 35.520 -14.065 1.00 71.09 ? ? ? ? ? ? 40 LYS A N 1
+ATOM 237 C CA . LYS A 1 38 ? -0.646 35.219 -14.127 1.00 67.44 ? ? ? ? ? ? 40 LYS A CA 1
+ATOM 238 C C . LYS A 1 38 ? -1.246 35.395 -15.514 1.00 65.75 ? ? ? ? ? ? 40 LYS A C 1
+ATOM 239 O O . LYS A 1 38 ? -1.274 36.506 -16.038 1.00 66.82 ? ? ? ? ? ? 40 LYS A O 1
+ATOM 240 C CB . LYS A 1 38 ? -1.408 36.092 -13.130 1.00 67.43 ? ? ? ? ? ? 40 LYS A CB 1
+ATOM 241 C CG . LYS A 1 38 ? -2.847 35.692 -12.912 1.00 65.33 ? ? ? ? ? ? 40 LYS A CG 1
+ATOM 242 C CD . LYS A 1 38 ? -3.496 36.530 -11.819 1.00 65.17 ? ? ? ? ? ? 40 LYS A CD 1
+ATOM 243 C CE . LYS A 1 38 ? -4.727 35.828 -11.238 1.00 64.58 ? ? ? ? ? ? 40 LYS A CE 1
+ATOM 244 N NZ . LYS A 1 38 ? -5.911 36.738 -11.093 1.00 64.29 ? ? ? ? ? ? 40 LYS A NZ 1
+ATOM 245 N N . GLY A 1 39 ? -1.710 34.288 -16.097 1.00 62.75 ? ? ? ? ? ? 41 GLY A N 1
+ATOM 246 C CA . GLY A 1 39 ? -2.358 34.280 -17.410 1.00 60.49 ? ? ? ? ? ? 41 GLY A CA 1
+ATOM 247 C C . GLY A 1 39 ? -1.471 33.947 -18.599 1.00 60.30 ? ? ? ? ? ? 41 GLY A C 1
+ATOM 248 O O . GLY A 1 39 ? -1.957 33.805 -19.718 1.00 58.95 ? ? ? ? ? ? 41 GLY A O 1
+ATOM 249 N N . GLU A 1 40 ? -0.167 33.843 -18.366 1.00 61.59 ? ? ? ? ? ? 42 GLU A N 1
+ATOM 250 C CA . GLU A 1 40 ? 0.777 33.499 -19.424 1.00 62.43 ? ? ? ? ? ? 42 GLU A CA 1
+ATOM 251 C C . GLU A 1 40 ? 0.720 32.015 -19.667 1.00 59.62 ? ? ? ? ? ? 42 GLU A C 1
+ATOM 252 O O . GLU A 1 40 ? 0.425 31.239 -18.761 1.00 58.37 ? ? ? ? ? ? 42 GLU A O 1
+ATOM 253 C CB . GLU A 1 40 ? 2.200 33.917 -19.056 1.00 65.52 ? ? ? ? ? ? 42 GLU A CB 1
+ATOM 254 C CG . GLU A 1 40 ? 2.523 35.352 -19.404 1.00 71.75 ? ? ? ? ? ? 42 GLU A CG 1
+ATOM 255 C CD . GLU A 1 40 ? 3.754 35.879 -18.701 1.00 79.02 ? ? ? ? ? ? 42 GLU A CD 1
+ATOM 256 O OE1 . GLU A 1 40 ? 4.375 35.124 -17.926 1.00 79.96 ? ? ? ? ? ? 42 GLU A OE1 1
+ATOM 257 O OE2 . GLU A 1 40 ? 4.097 37.059 -18.923 1.00 83.29 ? ? ? ? ? ? 42 GLU A OE2 1
+ATOM 258 N N . VAL A 1 41 ? 1.004 31.619 -20.895 1.00 58.12 ? ? ? ? ? ? 43 VAL A N 1
+ATOM 259 C CA . VAL A 1 41 ? 0.931 30.221 -21.282 1.00 55.42 ? ? ? ? ? ? 43 VAL A CA 1
+ATOM 260 C C . VAL A 1 41 ? 2.254 29.747 -21.855 1.00 57.22 ? ? ? ? ? ? 43 VAL A C 1
+ATOM 261 O O . VAL A 1 41 ? 2.823 30.381 -22.755 1.00 58.88 ? ? ? ? ? ? 43 VAL A O 1
+ATOM 262 C CB . VAL A 1 41 ? -0.180 29.994 -22.309 1.00 53.28 ? ? ? ? ? ? 43 VAL A CB 1
+ATOM 263 C CG1 . VAL A 1 41 ? -0.060 28.645 -22.920 1.00 50.49 ? ? ? ? ? ? 43 VAL A CG1 1
+ATOM 264 C CG2 . VAL A 1 41 ? -1.523 30.132 -21.664 1.00 49.78 ? ? ? ? ? ? 43 VAL A CG2 1
+ATOM 265 N N . LEU A 1 42 ? 2.738 28.629 -21.323 1.00 57.21 ? ? ? ? ? ? 44 LEU A N 1
+ATOM 266 C CA . LEU A 1 42 ? 3.960 28.037 -21.813 1.00 58.54 ? ? ? ? ? ? 44 LEU A CA 1
+ATOM 267 C C . LEU A 1 42 ? 3.633 26.718 -22.458 1.00 56.54 ? ? ? ? ? ? 44 LEU A C 1
+ATOM 268 O O . LEU A 1 42 ? 2.882 25.928 -21.899 1.00 54.68 ? ? ? ? ? ? 44 LEU A O 1
+ATOM 269 C CB . LEU A 1 42 ? 4.954 27.852 -20.680 1.00 60.35 ? ? ? ? ? ? 44 LEU A CB 1
+ATOM 270 C CG . LEU A 1 42 ? 6.378 27.476 -21.074 1.00 64.66 ? ? ? ? ? ? 44 LEU A CG 1
+ATOM 271 C CD1 . LEU A 1 42 ? 7.071 28.595 -21.816 1.00 69.92 ? ? ? ? ? ? 44 LEU A CD1 1
+ATOM 272 C CD2 . LEU A 1 42 ? 7.171 27.112 -19.839 1.00 67.81 ? ? ? ? ? ? 44 LEU A CD2 1
+ATOM 273 N N . ILE A 1 43 ? 4.162 26.504 -23.657 1.00 56.61 ? ? ? ? ? ? 45 ILE A N 1
+ATOM 274 C CA . ILE A 1 43 ? 4.086 25.207 -24.298 1.00 55.49 ? ? ? ? ? ? 45 ILE A CA 1
+ATOM 275 C C . ILE A 1 43 ? 5.487 24.630 -24.267 1.00 57.96 ? ? ? ? ? ? 45 ILE A C 1
+ATOM 276 O O . ILE A 1 43 ? 6.345 25.038 -25.046 1.00 60.01 ? ? ? ? ? ? 45 ILE A O 1
+ATOM 277 C CB . ILE A 1 43 ? 3.621 25.276 -25.757 1.00 54.45 ? ? ? ? ? ? 45 ILE A CB 1
+ATOM 278 C CG1 . ILE A 1 43 ? 2.749 26.525 -26.016 1.00 53.11 ? ? ? ? ? ? 45 ILE A CG1 1
+ATOM 279 C CG2 . ILE A 1 43 ? 2.966 23.955 -26.167 1.00 50.96 ? ? ? ? ? ? 45 ILE A CG2 1
+ATOM 280 C CD1 . ILE A 1 43 ? 1.330 26.489 -25.511 1.00 48.47 ? ? ? ? ? ? 45 ILE A CD1 1
+ATOM 281 N N . ALA A 1 44 ? 5.708 23.687 -23.351 1.00 58.61 ? ? ? ? ? ? 46 ALA A N 1
+ATOM 282 C CA . ALA A 1 44 ? 7.019 23.104 -23.115 1.00 60.53 ? ? ? ? ? ? 46 ALA A CA 1
+ATOM 283 C C . ALA A 1 44 ? 7.098 21.728 -23.724 1.00 60.54 ? ? ? ? ? ? 46 ALA A C 1
+ATOM 284 O O . ALA A 1 44 ? 6.238 20.893 -23.489 1.00 58.05 ? ? ? ? ? ? 46 ALA A O 1
+ATOM 285 C CB . ALA A 1 44 ? 7.298 23.026 -21.643 1.00 61.04 ? ? ? ? ? ? 46 ALA A CB 1
+ATOM 286 N N . GLN A 1 45 ? 8.142 21.522 -24.518 1.00 63.39 ? ? ? ? ? ? 47 GLN A N 1
+ATOM 287 C CA . GLN A 1 45 ? 8.433 20.236 -25.131 1.00 64.77 ? ? ? ? ? ? 47 GLN A CA 1
+ATOM 288 C C . GLN A 1 45 ? 9.599 19.592 -24.406 1.00 67.08 ? ? ? ? ? ? 47 GLN A C 1
+ATOM 289 O O . GLN A 1 45 ? 10.492 20.287 -23.920 1.00 69.41 ? ? ? ? ? ? 47 GLN A O 1
+ATOM 290 C CB . GLN A 1 45 ? 8.791 20.423 -26.602 1.00 65.44 ? ? ? ? ? ? 47 GLN A CB 1
+ATOM 291 C CG . GLN A 1 45 ? 8.796 19.131 -27.399 1.00 65.31 ? ? ? ? ? ? 47 GLN A CG 1
+ATOM 292 C CD . GLN A 1 45 ? 9.318 19.305 -28.829 1.00 68.03 ? ? ? ? ? ? 47 GLN A CD 1
+ATOM 293 O OE1 . GLN A 1 45 ? 10.214 20.129 -29.090 1.00 70.64 ? ? ? ? ? ? 47 GLN A OE1 1
+ATOM 294 N NE2 . GLN A 1 45 ? 8.757 18.518 -29.767 1.00 65.95 ? ? ? ? ? ? 47 GLN A NE2 1
+ATOM 295 N N . PHE A 1 46 ? 9.590 18.266 -24.339 1.00 67.71 ? ? ? ? ? ? 48 PHE A N 1
+ATOM 296 C CA . PHE A 1 46 ? 10.706 17.526 -23.777 1.00 70.43 ? ? ? ? ? ? 48 PHE A CA 1
+ATOM 297 C C . PHE A 1 46 ? 11.857 17.437 -24.766 1.00 74.96 ? ? ? ? ? ? 48 PHE A C 1
+ATOM 298 O O . PHE A 1 46 ? 11.675 16.991 -25.907 1.00 74.94 ? ? ? ? ? ? 48 PHE A O 1
+ATOM 299 C CB . PHE A 1 46 ? 10.269 16.127 -23.384 1.00 67.85 ? ? ? ? ? ? 48 PHE A CB 1
+ATOM 300 C CG . PHE A 1 46 ? 9.527 16.081 -22.099 1.00 64.51 ? ? ? ? ? ? 48 PHE A CG 1
+ATOM 301 C CD1 . PHE A 1 46 ? 10.218 16.130 -20.894 1.00 65.87 ? ? ? ? ? ? 48 PHE A CD1 1
+ATOM 302 C CD2 . PHE A 1 46 ? 8.130 15.992 -22.085 1.00 59.45 ? ? ? ? ? ? 48 PHE A CD2 1
+ATOM 303 C CE1 . PHE A 1 46 ? 9.533 16.094 -19.687 1.00 63.95 ? ? ? ? ? ? 48 PHE A CE1 1
+ATOM 304 C CE2 . PHE A 1 46 ? 7.427 15.953 -20.885 1.00 57.67 ? ? ? ? ? ? 48 PHE A CE2 1
+ATOM 305 C CZ . PHE A 1 46 ? 8.130 16.002 -19.680 1.00 60.02 ? ? ? ? ? ? 48 PHE A CZ 1
+ATOM 306 N N . THR A 1 47 ? 13.038 17.869 -24.334 1.00 80.48 ? ? ? ? ? ? 49 THR A N 1
+ATOM 307 C CA . THR A 1 47 ? 14.238 17.712 -25.140 1.00 86.44 ? ? ? ? ? ? 49 THR A CA 1
+ATOM 308 C C . THR A 1 47 ? 14.993 16.474 -24.653 1.00 88.73 ? ? ? ? ? ? 49 THR A C 1
+ATOM 309 O O . THR A 1 47 ? 14.523 15.780 -23.752 1.00 86.98 ? ? ? ? ? ? 49 THR A O 1
+ATOM 310 C CB . THR A 1 47 ? 15.135 18.969 -25.068 1.00 89.11 ? ? ? ? ? ? 49 THR A CB 1
+ATOM 311 O OG1 . THR A 1 47 ? 15.953 18.934 -23.892 1.00 92.76 ? ? ? ? ? ? 49 THR A OG1 1
+ATOM 312 C CG2 . THR A 1 47 ? 14.285 20.230 -25.055 1.00 88.83 ? ? ? ? ? ? 49 THR A CG2 1
+ATOM 313 N N . GLU A 1 48 ? 16.145 16.187 -25.257 1.00 93.73 ? ? ? ? ? ? 50 GLU A N 1
+ATOM 314 C CA . GLU A 1 48 ? 17.052 15.170 -24.714 1.00 98.04 ? ? ? ? ? ? 50 GLU A CA 1
+ATOM 315 C C . GLU A 1 48 ? 17.700 15.685 -23.409 1.00 99.89 ? ? ? ? ? ? 50 GLU A C 1
+ATOM 316 O O . GLU A 1 48 ? 17.792 14.952 -22.420 1.00 99.46 ? ? ? ? ? ? 50 GLU A O 1
+ATOM 317 C CB . GLU A 1 48 ? 18.103 14.731 -25.754 1.00 100.79 ? ? ? ? ? ? 50 GLU A CB 1
+ATOM 318 C CG . GLU A 1 48 ? 19.096 15.818 -26.196 0.50 107.62 ? ? ? ? ? ? 50 GLU A CG 1
+ATOM 319 C CD . GLU A 1 48 ? 20.357 15.251 -26.838 0.50 115.10 ? ? ? ? ? ? 50 GLU A CD 1
+ATOM 320 O OE1 . GLU A 1 48 ? 21.467 15.702 -26.482 0.50 120.30 ? ? ? ? ? ? 50 GLU A OE1 1
+ATOM 321 O OE2 . GLU A 1 48 ? 20.241 14.354 -27.697 0.50 115.44 ? ? ? ? ? ? 50 GLU A OE2 1
+ATOM 322 N N . HIS A 1 49 ? 18.108 16.957 -23.422 1.00 102.54 ? ? ? ? ? ? 51 HIS A N 1
+ATOM 323 C CA . HIS A 1 49 ? 18.615 17.674 -22.247 1.00 104.56 ? ? ? ? ? ? 51 HIS A CA 1
+ATOM 324 C C . HIS A 1 49 ? 17.684 17.578 -21.032 1.00 100.90 ? ? ? ? ? ? 51 HIS A C 1
+ATOM 325 O O . HIS A 1 49 ? 18.145 17.604 -19.888 1.00 102.24 ? ? ? ? ? ? 51 HIS A O 1
+ATOM 326 C CB . HIS A 1 49 ? 18.790 19.162 -22.576 1.00 107.45 ? ? ? ? ? ? 51 HIS A CB 1
+ATOM 327 C CG . HIS A 1 49 ? 19.959 19.466 -23.458 1.00 115.35 ? ? ? ? ? ? 51 HIS A CG 1
+ATOM 328 N ND1 . HIS A 1 49 ? 19.964 19.199 -24.811 1.00 117.92 ? ? ? ? ? ? 51 HIS A ND1 1
+ATOM 329 C CD2 . HIS A 1 49 ? 21.153 20.047 -23.185 1.00 122.56 ? ? ? ? ? ? 51 HIS A CD2 1
+ATOM 330 C CE1 . HIS A 1 49 ? 21.117 19.586 -25.330 1.00 123.61 ? ? ? ? ? ? 51 HIS A CE1 1
+ATOM 331 N NE2 . HIS A 1 49 ? 21.855 20.106 -24.366 1.00 126.48 ? ? ? ? ? ? 51 HIS A NE2 1
+ATOM 332 N N . THR A 1 50 ? 16.377 17.481 -21.294 1.00 95.68 ? ? ? ? ? ? 52 THR A N 1
+ATOM 333 C CA . THR A 1 50 ? 15.340 17.640 -20.268 1.00 90.19 ? ? ? ? ? ? 52 THR A CA 1
+ATOM 334 C C . THR A 1 50 ? 14.528 16.370 -20.027 1.00 86.57 ? ? ? ? ? ? 52 THR A C 1
+ATOM 335 O O . THR A 1 50 ? 13.629 16.031 -20.795 1.00 83.93 ? ? ? ? ? ? 52 THR A O 1
+ATOM 336 C CB . THR A 1 50 ? 14.419 18.847 -20.596 1.00 89.09 ? ? ? ? ? ? 52 THR A CB 1
+ATOM 337 O OG1 . THR A 1 50 ? 15.128 20.061 -20.323 1.00 91.82 ? ? ? ? ? ? 52 THR A OG1 1
+ATOM 338 C CG2 . THR A 1 50 ? 13.158 18.832 -19.761 1.00 84.32 ? ? ? ? ? ? 52 THR A CG2 1
+ATOM 339 N N . SER A 1 51 ? 14.863 15.686 -18.938 1.00 85.07 ? ? ? ? ? ? 53 SER A N 1
+ATOM 340 C CA . SER A 1 51 ? 14.183 14.465 -18.518 1.00 82.20 ? ? ? ? ? ? 53 SER A CA 1
+ATOM 341 C C . SER A 1 51 ? 12.860 14.724 -17.792 1.00 78.23 ? ? ? ? ? ? 53 SER A C 1
+ATOM 342 O O . SER A 1 51 ? 11.863 14.057 -18.069 1.00 75.30 ? ? ? ? ? ? 53 SER A O 1
+ATOM 343 C CB . SER A 1 51 ? 15.103 13.617 -17.631 1.00 84.25 ? ? ? ? ? ? 53 SER A CB 1
+ATOM 344 O OG . SER A 1 51 ? 15.508 14.324 -16.475 1.00 87.22 ? ? ? ? ? ? 53 SER A OG 1
+ATOM 345 N N . ALA A 1 52 ? 12.855 15.681 -16.867 1.00 76.66 ? ? ? ? ? ? 54 ALA A N 1
+ATOM 346 C CA . ALA A 1 52 ? 11.660 15.983 -16.082 1.00 73.63 ? ? ? ? ? ? 54 ALA A CA 1
+ATOM 347 C C . ALA A 1 52 ? 11.347 17.470 -16.020 1.00 72.67 ? ? ? ? ? ? 54 ALA A C 1
+ATOM 348 O O . ALA A 1 52 ? 12.231 18.295 -16.168 1.00 74.97 ? ? ? ? ? ? 54 ALA A O 1
+ATOM 349 C CB . ALA A 1 52 ? 11.807 15.427 -14.697 1.00 73.72 ? ? ? ? ? ? 54 ALA A CB 1
+ATOM 350 N N . ILE A 1 53 ? 10.078 17.799 -15.808 1.00 69.28 ? ? ? ? ? ? 55 ILE A N 1
+ATOM 351 C CA . ILE A 1 53 ? 9.644 19.182 -15.648 1.00 67.60 ? ? ? ? ? ? 55 ILE A CA 1
+ATOM 352 C C . ILE A 1 53 ? 8.807 19.315 -14.386 1.00 66.31 ? ? ? ? ? ? 55 ILE A C 1
+ATOM 353 O O . ILE A 1 53 ? 7.813 18.615 -14.234 1.00 63.74 ? ? ? ? ? ? 55 ILE A O 1
+ATOM 354 C CB . ILE A 1 53 ? 8.816 19.679 -16.852 1.00 66.27 ? ? ? ? ? ? 55 ILE A CB 1
+ATOM 355 C CG1 . ILE A 1 53 ? 9.678 19.756 -18.104 1.00 67.47 ? ? ? ? ? ? 55 ILE A CG1 1
+ATOM 356 C CG2 . ILE A 1 53 ? 8.217 21.057 -16.579 1.00 65.21 ? ? ? ? ? ? 55 ILE A CG2 1
+ATOM 357 C CD1 . ILE A 1 53 ? 8.873 19.776 -19.383 1.00 65.20 ? ? ? ? ? ? 55 ILE A CD1 1
+ATOM 358 N N . LYS A 1 54 ? 9.212 20.225 -13.498 1.00 67.56 ? ? ? ? ? ? 56 LYS A N 1
+ATOM 359 C CA . LYS A 1 54 ? 8.518 20.471 -12.242 1.00 66.86 ? ? ? ? ? ? 56 LYS A CA 1
+ATOM 360 C C . LYS A 1 54 ? 7.790 21.787 -12.345 1.00 66.25 ? ? ? ? ? ? 56 LYS A C 1
+ATOM 361 O O . LYS A 1 54 ? 8.325 22.736 -12.899 1.00 67.88 ? ? ? ? ? ? 56 LYS A O 1
+ATOM 362 C CB . LYS A 1 54 ? 9.524 20.526 -11.091 1.00 69.15 ? ? ? ? ? ? 56 LYS A CB 1
+ATOM 363 C CG . LYS A 1 54 ? 8.919 20.527 -9.688 1.00 66.38 ? ? ? ? ? ? 56 LYS A CG 1
+ATOM 364 C CD . LYS A 1 54 ? 9.898 21.069 -8.644 1.00 66.41 ? ? ? ? ? ? 56 LYS A CD 1
+ATOM 365 C CE . LYS A 1 54 ? 10.805 19.996 -8.061 1.00 66.08 ? ? ? ? ? ? 56 LYS A CE 1
+ATOM 366 N NZ . LYS A 1 54 ? 11.738 20.531 -7.020 1.00 66.38 ? ? ? ? ? ? 56 LYS A NZ 1
+ATOM 367 N N . VAL A 1 55 ? 6.569 21.843 -11.826 1.00 63.79 ? ? ? ? ? ? 57 VAL A N 1
+ATOM 368 C CA . VAL A 1 55 ? 5.805 23.088 -11.783 1.00 62.60 ? ? ? ? ? ? 57 VAL A CA 1
+ATOM 369 C C . VAL A 1 55 ? 5.508 23.478 -10.335 1.00 63.99 ? ? ? ? ? ? 57 VAL A C 1
+ATOM 370 O O . VAL A 1 55 ? 4.827 22.751 -9.607 1.00 62.58 ? ? ? ? ? ? 57 VAL A O 1
+ATOM 371 C CB . VAL A 1 55 ? 4.491 22.999 -12.582 1.00 60.05 ? ? ? ? ? ? 57 VAL A CB 1
+ATOM 372 C CG1 . VAL A 1 55 ? 3.777 24.330 -12.592 1.00 58.65 ? ? ? ? ? ? 57 VAL A CG1 1
+ATOM 373 C CG2 . VAL A 1 55 ? 4.759 22.561 -14.001 1.00 57.89 ? ? ? ? ? ? 57 VAL A CG2 1
+ATOM 374 N N . ARG A 1 56 ? 6.046 24.625 -9.926 1.00 67.06 ? ? ? ? ? ? 58 ARG A N 1
+ATOM 375 C CA . ARG A 1 56 ? 5.822 25.201 -8.602 1.00 68.68 ? ? ? ? ? ? 58 ARG A CA 1
+ATOM 376 C C . ARG A 1 56 ? 4.944 26.430 -8.775 1.00 68.31 ? ? ? ? ? ? 58 ARG A C 1
+ATOM 377 O O . ARG A 1 56 ? 5.295 27.346 -9.516 1.00 69.78 ? ? ? ? ? ? 58 ARG A O 1
+ATOM 378 C CB . ARG A 1 56 ? 7.149 25.622 -7.961 1.00 71.82 ? ? ? ? ? ? 58 ARG A CB 1
+ATOM 379 C CG . ARG A 1 56 ? 7.919 24.540 -7.264 1.00 71.32 ? ? ? ? ? ? 58 ARG A CG 1
+ATOM 380 C CD . ARG A 1 56 ? 8.899 25.124 -6.251 1.00 74.34 ? ? ? ? ? ? 58 ARG A CD 1
+ATOM 381 N NE . ARG A 1 56 ? 10.303 24.967 -6.641 1.00 76.63 ? ? ? ? ? ? 58 ARG A NE 1
+ATOM 382 C CZ . ARG A 1 56 ? 11.114 24.011 -6.180 1.00 77.74 ? ? ? ? ? ? 58 ARG A CZ 1
+ATOM 383 N NH1 . ARG A 1 56 ? 10.668 23.111 -5.308 1.00 77.26 ? ? ? ? ? ? 58 ARG A NH1 1
+ATOM 384 N NH2 . ARG A 1 56 ? 12.380 23.947 -6.590 1.00 79.00 ? ? ? ? ? ? 58 ARG A NH2 1
+ATOM 385 N N . GLY A 1 57 ? 3.795 26.450 -8.116 1.00 66.23 ? ? ? ? ? ? 59 GLY A N 1
+ATOM 386 C CA . GLY A 1 57 ? 2.891 27.591 -8.224 1.00 64.54 ? ? ? ? ? ? 59 GLY A CA 1
+ATOM 387 C C . GLY A 1 57 ? 1.515 27.161 -8.671 1.00 61.40 ? ? ? ? ? ? 59 GLY A C 1
+ATOM 388 O O . GLY A 1 57 ? 1.324 26.011 -9.023 1.00 60.50 ? ? ? ? ? ? 59 GLY A O 1
+ATOM 389 N N . LYS A 1 58 ? 0.553 28.077 -8.652 1.00 59.63 ? ? ? ? ? ? 60 LYS A N 1
+ATOM 390 C CA . LYS A 1 58 ? -0.823 27.767 -9.030 1.00 56.33 ? ? ? ? ? ? 60 LYS A CA 1
+ATOM 391 C C . LYS A 1 58 ? -0.937 27.782 -10.560 1.00 54.36 ? ? ? ? ? ? 60 LYS A C 1
+ATOM 392 O O . LYS A 1 58 ? -0.806 28.840 -11.173 1.00 55.40 ? ? ? ? ? ? 60 LYS A O 1
+ATOM 393 C CB . LYS A 1 58 ? -1.776 28.800 -8.402 1.00 56.75 ? ? ? ? ? ? 60 LYS A CB 1
+ATOM 394 C CG . LYS A 1 58 ? -3.130 28.251 -7.937 1.00 56.71 ? ? ? ? ? ? 60 LYS A CG 1
+ATOM 395 C CD . LYS A 1 58 ? -3.097 27.743 -6.485 1.00 57.00 ? ? ? ? ? ? 60 LYS A CD 1
+ATOM 396 C CE . LYS A 1 58 ? -4.401 27.012 -6.119 1.00 56.07 ? ? ? ? ? ? 60 LYS A CE 1
+ATOM 397 N N . ALA A 1 59 ? -1.157 26.623 -11.185 1.00 50.90 ? ? ? ? ? ? 61 ALA A N 1
+ATOM 398 C CA . ALA A 1 59 ? -1.229 26.563 -12.652 1.00 48.01 ? ? ? ? ? ? 61 ALA A CA 1
+ATOM 399 C C . ALA A 1 59 ? -2.205 25.512 -13.166 1.00 44.63 ? ? ? ? ? ? 61 ALA A C 1
+ATOM 400 O O . ALA A 1 59 ? -2.516 24.556 -12.458 1.00 43.62 ? ? ? ? ? ? 61 ALA A O 1
+ATOM 401 C CB . ALA A 1 59 ? 0.153 26.320 -13.244 1.00 49.49 ? ? ? ? ? ? 61 ALA A CB 1
+ATOM 402 N N . TYR A 1 60 ? -2.667 25.686 -14.404 1.00 41.70 ? ? ? ? ? ? 62 TYR A N 1
+ATOM 403 C CA . TYR A 1 60 ? -3.493 24.707 -15.082 1.00 38.07 ? ? ? ? ? ? 62 TYR A CA 1
+ATOM 404 C C . TYR A 1 60 ? -2.627 24.044 -16.134 1.00 37.82 ? ? ? ? ? ? 62 TYR A C 1
+ATOM 405 O O . TYR A 1 60 ? -1.998 24.722 -16.954 1.00 38.91 ? ? ? ? ? ? 62 TYR A O 1
+ATOM 406 C CB . TYR A 1 60 ? -4.671 25.417 -15.716 1.00 36.81 ? ? ? ? ? ? 62 TYR A CB 1
+ATOM 407 C CG . TYR A 1 60 ? -5.719 24.566 -16.417 1.00 33.24 ? ? ? ? ? ? 62 TYR A CG 1
+ATOM 408 C CD1 . TYR A 1 60 ? -6.553 23.709 -15.702 1.00 30.81 ? ? ? ? ? ? 62 TYR A CD1 1
+ATOM 409 C CD2 . TYR A 1 60 ? -5.925 24.669 -17.795 1.00 32.16 ? ? ? ? ? ? 62 TYR A CD2 1
+ATOM 410 C CE1 . TYR A 1 60 ? -7.554 22.938 -16.349 1.00 26.98 ? ? ? ? ? ? 62 TYR A CE1 1
+ATOM 411 C CE2 . TYR A 1 60 ? -6.915 23.914 -18.446 1.00 29.38 ? ? ? ? ? ? 62 TYR A CE2 1
+ATOM 412 C CZ . TYR A 1 60 ? -7.728 23.053 -17.716 1.00 26.79 ? ? ? ? ? ? 62 TYR A CZ 1
+ATOM 413 O OH . TYR A 1 60 ? -8.701 22.329 -18.381 1.00 24.12 ? ? ? ? ? ? 62 TYR A OH 1
+ATOM 414 N N . ILE A 1 61 ? -2.579 22.717 -16.097 1.00 36.07 ? ? ? ? ? ? 63 ILE A N 1
+ATOM 415 C CA . ILE A 1 61 ? -1.662 21.980 -16.938 1.00 35.83 ? ? ? ? ? ? 63 ILE A CA 1
+ATOM 416 C C . ILE A 1 61 ? -2.384 20.971 -17.798 1.00 33.41 ? ? ? ? ? ? 63 ILE A C 1
+ATOM 417 O O . ILE A 1 61 ? -3.202 20.217 -17.298 1.00 31.94 ? ? ? ? ? ? 63 ILE A O 1
+ATOM 418 C CB . ILE A 1 61 ? -0.610 21.239 -16.097 1.00 37.09 ? ? ? ? ? ? 63 ILE A CB 1
+ATOM 419 C CG1 . ILE A 1 61 ? 0.153 22.208 -15.183 1.00 40.08 ? ? ? ? ? ? 63 ILE A CG1 1
+ATOM 420 C CG2 . ILE A 1 61 ? 0.358 20.461 -17.018 1.00 38.40 ? ? ? ? ? ? 63 ILE A CG2 1
+ATOM 421 C CD1 . ILE A 1 61 ? 0.912 21.521 -14.083 1.00 42.02 ? ? ? ? ? ? 63 ILE A CD1 1
+ATOM 422 N N . GLN A 1 62 ? -2.075 20.961 -19.094 1.00 32.65 ? ? ? ? ? ? 64 GLN A N 1
+ATOM 423 C CA . GLN A 1 62 ? -2.645 19.966 -20.035 1.00 31.02 ? ? ? ? ? ? 64 GLN A CA 1
+ATOM 424 C C . GLN A 1 62 ? -1.536 19.076 -20.577 1.00 31.29 ? ? ? ? ? ? 64 GLN A C 1
+ATOM 425 O O . GLN A 1 62 ? -0.503 19.573 -21.072 1.00 33.32 ? ? ? ? ? ? 64 GLN A O 1
+ATOM 426 C CB . GLN A 1 62 ? -3.321 20.649 -21.251 1.00 30.42 ? ? ? ? ? ? 64 GLN A CB 1
+ATOM 427 C CG . GLN A 1 62 ? -4.366 21.714 -20.928 1.00 29.89 ? ? ? ? ? ? 64 GLN A CG 1
+ATOM 428 C CD . GLN A 1 62 ? -5.024 22.308 -22.172 1.00 30.22 ? ? ? ? ? ? 64 GLN A CD 1
+ATOM 429 O OE1 . GLN A 1 62 ? -4.345 22.746 -23.129 1.00 31.89 ? ? ? ? ? ? 64 GLN A OE1 1
+ATOM 430 N NE2 . GLN A 1 62 ? -6.362 22.351 -22.155 1.00 28.53 ? ? ? ? ? ? 64 GLN A NE2 1
+ATOM 431 N N . THR A 1 63 ? -1.751 17.773 -20.518 1.00 29.70 ? ? ? ? ? ? 65 THR A N 1
+ATOM 432 C CA . THR A 1 63 ? -0.825 16.842 -21.142 1.00 29.95 ? ? ? ? ? ? 65 THR A CA 1
+ATOM 433 C C . THR A 1 63 ? -1.610 15.830 -21.967 1.00 28.22 ? ? ? ? ? ? 65 THR A C 1
+ATOM 434 O O . THR A 1 63 ? -2.852 15.745 -21.879 1.00 26.39 ? ? ? ? ? ? 65 THR A O 1
+ATOM 435 C CB . THR A 1 63 ? -0.010 16.071 -20.095 1.00 30.81 ? ? ? ? ? ? 65 THR A CB 1
+ATOM 436 O OG1 . THR A 1 63 ? -0.897 15.297 -19.248 1.00 30.42 ? ? ? ? ? ? 65 THR A OG1 1
+ATOM 437 C CG2 . THR A 1 63 ? 0.824 17.023 -19.275 1.00 33.74 ? ? ? ? ? ? 65 THR A CG2 1
+ATOM 438 N N . ARG A 1 64 ? -0.886 15.027 -22.737 1.00 28.10 ? ? ? ? ? ? 66 ARG A N 1
+ATOM 439 C CA . ARG A 1 64 ? -1.516 13.903 -23.389 1.00 26.73 ? ? ? ? ? ? 66 ARG A CA 1
+ATOM 440 C C . ARG A 1 64 ? -2.410 13.108 -22.409 1.00 25.08 ? ? ? ? ? ? 66 ARG A C 1
+ATOM 441 O O . ARG A 1 64 ? -3.376 12.454 -22.828 1.00 23.73 ? ? ? ? ? ? 66 ARG A O 1
+ATOM 442 C CB . ARG A 1 64 ? -0.460 13.014 -24.044 1.00 27.91 ? ? ? ? ? ? 66 ARG A CB 1
+ATOM 443 C CG . ARG A 1 64 ? -1.032 11.692 -24.648 1.00 29.01 ? ? ? ? ? ? 66 ARG A CG 1
+ATOM 444 C CD . ARG A 1 64 ? -0.213 11.224 -25.909 1.00 33.87 ? ? ? ? ? ? 66 ARG A CD 1
+ATOM 445 N NE . ARG A 1 64 ? 1.113 10.719 -25.542 1.00 39.87 ? ? ? ? ? ? 66 ARG A NE 1
+ATOM 446 C CZ . ARG A 1 64 ? 1.273 9.451 -25.149 1.00 45.46 ? ? ? ? ? ? 66 ARG A CZ 1
+ATOM 447 N NH1 . ARG A 1 64 ? 2.466 9.006 -24.775 1.00 48.49 ? ? ? ? ? ? 66 ARG A NH1 1
+ATOM 448 N NH2 . ARG A 1 64 ? 0.208 8.625 -25.112 1.00 45.95 ? ? ? ? ? ? 66 ARG A NH2 1
+ATOM 449 N N . HIS A 1 65 ? -2.111 13.173 -21.107 1.00 24.86 ? ? ? ? ? ? 67 HIS A N 1
+ATOM 450 C CA . HIS A 1 65 ? -2.841 12.331 -20.131 1.00 24.10 ? ? ? ? ? ? 67 HIS A CA 1
+ATOM 451 C C . HIS A 1 65 ? -4.020 13.013 -19.469 1.00 23.34 ? ? ? ? ? ? 67 HIS A C 1
+ATOM 452 O O . HIS A 1 65 ? -4.610 12.431 -18.508 1.00 22.91 ? ? ? ? ? ? 67 HIS A O 1
+ATOM 453 C CB . HIS A 1 65 ? -1.918 11.730 -19.064 1.00 24.80 ? ? ? ? ? ? 67 HIS A CB 1
+ATOM 454 C CG . HIS A 1 65 ? -0.816 10.907 -19.640 1.00 27.48 ? ? ? ? ? ? 67 HIS A CG 1
+ATOM 455 N ND1 . HIS A 1 65 ? -0.956 10.191 -20.818 1.00 28.09 ? ? ? ? ? ? 67 HIS A ND1 1
+ATOM 456 C CD2 . HIS A 1 65 ? 0.447 10.682 -19.209 1.00 30.60 ? ? ? ? ? ? 67 HIS A CD2 1
+ATOM 457 C CE1 . HIS A 1 65 ? 0.181 9.571 -21.091 1.00 30.69 ? ? ? ? ? ? 67 HIS A CE1 1
+ATOM 458 N NE2 . HIS A 1 65 ? 1.041 9.835 -20.121 1.00 32.56 ? ? ? ? ? ? 67 HIS A NE2 1
+ATOM 459 N N . GLY A 1 66 ? -4.357 14.217 -19.977 1.00 23.45 ? ? ? ? ? ? 68 GLY A N 1
+ATOM 460 C CA . GLY A 1 66 ? -5.543 14.957 -19.528 1.00 23.05 ? ? ? ? ? ? 68 GLY A CA 1
+ATOM 461 C C . GLY A 1 66 ? -5.125 16.212 -18.813 1.00 23.58 ? ? ? ? ? ? 68 GLY A C 1
+ATOM 462 O O . GLY A 1 66 ? -3.974 16.630 -18.952 1.00 24.68 ? ? ? ? ? ? 68 GLY A O 1
+ATOM 463 N N . VAL A 1 67 ? -6.046 16.822 -18.054 1.00 23.73 ? ? ? ? ? ? 69 VAL A N 1
+ATOM 464 C CA . VAL A 1 67 ? -5.685 18.035 -17.310 1.00 25.29 ? ? ? ? ? ? 69 VAL A CA 1
+ATOM 465 C C . VAL A 1 67 ? -5.378 17.774 -15.842 1.00 27.38 ? ? ? ? ? ? 69 VAL A C 1
+ATOM 466 O O . VAL A 1 67 ? -5.799 16.787 -15.265 1.00 26.03 ? ? ? ? ? ? 69 VAL A O 1
+ATOM 467 C CB . VAL A 1 67 ? -6.706 19.173 -17.463 1.00 24.18 ? ? ? ? ? ? 69 VAL A CB 1
+ATOM 468 C CG1 . VAL A 1 67 ? -7.328 19.087 -18.796 1.00 23.47 ? ? ? ? ? ? 69 VAL A CG1 1
+ATOM 469 C CG2 . VAL A 1 67 ? -7.792 19.078 -16.407 1.00 23.38 ? ? ? ? ? ? 69 VAL A CG2 1
+ATOM 470 N N . ILE A 1 68 ? -4.609 18.685 -15.274 1.00 31.58 ? ? ? ? ? ? 70 ILE A N 1
+ATOM 471 C CA . ILE A 1 68 ? -4.257 18.667 -13.875 1.00 35.85 ? ? ? ? ? ? 70 ILE A CA 1
+ATOM 472 C C . ILE A 1 68 ? -3.894 20.103 -13.437 1.00 40.48 ? ? ? ? ? ? 70 ILE A C 1
+ATOM 473 O O . ILE A 1 68 ? -3.442 20.943 -14.252 1.00 41.26 ? ? ? ? ? ? 70 ILE A O 1
+ATOM 474 C CB . ILE A 1 68 ? -3.137 17.660 -13.591 1.00 35.31 ? ? ? ? ? ? 70 ILE A CB 1
+ATOM 475 C CG1 . ILE A 1 68 ? -3.062 17.400 -12.099 1.00 34.94 ? ? ? ? ? ? 70 ILE A CG1 1
+ATOM 476 C CG2 . ILE A 1 68 ? -1.813 18.148 -14.144 1.00 36.89 ? ? ? ? ? ? 70 ILE A CG2 1
+ATOM 477 C CD1 . ILE A 1 68 ? -2.514 16.052 -11.774 1.00 34.03 ? ? ? ? ? ? 70 ILE A CD1 1
+ATOM 478 N N . GLU A 1 69 ? -4.123 20.367 -12.150 1.00 45.39 ? ? ? ? ? ? 71 GLU A N 1
+ATOM 479 C CA . GLU A 1 69 ? -3.959 21.684 -11.556 1.00 51.34 ? ? ? ? ? ? 71 GLU A CA 1
+ATOM 480 C C . GLU A 1 69 ? -2.832 21.594 -10.527 1.00 55.11 ? ? ? ? ? ? 71 GLU A C 1
+ATOM 481 O O . GLU A 1 69 ? -2.859 20.721 -9.664 1.00 55.41 ? ? ? ? ? ? 71 GLU A O 1
+ATOM 482 C CB . GLU A 1 69 ? -5.285 22.073 -10.896 1.00 50.78 ? ? ? ? ? ? 71 GLU A CB 1
+ATOM 483 C CG . GLU A 1 69 ? -5.358 23.453 -10.275 1.00 56.29 ? ? ? ? ? ? 71 GLU A CG 1
+ATOM 484 C CD . GLU A 1 69 ? -6.733 23.756 -9.687 1.00 59.81 ? ? ? ? ? ? 71 GLU A CD 1
+ATOM 485 O OE1 . GLU A 1 69 ? -6.805 24.062 -8.476 1.00 61.66 ? ? ? ? ? ? 71 GLU A OE1 1
+ATOM 486 O OE2 . GLU A 1 69 ? -7.742 23.685 -10.439 1.00 59.40 ? ? ? ? ? ? 71 GLU A OE2 1
+ATOM 487 N N . SER A 1 70 ? -1.830 22.463 -10.633 1.00 60.26 ? ? ? ? ? ? 72 SER A N 1
+ATOM 488 C CA . SER A 1 70 ? -0.785 22.528 -9.618 1.00 65.19 ? ? ? ? ? ? 72 SER A CA 1
+ATOM 489 C C . SER A 1 70 ? -1.191 23.554 -8.582 1.00 67.72 ? ? ? ? ? ? 72 SER A C 1
+ATOM 490 O O . SER A 1 70 ? -1.586 24.664 -8.933 1.00 68.67 ? ? ? ? ? ? 72 SER A O 1
+ATOM 491 C CB . SER A 1 70 ? 0.566 22.885 -10.232 1.00 66.81 ? ? ? ? ? ? 72 SER A CB 1
+ATOM 492 O OG . SER A 1 70 ? 0.520 24.141 -10.869 1.00 69.19 ? ? ? ? ? ? 72 SER A OG 1
+ATOM 493 N N . GLU A 1 71 ? -1.109 23.173 -7.312 1.00 70.07 ? ? ? ? ? ? 73 GLU A N 1
+ATOM 494 C CA . GLU A 1 71 ? -1.494 24.038 -6.212 1.00 72.36 ? ? ? ? ? ? 73 GLU A CA 1
+ATOM 495 C C . GLU A 1 71 ? -0.236 24.266 -5.347 1.00 75.16 ? ? ? ? ? ? 73 GLU A C 1
+ATOM 496 O O . GLU A 1 71 ? -0.249 24.010 -4.173 1.00 77.08 ? ? ? ? ? ? 73 GLU A O 1
+ATOM 497 C CB . GLU A 1 71 ? -2.606 23.360 -5.394 1.00 71.07 ? ? ? ? ? ? 73 GLU A CB 1
+ATOM 498 C CG . GLU A 1 71 ? -3.410 22.310 -6.167 1.00 69.29 ? ? ? ? ? ? 73 GLU A CG 1
+ATOM 499 C CD . GLU A 1 71 ? -4.836 22.110 -5.652 1.00 67.49 ? ? ? ? ? ? 73 GLU A CD 1
+ATOM 500 O OE1 . GLU A 1 71 ? -5.627 23.072 -5.780 1.00 67.26 ? ? ? ? ? ? 73 GLU A OE1 1
+ATOM 501 O OE2 . GLU A 1 71 ? -5.169 20.998 -5.157 1.00 64.72 ? ? ? ? ? ? 73 GLU A OE2 1
+ATOM 502 N N . GLY A 1 72 ? 0.917 24.600 -5.926 1.00 75.64 ? ? ? ? ? ? 74 GLY A N 1
+ATOM 503 C CA . GLY A 1 72 ? 2.179 24.627 -5.145 1.00 76.28 ? ? ? ? ? ? 74 GLY A CA 1
+ATOM 504 C C . GLY A 1 72 ? 2.532 25.958 -4.485 1.00 77.39 ? ? ? ? ? ? 74 GLY A C 1
+ATOM 505 O O . GLY A 1 72 ? 1.761 26.914 -4.592 1.00 77.60 ? ? ? ? ? ? 74 GLY A O 1
+ATOM 506 N N . LYS A 1 73 ? 3.692 26.048 -3.818 1.00 78.11 ? ? ? ? ? ? 75 LYS A N 1
+ATOM 507 C CA . LYS A 1 73 ? 4.129 27.336 -3.223 1.00 79.14 ? ? ? ? ? ? 75 LYS A CA 1
+ATOM 508 C C . LYS A 1 73 ? 4.479 28.474 -4.244 1.00 79.69 ? ? ? ? ? ? 75 LYS A C 1
+ATOM 509 O O . LYS A 1 73 ? 5.535 28.516 -4.903 1.00 79.72 ? ? ? ? ? ? 75 LYS A O 1
+ATOM 510 C CB . LYS A 1 73 ? 5.211 27.143 -2.149 1.00 79.82 ? ? ? ? ? ? 75 LYS A CB 1
+ATOM 511 C CG . LYS A 1 73 ? 6.646 27.001 -2.680 1.00 82.03 ? ? ? ? ? ? 75 LYS A CG 1
+ATOM 512 C CD . LYS A 1 73 ? 7.702 26.968 -1.556 1.00 83.81 ? ? ? ? ? ? 75 LYS A CD 1
+ATOM 513 C CE . LYS A 1 73 ? 9.130 26.847 -2.110 1.00 84.65 ? ? ? ? ? ? 75 LYS A CE 1
+ATOM 514 N NZ . LYS A 1 73 ? 10.106 26.489 -1.037 1.00 84.64 ? ? ? ? ? ? 75 LYS A NZ 1
diff --git a/modules/seq/alg/tests/testfiles/validate_segres_aln_breakage.mmcif b/modules/seq/alg/tests/testfiles/validate_segres_aln_breakage.mmcif
new file mode 100644
index 0000000000000000000000000000000000000000..0d66b8fa227e343ff23e6c413a9de746b19c68af
--- /dev/null
+++ b/modules/seq/alg/tests/testfiles/validate_segres_aln_breakage.mmcif
@@ -0,0 +1,560 @@
+data_3BAR
+# based on 3AQD
+_entry.id 3BAR
+#
+loop_
+_entity.id
+_entity.type
+_entity.src_method
+_entity.pdbx_description
+_entity.formula_weight
+_entity.pdbx_number_of_molecules
+_entity.details
+1 polymer man 'Transcription attenuation protein mtrB' 8257.458 22 ?
+2 water nat water 18.015 7 ?
+#
+_entity_poly.entity_id 1
+_entity_poly.type 'polypeptide(L)'
+_entity_poly.nstd_linkage no
+_entity_poly.nstd_monomer no
+_entity_poly.pdbx_seq_one_letter_code MYTNSDFVVIKALEDGVNVIGLTRGADTRFHHSEKLDKGEVLIAQFTEHTSAIKVRGKAYIQTRHGVIESEKK
+_entity_poly.pdbx_seq_one_letter_code_can MYTNSDFVVIKALEDGVNVIGLTRGADTRFHHSEKLDKGEVLIAQFTEHTSAIKVRGKAYIQTRHGVIESEKK
+_entity_poly.pdbx_strand_id A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V
+#
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_entity_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.B_iso_or_equiv
+_atom_site.Cartn_x_esd
+_atom_site.Cartn_y_esd
+_atom_site.Cartn_z_esd
+_atom_site.occupancy_esd
+_atom_site.B_iso_or_equiv_esd
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_comp_id
+_atom_site.auth_asym_id
+_atom_site.auth_atom_id
+_atom_site.pdbx_PDB_model_num
+ATOM 1 N N . SER A 1 5 ? 8.892 13.236 -28.550 1.00 81.62 ? ? ? ? ? ? 7 SER A N 1
+ATOM 2 C CA . SER A 1 5 ? 8.449 14.550 -29.128 1.00 80.98 ? ? ? ? ? ? 7 SER A CA 1
+ATOM 3 C C . SER A 1 5 ? 7.181 15.159 -28.476 1.00 77.44 ? ? ? ? ? ? 7 SER A C 1
+ATOM 4 O O . SER A 1 5 ? 6.463 15.940 -29.117 1.00 76.80 ? ? ? ? ? ? 7 SER A O 1
+ATOM 5 C CB . SER A 1 5 ? 8.239 14.416 -30.651 1.00 81.96 ? ? ? ? ? ? 7 SER A CB 1
+ATOM 6 O OG . SER A 1 5 ? 9.441 14.629 -31.378 1.00 87.04 ? ? ? ? ? ? 7 SER A OG 1
+ATOM 7 N N . ASP A 1 6 ? 6.910 14.822 -27.217 1.00 73.87 ? ? ? ? ? ? 8 ASP A N 1
+ATOM 8 C CA . ASP A 1 6 ? 5.670 15.258 -26.582 1.00 69.40 ? ? ? ? ? ? 8 ASP A CA 1
+ATOM 9 C C . ASP A 1 6 ? 5.834 16.550 -25.785 1.00 68.43 ? ? ? ? ? ? 8 ASP A C 1
+ATOM 10 O O . ASP A 1 6 ? 6.944 16.907 -25.403 1.00 70.90 ? ? ? ? ? ? 8 ASP A O 1
+ATOM 11 C CB . ASP A 1 6 ? 5.104 14.146 -25.703 1.00 67.64 ? ? ? ? ? ? 8 ASP A CB 1
+ATOM 12 C CG . ASP A 1 6 ? 3.570 14.083 -25.751 1.00 64.57 ? ? ? ? ? ? 8 ASP A CG 1
+ATOM 13 O OD1 . ASP A 1 6 ? 2.949 15.085 -26.195 1.00 63.11 ? ? ? ? ? ? 8 ASP A OD1 1
+ATOM 14 O OD2 . ASP A 1 6 ? 2.984 13.032 -25.353 1.00 62.17 ? ? ? ? ? ? 8 ASP A OD2 1
+ATOM 15 N N . PHE A 1 7 ? 4.726 17.246 -25.545 1.00 64.53 ? ? ? ? ? ? 9 PHE A N 1
+ATOM 16 C CA . PHE A 1 7 ? 4.750 18.548 -24.879 1.00 61.94 ? ? ? ? ? ? 9 PHE A CA 1
+ATOM 17 C C . PHE A 1 7 ? 3.673 18.732 -23.796 1.00 57.92 ? ? ? ? ? ? 9 PHE A C 1
+ATOM 18 O O . PHE A 1 7 ? 2.693 17.987 -23.744 1.00 55.70 ? ? ? ? ? ? 9 PHE A O 1
+ATOM 19 C CB . PHE A 1 7 ? 4.618 19.664 -25.915 1.00 63.43 ? ? ? ? ? ? 9 PHE A CB 1
+ATOM 20 C CG . PHE A 1 7 ? 3.282 19.718 -26.567 1.00 62.41 ? ? ? ? ? ? 9 PHE A CG 1
+ATOM 21 C CD1 . PHE A 1 7 ? 2.231 20.382 -25.970 1.00 61.82 ? ? ? ? ? ? 9 PHE A CD1 1
+ATOM 22 C CD2 . PHE A 1 7 ? 3.075 19.105 -27.775 1.00 64.02 ? ? ? ? ? ? 9 PHE A CD2 1
+ATOM 23 C CE1 . PHE A 1 7 ? 0.988 20.428 -26.567 1.00 60.16 ? ? ? ? ? ? 9 PHE A CE1 1
+ATOM 24 C CE2 . PHE A 1 7 ? 1.832 19.145 -28.383 1.00 62.57 ? ? ? ? ? ? 9 PHE A CE2 1
+ATOM 25 C CZ . PHE A 1 7 ? 0.783 19.808 -27.775 1.00 60.25 ? ? ? ? ? ? 9 PHE A CZ 1
+ATOM 26 N N . VAL A 1 8 ? 3.861 19.735 -22.938 1.00 55.04 ? ? ? ? ? ? 10 VAL A N 1
+ATOM 27 C CA . VAL A 1 8 ? 2.861 20.095 -21.949 1.00 50.88 ? ? ? ? ? ? 10 VAL A CA 1
+ATOM 28 C C . VAL A 1 8 ? 2.487 21.551 -22.098 1.00 49.54 ? ? ? ? ? ? 10 VAL A C 1
+ATOM 29 O O . VAL A 1 8 ? 3.323 22.385 -22.446 1.00 50.85 ? ? ? ? ? ? 10 VAL A O 1
+ATOM 30 C CB . VAL A 1 8 ? 3.326 19.851 -20.511 1.00 51.03 ? ? ? ? ? ? 10 VAL A CB 1
+ATOM 31 C CG1 . VAL A 1 8 ? 3.832 18.442 -20.371 1.00 50.13 ? ? ? ? ? ? 10 VAL A CG1 1
+ATOM 32 C CG2 . VAL A 1 8 ? 4.402 20.826 -20.090 1.00 53.19 ? ? ? ? ? ? 10 VAL A CG2 1
+ATOM 33 N N . VAL A 1 9 ? 1.215 21.844 -21.842 1.00 46.06 ? ? ? ? ? ? 11 VAL A N 1
+ATOM 34 C CA . VAL A 1 9 ? 0.687 23.206 -21.880 1.00 44.00 ? ? ? ? ? ? 11 VAL A CA 1
+ATOM 35 C C . VAL A 1 9 ? 0.489 23.603 -20.434 1.00 44.21 ? ? ? ? ? ? 11 VAL A C 1
+ATOM 36 O O . VAL A 1 9 ? -0.170 22.877 -19.678 1.00 42.41 ? ? ? ? ? ? 11 VAL A O 1
+ATOM 37 C CB . VAL A 1 9 ? -0.661 23.252 -22.624 1.00 42.00 ? ? ? ? ? ? 11 VAL A CB 1
+ATOM 38 C CG1 . VAL A 1 9 ? -1.295 24.607 -22.528 1.00 40.79 ? ? ? ? ? ? 11 VAL A CG1 1
+ATOM 39 C CG2 . VAL A 1 9 ? -0.455 22.906 -24.078 1.00 40.13 ? ? ? ? ? ? 11 VAL A CG2 1
+ATOM 40 N N . ILE A 1 10 ? 1.076 24.738 -20.056 1.00 46.10 ? ? ? ? ? ? 12 ILE A N 1
+ATOM 41 C CA . ILE A 1 10 ? 1.003 25.240 -18.696 1.00 47.51 ? ? ? ? ? ? 12 ILE A CA 1
+ATOM 42 C C . ILE A 1 10 ? 0.516 26.657 -18.743 1.00 48.05 ? ? ? ? ? ? 12 ILE A C 1
+ATOM 43 O O . ILE A 1 10 ? 1.137 27.508 -19.380 1.00 49.65 ? ? ? ? ? ? 12 ILE A O 1
+ATOM 44 C CB . ILE A 1 10 ? 2.374 25.247 -18.012 1.00 49.28 ? ? ? ? ? ? 12 ILE A CB 1
+ATOM 45 C CG1 . ILE A 1 10 ? 2.981 23.848 -18.003 1.00 49.95 ? ? ? ? ? ? 12 ILE A CG1 1
+ATOM 46 C CG2 . ILE A 1 10 ? 2.247 25.753 -16.603 1.00 50.91 ? ? ? ? ? ? 12 ILE A CG2 1
+ATOM 47 C CD1 . ILE A 1 10 ? 4.435 23.827 -17.677 1.00 54.16 ? ? ? ? ? ? 12 ILE A CD1 1
+ATOM 48 N N . LYS A 1 11 ? -0.606 26.901 -18.076 1.00 47.39 ? ? ? ? ? ? 13 LYS A N 1
+ATOM 49 C CA . LYS A 1 11 ? -1.139 28.252 -17.917 1.00 48.23 ? ? ? ? ? ? 13 LYS A CA 1
+ATOM 50 C C . LYS A 1 11 ? -0.998 28.660 -16.473 1.00 50.10 ? ? ? ? ? ? 13 LYS A C 1
+ATOM 51 O O . LYS A 1 11 ? -1.441 27.931 -15.579 1.00 49.40 ? ? ? ? ? ? 13 LYS A O 1
+ATOM 52 C CB . LYS A 1 11 ? -2.609 28.311 -18.304 1.00 46.00 ? ? ? ? ? ? 13 LYS A CB 1
+ATOM 53 C CG . LYS A 1 11 ? -3.144 29.706 -18.267 1.00 45.91 ? ? ? ? ? ? 13 LYS A CG 1
+ATOM 54 C CD . LYS A 1 11 ? -4.640 29.741 -18.402 1.00 43.12 ? ? ? ? ? ? 13 LYS A CD 1
+ATOM 55 C CE . LYS A 1 11 ? -5.103 31.182 -18.619 1.00 44.02 ? ? ? ? ? ? 13 LYS A CE 1
+ATOM 56 N NZ . LYS A 1 11 ? -6.563 31.312 -18.363 1.00 43.35 ? ? ? ? ? ? 13 LYS A NZ 1
+ATOM 57 N N . ALA A 1 12 ? -0.379 29.818 -16.242 1.00 53.49 ? ? ? ? ? ? 14 ALA A N 1
+ATOM 58 C CA . ALA A 1 12 ? -0.115 30.296 -14.876 1.00 55.56 ? ? ? ? ? ? 14 ALA A CA 1
+ATOM 59 C C . ALA A 1 12 ? -1.354 30.960 -14.272 1.00 55.44 ? ? ? ? ? ? 14 ALA A C 1
+ATOM 60 O O . ALA A 1 12 ? -1.938 31.848 -14.881 1.00 55.76 ? ? ? ? ? ? 14 ALA A O 1
+ATOM 61 C CB . ALA A 1 12 ? 1.042 31.240 -14.890 1.00 58.43 ? ? ? ? ? ? 14 ALA A CB 1
+ATOM 62 N N . LEU A 1 13 ? -1.767 30.514 -13.093 1.00 55.02 ? ? ? ? ? ? 15 LEU A N 1
+ATOM 63 C CA . LEU A 1 13 ? -2.966 31.063 -12.438 1.00 55.23 ? ? ? ? ? ? 15 LEU A CA 1
+ATOM 64 C C . LEU A 1 13 ? -2.665 32.145 -11.380 1.00 58.70 ? ? ? ? ? ? 15 LEU A C 1
+ATOM 65 O O . LEU A 1 13 ? -3.574 32.758 -10.809 1.00 58.84 ? ? ? ? ? ? 15 LEU A O 1
+ATOM 66 C CB . LEU A 1 13 ? -3.811 29.932 -11.832 1.00 52.50 ? ? ? ? ? ? 15 LEU A CB 1
+ATOM 67 C CG . LEU A 1 13 ? -4.415 28.951 -12.839 1.00 47.91 ? ? ? ? ? ? 15 LEU A CG 1
+ATOM 68 C CD1 . LEU A 1 13 ? -4.953 27.698 -12.151 1.00 44.21 ? ? ? ? ? ? 15 LEU A CD1 1
+ATOM 69 C CD2 . LEU A 1 13 ? -5.494 29.672 -13.668 1.00 46.05 ? ? ? ? ? ? 15 LEU A CD2 1
+ATOM 70 N N . GLU A 1 14 ? -1.379 32.359 -11.120 1.00 62.66 ? ? ? ? ? ? 16 GLU A N 1
+ATOM 71 C CA . GLU A 1 14 ? -0.899 33.425 -10.252 1.00 67.00 ? ? ? ? ? ? 16 GLU A CA 1
+ATOM 72 C C . GLU A 1 14 ? 0.409 33.922 -10.836 1.00 70.32 ? ? ? ? ? ? 16 GLU A C 1
+ATOM 73 O O . GLU A 1 14 ? 0.914 33.339 -11.785 1.00 70.03 ? ? ? ? ? ? 16 GLU A O 1
+ATOM 74 C CB . GLU A 1 14 ? -0.696 32.923 -8.819 1.00 67.19 ? ? ? ? ? ? 16 GLU A CB 1
+ATOM 75 C CG . GLU A 1 14 ? 0.432 31.895 -8.625 1.00 68.58 ? ? ? ? ? ? 16 GLU A CG 1
+ATOM 76 C CD . GLU A 1 14 ? 0.454 31.270 -7.222 1.00 70.39 ? ? ? ? ? ? 16 GLU A CD 1
+ATOM 77 O OE1 . GLU A 1 14 ? -0.457 31.541 -6.412 1.00 71.02 ? ? ? ? ? ? 16 GLU A OE1 1
+ATOM 78 O OE2 . GLU A 1 14 ? 1.387 30.491 -6.926 1.00 71.29 ? ? ? ? ? ? 16 GLU A OE2 1
+ATOM 79 N N . ASP A 1 15 ? 0.955 35.001 -10.285 1.00 74.75 ? ? ? ? ? ? 17 ASP A N 1
+ATOM 80 C CA . ASP A 1 15 ? 2.250 35.491 -10.740 1.00 78.78 ? ? ? ? ? ? 17 ASP A CA 1
+ATOM 81 C C . ASP A 1 15 ? 3.325 34.615 -10.138 1.00 79.87 ? ? ? ? ? ? 17 ASP A C 1
+ATOM 82 O O . ASP A 1 15 ? 3.099 33.950 -9.124 1.00 79.33 ? ? ? ? ? ? 17 ASP A O 1
+ATOM 83 C CB . ASP A 1 15 ? 2.475 36.953 -10.336 1.00 81.65 ? ? ? ? ? ? 17 ASP A CB 1
+ATOM 84 C CG . ASP A 1 15 ? 1.621 37.937 -11.140 1.00 83.16 ? ? ? ? ? ? 17 ASP A CG 1
+ATOM 85 O OD1 . ASP A 1 15 ? 1.344 37.691 -12.326 1.00 82.40 ? ? ? ? ? ? 17 ASP A OD1 1
+ATOM 86 O OD2 . ASP A 1 15 ? 1.231 38.982 -10.589 1.00 86.46 ? ? ? ? ? ? 17 ASP A OD2 1
+ATOM 87 N N . GLY A 1 16 ? 4.489 34.606 -10.778 1.00 81.58 ? ? ? ? ? ? 18 GLY A N 1
+ATOM 88 C CA . GLY A 1 16 ? 5.660 33.903 -10.248 1.00 82.57 ? ? ? ? ? ? 18 GLY A CA 1
+ATOM 89 C C . GLY A 1 16 ? 5.555 32.392 -10.154 1.00 80.35 ? ? ? ? ? ? 18 GLY A C 1
+ATOM 90 O O . GLY A 1 16 ? 6.059 31.793 -9.215 1.00 81.29 ? ? ? ? ? ? 18 GLY A O 1
+ATOM 91 N N . VAL A 1 17 ? 4.892 31.781 -11.128 1.00 77.56 ? ? ? ? ? ? 19 VAL A N 1
+ATOM 92 C CA . VAL A 1 17 ? 4.885 30.336 -11.259 1.00 74.50 ? ? ? ? ? ? 19 VAL A CA 1
+ATOM 93 C C . VAL A 1 17 ? 6.239 29.942 -11.826 1.00 76.68 ? ? ? ? ? ? 19 VAL A C 1
+ATOM 94 O O . VAL A 1 17 ? 6.799 30.655 -12.655 1.00 78.24 ? ? ? ? ? ? 19 VAL A O 1
+ATOM 95 C CB . VAL A 1 17 ? 3.755 29.861 -12.187 1.00 71.56 ? ? ? ? ? ? 19 VAL A CB 1
+ATOM 96 C CG1 . VAL A 1 17 ? 3.820 28.364 -12.384 1.00 67.63 ? ? ? ? ? ? 19 VAL A CG1 1
+ATOM 97 C CG2 . VAL A 1 17 ? 2.409 30.247 -11.611 1.00 67.92 ? ? ? ? ? ? 19 VAL A CG2 1
+ATOM 98 N N . ASN A 1 18 ? 6.764 28.812 -11.381 1.00 77.33 ? ? ? ? ? ? 20 ASN A N 1
+ATOM 99 C CA . ASN A 1 18 ? 8.086 28.396 -11.775 1.00 79.46 ? ? ? ? ? ? 20 ASN A CA 1
+ATOM 100 C C . ASN A 1 18 ? 8.067 27.069 -12.528 1.00 77.29 ? ? ? ? ? ? 20 ASN A C 1
+ATOM 101 O O . ASN A 1 18 ? 7.635 26.058 -11.989 1.00 75.60 ? ? ? ? ? ? 20 ASN A O 1
+ATOM 102 C CB . ASN A 1 18 ? 8.941 28.291 -10.526 1.00 82.30 ? ? ? ? ? ? 20 ASN A CB 1
+ATOM 103 C CG . ASN A 1 18 ? 10.360 28.739 -10.753 1.00 89.13 ? ? ? ? ? ? 20 ASN A CG 1
+ATOM 104 O OD1 . ASN A 1 18 ? 10.690 29.305 -11.791 1.00 92.93 ? ? ? ? ? ? 20 ASN A OD1 1
+ATOM 105 N ND2 . ASN A 1 18 ? 11.217 28.488 -9.773 1.00 94.39 ? ? ? ? ? ? 20 ASN A ND2 1
+ATOM 106 N N . VAL A 1 19 ? 8.521 27.077 -13.779 1.00 76.88 ? ? ? ? ? ? 21 VAL A N 1
+ATOM 107 C CA . VAL A 1 19 ? 8.542 25.871 -14.600 1.00 75.28 ? ? ? ? ? ? 21 VAL A CA 1
+ATOM 108 C C . VAL A 1 19 ? 9.970 25.398 -14.720 1.00 78.52 ? ? ? ? ? ? 21 VAL A C 1
+ATOM 109 O O . VAL A 1 19 ? 10.747 25.948 -15.489 1.00 80.53 ? ? ? ? ? ? 21 VAL A O 1
+ATOM 110 C CB . VAL A 1 19 ? 7.946 26.104 -16.005 1.00 73.54 ? ? ? ? ? ? 21 VAL A CB 1
+ATOM 111 C CG1 . VAL A 1 19 ? 7.966 24.838 -16.807 1.00 70.33 ? ? ? ? ? ? 21 VAL A CG1 1
+ATOM 112 C CG2 . VAL A 1 19 ? 6.528 26.602 -15.913 1.00 69.44 ? ? ? ? ? ? 21 VAL A CG2 1
+ATOM 113 N N . ILE A 1 20 ? 10.305 24.368 -13.960 1.00 80.07 ? ? ? ? ? ? 22 ILE A N 1
+ATOM 114 C CA . ILE A 1 20 ? 11.683 23.949 -13.817 1.00 83.77 ? ? ? ? ? ? 22 ILE A CA 1
+ATOM 115 C C . ILE A 1 20 ? 12.004 22.729 -14.664 1.00 83.74 ? ? ? ? ? ? 22 ILE A C 1
+ATOM 116 O O . ILE A 1 20 ? 11.349 21.705 -14.536 1.00 81.42 ? ? ? ? ? ? 22 ILE A O 1
+ATOM 117 C CB . ILE A 1 20 ? 12.014 23.661 -12.348 1.00 84.59 ? ? ? ? ? ? 22 ILE A CB 1
+ATOM 118 C CG1 . ILE A 1 20 ? 11.522 24.802 -11.467 1.00 85.96 ? ? ? ? ? ? 22 ILE A CG1 1
+ATOM 119 C CG2 . ILE A 1 20 ? 13.511 23.484 -12.166 1.00 89.81 ? ? ? ? ? ? 22 ILE A CG2 1
+ATOM 120 C CD1 . ILE A 1 20 ? 11.484 24.464 -9.998 1.00 87.43 ? ? ? ? ? ? 22 ILE A CD1 1
+ATOM 121 N N . GLY A 1 21 ? 13.019 22.862 -15.520 1.00 86.57 ? ? ? ? ? ? 23 GLY A N 1
+ATOM 122 C CA . GLY A 1 21 ? 13.522 21.775 -16.358 1.00 88.60 ? ? ? ? ? ? 23 GLY A CA 1
+ATOM 123 C C . GLY A 1 21 ? 14.674 21.070 -15.675 1.00 91.29 ? ? ? ? ? ? 23 GLY A C 1
+ATOM 124 O O . GLY A 1 21 ? 15.573 21.716 -15.154 1.00 94.14 ? ? ? ? ? ? 23 GLY A O 1
+ATOM 125 N N . LEU A 1 22 ? 14.642 19.743 -15.672 1.00 91.36 ? ? ? ? ? ? 24 LEU A N 1
+ATOM 126 C CA . LEU A 1 22 ? 15.603 18.932 -14.926 1.00 92.96 ? ? ? ? ? ? 24 LEU A CA 1
+ATOM 127 C C . LEU A 1 22 ? 16.447 18.089 -15.876 1.00 94.68 ? ? ? ? ? ? 24 LEU A C 1
+ATOM 128 O O . LEU A 1 22 ? 15.939 17.601 -16.885 1.00 94.04 ? ? ? ? ? ? 24 LEU A O 1
+ATOM 129 C CB . LEU A 1 22 ? 14.860 18.047 -13.924 1.00 91.08 ? ? ? ? ? ? 24 LEU A CB 1
+ATOM 130 C CG . LEU A 1 22 ? 14.551 18.518 -12.493 1.00 90.38 ? ? ? ? ? ? 24 LEU A CG 1
+ATOM 131 C CD1 . LEU A 1 22 ? 14.342 20.009 -12.384 1.00 91.01 ? ? ? ? ? ? 24 LEU A CD1 1
+ATOM 132 C CD2 . LEU A 1 22 ? 13.342 17.791 -11.921 1.00 85.41 ? ? ? ? ? ? 24 LEU A CD2 1
+ATOM 133 N N . THR A 1 23 ? 17.733 17.926 -15.565 1.00 96.47 ? ? ? ? ? ? 25 THR A N 1
+ATOM 134 C CA . THR A 1 23 ? 18.688 17.343 -16.531 1.00 98.30 ? ? ? ? ? ? 25 THR A CA 1
+ATOM 135 C C . THR A 1 23 ? 19.007 15.862 -16.352 1.00 98.49 ? ? ? ? ? ? 25 THR A C 1
+ATOM 136 O O . THR A 1 23 ? 18.826 15.304 -15.266 1.00 98.19 ? ? ? ? ? ? 25 THR A O 1
+ATOM 137 C CB . THR A 1 23 ? 20.028 18.102 -16.553 1.00 100.21 ? ? ? ? ? ? 25 THR A CB 1
+ATOM 138 O OG1 . THR A 1 23 ? 20.490 18.282 -15.208 1.00 101.37 ? ? ? ? ? ? 25 THR A OG1 1
+ATOM 139 C CG2 . THR A 1 23 ? 19.883 19.457 -17.252 1.00 100.72 ? ? ? ? ? ? 25 THR A CG2 1
+ATOM 140 N N . ARG A 1 24 ? 19.501 15.246 -17.430 1.00 99.49 ? ? ? ? ? ? 26 ARG A N 1
+ATOM 141 C CA . ARG A 1 24 ? 19.857 13.819 -17.452 1.00 99.94 ? ? ? ? ? ? 26 ARG A CA 1
+ATOM 142 C C . ARG A 1 24 ? 21.154 13.541 -16.693 1.00 101.44 ? ? ? ? ? ? 26 ARG A C 1
+ATOM 143 O O . ARG A 1 24 ? 22.240 13.904 -17.147 1.00 103.26 ? ? ? ? ? ? 26 ARG A O 1
+ATOM 144 C CB . ARG A 1 24 ? 19.955 13.281 -18.893 1.00 100.14 ? ? ? ? ? ? 26 ARG A CB 1
+ATOM 145 C CG . ARG A 1 24 ? 18.620 13.217 -19.642 1.00 99.36 ? ? ? ? ? ? 26 ARG A CG 1
+ATOM 146 C CD . ARG A 1 24 ? 18.634 12.164 -20.759 1.00 100.98 ? ? ? ? ? ? 26 ARG A CD 1
+ATOM 147 N NE . ARG A 1 24 ? 17.552 12.352 -21.740 1.00 100.55 ? ? ? ? ? ? 26 ARG A NE 1
+ATOM 148 C CZ . ARG A 1 24 ? 17.231 11.494 -22.716 1.00 99.98 ? ? ? ? ? ? 26 ARG A CZ 1
+ATOM 149 N NH1 . ARG A 1 24 ? 17.891 10.344 -22.876 1.00 99.60 ? ? ? ? ? ? 26 ARG A NH1 1
+ATOM 150 N NH2 . ARG A 1 24 ? 16.229 11.791 -23.537 1.00 99.33 ? ? ? ? ? ? 26 ARG A NH2 1
+ATOM 151 N N . THR A 1 28 ? 22.527 16.428 -12.721 1.00 120.13 ? ? ? ? ? ? 30 THR A N 1
+ATOM 152 C CA . THR A 1 28 ? 21.235 15.835 -13.090 1.00 118.47 ? ? ? ? ? ? 30 THR A CA 1
+ATOM 153 C C . THR A 1 28 ? 20.021 16.467 -12.351 1.00 117.17 ? ? ? ? ? ? 30 THR A C 1
+ATOM 154 O O . THR A 1 28 ? 18.867 16.073 -12.593 1.00 115.70 ? ? ? ? ? ? 30 THR A O 1
+ATOM 155 C CB . THR A 1 28 ? 21.259 14.241 -13.007 1.00 118.06 ? ? ? ? ? ? 30 THR A CB 1
+ATOM 156 O OG1 . THR A 1 28 ? 19.946 13.697 -13.234 1.00 116.11 ? ? ? ? ? ? 30 THR A OG1 1
+ATOM 157 C CG2 . THR A 1 28 ? 21.822 13.727 -11.660 1.00 118.37 ? ? ? ? ? ? 30 THR A CG2 1
+ATOM 158 N N . ARG A 1 29 ? 20.289 17.464 -11.492 1.00 117.71 ? ? ? ? ? ? 31 ARG A N 1
+ATOM 159 C CA . ARG A 1 29 ? 19.261 18.091 -10.604 1.00 116.35 ? ? ? ? ? ? 31 ARG A CA 1
+ATOM 160 C C . ARG A 1 29 ? 18.477 19.294 -11.195 1.00 115.56 ? ? ? ? ? ? 31 ARG A C 1
+ATOM 161 O O . ARG A 1 29 ? 18.271 19.360 -12.420 1.00 115.47 ? ? ? ? ? ? 31 ARG A O 1
+ATOM 162 C CB . ARG A 1 29 ? 19.840 18.428 -9.204 1.00 117.16 ? ? ? ? ? ? 31 ARG A CB 1
+ATOM 163 C CG . ARG A 1 29 ? 21.320 18.904 -9.113 1.00 119.11 ? ? ? ? ? ? 31 ARG A CG 1
+ATOM 164 C CD . ARG A 1 29 ? 21.638 20.210 -9.857 1.00 119.60 ? ? ? ? ? ? 31 ARG A CD 1
+ATOM 165 N NE . ARG A 1 29 ? 22.419 19.952 -11.068 1.00 120.44 ? ? ? ? ? ? 31 ARG A NE 1
+ATOM 166 C CZ . ARG A 1 29 ? 21.980 20.123 -12.315 1.00 119.80 ? ? ? ? ? ? 31 ARG A CZ 1
+ATOM 167 N NH1 . ARG A 1 29 ? 22.780 19.853 -13.337 1.00 121.30 ? ? ? ? ? ? 31 ARG A NH1 1
+ATOM 168 N NH2 . ARG A 1 29 ? 20.756 20.576 -12.552 1.00 117.87 ? ? ? ? ? ? 31 ARG A NH2 1
+ATOM 169 N N . PHE A 1 30 ? 18.052 20.228 -10.323 1.00 114.83 ? ? ? ? ? ? 32 PHE A N 1
+ATOM 170 C CA . PHE A 1 30 ? 17.248 21.413 -10.728 1.00 113.80 ? ? ? ? ? ? 32 PHE A CA 1
+ATOM 171 C C . PHE A 1 30 ? 18.047 22.475 -11.541 1.00 114.52 ? ? ? ? ? ? 32 PHE A C 1
+ATOM 172 O O . PHE A 1 30 ? 18.937 23.145 -11.001 1.00 115.82 ? ? ? ? ? ? 32 PHE A O 1
+ATOM 173 C CB . PHE A 1 30 ? 16.487 22.093 -9.541 1.00 113.41 ? ? ? ? ? ? 32 PHE A CB 1
+ATOM 174 C CG . PHE A 1 30 ? 16.144 21.179 -8.346 1.00 112.64 ? ? ? ? ? ? 32 PHE A CG 1
+ATOM 175 C CD1 . PHE A 1 30 ? 15.540 21.740 -7.207 1.00 112.23 ? ? ? ? ? ? 32 PHE A CD1 1
+ATOM 176 C CD2 . PHE A 1 30 ? 16.423 19.805 -8.338 1.00 111.84 ? ? ? ? ? ? 32 PHE A CD2 1
+ATOM 177 C CE1 . PHE A 1 30 ? 15.212 20.957 -6.091 1.00 111.54 ? ? ? ? ? ? 32 PHE A CE1 1
+ATOM 178 C CE2 . PHE A 1 30 ? 16.110 19.015 -7.218 1.00 111.19 ? ? ? ? ? ? 32 PHE A CE2 1
+ATOM 179 C CZ . PHE A 1 30 ? 15.497 19.590 -6.097 1.00 111.08 ? ? ? ? ? ? 32 PHE A CZ 1
+ATOM 180 N N . HIS A 1 31 ? 17.677 22.645 -12.817 1.00 113.18 ? ? ? ? ? ? 33 HIS A N 1
+ATOM 181 C CA . HIS A 1 31 ? 18.505 23.317 -13.836 1.00 113.51 ? ? ? ? ? ? 33 HIS A CA 1
+ATOM 182 C C . HIS A 1 31 ? 17.843 24.573 -14.459 1.00 112.40 ? ? ? ? ? ? 33 HIS A C 1
+ATOM 183 O O . HIS A 1 31 ? 17.840 25.650 -13.849 1.00 112.91 ? ? ? ? ? ? 33 HIS A O 1
+ATOM 184 C CB . HIS A 1 31 ? 18.897 22.274 -14.908 1.00 113.74 ? ? ? ? ? ? 33 HIS A CB 1
+ATOM 185 C CG . HIS A 1 31 ? 19.881 22.761 -15.933 1.00 116.22 ? ? ? ? ? ? 33 HIS A CG 1
+ATOM 186 N ND1 . HIS A 1 31 ? 21.201 23.036 -15.635 1.00 118.98 ? ? ? ? ? ? 33 HIS A ND1 1
+ATOM 187 C CD2 . HIS A 1 31 ? 19.743 22.976 -17.264 1.00 116.72 ? ? ? ? ? ? 33 HIS A CD2 1
+ATOM 188 C CE1 . HIS A 1 31 ? 21.826 23.425 -16.734 1.00 120.25 ? ? ? ? ? ? 33 HIS A CE1 1
+ATOM 189 N NE2 . HIS A 1 31 ? 20.964 23.395 -17.736 1.00 119.10 ? ? ? ? ? ? 33 HIS A NE2 1
+ATOM 190 N N . HIS A 1 32 ? 17.298 24.431 -15.670 1.00 110.63 ? ? ? ? ? ? 34 HIS A N 1
+ATOM 191 C CA . HIS A 1 32 ? 16.630 25.529 -16.377 1.00 108.57 ? ? ? ? ? ? 34 HIS A CA 1
+ATOM 192 C C . HIS A 1 32 ? 15.315 25.908 -15.701 1.00 105.41 ? ? ? ? ? ? 34 HIS A C 1
+ATOM 193 O O . HIS A 1 32 ? 14.336 25.165 -15.760 1.00 102.47 ? ? ? ? ? ? 34 HIS A O 1
+ATOM 194 C CB . HIS A 1 32 ? 16.384 25.161 -17.858 1.00 108.29 ? ? ? ? ? ? 34 HIS A CB 1
+ATOM 195 C CG . HIS A 1 32 ? 15.859 26.296 -18.697 1.00 108.03 ? ? ? ? ? ? 34 HIS A CG 1
+ATOM 196 N ND1 . HIS A 1 32 ? 16.492 27.522 -18.778 1.00 111.34 ? ? ? ? ? ? 34 HIS A ND1 1
+ATOM 197 C CD2 . HIS A 1 32 ? 14.778 26.380 -19.511 1.00 103.90 ? ? ? ? ? ? 34 HIS A CD2 1
+ATOM 198 C CE1 . HIS A 1 32 ? 15.812 28.317 -19.586 1.00 109.77 ? ? ? ? ? ? 34 HIS A CE1 1
+ATOM 199 N NE2 . HIS A 1 32 ? 14.772 27.647 -20.051 1.00 105.66 ? ? ? ? ? ? 34 HIS A NE2 1
+ATOM 200 N N . SER A 1 33 ? 15.303 27.064 -15.056 1.00 104.75 ? ? ? ? ? ? 35 SER A N 1
+ATOM 201 C CA . SER A 1 33 ? 14.079 27.599 -14.485 1.00 101.92 ? ? ? ? ? ? 35 SER A CA 1
+ATOM 202 C C . SER A 1 33 ? 13.450 28.601 -15.456 1.00 99.94 ? ? ? ? ? ? 35 SER A C 1
+ATOM 203 O O . SER A 1 33 ? 14.146 29.196 -16.272 1.00 101.93 ? ? ? ? ? ? 35 SER A O 1
+ATOM 204 C CB . SER A 1 33 ? 14.372 28.236 -13.124 1.00 103.64 ? ? ? ? ? ? 35 SER A CB 1
+ATOM 205 O OG . SER A 1 33 ? 13.401 29.202 -12.771 1.00 103.74 ? ? ? ? ? ? 35 SER A OG 1
+ATOM 206 N N . GLU A 1 34 ? 12.136 28.778 -15.372 1.00 95.30 ? ? ? ? ? ? 36 GLU A N 1
+ATOM 207 C CA . GLU A 1 34 ? 11.425 29.699 -16.249 1.00 92.35 ? ? ? ? ? ? 36 GLU A CA 1
+ATOM 208 C C . GLU A 1 34 ? 10.221 30.272 -15.520 1.00 90.03 ? ? ? ? ? ? 36 GLU A C 1
+ATOM 209 O O . GLU A 1 34 ? 9.296 29.543 -15.201 1.00 87.29 ? ? ? ? ? ? 36 GLU A O 1
+ATOM 210 C CB . GLU A 1 34 ? 10.977 28.964 -17.511 1.00 90.67 ? ? ? ? ? ? 36 GLU A CB 1
+ATOM 211 C CG . GLU A 1 34 ? 10.555 29.867 -18.650 1.00 90.72 ? ? ? ? ? ? 36 GLU A CG 1
+ATOM 212 C CD . GLU A 1 34 ? 11.736 30.565 -19.310 1.00 96.24 ? ? ? ? ? ? 36 GLU A CD 1
+ATOM 213 O OE1 . GLU A 1 34 ? 12.815 29.937 -19.462 1.00 99.38 ? ? ? ? ? ? 36 GLU A OE1 1
+ATOM 214 O OE2 . GLU A 1 34 ? 11.578 31.748 -19.685 1.00 98.37 ? ? ? ? ? ? 36 GLU A OE2 1
+ATOM 215 N N . LYS A 1 35 ? 10.235 31.569 -15.239 1.00 90.36 ? ? ? ? ? ? 37 LYS A N 1
+ATOM 216 C CA . LYS A 1 35 ? 9.139 32.178 -14.506 1.00 88.38 ? ? ? ? ? ? 37 LYS A CA 1
+ATOM 217 C C . LYS A 1 35 ? 7.977 32.484 -15.433 1.00 85.67 ? ? ? ? ? ? 37 LYS A C 1
+ATOM 218 O O . LYS A 1 35 ? 8.172 32.833 -16.592 1.00 86.06 ? ? ? ? ? ? 37 LYS A O 1
+ATOM 219 C CB . LYS A 1 35 ? 9.601 33.433 -13.768 1.00 91.44 ? ? ? ? ? ? 37 LYS A CB 1
+ATOM 220 N N . LEU A 1 36 ? 6.766 32.325 -14.915 1.00 81.92 ? ? ? ? ? ? 38 LEU A N 1
+ATOM 221 C CA . LEU A 1 36 ? 5.539 32.641 -15.640 1.00 78.89 ? ? ? ? ? ? 38 LEU A CA 1
+ATOM 222 C C . LEU A 1 36 ? 4.640 33.528 -14.797 1.00 78.12 ? ? ? ? ? ? 38 LEU A C 1
+ATOM 223 O O . LEU A 1 36 ? 4.498 33.299 -13.601 1.00 77.83 ? ? ? ? ? ? 38 LEU A O 1
+ATOM 224 C CB . LEU A 1 36 ? 4.770 31.368 -15.979 1.00 77.62 ? ? ? ? ? ? 38 LEU A CB 1
+ATOM 225 C CG . LEU A 1 36 ? 4.861 30.675 -17.336 1.00 76.31 ? ? ? ? ? ? 38 LEU A CG 1
+ATOM 226 C CD1 . LEU A 1 36 ? 3.481 30.149 -17.653 1.00 74.28 ? ? ? ? ? ? 38 LEU A CD1 1
+ATOM 227 C CD2 . LEU A 1 36 ? 5.328 31.599 -18.436 1.00 76.23 ? ? ? ? ? ? 38 LEU A CD2 1
+ATOM 228 N N . ASP A 1 37 ? 4.015 34.523 -15.417 1.00 77.70 ? ? ? ? ? ? 39 ASP A N 1
+ATOM 229 C CA . ASP A 1 37 ? 3.127 35.429 -14.691 1.00 77.42 ? ? ? ? ? ? 39 ASP A CA 1
+ATOM 230 C C . ASP A 1 37 ? 1.666 35.169 -15.004 1.00 73.58 ? ? ? ? ? ? 39 ASP A C 1
+ATOM 231 O O . ASP A 1 37 ? 1.352 34.676 -16.075 1.00 72.04 ? ? ? ? ? ? 39 ASP A O 1
+ATOM 232 C CB . ASP A 1 37 ? 3.473 36.886 -14.995 1.00 80.86 ? ? ? ? ? ? 39 ASP A CB 1
+ATOM 233 C CG . ASP A 1 37 ? 4.632 37.408 -14.159 1.00 86.94 ? ? ? ? ? ? 39 ASP A CG 1
+ATOM 234 O OD1 . ASP A 1 37 ? 4.986 36.781 -13.125 1.00 88.70 ? ? ? ? ? ? 39 ASP A OD1 1
+ATOM 235 O OD2 . ASP A 1 37 ? 5.178 38.463 -14.548 1.00 92.58 ? ? ? ? ? ? 39 ASP A OD2 1
+ATOM 236 N N . LYS A 1 38 ? 0.788 35.520 -14.065 1.00 71.09 ? ? ? ? ? ? 40 LYS A N 1
+ATOM 237 C CA . LYS A 1 38 ? -0.646 35.219 -14.127 1.00 67.44 ? ? ? ? ? ? 40 LYS A CA 1
+ATOM 238 C C . LYS A 1 38 ? -1.246 35.395 -15.514 1.00 65.75 ? ? ? ? ? ? 40 LYS A C 1
+ATOM 239 O O . LYS A 1 38 ? -1.274 36.506 -16.038 1.00 66.82 ? ? ? ? ? ? 40 LYS A O 1
+ATOM 240 C CB . LYS A 1 38 ? -1.408 36.092 -13.130 1.00 67.43 ? ? ? ? ? ? 40 LYS A CB 1
+ATOM 241 C CG . LYS A 1 38 ? -2.847 35.692 -12.912 1.00 65.33 ? ? ? ? ? ? 40 LYS A CG 1
+ATOM 242 C CD . LYS A 1 38 ? -3.496 36.530 -11.819 1.00 65.17 ? ? ? ? ? ? 40 LYS A CD 1
+ATOM 243 C CE . LYS A 1 38 ? -4.727 35.828 -11.238 1.00 64.58 ? ? ? ? ? ? 40 LYS A CE 1
+ATOM 244 N NZ . LYS A 1 38 ? -5.911 36.738 -11.093 1.00 64.29 ? ? ? ? ? ? 40 LYS A NZ 1
+ATOM 245 N N . GLY A 1 39 ? -1.710 34.288 -16.097 1.00 62.75 ? ? ? ? ? ? 41 GLY A N 1
+ATOM 246 C CA . GLY A 1 39 ? -2.358 34.280 -17.410 1.00 60.49 ? ? ? ? ? ? 41 GLY A CA 1
+ATOM 247 C C . GLY A 1 39 ? -1.471 33.947 -18.599 1.00 60.30 ? ? ? ? ? ? 41 GLY A C 1
+ATOM 248 O O . GLY A 1 39 ? -1.957 33.805 -19.718 1.00 58.95 ? ? ? ? ? ? 41 GLY A O 1
+ATOM 249 N N . GLU A 1 40 ? -0.167 33.843 -18.366 1.00 61.59 ? ? ? ? ? ? 42 GLU A N 1
+ATOM 250 C CA . GLU A 1 40 ? 0.777 33.499 -19.424 1.00 62.43 ? ? ? ? ? ? 42 GLU A CA 1
+ATOM 251 C C . GLU A 1 40 ? 0.720 32.015 -19.667 1.00 59.62 ? ? ? ? ? ? 42 GLU A C 1
+ATOM 252 O O . GLU A 1 40 ? 0.425 31.239 -18.761 1.00 58.37 ? ? ? ? ? ? 42 GLU A O 1
+ATOM 253 C CB . GLU A 1 40 ? 2.200 33.917 -19.056 1.00 65.52 ? ? ? ? ? ? 42 GLU A CB 1
+ATOM 254 C CG . GLU A 1 40 ? 2.523 35.352 -19.404 1.00 71.75 ? ? ? ? ? ? 42 GLU A CG 1
+ATOM 255 C CD . GLU A 1 40 ? 3.754 35.879 -18.701 1.00 79.02 ? ? ? ? ? ? 42 GLU A CD 1
+ATOM 256 O OE1 . GLU A 1 40 ? 4.375 35.124 -17.926 1.00 79.96 ? ? ? ? ? ? 42 GLU A OE1 1
+ATOM 257 O OE2 . GLU A 1 40 ? 4.097 37.059 -18.923 1.00 83.29 ? ? ? ? ? ? 42 GLU A OE2 1
+ATOM 258 N N . VAL A 1 41 ? 1.004 31.619 -20.895 1.00 58.12 ? ? ? ? ? ? 43 VAL A N 1
+ATOM 259 C CA . VAL A 1 41 ? 0.931 30.221 -21.282 1.00 55.42 ? ? ? ? ? ? 43 VAL A CA 1
+ATOM 260 C C . VAL A 1 41 ? 2.254 29.747 -21.855 1.00 57.22 ? ? ? ? ? ? 43 VAL A C 1
+ATOM 261 O O . VAL A 1 41 ? 2.823 30.381 -22.755 1.00 58.88 ? ? ? ? ? ? 43 VAL A O 1
+ATOM 262 C CB . VAL A 1 41 ? -0.180 29.994 -22.309 1.00 53.28 ? ? ? ? ? ? 43 VAL A CB 1
+ATOM 263 C CG1 . VAL A 1 41 ? -0.060 28.645 -22.920 1.00 50.49 ? ? ? ? ? ? 43 VAL A CG1 1
+ATOM 264 C CG2 . VAL A 1 41 ? -1.523 30.132 -21.664 1.00 49.78 ? ? ? ? ? ? 43 VAL A CG2 1
+ATOM 265 N N . LEU A 1 42 ? 2.738 28.629 -21.323 1.00 57.21 ? ? ? ? ? ? 44 LEU A N 1
+ATOM 266 C CA . LEU A 1 42 ? 3.960 28.037 -21.813 1.00 58.54 ? ? ? ? ? ? 44 LEU A CA 1
+ATOM 267 C C . LEU A 1 42 ? 3.633 26.718 -22.458 1.00 56.54 ? ? ? ? ? ? 44 LEU A C 1
+ATOM 268 O O . LEU A 1 42 ? 2.882 25.928 -21.899 1.00 54.68 ? ? ? ? ? ? 44 LEU A O 1
+ATOM 269 C CB . LEU A 1 42 ? 4.954 27.852 -20.680 1.00 60.35 ? ? ? ? ? ? 44 LEU A CB 1
+ATOM 270 C CG . LEU A 1 42 ? 6.378 27.476 -21.074 1.00 64.66 ? ? ? ? ? ? 44 LEU A CG 1
+ATOM 271 C CD1 . LEU A 1 42 ? 7.071 28.595 -21.816 1.00 69.92 ? ? ? ? ? ? 44 LEU A CD1 1
+ATOM 272 C CD2 . LEU A 1 42 ? 7.171 27.112 -19.839 1.00 67.81 ? ? ? ? ? ? 44 LEU A CD2 1
+ATOM 273 N N . ILE A 1 43 ? 4.162 26.504 -23.657 1.00 56.61 ? ? ? ? ? ? 45 ILE A N 1
+ATOM 274 C CA . ILE A 1 43 ? 4.086 25.207 -24.298 1.00 55.49 ? ? ? ? ? ? 45 ILE A CA 1
+ATOM 275 C C . ILE A 1 43 ? 5.487 24.630 -24.267 1.00 57.96 ? ? ? ? ? ? 45 ILE A C 1
+ATOM 276 O O . ILE A 1 43 ? 6.345 25.038 -25.046 1.00 60.01 ? ? ? ? ? ? 45 ILE A O 1
+ATOM 277 C CB . ILE A 1 43 ? 3.621 25.276 -25.757 1.00 54.45 ? ? ? ? ? ? 45 ILE A CB 1
+ATOM 278 C CG1 . ILE A 1 43 ? 2.749 26.525 -26.016 1.00 53.11 ? ? ? ? ? ? 45 ILE A CG1 1
+ATOM 279 C CG2 . ILE A 1 43 ? 2.966 23.955 -26.167 1.00 50.96 ? ? ? ? ? ? 45 ILE A CG2 1
+ATOM 280 C CD1 . ILE A 1 43 ? 1.330 26.489 -25.511 1.00 48.47 ? ? ? ? ? ? 45 ILE A CD1 1
+ATOM 281 N N . ALA A 1 44 ? 5.708 23.687 -23.351 1.00 58.61 ? ? ? ? ? ? 46 ALA A N 1
+ATOM 282 C CA . ALA A 1 44 ? 7.019 23.104 -23.115 1.00 60.53 ? ? ? ? ? ? 46 ALA A CA 1
+ATOM 283 C C . ALA A 1 44 ? 7.098 21.728 -23.724 1.00 60.54 ? ? ? ? ? ? 46 ALA A C 1
+ATOM 284 O O . ALA A 1 44 ? 6.238 20.893 -23.489 1.00 58.05 ? ? ? ? ? ? 46 ALA A O 1
+ATOM 285 C CB . ALA A 1 44 ? 7.298 23.026 -21.643 1.00 61.04 ? ? ? ? ? ? 46 ALA A CB 1
+ATOM 286 N N . GLN A 1 45 ? 8.142 21.522 -24.518 1.00 63.39 ? ? ? ? ? ? 47 GLN A N 1
+ATOM 287 C CA . GLN A 1 45 ? 8.433 20.236 -25.131 1.00 64.77 ? ? ? ? ? ? 47 GLN A CA 1
+ATOM 288 C C . GLN A 1 45 ? 9.599 19.592 -24.406 1.00 67.08 ? ? ? ? ? ? 47 GLN A C 1
+ATOM 289 O O . GLN A 1 45 ? 10.492 20.287 -23.920 1.00 69.41 ? ? ? ? ? ? 47 GLN A O 1
+ATOM 290 C CB . GLN A 1 45 ? 8.791 20.423 -26.602 1.00 65.44 ? ? ? ? ? ? 47 GLN A CB 1
+ATOM 291 C CG . GLN A 1 45 ? 8.796 19.131 -27.399 1.00 65.31 ? ? ? ? ? ? 47 GLN A CG 1
+ATOM 292 C CD . GLN A 1 45 ? 9.318 19.305 -28.829 1.00 68.03 ? ? ? ? ? ? 47 GLN A CD 1
+ATOM 293 O OE1 . GLN A 1 45 ? 10.214 20.129 -29.090 1.00 70.64 ? ? ? ? ? ? 47 GLN A OE1 1
+ATOM 294 N NE2 . GLN A 1 45 ? 8.757 18.518 -29.767 1.00 65.95 ? ? ? ? ? ? 47 GLN A NE2 1
+ATOM 295 N N . PHE A 1 46 ? 9.590 18.266 -24.339 1.00 67.71 ? ? ? ? ? ? 48 PHE A N 1
+ATOM 296 C CA . PHE A 1 46 ? 10.706 17.526 -23.777 1.00 70.43 ? ? ? ? ? ? 48 PHE A CA 1
+ATOM 297 C C . PHE A 1 46 ? 11.857 17.437 -24.766 1.00 74.96 ? ? ? ? ? ? 48 PHE A C 1
+ATOM 298 O O . PHE A 1 46 ? 11.675 16.991 -25.907 1.00 74.94 ? ? ? ? ? ? 48 PHE A O 1
+ATOM 299 C CB . PHE A 1 46 ? 10.269 16.127 -23.384 1.00 67.85 ? ? ? ? ? ? 48 PHE A CB 1
+ATOM 300 C CG . PHE A 1 46 ? 9.527 16.081 -22.099 1.00 64.51 ? ? ? ? ? ? 48 PHE A CG 1
+ATOM 301 C CD1 . PHE A 1 46 ? 10.218 16.130 -20.894 1.00 65.87 ? ? ? ? ? ? 48 PHE A CD1 1
+ATOM 302 C CD2 . PHE A 1 46 ? 8.130 15.992 -22.085 1.00 59.45 ? ? ? ? ? ? 48 PHE A CD2 1
+ATOM 303 C CE1 . PHE A 1 46 ? 9.533 16.094 -19.687 1.00 63.95 ? ? ? ? ? ? 48 PHE A CE1 1
+ATOM 304 C CE2 . PHE A 1 46 ? 7.427 15.953 -20.885 1.00 57.67 ? ? ? ? ? ? 48 PHE A CE2 1
+ATOM 305 C CZ . PHE A 1 46 ? 8.130 16.002 -19.680 1.00 60.02 ? ? ? ? ? ? 48 PHE A CZ 1
+ATOM 306 N N . THR A 1 47 ? 13.038 17.869 -24.334 1.00 80.48 ? ? ? ? ? ? 49 THR A N 1
+ATOM 307 C CA . THR A 1 47 ? 14.238 17.712 -25.140 1.00 86.44 ? ? ? ? ? ? 49 THR A CA 1
+ATOM 308 C C . THR A 1 47 ? 14.993 16.474 -24.653 1.00 88.73 ? ? ? ? ? ? 49 THR A C 1
+ATOM 309 O O . THR A 1 47 ? 14.523 15.780 -23.752 1.00 86.98 ? ? ? ? ? ? 49 THR A O 1
+ATOM 310 C CB . THR A 1 47 ? 15.135 18.969 -25.068 1.00 89.11 ? ? ? ? ? ? 49 THR A CB 1
+ATOM 311 O OG1 . THR A 1 47 ? 15.953 18.934 -23.892 1.00 92.76 ? ? ? ? ? ? 49 THR A OG1 1
+ATOM 312 C CG2 . THR A 1 47 ? 14.285 20.230 -25.055 1.00 88.83 ? ? ? ? ? ? 49 THR A CG2 1
+ATOM 313 N N . GLU A 1 48 ? 16.145 16.187 -25.257 1.00 93.73 ? ? ? ? ? ? 50 GLU A N 1
+ATOM 314 C CA . GLU A 1 48 ? 17.052 15.170 -24.714 1.00 98.04 ? ? ? ? ? ? 50 GLU A CA 1
+ATOM 315 C C . GLU A 1 48 ? 17.700 15.685 -23.409 1.00 99.89 ? ? ? ? ? ? 50 GLU A C 1
+ATOM 316 O O . GLU A 1 48 ? 17.792 14.952 -22.420 1.00 99.46 ? ? ? ? ? ? 50 GLU A O 1
+ATOM 317 C CB . GLU A 1 48 ? 18.103 14.731 -25.754 1.00 100.79 ? ? ? ? ? ? 50 GLU A CB 1
+ATOM 318 C CG . GLU A 1 48 ? 19.096 15.818 -26.196 0.50 107.62 ? ? ? ? ? ? 50 GLU A CG 1
+ATOM 319 C CD . GLU A 1 48 ? 20.357 15.251 -26.838 0.50 115.10 ? ? ? ? ? ? 50 GLU A CD 1
+ATOM 320 O OE1 . GLU A 1 48 ? 21.467 15.702 -26.482 0.50 120.30 ? ? ? ? ? ? 50 GLU A OE1 1
+ATOM 321 O OE2 . GLU A 1 48 ? 20.241 14.354 -27.697 0.50 115.44 ? ? ? ? ? ? 50 GLU A OE2 1
+ATOM 322 N N . HIS A 1 49 ? 18.108 16.957 -23.422 1.00 102.54 ? ? ? ? ? ? 51 HIS A N 1
+ATOM 323 C CA . HIS A 1 49 ? 18.615 17.674 -22.247 1.00 104.56 ? ? ? ? ? ? 51 HIS A CA 1
+ATOM 324 C C . HIS A 1 49 ? 17.684 17.578 -21.032 1.00 100.90 ? ? ? ? ? ? 51 HIS A C 1
+ATOM 325 O O . HIS A 1 49 ? 18.145 17.604 -19.888 1.00 102.24 ? ? ? ? ? ? 51 HIS A O 1
+ATOM 326 C CB . HIS A 1 49 ? 18.790 19.162 -22.576 1.00 107.45 ? ? ? ? ? ? 51 HIS A CB 1
+ATOM 327 C CG . HIS A 1 49 ? 19.959 19.466 -23.458 1.00 115.35 ? ? ? ? ? ? 51 HIS A CG 1
+ATOM 328 N ND1 . HIS A 1 49 ? 19.964 19.199 -24.811 1.00 117.92 ? ? ? ? ? ? 51 HIS A ND1 1
+ATOM 329 C CD2 . HIS A 1 49 ? 21.153 20.047 -23.185 1.00 122.56 ? ? ? ? ? ? 51 HIS A CD2 1
+ATOM 330 C CE1 . HIS A 1 49 ? 21.117 19.586 -25.330 1.00 123.61 ? ? ? ? ? ? 51 HIS A CE1 1
+ATOM 331 N NE2 . HIS A 1 49 ? 21.855 20.106 -24.366 1.00 126.48 ? ? ? ? ? ? 51 HIS A NE2 1
+ATOM 332 N N . THR A 1 50 ? 16.377 17.481 -21.294 1.00 95.68 ? ? ? ? ? ? 52 THR A N 1
+ATOM 333 C CA . THR A 1 50 ? 15.340 17.640 -20.268 1.00 90.19 ? ? ? ? ? ? 52 THR A CA 1
+ATOM 334 C C . THR A 1 50 ? 14.528 16.370 -20.027 1.00 86.57 ? ? ? ? ? ? 52 THR A C 1
+ATOM 335 O O . THR A 1 50 ? 13.629 16.031 -20.795 1.00 83.93 ? ? ? ? ? ? 52 THR A O 1
+ATOM 336 C CB . THR A 1 50 ? 14.419 18.847 -20.596 1.00 89.09 ? ? ? ? ? ? 52 THR A CB 1
+ATOM 337 O OG1 . THR A 1 50 ? 15.128 20.061 -20.323 1.00 91.82 ? ? ? ? ? ? 52 THR A OG1 1
+ATOM 338 C CG2 . THR A 1 50 ? 13.158 18.832 -19.761 1.00 84.32 ? ? ? ? ? ? 52 THR A CG2 1
+ATOM 339 N N . SER A 1 51 ? 14.863 15.686 -18.938 1.00 85.07 ? ? ? ? ? ? 53 SER A N 1
+ATOM 340 C CA . SER A 1 51 ? 14.183 14.465 -18.518 1.00 82.20 ? ? ? ? ? ? 53 SER A CA 1
+ATOM 341 C C . SER A 1 51 ? 12.860 14.724 -17.792 1.00 78.23 ? ? ? ? ? ? 53 SER A C 1
+ATOM 342 O O . SER A 1 51 ? 11.863 14.057 -18.069 1.00 75.30 ? ? ? ? ? ? 53 SER A O 1
+ATOM 343 C CB . SER A 1 51 ? 15.103 13.617 -17.631 1.00 84.25 ? ? ? ? ? ? 53 SER A CB 1
+ATOM 344 O OG . SER A 1 51 ? 15.508 14.324 -16.475 1.00 87.22 ? ? ? ? ? ? 53 SER A OG 1
+ATOM 345 N N . ALA A 1 52 ? 12.855 15.681 -16.867 1.00 76.66 ? ? ? ? ? ? 54 ALA A N 1
+ATOM 346 C CA . ALA A 1 52 ? 11.660 15.983 -16.082 1.00 73.63 ? ? ? ? ? ? 54 ALA A CA 1
+ATOM 347 C C . ALA A 1 52 ? 11.347 17.470 -16.020 1.00 72.67 ? ? ? ? ? ? 54 ALA A C 1
+ATOM 348 O O . ALA A 1 52 ? 12.231 18.295 -16.168 1.00 74.97 ? ? ? ? ? ? 54 ALA A O 1
+ATOM 349 C CB . ALA A 1 52 ? 11.807 15.427 -14.697 1.00 73.72 ? ? ? ? ? ? 54 ALA A CB 1
+ATOM 350 N N . ILE A 1 53 ? 10.078 17.799 -15.808 1.00 69.28 ? ? ? ? ? ? 55 ILE A N 1
+ATOM 351 C CA . ILE A 1 53 ? 9.644 19.182 -15.648 1.00 67.60 ? ? ? ? ? ? 55 ILE A CA 1
+ATOM 352 C C . ILE A 1 53 ? 8.807 19.315 -14.386 1.00 66.31 ? ? ? ? ? ? 55 ILE A C 1
+ATOM 353 O O . ILE A 1 53 ? 7.813 18.615 -14.234 1.00 63.74 ? ? ? ? ? ? 55 ILE A O 1
+ATOM 354 C CB . ILE A 1 53 ? 8.816 19.679 -16.852 1.00 66.27 ? ? ? ? ? ? 55 ILE A CB 1
+ATOM 355 C CG1 . ILE A 1 53 ? 9.678 19.756 -18.104 1.00 67.47 ? ? ? ? ? ? 55 ILE A CG1 1
+ATOM 356 C CG2 . ILE A 1 53 ? 8.217 21.057 -16.579 1.00 65.21 ? ? ? ? ? ? 55 ILE A CG2 1
+ATOM 357 C CD1 . ILE A 1 53 ? 8.873 19.776 -19.383 1.00 65.20 ? ? ? ? ? ? 55 ILE A CD1 1
+ATOM 358 N N . LYS A 1 54 ? 9.212 20.225 -13.498 1.00 67.56 ? ? ? ? ? ? 56 LYS A N 1
+ATOM 359 C CA . LYS A 1 54 ? 8.518 20.471 -12.242 1.00 66.86 ? ? ? ? ? ? 56 LYS A CA 1
+ATOM 360 C C . LYS A 1 54 ? 7.790 21.787 -12.345 1.00 66.25 ? ? ? ? ? ? 56 LYS A C 1
+ATOM 361 O O . LYS A 1 54 ? 8.325 22.736 -12.899 1.00 67.88 ? ? ? ? ? ? 56 LYS A O 1
+ATOM 362 C CB . LYS A 1 54 ? 9.524 20.526 -11.091 1.00 69.15 ? ? ? ? ? ? 56 LYS A CB 1
+ATOM 363 C CG . LYS A 1 54 ? 8.919 20.527 -9.688 1.00 66.38 ? ? ? ? ? ? 56 LYS A CG 1
+ATOM 364 C CD . LYS A 1 54 ? 9.898 21.069 -8.644 1.00 66.41 ? ? ? ? ? ? 56 LYS A CD 1
+ATOM 365 C CE . LYS A 1 54 ? 10.805 19.996 -8.061 1.00 66.08 ? ? ? ? ? ? 56 LYS A CE 1
+ATOM 366 N NZ . LYS A 1 54 ? 11.738 20.531 -7.020 1.00 66.38 ? ? ? ? ? ? 56 LYS A NZ 1
+ATOM 367 N N . VAL A 1 55 ? 6.569 21.843 -11.826 1.00 63.79 ? ? ? ? ? ? 57 VAL A N 1
+ATOM 368 C CA . VAL A 1 55 ? 5.805 23.088 -11.783 1.00 62.60 ? ? ? ? ? ? 57 VAL A CA 1
+ATOM 369 C C . VAL A 1 55 ? 5.508 23.478 -10.335 1.00 63.99 ? ? ? ? ? ? 57 VAL A C 1
+ATOM 370 O O . VAL A 1 55 ? 4.827 22.751 -9.607 1.00 62.58 ? ? ? ? ? ? 57 VAL A O 1
+ATOM 371 C CB . VAL A 1 55 ? 4.491 22.999 -12.582 1.00 60.05 ? ? ? ? ? ? 57 VAL A CB 1
+ATOM 372 C CG1 . VAL A 1 55 ? 3.777 24.330 -12.592 1.00 58.65 ? ? ? ? ? ? 57 VAL A CG1 1
+ATOM 373 C CG2 . VAL A 1 55 ? 4.759 22.561 -14.001 1.00 57.89 ? ? ? ? ? ? 57 VAL A CG2 1
+ATOM 374 N N . ARG A 1 56 ? 6.046 24.625 -9.926 1.00 67.06 ? ? ? ? ? ? 58 ARG A N 1
+ATOM 375 C CA . ARG A 1 56 ? 5.822 25.201 -8.602 1.00 68.68 ? ? ? ? ? ? 58 ARG A CA 1
+ATOM 376 C C . ARG A 1 56 ? 4.944 26.430 -8.775 1.00 68.31 ? ? ? ? ? ? 58 ARG A C 1
+ATOM 377 O O . ARG A 1 56 ? 5.295 27.346 -9.516 1.00 69.78 ? ? ? ? ? ? 58 ARG A O 1
+ATOM 378 C CB . ARG A 1 56 ? 7.149 25.622 -7.961 1.00 71.82 ? ? ? ? ? ? 58 ARG A CB 1
+ATOM 379 C CG . ARG A 1 56 ? 7.919 24.540 -7.264 1.00 71.32 ? ? ? ? ? ? 58 ARG A CG 1
+ATOM 380 C CD . ARG A 1 56 ? 8.899 25.124 -6.251 1.00 74.34 ? ? ? ? ? ? 58 ARG A CD 1
+ATOM 381 N NE . ARG A 1 56 ? 10.303 24.967 -6.641 1.00 76.63 ? ? ? ? ? ? 58 ARG A NE 1
+ATOM 382 C CZ . ARG A 1 56 ? 11.114 24.011 -6.180 1.00 77.74 ? ? ? ? ? ? 58 ARG A CZ 1
+ATOM 383 N NH1 . ARG A 1 56 ? 10.668 23.111 -5.308 1.00 77.26 ? ? ? ? ? ? 58 ARG A NH1 1
+ATOM 384 N NH2 . ARG A 1 56 ? 12.380 23.947 -6.590 1.00 79.00 ? ? ? ? ? ? 58 ARG A NH2 1
+ATOM 385 N N . GLY A 1 57 ? 3.795 26.450 -8.116 1.00 66.23 ? ? ? ? ? ? 59 GLY A N 1
+ATOM 386 C CA . GLY A 1 57 ? 2.891 27.591 -8.224 1.00 64.54 ? ? ? ? ? ? 59 GLY A CA 1
+ATOM 387 C C . GLY A 1 57 ? 1.515 27.161 -8.671 1.00 61.40 ? ? ? ? ? ? 59 GLY A C 1
+ATOM 388 O O . GLY A 1 57 ? 1.324 26.011 -9.023 1.00 60.50 ? ? ? ? ? ? 59 GLY A O 1
+ATOM 389 N N . LYS A 1 58 ? 0.553 28.077 -8.652 1.00 59.63 ? ? ? ? ? ? 60 LYS A N 1
+ATOM 390 C CA . LYS A 1 58 ? -0.823 27.767 -9.030 1.00 56.33 ? ? ? ? ? ? 60 LYS A CA 1
+ATOM 391 C C . LYS A 1 58 ? -0.937 27.782 -10.560 1.00 54.36 ? ? ? ? ? ? 60 LYS A C 1
+ATOM 392 O O . LYS A 1 58 ? -0.806 28.840 -11.173 1.00 55.40 ? ? ? ? ? ? 60 LYS A O 1
+ATOM 393 C CB . LYS A 1 58 ? -1.776 28.800 -8.402 1.00 56.75 ? ? ? ? ? ? 60 LYS A CB 1
+ATOM 394 C CG . LYS A 1 58 ? -3.130 28.251 -7.937 1.00 56.71 ? ? ? ? ? ? 60 LYS A CG 1
+ATOM 395 C CD . LYS A 1 58 ? -3.097 27.743 -6.485 1.00 57.00 ? ? ? ? ? ? 60 LYS A CD 1
+ATOM 396 C CE . LYS A 1 58 ? -4.401 27.012 -6.119 1.00 56.07 ? ? ? ? ? ? 60 LYS A CE 1
+ATOM 397 N N . ALA A 1 59 ? -1.157 26.623 -11.185 1.00 50.90 ? ? ? ? ? ? 61 ALA A N 1
+ATOM 398 C CA . ALA A 1 59 ? -1.229 26.563 -12.652 1.00 48.01 ? ? ? ? ? ? 61 ALA A CA 1
+ATOM 399 C C . ALA A 1 59 ? -2.205 25.512 -13.166 1.00 44.63 ? ? ? ? ? ? 61 ALA A C 1
+ATOM 400 O O . ALA A 1 59 ? -2.516 24.556 -12.458 1.00 43.62 ? ? ? ? ? ? 61 ALA A O 1
+ATOM 401 C CB . ALA A 1 59 ? 0.153 26.320 -13.244 1.00 49.49 ? ? ? ? ? ? 61 ALA A CB 1
+ATOM 402 N N . TYR A 1 60 ? -2.667 25.686 -14.404 1.00 41.70 ? ? ? ? ? ? 62 TYR A N 1
+ATOM 403 C CA . TYR A 1 60 ? -3.493 24.707 -15.082 1.00 38.07 ? ? ? ? ? ? 62 TYR A CA 1
+ATOM 404 C C . TYR A 1 60 ? -2.627 24.044 -16.134 1.00 37.82 ? ? ? ? ? ? 62 TYR A C 1
+ATOM 405 O O . TYR A 1 60 ? -1.998 24.722 -16.954 1.00 38.91 ? ? ? ? ? ? 62 TYR A O 1
+ATOM 406 C CB . TYR A 1 60 ? -4.671 25.417 -15.716 1.00 36.81 ? ? ? ? ? ? 62 TYR A CB 1
+ATOM 407 C CG . TYR A 1 60 ? -5.719 24.566 -16.417 1.00 33.24 ? ? ? ? ? ? 62 TYR A CG 1
+ATOM 408 C CD1 . TYR A 1 60 ? -6.553 23.709 -15.702 1.00 30.81 ? ? ? ? ? ? 62 TYR A CD1 1
+ATOM 409 C CD2 . TYR A 1 60 ? -5.925 24.669 -17.795 1.00 32.16 ? ? ? ? ? ? 62 TYR A CD2 1
+ATOM 410 C CE1 . TYR A 1 60 ? -7.554 22.938 -16.349 1.00 26.98 ? ? ? ? ? ? 62 TYR A CE1 1
+ATOM 411 C CE2 . TYR A 1 60 ? -6.915 23.914 -18.446 1.00 29.38 ? ? ? ? ? ? 62 TYR A CE2 1
+ATOM 412 C CZ . TYR A 1 60 ? -7.728 23.053 -17.716 1.00 26.79 ? ? ? ? ? ? 62 TYR A CZ 1
+ATOM 413 O OH . TYR A 1 60 ? -8.701 22.329 -18.381 1.00 24.12 ? ? ? ? ? ? 62 TYR A OH 1
+ATOM 414 N N . ILE A 1 61 ? -2.579 22.717 -16.097 1.00 36.07 ? ? ? ? ? ? 63 ILE A N 1
+ATOM 415 C CA . ILE A 1 61 ? -1.662 21.980 -16.938 1.00 35.83 ? ? ? ? ? ? 63 ILE A CA 1
+ATOM 416 C C . ILE A 1 61 ? -2.384 20.971 -17.798 1.00 33.41 ? ? ? ? ? ? 63 ILE A C 1
+ATOM 417 O O . ILE A 1 61 ? -3.202 20.217 -17.298 1.00 31.94 ? ? ? ? ? ? 63 ILE A O 1
+ATOM 418 C CB . ILE A 1 61 ? -0.610 21.239 -16.097 1.00 37.09 ? ? ? ? ? ? 63 ILE A CB 1
+ATOM 419 C CG1 . ILE A 1 61 ? 0.153 22.208 -15.183 1.00 40.08 ? ? ? ? ? ? 63 ILE A CG1 1
+ATOM 420 C CG2 . ILE A 1 61 ? 0.358 20.461 -17.018 1.00 38.40 ? ? ? ? ? ? 63 ILE A CG2 1
+ATOM 421 C CD1 . ILE A 1 61 ? 0.912 21.521 -14.083 1.00 42.02 ? ? ? ? ? ? 63 ILE A CD1 1
+ATOM 422 N N . GLN A 1 62 ? -2.075 20.961 -19.094 1.00 32.65 ? ? ? ? ? ? 64 GLN A N 1
+ATOM 423 C CA . GLN A 1 62 ? -2.645 19.966 -20.035 1.00 31.02 ? ? ? ? ? ? 64 GLN A CA 1
+ATOM 424 C C . GLN A 1 62 ? -1.536 19.076 -20.577 1.00 31.29 ? ? ? ? ? ? 64 GLN A C 1
+ATOM 425 O O . GLN A 1 62 ? -0.503 19.573 -21.072 1.00 33.32 ? ? ? ? ? ? 64 GLN A O 1
+ATOM 426 C CB . GLN A 1 62 ? -3.321 20.649 -21.251 1.00 30.42 ? ? ? ? ? ? 64 GLN A CB 1
+ATOM 427 C CG . GLN A 1 62 ? -4.366 21.714 -20.928 1.00 29.89 ? ? ? ? ? ? 64 GLN A CG 1
+ATOM 428 C CD . GLN A 1 62 ? -5.024 22.308 -22.172 1.00 30.22 ? ? ? ? ? ? 64 GLN A CD 1
+ATOM 429 O OE1 . GLN A 1 62 ? -4.345 22.746 -23.129 1.00 31.89 ? ? ? ? ? ? 64 GLN A OE1 1
+ATOM 430 N NE2 . GLN A 1 62 ? -6.362 22.351 -22.155 1.00 28.53 ? ? ? ? ? ? 64 GLN A NE2 1
+ATOM 431 N N . THR A 1 63 ? -1.751 17.773 -20.518 1.00 29.70 ? ? ? ? ? ? 65 THR A N 1
+ATOM 432 C CA . THR A 1 63 ? -0.825 16.842 -21.142 1.00 29.95 ? ? ? ? ? ? 65 THR A CA 1
+ATOM 433 C C . THR A 1 63 ? -1.610 15.830 -21.967 1.00 28.22 ? ? ? ? ? ? 65 THR A C 1
+ATOM 434 O O . THR A 1 63 ? -2.852 15.745 -21.879 1.00 26.39 ? ? ? ? ? ? 65 THR A O 1
+ATOM 435 C CB . THR A 1 63 ? -0.010 16.071 -20.095 1.00 30.81 ? ? ? ? ? ? 65 THR A CB 1
+ATOM 436 O OG1 . THR A 1 63 ? -0.897 15.297 -19.248 1.00 30.42 ? ? ? ? ? ? 65 THR A OG1 1
+ATOM 437 C CG2 . THR A 1 63 ? 0.824 17.023 -19.275 1.00 33.74 ? ? ? ? ? ? 65 THR A CG2 1
+ATOM 438 N N . ARG A 1 64 ? -0.886 15.027 -22.737 1.00 28.10 ? ? ? ? ? ? 66 ARG A N 1
+ATOM 439 C CA . ARG A 1 64 ? -1.516 13.903 -23.389 1.00 26.73 ? ? ? ? ? ? 66 ARG A CA 1
+ATOM 440 C C . ARG A 1 64 ? -2.410 13.108 -22.409 1.00 25.08 ? ? ? ? ? ? 66 ARG A C 1
+ATOM 441 O O . ARG A 1 64 ? -3.376 12.454 -22.828 1.00 23.73 ? ? ? ? ? ? 66 ARG A O 1
+ATOM 442 C CB . ARG A 1 64 ? -0.460 13.014 -24.044 1.00 27.91 ? ? ? ? ? ? 66 ARG A CB 1
+ATOM 443 C CG . ARG A 1 64 ? -1.032 11.692 -24.648 1.00 29.01 ? ? ? ? ? ? 66 ARG A CG 1
+ATOM 444 C CD . ARG A 1 64 ? -0.213 11.224 -25.909 1.00 33.87 ? ? ? ? ? ? 66 ARG A CD 1
+ATOM 445 N NE . ARG A 1 64 ? 1.113 10.719 -25.542 1.00 39.87 ? ? ? ? ? ? 66 ARG A NE 1
+ATOM 446 C CZ . ARG A 1 64 ? 1.273 9.451 -25.149 1.00 45.46 ? ? ? ? ? ? 66 ARG A CZ 1
+ATOM 447 N NH1 . ARG A 1 64 ? 2.466 9.006 -24.775 1.00 48.49 ? ? ? ? ? ? 66 ARG A NH1 1
+ATOM 448 N NH2 . ARG A 1 64 ? 0.208 8.625 -25.112 1.00 45.95 ? ? ? ? ? ? 66 ARG A NH2 1
+ATOM 449 N N . HIS A 1 65 ? -2.111 13.173 -21.107 1.00 24.86 ? ? ? ? ? ? 67 HIS A N 1
+ATOM 450 C CA . HIS A 1 65 ? -2.841 12.331 -20.131 1.00 24.10 ? ? ? ? ? ? 67 HIS A CA 1
+ATOM 451 C C . HIS A 1 65 ? -4.020 13.013 -19.469 1.00 23.34 ? ? ? ? ? ? 67 HIS A C 1
+ATOM 452 O O . HIS A 1 65 ? -4.610 12.431 -18.508 1.00 22.91 ? ? ? ? ? ? 67 HIS A O 1
+ATOM 453 C CB . HIS A 1 65 ? -1.918 11.730 -19.064 1.00 24.80 ? ? ? ? ? ? 67 HIS A CB 1
+ATOM 454 C CG . HIS A 1 65 ? -0.816 10.907 -19.640 1.00 27.48 ? ? ? ? ? ? 67 HIS A CG 1
+ATOM 455 N ND1 . HIS A 1 65 ? -0.956 10.191 -20.818 1.00 28.09 ? ? ? ? ? ? 67 HIS A ND1 1
+ATOM 456 C CD2 . HIS A 1 65 ? 0.447 10.682 -19.209 1.00 30.60 ? ? ? ? ? ? 67 HIS A CD2 1
+ATOM 457 C CE1 . HIS A 1 65 ? 0.181 9.571 -21.091 1.00 30.69 ? ? ? ? ? ? 67 HIS A CE1 1
+ATOM 458 N NE2 . HIS A 1 65 ? 1.041 9.835 -20.121 1.00 32.56 ? ? ? ? ? ? 67 HIS A NE2 1
+ATOM 459 N N . GLY A 1 66 ? -4.357 14.217 -19.977 1.00 23.45 ? ? ? ? ? ? 68 GLY A N 1
+ATOM 460 C CA . GLY A 1 66 ? -5.543 14.957 -19.528 1.00 23.05 ? ? ? ? ? ? 68 GLY A CA 1
+ATOM 461 C C . GLY A 1 66 ? -5.125 16.212 -18.813 1.00 23.58 ? ? ? ? ? ? 68 GLY A C 1
+ATOM 462 O O . GLY A 1 66 ? -3.974 16.630 -18.952 1.00 24.68 ? ? ? ? ? ? 68 GLY A O 1
+ATOM 463 N N . VAL A 1 67 ? -6.046 16.822 -18.054 1.00 23.73 ? ? ? ? ? ? 69 VAL A N 1
+ATOM 464 C CA . VAL A 1 67 ? -5.685 18.035 -17.310 1.00 25.29 ? ? ? ? ? ? 69 VAL A CA 1
+ATOM 465 C C . VAL A 1 67 ? -5.378 17.774 -15.842 1.00 27.38 ? ? ? ? ? ? 69 VAL A C 1
+ATOM 466 O O . VAL A 1 67 ? -5.799 16.787 -15.265 1.00 26.03 ? ? ? ? ? ? 69 VAL A O 1
+ATOM 467 C CB . VAL A 1 67 ? -6.706 19.173 -17.463 1.00 24.18 ? ? ? ? ? ? 69 VAL A CB 1
+ATOM 468 C CG1 . VAL A 1 67 ? -7.328 19.087 -18.796 1.00 23.47 ? ? ? ? ? ? 69 VAL A CG1 1
+ATOM 469 C CG2 . VAL A 1 67 ? -7.792 19.078 -16.407 1.00 23.38 ? ? ? ? ? ? 69 VAL A CG2 1
+ATOM 470 N N . ILE A 1 68 ? -4.609 18.685 -15.274 1.00 31.58 ? ? ? ? ? ? 70 ILE A N 1
+ATOM 471 C CA . ILE A 1 68 ? -4.257 18.667 -13.875 1.00 35.85 ? ? ? ? ? ? 70 ILE A CA 1
+ATOM 472 C C . ILE A 1 68 ? -3.894 20.103 -13.437 1.00 40.48 ? ? ? ? ? ? 70 ILE A C 1
+ATOM 473 O O . ILE A 1 68 ? -3.442 20.943 -14.252 1.00 41.26 ? ? ? ? ? ? 70 ILE A O 1
+ATOM 474 C CB . ILE A 1 68 ? -3.137 17.660 -13.591 1.00 35.31 ? ? ? ? ? ? 70 ILE A CB 1
+ATOM 475 C CG1 . ILE A 1 68 ? -3.062 17.400 -12.099 1.00 34.94 ? ? ? ? ? ? 70 ILE A CG1 1
+ATOM 476 C CG2 . ILE A 1 68 ? -1.813 18.148 -14.144 1.00 36.89 ? ? ? ? ? ? 70 ILE A CG2 1
+ATOM 477 C CD1 . ILE A 1 68 ? -2.514 16.052 -11.774 1.00 34.03 ? ? ? ? ? ? 70 ILE A CD1 1
+ATOM 478 N N . GLU A 1 69 ? -4.123 20.367 -12.150 1.00 45.39 ? ? ? ? ? ? 71 GLU A N 1
+ATOM 479 C CA . GLU A 1 69 ? -3.959 21.684 -11.556 1.00 51.34 ? ? ? ? ? ? 71 GLU A CA 1
+ATOM 480 C C . GLU A 1 69 ? -2.832 21.594 -10.527 1.00 55.11 ? ? ? ? ? ? 71 GLU A C 1
+ATOM 481 O O . GLU A 1 69 ? -2.859 20.721 -9.664 1.00 55.41 ? ? ? ? ? ? 71 GLU A O 1
+ATOM 482 C CB . GLU A 1 69 ? -5.285 22.073 -10.896 1.00 50.78 ? ? ? ? ? ? 71 GLU A CB 1
+ATOM 483 C CG . GLU A 1 69 ? -5.358 23.453 -10.275 1.00 56.29 ? ? ? ? ? ? 71 GLU A CG 1
+ATOM 484 C CD . GLU A 1 69 ? -6.733 23.756 -9.687 1.00 59.81 ? ? ? ? ? ? 71 GLU A CD 1
+ATOM 485 O OE1 . GLU A 1 69 ? -6.805 24.062 -8.476 1.00 61.66 ? ? ? ? ? ? 71 GLU A OE1 1
+ATOM 486 O OE2 . GLU A 1 69 ? -7.742 23.685 -10.439 1.00 59.40 ? ? ? ? ? ? 71 GLU A OE2 1
+ATOM 487 N N . SER A 1 70 ? -1.830 22.463 -10.633 1.00 60.26 ? ? ? ? ? ? 72 SER A N 1
+ATOM 488 C CA . SER A 1 70 ? -0.785 22.528 -9.618 1.00 65.19 ? ? ? ? ? ? 72 SER A CA 1
+ATOM 489 C C . SER A 1 70 ? -1.191 23.554 -8.582 1.00 67.72 ? ? ? ? ? ? 72 SER A C 1
+ATOM 490 O O . SER A 1 70 ? -1.586 24.664 -8.933 1.00 68.67 ? ? ? ? ? ? 72 SER A O 1
+ATOM 491 C CB . SER A 1 70 ? 0.566 22.885 -10.232 1.00 66.81 ? ? ? ? ? ? 72 SER A CB 1
+ATOM 492 O OG . SER A 1 70 ? 0.520 24.141 -10.869 1.00 69.19 ? ? ? ? ? ? 72 SER A OG 1
+ATOM 493 N N . GLU A 1 71 ? -1.109 23.173 -7.312 1.00 70.07 ? ? ? ? ? ? 73 GLU A N 1
+ATOM 494 C CA . GLU A 1 71 ? -1.494 24.038 -6.212 1.00 72.36 ? ? ? ? ? ? 73 GLU A CA 1
+ATOM 495 C C . GLU A 1 71 ? -0.236 24.266 -5.347 1.00 75.16 ? ? ? ? ? ? 73 GLU A C 1
+ATOM 496 O O . GLU A 1 71 ? -0.249 24.010 -4.173 1.00 77.08 ? ? ? ? ? ? 73 GLU A O 1
+ATOM 497 C CB . GLU A 1 71 ? -2.606 23.360 -5.394 1.00 71.07 ? ? ? ? ? ? 73 GLU A CB 1
+ATOM 498 C CG . GLU A 1 71 ? -3.410 22.310 -6.167 1.00 69.29 ? ? ? ? ? ? 73 GLU A CG 1
+ATOM 499 C CD . GLU A 1 71 ? -4.836 22.110 -5.652 1.00 67.49 ? ? ? ? ? ? 73 GLU A CD 1
+ATOM 500 O OE1 . GLU A 1 71 ? -5.627 23.072 -5.780 1.00 67.26 ? ? ? ? ? ? 73 GLU A OE1 1
+ATOM 501 O OE2 . GLU A 1 71 ? -5.169 20.998 -5.157 1.00 64.72 ? ? ? ? ? ? 73 GLU A OE2 1
+ATOM 506 N N . LYS A 1 72 ? 3.692 26.048 -3.818 1.00 78.11 ? ? ? ? ? ? 75 LYS A N 1
+ATOM 507 C CA . LYS A 1 72 ? 4.129 27.336 -3.223 1.00 79.14 ? ? ? ? ? ? 75 LYS A CA 1
+ATOM 508 C C . LYS A 1 72 ? 4.479 28.474 -4.244 1.00 79.69 ? ? ? ? ? ? 75 LYS A C 1
+ATOM 509 O O . LYS A 1 72 ? 5.535 28.516 -4.903 1.00 79.72 ? ? ? ? ? ? 75 LYS A O 1
+ATOM 510 C CB . LYS A 1 72 ? 5.211 27.143 -2.149 1.00 79.82 ? ? ? ? ? ? 75 LYS A CB 1
+ATOM 511 C CG . LYS A 1 72 ? 6.646 27.001 -2.680 1.00 82.03 ? ? ? ? ? ? 75 LYS A CG 1
+ATOM 512 C CD . LYS A 1 72 ? 7.702 26.968 -1.556 1.00 83.81 ? ? ? ? ? ? 75 LYS A CD 1
+ATOM 513 C CE . LYS A 1 72 ? 9.130 26.847 -2.110 1.00 84.65 ? ? ? ? ? ? 75 LYS A CE 1
+ATOM 514 N NZ . LYS A 1 72 ? 10.106 26.489 -1.037 1.00 84.64 ? ? ? ? ? ? 75 LYS A NZ 1
diff --git a/modules/seq/alg/tests/testfiles/validate_seqres_aln_connected.mmcif b/modules/seq/alg/tests/testfiles/validate_seqres_aln_connected.mmcif
new file mode 100644
index 0000000000000000000000000000000000000000..2e76cf323b55cd273db4cfd97b9b9d53a6aac9f3
--- /dev/null
+++ b/modules/seq/alg/tests/testfiles/validate_seqres_aln_connected.mmcif
@@ -0,0 +1,564 @@
+data_3BAR
+# based on 3AQD
+_entry.id 3BAR
+#
+loop_
+_entity.id
+_entity.type
+_entity.src_method
+_entity.pdbx_description
+_entity.formula_weight
+_entity.pdbx_number_of_molecules
+_entity.details
+1 polymer man 'Transcription attenuation protein mtrB' 8257.458 22 ?
+2 water nat water 18.015 7 ?
+#
+_entity_poly.entity_id 1
+_entity_poly.type 'polypeptide(L)'
+_entity_poly.nstd_linkage no
+_entity_poly.nstd_monomer no
+_entity_poly.pdbx_seq_one_letter_code MYTNSDFVVIKALEDGVNVIGLTRGADTRFHHSEKLDKGEVLIAQFTEHTSAIKVRGKAYIQTRHGVIESEGGKK
+_entity_poly.pdbx_seq_one_letter_code_can MYTNSDFVVIKALEDGVNVIGLTRGADTRFHHSEKLDKGEVLIAQFTEHTSAIKVRGKAYIQTRHGVIESEGGKK
+_entity_poly.pdbx_strand_id A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V
+#
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_entity_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.B_iso_or_equiv
+_atom_site.Cartn_x_esd
+_atom_site.Cartn_y_esd
+_atom_site.Cartn_z_esd
+_atom_site.occupancy_esd
+_atom_site.B_iso_or_equiv_esd
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_comp_id
+_atom_site.auth_asym_id
+_atom_site.auth_atom_id
+_atom_site.pdbx_PDB_model_num
+ATOM 1 N N . SER A 1 5 ? 8.892 13.236 -28.550 1.00 81.62 ? ? ? ? ? ? 7 SER A N 1
+ATOM 2 C CA . SER A 1 5 ? 8.449 14.550 -29.128 1.00 80.98 ? ? ? ? ? ? 7 SER A CA 1
+ATOM 3 C C . SER A 1 5 ? 7.181 15.159 -28.476 1.00 77.44 ? ? ? ? ? ? 7 SER A C 1
+ATOM 4 O O . SER A 1 5 ? 6.463 15.940 -29.117 1.00 76.80 ? ? ? ? ? ? 7 SER A O 1
+ATOM 5 C CB . SER A 1 5 ? 8.239 14.416 -30.651 1.00 81.96 ? ? ? ? ? ? 7 SER A CB 1
+ATOM 6 O OG . SER A 1 5 ? 9.441 14.629 -31.378 1.00 87.04 ? ? ? ? ? ? 7 SER A OG 1
+ATOM 7 N N . ASP A 1 6 ? 6.910 14.822 -27.217 1.00 73.87 ? ? ? ? ? ? 8 ASP A N 1
+ATOM 8 C CA . ASP A 1 6 ? 5.670 15.258 -26.582 1.00 69.40 ? ? ? ? ? ? 8 ASP A CA 1
+ATOM 9 C C . ASP A 1 6 ? 5.834 16.550 -25.785 1.00 68.43 ? ? ? ? ? ? 8 ASP A C 1
+ATOM 10 O O . ASP A 1 6 ? 6.944 16.907 -25.403 1.00 70.90 ? ? ? ? ? ? 8 ASP A O 1
+ATOM 11 C CB . ASP A 1 6 ? 5.104 14.146 -25.703 1.00 67.64 ? ? ? ? ? ? 8 ASP A CB 1
+ATOM 12 C CG . ASP A 1 6 ? 3.570 14.083 -25.751 1.00 64.57 ? ? ? ? ? ? 8 ASP A CG 1
+ATOM 13 O OD1 . ASP A 1 6 ? 2.949 15.085 -26.195 1.00 63.11 ? ? ? ? ? ? 8 ASP A OD1 1
+ATOM 14 O OD2 . ASP A 1 6 ? 2.984 13.032 -25.353 1.00 62.17 ? ? ? ? ? ? 8 ASP A OD2 1
+ATOM 15 N N . PHE A 1 7 ? 4.726 17.246 -25.545 1.00 64.53 ? ? ? ? ? ? 9 PHE A N 1
+ATOM 16 C CA . PHE A 1 7 ? 4.750 18.548 -24.879 1.00 61.94 ? ? ? ? ? ? 9 PHE A CA 1
+ATOM 17 C C . PHE A 1 7 ? 3.673 18.732 -23.796 1.00 57.92 ? ? ? ? ? ? 9 PHE A C 1
+ATOM 18 O O . PHE A 1 7 ? 2.693 17.987 -23.744 1.00 55.70 ? ? ? ? ? ? 9 PHE A O 1
+ATOM 19 C CB . PHE A 1 7 ? 4.618 19.664 -25.915 1.00 63.43 ? ? ? ? ? ? 9 PHE A CB 1
+ATOM 20 C CG . PHE A 1 7 ? 3.282 19.718 -26.567 1.00 62.41 ? ? ? ? ? ? 9 PHE A CG 1
+ATOM 21 C CD1 . PHE A 1 7 ? 2.231 20.382 -25.970 1.00 61.82 ? ? ? ? ? ? 9 PHE A CD1 1
+ATOM 22 C CD2 . PHE A 1 7 ? 3.075 19.105 -27.775 1.00 64.02 ? ? ? ? ? ? 9 PHE A CD2 1
+ATOM 23 C CE1 . PHE A 1 7 ? 0.988 20.428 -26.567 1.00 60.16 ? ? ? ? ? ? 9 PHE A CE1 1
+ATOM 24 C CE2 . PHE A 1 7 ? 1.832 19.145 -28.383 1.00 62.57 ? ? ? ? ? ? 9 PHE A CE2 1
+ATOM 25 C CZ . PHE A 1 7 ? 0.783 19.808 -27.775 1.00 60.25 ? ? ? ? ? ? 9 PHE A CZ 1
+ATOM 26 N N . VAL A 1 8 ? 3.861 19.735 -22.938 1.00 55.04 ? ? ? ? ? ? 10 VAL A N 1
+ATOM 27 C CA . VAL A 1 8 ? 2.861 20.095 -21.949 1.00 50.88 ? ? ? ? ? ? 10 VAL A CA 1
+ATOM 28 C C . VAL A 1 8 ? 2.487 21.551 -22.098 1.00 49.54 ? ? ? ? ? ? 10 VAL A C 1
+ATOM 29 O O . VAL A 1 8 ? 3.323 22.385 -22.446 1.00 50.85 ? ? ? ? ? ? 10 VAL A O 1
+ATOM 30 C CB . VAL A 1 8 ? 3.326 19.851 -20.511 1.00 51.03 ? ? ? ? ? ? 10 VAL A CB 1
+ATOM 31 C CG1 . VAL A 1 8 ? 3.832 18.442 -20.371 1.00 50.13 ? ? ? ? ? ? 10 VAL A CG1 1
+ATOM 32 C CG2 . VAL A 1 8 ? 4.402 20.826 -20.090 1.00 53.19 ? ? ? ? ? ? 10 VAL A CG2 1
+ATOM 33 N N . VAL A 1 9 ? 1.215 21.844 -21.842 1.00 46.06 ? ? ? ? ? ? 11 VAL A N 1
+ATOM 34 C CA . VAL A 1 9 ? 0.687 23.206 -21.880 1.00 44.00 ? ? ? ? ? ? 11 VAL A CA 1
+ATOM 35 C C . VAL A 1 9 ? 0.489 23.603 -20.434 1.00 44.21 ? ? ? ? ? ? 11 VAL A C 1
+ATOM 36 O O . VAL A 1 9 ? -0.170 22.877 -19.678 1.00 42.41 ? ? ? ? ? ? 11 VAL A O 1
+ATOM 37 C CB . VAL A 1 9 ? -0.661 23.252 -22.624 1.00 42.00 ? ? ? ? ? ? 11 VAL A CB 1
+ATOM 38 C CG1 . VAL A 1 9 ? -1.295 24.607 -22.528 1.00 40.79 ? ? ? ? ? ? 11 VAL A CG1 1
+ATOM 39 C CG2 . VAL A 1 9 ? -0.455 22.906 -24.078 1.00 40.13 ? ? ? ? ? ? 11 VAL A CG2 1
+ATOM 40 N N . ILE A 1 10 ? 1.076 24.738 -20.056 1.00 46.10 ? ? ? ? ? ? 12 ILE A N 1
+ATOM 41 C CA . ILE A 1 10 ? 1.003 25.240 -18.696 1.00 47.51 ? ? ? ? ? ? 12 ILE A CA 1
+ATOM 42 C C . ILE A 1 10 ? 0.516 26.657 -18.743 1.00 48.05 ? ? ? ? ? ? 12 ILE A C 1
+ATOM 43 O O . ILE A 1 10 ? 1.137 27.508 -19.380 1.00 49.65 ? ? ? ? ? ? 12 ILE A O 1
+ATOM 44 C CB . ILE A 1 10 ? 2.374 25.247 -18.012 1.00 49.28 ? ? ? ? ? ? 12 ILE A CB 1
+ATOM 45 C CG1 . ILE A 1 10 ? 2.981 23.848 -18.003 1.00 49.95 ? ? ? ? ? ? 12 ILE A CG1 1
+ATOM 46 C CG2 . ILE A 1 10 ? 2.247 25.753 -16.603 1.00 50.91 ? ? ? ? ? ? 12 ILE A CG2 1
+ATOM 47 C CD1 . ILE A 1 10 ? 4.435 23.827 -17.677 1.00 54.16 ? ? ? ? ? ? 12 ILE A CD1 1
+ATOM 48 N N . LYS A 1 11 ? -0.606 26.901 -18.076 1.00 47.39 ? ? ? ? ? ? 13 LYS A N 1
+ATOM 49 C CA . LYS A 1 11 ? -1.139 28.252 -17.917 1.00 48.23 ? ? ? ? ? ? 13 LYS A CA 1
+ATOM 50 C C . LYS A 1 11 ? -0.998 28.660 -16.473 1.00 50.10 ? ? ? ? ? ? 13 LYS A C 1
+ATOM 51 O O . LYS A 1 11 ? -1.441 27.931 -15.579 1.00 49.40 ? ? ? ? ? ? 13 LYS A O 1
+ATOM 52 C CB . LYS A 1 11 ? -2.609 28.311 -18.304 1.00 46.00 ? ? ? ? ? ? 13 LYS A CB 1
+ATOM 53 C CG . LYS A 1 11 ? -3.144 29.706 -18.267 1.00 45.91 ? ? ? ? ? ? 13 LYS A CG 1
+ATOM 54 C CD . LYS A 1 11 ? -4.640 29.741 -18.402 1.00 43.12 ? ? ? ? ? ? 13 LYS A CD 1
+ATOM 55 C CE . LYS A 1 11 ? -5.103 31.182 -18.619 1.00 44.02 ? ? ? ? ? ? 13 LYS A CE 1
+ATOM 56 N NZ . LYS A 1 11 ? -6.563 31.312 -18.363 1.00 43.35 ? ? ? ? ? ? 13 LYS A NZ 1
+ATOM 57 N N . ALA A 1 12 ? -0.379 29.818 -16.242 1.00 53.49 ? ? ? ? ? ? 14 ALA A N 1
+ATOM 58 C CA . ALA A 1 12 ? -0.115 30.296 -14.876 1.00 55.56 ? ? ? ? ? ? 14 ALA A CA 1
+ATOM 59 C C . ALA A 1 12 ? -1.354 30.960 -14.272 1.00 55.44 ? ? ? ? ? ? 14 ALA A C 1
+ATOM 60 O O . ALA A 1 12 ? -1.938 31.848 -14.881 1.00 55.76 ? ? ? ? ? ? 14 ALA A O 1
+ATOM 61 C CB . ALA A 1 12 ? 1.042 31.240 -14.890 1.00 58.43 ? ? ? ? ? ? 14 ALA A CB 1
+ATOM 62 N N . LEU A 1 13 ? -1.767 30.514 -13.093 1.00 55.02 ? ? ? ? ? ? 15 LEU A N 1
+ATOM 63 C CA . LEU A 1 13 ? -2.966 31.063 -12.438 1.00 55.23 ? ? ? ? ? ? 15 LEU A CA 1
+ATOM 64 C C . LEU A 1 13 ? -2.665 32.145 -11.380 1.00 58.70 ? ? ? ? ? ? 15 LEU A C 1
+ATOM 65 O O . LEU A 1 13 ? -3.574 32.758 -10.809 1.00 58.84 ? ? ? ? ? ? 15 LEU A O 1
+ATOM 66 C CB . LEU A 1 13 ? -3.811 29.932 -11.832 1.00 52.50 ? ? ? ? ? ? 15 LEU A CB 1
+ATOM 67 C CG . LEU A 1 13 ? -4.415 28.951 -12.839 1.00 47.91 ? ? ? ? ? ? 15 LEU A CG 1
+ATOM 68 C CD1 . LEU A 1 13 ? -4.953 27.698 -12.151 1.00 44.21 ? ? ? ? ? ? 15 LEU A CD1 1
+ATOM 69 C CD2 . LEU A 1 13 ? -5.494 29.672 -13.668 1.00 46.05 ? ? ? ? ? ? 15 LEU A CD2 1
+ATOM 70 N N . GLU A 1 14 ? -1.379 32.359 -11.120 1.00 62.66 ? ? ? ? ? ? 16 GLU A N 1
+ATOM 71 C CA . GLU A 1 14 ? -0.899 33.425 -10.252 1.00 67.00 ? ? ? ? ? ? 16 GLU A CA 1
+ATOM 72 C C . GLU A 1 14 ? 0.409 33.922 -10.836 1.00 70.32 ? ? ? ? ? ? 16 GLU A C 1
+ATOM 73 O O . GLU A 1 14 ? 0.914 33.339 -11.785 1.00 70.03 ? ? ? ? ? ? 16 GLU A O 1
+ATOM 74 C CB . GLU A 1 14 ? -0.696 32.923 -8.819 1.00 67.19 ? ? ? ? ? ? 16 GLU A CB 1
+ATOM 75 C CG . GLU A 1 14 ? 0.432 31.895 -8.625 1.00 68.58 ? ? ? ? ? ? 16 GLU A CG 1
+ATOM 76 C CD . GLU A 1 14 ? 0.454 31.270 -7.222 1.00 70.39 ? ? ? ? ? ? 16 GLU A CD 1
+ATOM 77 O OE1 . GLU A 1 14 ? -0.457 31.541 -6.412 1.00 71.02 ? ? ? ? ? ? 16 GLU A OE1 1
+ATOM 78 O OE2 . GLU A 1 14 ? 1.387 30.491 -6.926 1.00 71.29 ? ? ? ? ? ? 16 GLU A OE2 1
+ATOM 79 N N . ASP A 1 15 ? 0.955 35.001 -10.285 1.00 74.75 ? ? ? ? ? ? 17 ASP A N 1
+ATOM 80 C CA . ASP A 1 15 ? 2.250 35.491 -10.740 1.00 78.78 ? ? ? ? ? ? 17 ASP A CA 1
+ATOM 81 C C . ASP A 1 15 ? 3.325 34.615 -10.138 1.00 79.87 ? ? ? ? ? ? 17 ASP A C 1
+ATOM 82 O O . ASP A 1 15 ? 3.099 33.950 -9.124 1.00 79.33 ? ? ? ? ? ? 17 ASP A O 1
+ATOM 83 C CB . ASP A 1 15 ? 2.475 36.953 -10.336 1.00 81.65 ? ? ? ? ? ? 17 ASP A CB 1
+ATOM 84 C CG . ASP A 1 15 ? 1.621 37.937 -11.140 1.00 83.16 ? ? ? ? ? ? 17 ASP A CG 1
+ATOM 85 O OD1 . ASP A 1 15 ? 1.344 37.691 -12.326 1.00 82.40 ? ? ? ? ? ? 17 ASP A OD1 1
+ATOM 86 O OD2 . ASP A 1 15 ? 1.231 38.982 -10.589 1.00 86.46 ? ? ? ? ? ? 17 ASP A OD2 1
+ATOM 87 N N . GLY A 1 16 ? 4.489 34.606 -10.778 1.00 81.58 ? ? ? ? ? ? 18 GLY A N 1
+ATOM 88 C CA . GLY A 1 16 ? 5.660 33.903 -10.248 1.00 82.57 ? ? ? ? ? ? 18 GLY A CA 1
+ATOM 89 C C . GLY A 1 16 ? 5.555 32.392 -10.154 1.00 80.35 ? ? ? ? ? ? 18 GLY A C 1
+ATOM 90 O O . GLY A 1 16 ? 6.059 31.793 -9.215 1.00 81.29 ? ? ? ? ? ? 18 GLY A O 1
+ATOM 91 N N . VAL A 1 17 ? 4.892 31.781 -11.128 1.00 77.56 ? ? ? ? ? ? 19 VAL A N 1
+ATOM 92 C CA . VAL A 1 17 ? 4.885 30.336 -11.259 1.00 74.50 ? ? ? ? ? ? 19 VAL A CA 1
+ATOM 93 C C . VAL A 1 17 ? 6.239 29.942 -11.826 1.00 76.68 ? ? ? ? ? ? 19 VAL A C 1
+ATOM 94 O O . VAL A 1 17 ? 6.799 30.655 -12.655 1.00 78.24 ? ? ? ? ? ? 19 VAL A O 1
+ATOM 95 C CB . VAL A 1 17 ? 3.755 29.861 -12.187 1.00 71.56 ? ? ? ? ? ? 19 VAL A CB 1
+ATOM 96 C CG1 . VAL A 1 17 ? 3.820 28.364 -12.384 1.00 67.63 ? ? ? ? ? ? 19 VAL A CG1 1
+ATOM 97 C CG2 . VAL A 1 17 ? 2.409 30.247 -11.611 1.00 67.92 ? ? ? ? ? ? 19 VAL A CG2 1
+ATOM 98 N N . ASN A 1 18 ? 6.764 28.812 -11.381 1.00 77.33 ? ? ? ? ? ? 20 ASN A N 1
+ATOM 99 C CA . ASN A 1 18 ? 8.086 28.396 -11.775 1.00 79.46 ? ? ? ? ? ? 20 ASN A CA 1
+ATOM 100 C C . ASN A 1 18 ? 8.067 27.069 -12.528 1.00 77.29 ? ? ? ? ? ? 20 ASN A C 1
+ATOM 101 O O . ASN A 1 18 ? 7.635 26.058 -11.989 1.00 75.60 ? ? ? ? ? ? 20 ASN A O 1
+ATOM 102 C CB . ASN A 1 18 ? 8.941 28.291 -10.526 1.00 82.30 ? ? ? ? ? ? 20 ASN A CB 1
+ATOM 103 C CG . ASN A 1 18 ? 10.360 28.739 -10.753 1.00 89.13 ? ? ? ? ? ? 20 ASN A CG 1
+ATOM 104 O OD1 . ASN A 1 18 ? 10.690 29.305 -11.791 1.00 92.93 ? ? ? ? ? ? 20 ASN A OD1 1
+ATOM 105 N ND2 . ASN A 1 18 ? 11.217 28.488 -9.773 1.00 94.39 ? ? ? ? ? ? 20 ASN A ND2 1
+ATOM 106 N N . VAL A 1 19 ? 8.521 27.077 -13.779 1.00 76.88 ? ? ? ? ? ? 21 VAL A N 1
+ATOM 107 C CA . VAL A 1 19 ? 8.542 25.871 -14.600 1.00 75.28 ? ? ? ? ? ? 21 VAL A CA 1
+ATOM 108 C C . VAL A 1 19 ? 9.970 25.398 -14.720 1.00 78.52 ? ? ? ? ? ? 21 VAL A C 1
+ATOM 109 O O . VAL A 1 19 ? 10.747 25.948 -15.489 1.00 80.53 ? ? ? ? ? ? 21 VAL A O 1
+ATOM 110 C CB . VAL A 1 19 ? 7.946 26.104 -16.005 1.00 73.54 ? ? ? ? ? ? 21 VAL A CB 1
+ATOM 111 C CG1 . VAL A 1 19 ? 7.966 24.838 -16.807 1.00 70.33 ? ? ? ? ? ? 21 VAL A CG1 1
+ATOM 112 C CG2 . VAL A 1 19 ? 6.528 26.602 -15.913 1.00 69.44 ? ? ? ? ? ? 21 VAL A CG2 1
+ATOM 113 N N . ILE A 1 20 ? 10.305 24.368 -13.960 1.00 80.07 ? ? ? ? ? ? 22 ILE A N 1
+ATOM 114 C CA . ILE A 1 20 ? 11.683 23.949 -13.817 1.00 83.77 ? ? ? ? ? ? 22 ILE A CA 1
+ATOM 115 C C . ILE A 1 20 ? 12.004 22.729 -14.664 1.00 83.74 ? ? ? ? ? ? 22 ILE A C 1
+ATOM 116 O O . ILE A 1 20 ? 11.349 21.705 -14.536 1.00 81.42 ? ? ? ? ? ? 22 ILE A O 1
+ATOM 117 C CB . ILE A 1 20 ? 12.014 23.661 -12.348 1.00 84.59 ? ? ? ? ? ? 22 ILE A CB 1
+ATOM 118 C CG1 . ILE A 1 20 ? 11.522 24.802 -11.467 1.00 85.96 ? ? ? ? ? ? 22 ILE A CG1 1
+ATOM 119 C CG2 . ILE A 1 20 ? 13.511 23.484 -12.166 1.00 89.81 ? ? ? ? ? ? 22 ILE A CG2 1
+ATOM 120 C CD1 . ILE A 1 20 ? 11.484 24.464 -9.998 1.00 87.43 ? ? ? ? ? ? 22 ILE A CD1 1
+ATOM 121 N N . GLY A 1 21 ? 13.019 22.862 -15.520 1.00 86.57 ? ? ? ? ? ? 23 GLY A N 1
+ATOM 122 C CA . GLY A 1 21 ? 13.522 21.775 -16.358 1.00 88.60 ? ? ? ? ? ? 23 GLY A CA 1
+ATOM 123 C C . GLY A 1 21 ? 14.674 21.070 -15.675 1.00 91.29 ? ? ? ? ? ? 23 GLY A C 1
+ATOM 124 O O . GLY A 1 21 ? 15.573 21.716 -15.154 1.00 94.14 ? ? ? ? ? ? 23 GLY A O 1
+ATOM 125 N N . LEU A 1 22 ? 14.642 19.743 -15.672 1.00 91.36 ? ? ? ? ? ? 24 LEU A N 1
+ATOM 126 C CA . LEU A 1 22 ? 15.603 18.932 -14.926 1.00 92.96 ? ? ? ? ? ? 24 LEU A CA 1
+ATOM 127 C C . LEU A 1 22 ? 16.447 18.089 -15.876 1.00 94.68 ? ? ? ? ? ? 24 LEU A C 1
+ATOM 128 O O . LEU A 1 22 ? 15.939 17.601 -16.885 1.00 94.04 ? ? ? ? ? ? 24 LEU A O 1
+ATOM 129 C CB . LEU A 1 22 ? 14.860 18.047 -13.924 1.00 91.08 ? ? ? ? ? ? 24 LEU A CB 1
+ATOM 130 C CG . LEU A 1 22 ? 14.551 18.518 -12.493 1.00 90.38 ? ? ? ? ? ? 24 LEU A CG 1
+ATOM 131 C CD1 . LEU A 1 22 ? 14.342 20.009 -12.384 1.00 91.01 ? ? ? ? ? ? 24 LEU A CD1 1
+ATOM 132 C CD2 . LEU A 1 22 ? 13.342 17.791 -11.921 1.00 85.41 ? ? ? ? ? ? 24 LEU A CD2 1
+ATOM 133 N N . THR A 1 23 ? 17.733 17.926 -15.565 1.00 96.47 ? ? ? ? ? ? 25 THR A N 1
+ATOM 134 C CA . THR A 1 23 ? 18.688 17.343 -16.531 1.00 98.30 ? ? ? ? ? ? 25 THR A CA 1
+ATOM 135 C C . THR A 1 23 ? 19.007 15.862 -16.352 1.00 98.49 ? ? ? ? ? ? 25 THR A C 1
+ATOM 136 O O . THR A 1 23 ? 18.826 15.304 -15.266 1.00 98.19 ? ? ? ? ? ? 25 THR A O 1
+ATOM 137 C CB . THR A 1 23 ? 20.028 18.102 -16.553 1.00 100.21 ? ? ? ? ? ? 25 THR A CB 1
+ATOM 138 O OG1 . THR A 1 23 ? 20.490 18.282 -15.208 1.00 101.37 ? ? ? ? ? ? 25 THR A OG1 1
+ATOM 139 C CG2 . THR A 1 23 ? 19.883 19.457 -17.252 1.00 100.72 ? ? ? ? ? ? 25 THR A CG2 1
+ATOM 140 N N . ARG A 1 24 ? 19.501 15.246 -17.430 1.00 99.49 ? ? ? ? ? ? 26 ARG A N 1
+ATOM 141 C CA . ARG A 1 24 ? 19.857 13.819 -17.452 1.00 99.94 ? ? ? ? ? ? 26 ARG A CA 1
+ATOM 142 C C . ARG A 1 24 ? 21.154 13.541 -16.693 1.00 101.44 ? ? ? ? ? ? 26 ARG A C 1
+ATOM 143 O O . ARG A 1 24 ? 22.240 13.904 -17.147 1.00 103.26 ? ? ? ? ? ? 26 ARG A O 1
+ATOM 144 C CB . ARG A 1 24 ? 19.955 13.281 -18.893 1.00 100.14 ? ? ? ? ? ? 26 ARG A CB 1
+ATOM 145 C CG . ARG A 1 24 ? 18.620 13.217 -19.642 1.00 99.36 ? ? ? ? ? ? 26 ARG A CG 1
+ATOM 146 C CD . ARG A 1 24 ? 18.634 12.164 -20.759 1.00 100.98 ? ? ? ? ? ? 26 ARG A CD 1
+ATOM 147 N NE . ARG A 1 24 ? 17.552 12.352 -21.740 1.00 100.55 ? ? ? ? ? ? 26 ARG A NE 1
+ATOM 148 C CZ . ARG A 1 24 ? 17.231 11.494 -22.716 1.00 99.98 ? ? ? ? ? ? 26 ARG A CZ 1
+ATOM 149 N NH1 . ARG A 1 24 ? 17.891 10.344 -22.876 1.00 99.60 ? ? ? ? ? ? 26 ARG A NH1 1
+ATOM 150 N NH2 . ARG A 1 24 ? 16.229 11.791 -23.537 1.00 99.33 ? ? ? ? ? ? 26 ARG A NH2 1
+ATOM 151 N N . THR A 1 28 ? 22.527 16.428 -12.721 1.00 120.13 ? ? ? ? ? ? 30 THR A N 1
+ATOM 152 C CA . THR A 1 28 ? 21.235 15.835 -13.090 1.00 118.47 ? ? ? ? ? ? 30 THR A CA 1
+ATOM 153 C C . THR A 1 28 ? 20.021 16.467 -12.351 1.00 117.17 ? ? ? ? ? ? 30 THR A C 1
+ATOM 154 O O . THR A 1 28 ? 18.867 16.073 -12.593 1.00 115.70 ? ? ? ? ? ? 30 THR A O 1
+ATOM 155 C CB . THR A 1 28 ? 21.259 14.241 -13.007 1.00 118.06 ? ? ? ? ? ? 30 THR A CB 1
+ATOM 156 O OG1 . THR A 1 28 ? 19.946 13.697 -13.234 1.00 116.11 ? ? ? ? ? ? 30 THR A OG1 1
+ATOM 157 C CG2 . THR A 1 28 ? 21.822 13.727 -11.660 1.00 118.37 ? ? ? ? ? ? 30 THR A CG2 1
+ATOM 158 N N . ARG A 1 29 ? 20.289 17.464 -11.492 1.00 117.71 ? ? ? ? ? ? 31 ARG A N 1
+ATOM 159 C CA . ARG A 1 29 ? 19.261 18.091 -10.604 1.00 116.35 ? ? ? ? ? ? 31 ARG A CA 1
+ATOM 160 C C . ARG A 1 29 ? 18.477 19.294 -11.195 1.00 115.56 ? ? ? ? ? ? 31 ARG A C 1
+ATOM 161 O O . ARG A 1 29 ? 18.271 19.360 -12.420 1.00 115.47 ? ? ? ? ? ? 31 ARG A O 1
+ATOM 162 C CB . ARG A 1 29 ? 19.840 18.428 -9.204 1.00 117.16 ? ? ? ? ? ? 31 ARG A CB 1
+ATOM 163 C CG . ARG A 1 29 ? 21.320 18.904 -9.113 1.00 119.11 ? ? ? ? ? ? 31 ARG A CG 1
+ATOM 164 C CD . ARG A 1 29 ? 21.638 20.210 -9.857 1.00 119.60 ? ? ? ? ? ? 31 ARG A CD 1
+ATOM 165 N NE . ARG A 1 29 ? 22.419 19.952 -11.068 1.00 120.44 ? ? ? ? ? ? 31 ARG A NE 1
+ATOM 166 C CZ . ARG A 1 29 ? 21.980 20.123 -12.315 1.00 119.80 ? ? ? ? ? ? 31 ARG A CZ 1
+ATOM 167 N NH1 . ARG A 1 29 ? 22.780 19.853 -13.337 1.00 121.30 ? ? ? ? ? ? 31 ARG A NH1 1
+ATOM 168 N NH2 . ARG A 1 29 ? 20.756 20.576 -12.552 1.00 117.87 ? ? ? ? ? ? 31 ARG A NH2 1
+ATOM 169 N N . PHE A 1 30 ? 18.052 20.228 -10.323 1.00 114.83 ? ? ? ? ? ? 32 PHE A N 1
+ATOM 170 C CA . PHE A 1 30 ? 17.248 21.413 -10.728 1.00 113.80 ? ? ? ? ? ? 32 PHE A CA 1
+ATOM 171 C C . PHE A 1 30 ? 18.047 22.475 -11.541 1.00 114.52 ? ? ? ? ? ? 32 PHE A C 1
+ATOM 172 O O . PHE A 1 30 ? 18.937 23.145 -11.001 1.00 115.82 ? ? ? ? ? ? 32 PHE A O 1
+ATOM 173 C CB . PHE A 1 30 ? 16.487 22.093 -9.541 1.00 113.41 ? ? ? ? ? ? 32 PHE A CB 1
+ATOM 174 C CG . PHE A 1 30 ? 16.144 21.179 -8.346 1.00 112.64 ? ? ? ? ? ? 32 PHE A CG 1
+ATOM 175 C CD1 . PHE A 1 30 ? 15.540 21.740 -7.207 1.00 112.23 ? ? ? ? ? ? 32 PHE A CD1 1
+ATOM 176 C CD2 . PHE A 1 30 ? 16.423 19.805 -8.338 1.00 111.84 ? ? ? ? ? ? 32 PHE A CD2 1
+ATOM 177 C CE1 . PHE A 1 30 ? 15.212 20.957 -6.091 1.00 111.54 ? ? ? ? ? ? 32 PHE A CE1 1
+ATOM 178 C CE2 . PHE A 1 30 ? 16.110 19.015 -7.218 1.00 111.19 ? ? ? ? ? ? 32 PHE A CE2 1
+ATOM 179 C CZ . PHE A 1 30 ? 15.497 19.590 -6.097 1.00 111.08 ? ? ? ? ? ? 32 PHE A CZ 1
+ATOM 180 N N . HIS A 1 31 ? 17.677 22.645 -12.817 1.00 113.18 ? ? ? ? ? ? 33 HIS A N 1
+ATOM 181 C CA . HIS A 1 31 ? 18.505 23.317 -13.836 1.00 113.51 ? ? ? ? ? ? 33 HIS A CA 1
+ATOM 182 C C . HIS A 1 31 ? 17.843 24.573 -14.459 1.00 112.40 ? ? ? ? ? ? 33 HIS A C 1
+ATOM 183 O O . HIS A 1 31 ? 17.840 25.650 -13.849 1.00 112.91 ? ? ? ? ? ? 33 HIS A O 1
+ATOM 184 C CB . HIS A 1 31 ? 18.897 22.274 -14.908 1.00 113.74 ? ? ? ? ? ? 33 HIS A CB 1
+ATOM 185 C CG . HIS A 1 31 ? 19.881 22.761 -15.933 1.00 116.22 ? ? ? ? ? ? 33 HIS A CG 1
+ATOM 186 N ND1 . HIS A 1 31 ? 21.201 23.036 -15.635 1.00 118.98 ? ? ? ? ? ? 33 HIS A ND1 1
+ATOM 187 C CD2 . HIS A 1 31 ? 19.743 22.976 -17.264 1.00 116.72 ? ? ? ? ? ? 33 HIS A CD2 1
+ATOM 188 C CE1 . HIS A 1 31 ? 21.826 23.425 -16.734 1.00 120.25 ? ? ? ? ? ? 33 HIS A CE1 1
+ATOM 189 N NE2 . HIS A 1 31 ? 20.964 23.395 -17.736 1.00 119.10 ? ? ? ? ? ? 33 HIS A NE2 1
+ATOM 190 N N . HIS A 1 32 ? 17.298 24.431 -15.670 1.00 110.63 ? ? ? ? ? ? 34 HIS A N 1
+ATOM 191 C CA . HIS A 1 32 ? 16.630 25.529 -16.377 1.00 108.57 ? ? ? ? ? ? 34 HIS A CA 1
+ATOM 192 C C . HIS A 1 32 ? 15.315 25.908 -15.701 1.00 105.41 ? ? ? ? ? ? 34 HIS A C 1
+ATOM 193 O O . HIS A 1 32 ? 14.336 25.165 -15.760 1.00 102.47 ? ? ? ? ? ? 34 HIS A O 1
+ATOM 194 C CB . HIS A 1 32 ? 16.384 25.161 -17.858 1.00 108.29 ? ? ? ? ? ? 34 HIS A CB 1
+ATOM 195 C CG . HIS A 1 32 ? 15.859 26.296 -18.697 1.00 108.03 ? ? ? ? ? ? 34 HIS A CG 1
+ATOM 196 N ND1 . HIS A 1 32 ? 16.492 27.522 -18.778 1.00 111.34 ? ? ? ? ? ? 34 HIS A ND1 1
+ATOM 197 C CD2 . HIS A 1 32 ? 14.778 26.380 -19.511 1.00 103.90 ? ? ? ? ? ? 34 HIS A CD2 1
+ATOM 198 C CE1 . HIS A 1 32 ? 15.812 28.317 -19.586 1.00 109.77 ? ? ? ? ? ? 34 HIS A CE1 1
+ATOM 199 N NE2 . HIS A 1 32 ? 14.772 27.647 -20.051 1.00 105.66 ? ? ? ? ? ? 34 HIS A NE2 1
+ATOM 200 N N . SER A 1 33 ? 15.303 27.064 -15.056 1.00 104.75 ? ? ? ? ? ? 35 SER A N 1
+ATOM 201 C CA . SER A 1 33 ? 14.079 27.599 -14.485 1.00 101.92 ? ? ? ? ? ? 35 SER A CA 1
+ATOM 202 C C . SER A 1 33 ? 13.450 28.601 -15.456 1.00 99.94 ? ? ? ? ? ? 35 SER A C 1
+ATOM 203 O O . SER A 1 33 ? 14.146 29.196 -16.272 1.00 101.93 ? ? ? ? ? ? 35 SER A O 1
+ATOM 204 C CB . SER A 1 33 ? 14.372 28.236 -13.124 1.00 103.64 ? ? ? ? ? ? 35 SER A CB 1
+ATOM 205 O OG . SER A 1 33 ? 13.401 29.202 -12.771 1.00 103.74 ? ? ? ? ? ? 35 SER A OG 1
+ATOM 206 N N . GLU A 1 34 ? 12.136 28.778 -15.372 1.00 95.30 ? ? ? ? ? ? 36 GLU A N 1
+ATOM 207 C CA . GLU A 1 34 ? 11.425 29.699 -16.249 1.00 92.35 ? ? ? ? ? ? 36 GLU A CA 1
+ATOM 208 C C . GLU A 1 34 ? 10.221 30.272 -15.520 1.00 90.03 ? ? ? ? ? ? 36 GLU A C 1
+ATOM 209 O O . GLU A 1 34 ? 9.296 29.543 -15.201 1.00 87.29 ? ? ? ? ? ? 36 GLU A O 1
+ATOM 210 C CB . GLU A 1 34 ? 10.977 28.964 -17.511 1.00 90.67 ? ? ? ? ? ? 36 GLU A CB 1
+ATOM 211 C CG . GLU A 1 34 ? 10.555 29.867 -18.650 1.00 90.72 ? ? ? ? ? ? 36 GLU A CG 1
+ATOM 212 C CD . GLU A 1 34 ? 11.736 30.565 -19.310 1.00 96.24 ? ? ? ? ? ? 36 GLU A CD 1
+ATOM 213 O OE1 . GLU A 1 34 ? 12.815 29.937 -19.462 1.00 99.38 ? ? ? ? ? ? 36 GLU A OE1 1
+ATOM 214 O OE2 . GLU A 1 34 ? 11.578 31.748 -19.685 1.00 98.37 ? ? ? ? ? ? 36 GLU A OE2 1
+ATOM 215 N N . LYS A 1 35 ? 10.235 31.569 -15.239 1.00 90.36 ? ? ? ? ? ? 37 LYS A N 1
+ATOM 216 C CA . LYS A 1 35 ? 9.139 32.178 -14.506 1.00 88.38 ? ? ? ? ? ? 37 LYS A CA 1
+ATOM 217 C C . LYS A 1 35 ? 7.977 32.484 -15.433 1.00 85.67 ? ? ? ? ? ? 37 LYS A C 1
+ATOM 218 O O . LYS A 1 35 ? 8.172 32.833 -16.592 1.00 86.06 ? ? ? ? ? ? 37 LYS A O 1
+ATOM 219 C CB . LYS A 1 35 ? 9.601 33.433 -13.768 1.00 91.44 ? ? ? ? ? ? 37 LYS A CB 1
+ATOM 220 N N . LEU A 1 36 ? 6.766 32.325 -14.915 1.00 81.92 ? ? ? ? ? ? 38 LEU A N 1
+ATOM 221 C CA . LEU A 1 36 ? 5.539 32.641 -15.640 1.00 78.89 ? ? ? ? ? ? 38 LEU A CA 1
+ATOM 222 C C . LEU A 1 36 ? 4.640 33.528 -14.797 1.00 78.12 ? ? ? ? ? ? 38 LEU A C 1
+ATOM 223 O O . LEU A 1 36 ? 4.498 33.299 -13.601 1.00 77.83 ? ? ? ? ? ? 38 LEU A O 1
+ATOM 224 C CB . LEU A 1 36 ? 4.770 31.368 -15.979 1.00 77.62 ? ? ? ? ? ? 38 LEU A CB 1
+ATOM 225 C CG . LEU A 1 36 ? 4.861 30.675 -17.336 1.00 76.31 ? ? ? ? ? ? 38 LEU A CG 1
+ATOM 226 C CD1 . LEU A 1 36 ? 3.481 30.149 -17.653 1.00 74.28 ? ? ? ? ? ? 38 LEU A CD1 1
+ATOM 227 C CD2 . LEU A 1 36 ? 5.328 31.599 -18.436 1.00 76.23 ? ? ? ? ? ? 38 LEU A CD2 1
+ATOM 228 N N . ASP A 1 37 ? 4.015 34.523 -15.417 1.00 77.70 ? ? ? ? ? ? 39 ASP A N 1
+ATOM 229 C CA . ASP A 1 37 ? 3.127 35.429 -14.691 1.00 77.42 ? ? ? ? ? ? 39 ASP A CA 1
+ATOM 230 C C . ASP A 1 37 ? 1.666 35.169 -15.004 1.00 73.58 ? ? ? ? ? ? 39 ASP A C 1
+ATOM 231 O O . ASP A 1 37 ? 1.352 34.676 -16.075 1.00 72.04 ? ? ? ? ? ? 39 ASP A O 1
+ATOM 232 C CB . ASP A 1 37 ? 3.473 36.886 -14.995 1.00 80.86 ? ? ? ? ? ? 39 ASP A CB 1
+ATOM 233 C CG . ASP A 1 37 ? 4.632 37.408 -14.159 1.00 86.94 ? ? ? ? ? ? 39 ASP A CG 1
+ATOM 234 O OD1 . ASP A 1 37 ? 4.986 36.781 -13.125 1.00 88.70 ? ? ? ? ? ? 39 ASP A OD1 1
+ATOM 235 O OD2 . ASP A 1 37 ? 5.178 38.463 -14.548 1.00 92.58 ? ? ? ? ? ? 39 ASP A OD2 1
+ATOM 236 N N . LYS A 1 38 ? 0.788 35.520 -14.065 1.00 71.09 ? ? ? ? ? ? 40 LYS A N 1
+ATOM 237 C CA . LYS A 1 38 ? -0.646 35.219 -14.127 1.00 67.44 ? ? ? ? ? ? 40 LYS A CA 1
+ATOM 238 C C . LYS A 1 38 ? -1.246 35.395 -15.514 1.00 65.75 ? ? ? ? ? ? 40 LYS A C 1
+ATOM 239 O O . LYS A 1 38 ? -1.274 36.506 -16.038 1.00 66.82 ? ? ? ? ? ? 40 LYS A O 1
+ATOM 240 C CB . LYS A 1 38 ? -1.408 36.092 -13.130 1.00 67.43 ? ? ? ? ? ? 40 LYS A CB 1
+ATOM 241 C CG . LYS A 1 38 ? -2.847 35.692 -12.912 1.00 65.33 ? ? ? ? ? ? 40 LYS A CG 1
+ATOM 242 C CD . LYS A 1 38 ? -3.496 36.530 -11.819 1.00 65.17 ? ? ? ? ? ? 40 LYS A CD 1
+ATOM 243 C CE . LYS A 1 38 ? -4.727 35.828 -11.238 1.00 64.58 ? ? ? ? ? ? 40 LYS A CE 1
+ATOM 244 N NZ . LYS A 1 38 ? -5.911 36.738 -11.093 1.00 64.29 ? ? ? ? ? ? 40 LYS A NZ 1
+ATOM 245 N N . GLY A 1 39 ? -1.710 34.288 -16.097 1.00 62.75 ? ? ? ? ? ? 41 GLY A N 1
+ATOM 246 C CA . GLY A 1 39 ? -2.358 34.280 -17.410 1.00 60.49 ? ? ? ? ? ? 41 GLY A CA 1
+ATOM 247 C C . GLY A 1 39 ? -1.471 33.947 -18.599 1.00 60.30 ? ? ? ? ? ? 41 GLY A C 1
+ATOM 248 O O . GLY A 1 39 ? -1.957 33.805 -19.718 1.00 58.95 ? ? ? ? ? ? 41 GLY A O 1
+ATOM 249 N N . GLU A 1 40 ? -0.167 33.843 -18.366 1.00 61.59 ? ? ? ? ? ? 42 GLU A N 1
+ATOM 250 C CA . GLU A 1 40 ? 0.777 33.499 -19.424 1.00 62.43 ? ? ? ? ? ? 42 GLU A CA 1
+ATOM 251 C C . GLU A 1 40 ? 0.720 32.015 -19.667 1.00 59.62 ? ? ? ? ? ? 42 GLU A C 1
+ATOM 252 O O . GLU A 1 40 ? 0.425 31.239 -18.761 1.00 58.37 ? ? ? ? ? ? 42 GLU A O 1
+ATOM 253 C CB . GLU A 1 40 ? 2.200 33.917 -19.056 1.00 65.52 ? ? ? ? ? ? 42 GLU A CB 1
+ATOM 254 C CG . GLU A 1 40 ? 2.523 35.352 -19.404 1.00 71.75 ? ? ? ? ? ? 42 GLU A CG 1
+ATOM 255 C CD . GLU A 1 40 ? 3.754 35.879 -18.701 1.00 79.02 ? ? ? ? ? ? 42 GLU A CD 1
+ATOM 256 O OE1 . GLU A 1 40 ? 4.375 35.124 -17.926 1.00 79.96 ? ? ? ? ? ? 42 GLU A OE1 1
+ATOM 257 O OE2 . GLU A 1 40 ? 4.097 37.059 -18.923 1.00 83.29 ? ? ? ? ? ? 42 GLU A OE2 1
+ATOM 258 N N . VAL A 1 41 ? 1.004 31.619 -20.895 1.00 58.12 ? ? ? ? ? ? 43 VAL A N 1
+ATOM 259 C CA . VAL A 1 41 ? 0.931 30.221 -21.282 1.00 55.42 ? ? ? ? ? ? 43 VAL A CA 1
+ATOM 260 C C . VAL A 1 41 ? 2.254 29.747 -21.855 1.00 57.22 ? ? ? ? ? ? 43 VAL A C 1
+ATOM 261 O O . VAL A 1 41 ? 2.823 30.381 -22.755 1.00 58.88 ? ? ? ? ? ? 43 VAL A O 1
+ATOM 262 C CB . VAL A 1 41 ? -0.180 29.994 -22.309 1.00 53.28 ? ? ? ? ? ? 43 VAL A CB 1
+ATOM 263 C CG1 . VAL A 1 41 ? -0.060 28.645 -22.920 1.00 50.49 ? ? ? ? ? ? 43 VAL A CG1 1
+ATOM 264 C CG2 . VAL A 1 41 ? -1.523 30.132 -21.664 1.00 49.78 ? ? ? ? ? ? 43 VAL A CG2 1
+ATOM 265 N N . LEU A 1 42 ? 2.738 28.629 -21.323 1.00 57.21 ? ? ? ? ? ? 44 LEU A N 1
+ATOM 266 C CA . LEU A 1 42 ? 3.960 28.037 -21.813 1.00 58.54 ? ? ? ? ? ? 44 LEU A CA 1
+ATOM 267 C C . LEU A 1 42 ? 3.633 26.718 -22.458 1.00 56.54 ? ? ? ? ? ? 44 LEU A C 1
+ATOM 268 O O . LEU A 1 42 ? 2.882 25.928 -21.899 1.00 54.68 ? ? ? ? ? ? 44 LEU A O 1
+ATOM 269 C CB . LEU A 1 42 ? 4.954 27.852 -20.680 1.00 60.35 ? ? ? ? ? ? 44 LEU A CB 1
+ATOM 270 C CG . LEU A 1 42 ? 6.378 27.476 -21.074 1.00 64.66 ? ? ? ? ? ? 44 LEU A CG 1
+ATOM 271 C CD1 . LEU A 1 42 ? 7.071 28.595 -21.816 1.00 69.92 ? ? ? ? ? ? 44 LEU A CD1 1
+ATOM 272 C CD2 . LEU A 1 42 ? 7.171 27.112 -19.839 1.00 67.81 ? ? ? ? ? ? 44 LEU A CD2 1
+ATOM 273 N N . ILE A 1 43 ? 4.162 26.504 -23.657 1.00 56.61 ? ? ? ? ? ? 45 ILE A N 1
+ATOM 274 C CA . ILE A 1 43 ? 4.086 25.207 -24.298 1.00 55.49 ? ? ? ? ? ? 45 ILE A CA 1
+ATOM 275 C C . ILE A 1 43 ? 5.487 24.630 -24.267 1.00 57.96 ? ? ? ? ? ? 45 ILE A C 1
+ATOM 276 O O . ILE A 1 43 ? 6.345 25.038 -25.046 1.00 60.01 ? ? ? ? ? ? 45 ILE A O 1
+ATOM 277 C CB . ILE A 1 43 ? 3.621 25.276 -25.757 1.00 54.45 ? ? ? ? ? ? 45 ILE A CB 1
+ATOM 278 C CG1 . ILE A 1 43 ? 2.749 26.525 -26.016 1.00 53.11 ? ? ? ? ? ? 45 ILE A CG1 1
+ATOM 279 C CG2 . ILE A 1 43 ? 2.966 23.955 -26.167 1.00 50.96 ? ? ? ? ? ? 45 ILE A CG2 1
+ATOM 280 C CD1 . ILE A 1 43 ? 1.330 26.489 -25.511 1.00 48.47 ? ? ? ? ? ? 45 ILE A CD1 1
+ATOM 281 N N . ALA A 1 44 ? 5.708 23.687 -23.351 1.00 58.61 ? ? ? ? ? ? 46 ALA A N 1
+ATOM 282 C CA . ALA A 1 44 ? 7.019 23.104 -23.115 1.00 60.53 ? ? ? ? ? ? 46 ALA A CA 1
+ATOM 283 C C . ALA A 1 44 ? 7.098 21.728 -23.724 1.00 60.54 ? ? ? ? ? ? 46 ALA A C 1
+ATOM 284 O O . ALA A 1 44 ? 6.238 20.893 -23.489 1.00 58.05 ? ? ? ? ? ? 46 ALA A O 1
+ATOM 285 C CB . ALA A 1 44 ? 7.298 23.026 -21.643 1.00 61.04 ? ? ? ? ? ? 46 ALA A CB 1
+ATOM 286 N N . GLN A 1 45 ? 8.142 21.522 -24.518 1.00 63.39 ? ? ? ? ? ? 47 GLN A N 1
+ATOM 287 C CA . GLN A 1 45 ? 8.433 20.236 -25.131 1.00 64.77 ? ? ? ? ? ? 47 GLN A CA 1
+ATOM 288 C C . GLN A 1 45 ? 9.599 19.592 -24.406 1.00 67.08 ? ? ? ? ? ? 47 GLN A C 1
+ATOM 289 O O . GLN A 1 45 ? 10.492 20.287 -23.920 1.00 69.41 ? ? ? ? ? ? 47 GLN A O 1
+ATOM 290 C CB . GLN A 1 45 ? 8.791 20.423 -26.602 1.00 65.44 ? ? ? ? ? ? 47 GLN A CB 1
+ATOM 291 C CG . GLN A 1 45 ? 8.796 19.131 -27.399 1.00 65.31 ? ? ? ? ? ? 47 GLN A CG 1
+ATOM 292 C CD . GLN A 1 45 ? 9.318 19.305 -28.829 1.00 68.03 ? ? ? ? ? ? 47 GLN A CD 1
+ATOM 293 O OE1 . GLN A 1 45 ? 10.214 20.129 -29.090 1.00 70.64 ? ? ? ? ? ? 47 GLN A OE1 1
+ATOM 294 N NE2 . GLN A 1 45 ? 8.757 18.518 -29.767 1.00 65.95 ? ? ? ? ? ? 47 GLN A NE2 1
+ATOM 295 N N . PHE A 1 46 ? 9.590 18.266 -24.339 1.00 67.71 ? ? ? ? ? ? 48 PHE A N 1
+ATOM 296 C CA . PHE A 1 46 ? 10.706 17.526 -23.777 1.00 70.43 ? ? ? ? ? ? 48 PHE A CA 1
+ATOM 297 C C . PHE A 1 46 ? 11.857 17.437 -24.766 1.00 74.96 ? ? ? ? ? ? 48 PHE A C 1
+ATOM 298 O O . PHE A 1 46 ? 11.675 16.991 -25.907 1.00 74.94 ? ? ? ? ? ? 48 PHE A O 1
+ATOM 299 C CB . PHE A 1 46 ? 10.269 16.127 -23.384 1.00 67.85 ? ? ? ? ? ? 48 PHE A CB 1
+ATOM 300 C CG . PHE A 1 46 ? 9.527 16.081 -22.099 1.00 64.51 ? ? ? ? ? ? 48 PHE A CG 1
+ATOM 301 C CD1 . PHE A 1 46 ? 10.218 16.130 -20.894 1.00 65.87 ? ? ? ? ? ? 48 PHE A CD1 1
+ATOM 302 C CD2 . PHE A 1 46 ? 8.130 15.992 -22.085 1.00 59.45 ? ? ? ? ? ? 48 PHE A CD2 1
+ATOM 303 C CE1 . PHE A 1 46 ? 9.533 16.094 -19.687 1.00 63.95 ? ? ? ? ? ? 48 PHE A CE1 1
+ATOM 304 C CE2 . PHE A 1 46 ? 7.427 15.953 -20.885 1.00 57.67 ? ? ? ? ? ? 48 PHE A CE2 1
+ATOM 305 C CZ . PHE A 1 46 ? 8.130 16.002 -19.680 1.00 60.02 ? ? ? ? ? ? 48 PHE A CZ 1
+ATOM 306 N N . THR A 1 47 ? 13.038 17.869 -24.334 1.00 80.48 ? ? ? ? ? ? 49 THR A N 1
+ATOM 307 C CA . THR A 1 47 ? 14.238 17.712 -25.140 1.00 86.44 ? ? ? ? ? ? 49 THR A CA 1
+ATOM 308 C C . THR A 1 47 ? 14.993 16.474 -24.653 1.00 88.73 ? ? ? ? ? ? 49 THR A C 1
+ATOM 309 O O . THR A 1 47 ? 14.523 15.780 -23.752 1.00 86.98 ? ? ? ? ? ? 49 THR A O 1
+ATOM 310 C CB . THR A 1 47 ? 15.135 18.969 -25.068 1.00 89.11 ? ? ? ? ? ? 49 THR A CB 1
+ATOM 311 O OG1 . THR A 1 47 ? 15.953 18.934 -23.892 1.00 92.76 ? ? ? ? ? ? 49 THR A OG1 1
+ATOM 312 C CG2 . THR A 1 47 ? 14.285 20.230 -25.055 1.00 88.83 ? ? ? ? ? ? 49 THR A CG2 1
+ATOM 313 N N . GLU A 1 48 ? 16.145 16.187 -25.257 1.00 93.73 ? ? ? ? ? ? 50 GLU A N 1
+ATOM 314 C CA . GLU A 1 48 ? 17.052 15.170 -24.714 1.00 98.04 ? ? ? ? ? ? 50 GLU A CA 1
+ATOM 315 C C . GLU A 1 48 ? 17.700 15.685 -23.409 1.00 99.89 ? ? ? ? ? ? 50 GLU A C 1
+ATOM 316 O O . GLU A 1 48 ? 17.792 14.952 -22.420 1.00 99.46 ? ? ? ? ? ? 50 GLU A O 1
+ATOM 317 C CB . GLU A 1 48 ? 18.103 14.731 -25.754 1.00 100.79 ? ? ? ? ? ? 50 GLU A CB 1
+ATOM 318 C CG . GLU A 1 48 ? 19.096 15.818 -26.196 0.50 107.62 ? ? ? ? ? ? 50 GLU A CG 1
+ATOM 319 C CD . GLU A 1 48 ? 20.357 15.251 -26.838 0.50 115.10 ? ? ? ? ? ? 50 GLU A CD 1
+ATOM 320 O OE1 . GLU A 1 48 ? 21.467 15.702 -26.482 0.50 120.30 ? ? ? ? ? ? 50 GLU A OE1 1
+ATOM 321 O OE2 . GLU A 1 48 ? 20.241 14.354 -27.697 0.50 115.44 ? ? ? ? ? ? 50 GLU A OE2 1
+ATOM 322 N N . HIS A 1 49 ? 18.108 16.957 -23.422 1.00 102.54 ? ? ? ? ? ? 51 HIS A N 1
+ATOM 323 C CA . HIS A 1 49 ? 18.615 17.674 -22.247 1.00 104.56 ? ? ? ? ? ? 51 HIS A CA 1
+ATOM 324 C C . HIS A 1 49 ? 17.684 17.578 -21.032 1.00 100.90 ? ? ? ? ? ? 51 HIS A C 1
+ATOM 325 O O . HIS A 1 49 ? 18.145 17.604 -19.888 1.00 102.24 ? ? ? ? ? ? 51 HIS A O 1
+ATOM 326 C CB . HIS A 1 49 ? 18.790 19.162 -22.576 1.00 107.45 ? ? ? ? ? ? 51 HIS A CB 1
+ATOM 327 C CG . HIS A 1 49 ? 19.959 19.466 -23.458 1.00 115.35 ? ? ? ? ? ? 51 HIS A CG 1
+ATOM 328 N ND1 . HIS A 1 49 ? 19.964 19.199 -24.811 1.00 117.92 ? ? ? ? ? ? 51 HIS A ND1 1
+ATOM 329 C CD2 . HIS A 1 49 ? 21.153 20.047 -23.185 1.00 122.56 ? ? ? ? ? ? 51 HIS A CD2 1
+ATOM 330 C CE1 . HIS A 1 49 ? 21.117 19.586 -25.330 1.00 123.61 ? ? ? ? ? ? 51 HIS A CE1 1
+ATOM 331 N NE2 . HIS A 1 49 ? 21.855 20.106 -24.366 1.00 126.48 ? ? ? ? ? ? 51 HIS A NE2 1
+ATOM 332 N N . THR A 1 50 ? 16.377 17.481 -21.294 1.00 95.68 ? ? ? ? ? ? 52 THR A N 1
+ATOM 333 C CA . THR A 1 50 ? 15.340 17.640 -20.268 1.00 90.19 ? ? ? ? ? ? 52 THR A CA 1
+ATOM 334 C C . THR A 1 50 ? 14.528 16.370 -20.027 1.00 86.57 ? ? ? ? ? ? 52 THR A C 1
+ATOM 335 O O . THR A 1 50 ? 13.629 16.031 -20.795 1.00 83.93 ? ? ? ? ? ? 52 THR A O 1
+ATOM 336 C CB . THR A 1 50 ? 14.419 18.847 -20.596 1.00 89.09 ? ? ? ? ? ? 52 THR A CB 1
+ATOM 337 O OG1 . THR A 1 50 ? 15.128 20.061 -20.323 1.00 91.82 ? ? ? ? ? ? 52 THR A OG1 1
+ATOM 338 C CG2 . THR A 1 50 ? 13.158 18.832 -19.761 1.00 84.32 ? ? ? ? ? ? 52 THR A CG2 1
+ATOM 339 N N . SER A 1 51 ? 14.863 15.686 -18.938 1.00 85.07 ? ? ? ? ? ? 53 SER A N 1
+ATOM 340 C CA . SER A 1 51 ? 14.183 14.465 -18.518 1.00 82.20 ? ? ? ? ? ? 53 SER A CA 1
+ATOM 341 C C . SER A 1 51 ? 12.860 14.724 -17.792 1.00 78.23 ? ? ? ? ? ? 53 SER A C 1
+ATOM 342 O O . SER A 1 51 ? 11.863 14.057 -18.069 1.00 75.30 ? ? ? ? ? ? 53 SER A O 1
+ATOM 343 C CB . SER A 1 51 ? 15.103 13.617 -17.631 1.00 84.25 ? ? ? ? ? ? 53 SER A CB 1
+ATOM 344 O OG . SER A 1 51 ? 15.508 14.324 -16.475 1.00 87.22 ? ? ? ? ? ? 53 SER A OG 1
+ATOM 345 N N . ALA A 1 52 ? 12.855 15.681 -16.867 1.00 76.66 ? ? ? ? ? ? 54 ALA A N 1
+ATOM 346 C CA . ALA A 1 52 ? 11.660 15.983 -16.082 1.00 73.63 ? ? ? ? ? ? 54 ALA A CA 1
+ATOM 347 C C . ALA A 1 52 ? 11.347 17.470 -16.020 1.00 72.67 ? ? ? ? ? ? 54 ALA A C 1
+ATOM 348 O O . ALA A 1 52 ? 12.231 18.295 -16.168 1.00 74.97 ? ? ? ? ? ? 54 ALA A O 1
+ATOM 349 C CB . ALA A 1 52 ? 11.807 15.427 -14.697 1.00 73.72 ? ? ? ? ? ? 54 ALA A CB 1
+ATOM 350 N N . ILE A 1 53 ? 10.078 17.799 -15.808 1.00 69.28 ? ? ? ? ? ? 55 ILE A N 1
+ATOM 351 C CA . ILE A 1 53 ? 9.644 19.182 -15.648 1.00 67.60 ? ? ? ? ? ? 55 ILE A CA 1
+ATOM 352 C C . ILE A 1 53 ? 8.807 19.315 -14.386 1.00 66.31 ? ? ? ? ? ? 55 ILE A C 1
+ATOM 353 O O . ILE A 1 53 ? 7.813 18.615 -14.234 1.00 63.74 ? ? ? ? ? ? 55 ILE A O 1
+ATOM 354 C CB . ILE A 1 53 ? 8.816 19.679 -16.852 1.00 66.27 ? ? ? ? ? ? 55 ILE A CB 1
+ATOM 355 C CG1 . ILE A 1 53 ? 9.678 19.756 -18.104 1.00 67.47 ? ? ? ? ? ? 55 ILE A CG1 1
+ATOM 356 C CG2 . ILE A 1 53 ? 8.217 21.057 -16.579 1.00 65.21 ? ? ? ? ? ? 55 ILE A CG2 1
+ATOM 357 C CD1 . ILE A 1 53 ? 8.873 19.776 -19.383 1.00 65.20 ? ? ? ? ? ? 55 ILE A CD1 1
+ATOM 358 N N . LYS A 1 54 ? 9.212 20.225 -13.498 1.00 67.56 ? ? ? ? ? ? 56 LYS A N 1
+ATOM 359 C CA . LYS A 1 54 ? 8.518 20.471 -12.242 1.00 66.86 ? ? ? ? ? ? 56 LYS A CA 1
+ATOM 360 C C . LYS A 1 54 ? 7.790 21.787 -12.345 1.00 66.25 ? ? ? ? ? ? 56 LYS A C 1
+ATOM 361 O O . LYS A 1 54 ? 8.325 22.736 -12.899 1.00 67.88 ? ? ? ? ? ? 56 LYS A O 1
+ATOM 362 C CB . LYS A 1 54 ? 9.524 20.526 -11.091 1.00 69.15 ? ? ? ? ? ? 56 LYS A CB 1
+ATOM 363 C CG . LYS A 1 54 ? 8.919 20.527 -9.688 1.00 66.38 ? ? ? ? ? ? 56 LYS A CG 1
+ATOM 364 C CD . LYS A 1 54 ? 9.898 21.069 -8.644 1.00 66.41 ? ? ? ? ? ? 56 LYS A CD 1
+ATOM 365 C CE . LYS A 1 54 ? 10.805 19.996 -8.061 1.00 66.08 ? ? ? ? ? ? 56 LYS A CE 1
+ATOM 366 N NZ . LYS A 1 54 ? 11.738 20.531 -7.020 1.00 66.38 ? ? ? ? ? ? 56 LYS A NZ 1
+ATOM 367 N N . VAL A 1 55 ? 6.569 21.843 -11.826 1.00 63.79 ? ? ? ? ? ? 57 VAL A N 1
+ATOM 368 C CA . VAL A 1 55 ? 5.805 23.088 -11.783 1.00 62.60 ? ? ? ? ? ? 57 VAL A CA 1
+ATOM 369 C C . VAL A 1 55 ? 5.508 23.478 -10.335 1.00 63.99 ? ? ? ? ? ? 57 VAL A C 1
+ATOM 370 O O . VAL A 1 55 ? 4.827 22.751 -9.607 1.00 62.58 ? ? ? ? ? ? 57 VAL A O 1
+ATOM 371 C CB . VAL A 1 55 ? 4.491 22.999 -12.582 1.00 60.05 ? ? ? ? ? ? 57 VAL A CB 1
+ATOM 372 C CG1 . VAL A 1 55 ? 3.777 24.330 -12.592 1.00 58.65 ? ? ? ? ? ? 57 VAL A CG1 1
+ATOM 373 C CG2 . VAL A 1 55 ? 4.759 22.561 -14.001 1.00 57.89 ? ? ? ? ? ? 57 VAL A CG2 1
+ATOM 374 N N . ARG A 1 56 ? 6.046 24.625 -9.926 1.00 67.06 ? ? ? ? ? ? 58 ARG A N 1
+ATOM 375 C CA . ARG A 1 56 ? 5.822 25.201 -8.602 1.00 68.68 ? ? ? ? ? ? 58 ARG A CA 1
+ATOM 376 C C . ARG A 1 56 ? 4.944 26.430 -8.775 1.00 68.31 ? ? ? ? ? ? 58 ARG A C 1
+ATOM 377 O O . ARG A 1 56 ? 5.295 27.346 -9.516 1.00 69.78 ? ? ? ? ? ? 58 ARG A O 1
+ATOM 378 C CB . ARG A 1 56 ? 7.149 25.622 -7.961 1.00 71.82 ? ? ? ? ? ? 58 ARG A CB 1
+ATOM 379 C CG . ARG A 1 56 ? 7.919 24.540 -7.264 1.00 71.32 ? ? ? ? ? ? 58 ARG A CG 1
+ATOM 380 C CD . ARG A 1 56 ? 8.899 25.124 -6.251 1.00 74.34 ? ? ? ? ? ? 58 ARG A CD 1
+ATOM 381 N NE . ARG A 1 56 ? 10.303 24.967 -6.641 1.00 76.63 ? ? ? ? ? ? 58 ARG A NE 1
+ATOM 382 C CZ . ARG A 1 56 ? 11.114 24.011 -6.180 1.00 77.74 ? ? ? ? ? ? 58 ARG A CZ 1
+ATOM 383 N NH1 . ARG A 1 56 ? 10.668 23.111 -5.308 1.00 77.26 ? ? ? ? ? ? 58 ARG A NH1 1
+ATOM 384 N NH2 . ARG A 1 56 ? 12.380 23.947 -6.590 1.00 79.00 ? ? ? ? ? ? 58 ARG A NH2 1
+ATOM 385 N N . GLY A 1 57 ? 3.795 26.450 -8.116 1.00 66.23 ? ? ? ? ? ? 59 GLY A N 1
+ATOM 386 C CA . GLY A 1 57 ? 2.891 27.591 -8.224 1.00 64.54 ? ? ? ? ? ? 59 GLY A CA 1
+ATOM 387 C C . GLY A 1 57 ? 1.515 27.161 -8.671 1.00 61.40 ? ? ? ? ? ? 59 GLY A C 1
+ATOM 388 O O . GLY A 1 57 ? 1.324 26.011 -9.023 1.00 60.50 ? ? ? ? ? ? 59 GLY A O 1
+ATOM 389 N N . LYS A 1 58 ? 0.553 28.077 -8.652 1.00 59.63 ? ? ? ? ? ? 60 LYS A N 1
+ATOM 390 C CA . LYS A 1 58 ? -0.823 27.767 -9.030 1.00 56.33 ? ? ? ? ? ? 60 LYS A CA 1
+ATOM 391 C C . LYS A 1 58 ? -0.937 27.782 -10.560 1.00 54.36 ? ? ? ? ? ? 60 LYS A C 1
+ATOM 392 O O . LYS A 1 58 ? -0.806 28.840 -11.173 1.00 55.40 ? ? ? ? ? ? 60 LYS A O 1
+ATOM 393 C CB . LYS A 1 58 ? -1.776 28.800 -8.402 1.00 56.75 ? ? ? ? ? ? 60 LYS A CB 1
+ATOM 394 C CG . LYS A 1 58 ? -3.130 28.251 -7.937 1.00 56.71 ? ? ? ? ? ? 60 LYS A CG 1
+ATOM 395 C CD . LYS A 1 58 ? -3.097 27.743 -6.485 1.00 57.00 ? ? ? ? ? ? 60 LYS A CD 1
+ATOM 396 C CE . LYS A 1 58 ? -4.401 27.012 -6.119 1.00 56.07 ? ? ? ? ? ? 60 LYS A CE 1
+ATOM 397 N N . ALA A 1 59 ? -1.157 26.623 -11.185 1.00 50.90 ? ? ? ? ? ? 61 ALA A N 1
+ATOM 398 C CA . ALA A 1 59 ? -1.229 26.563 -12.652 1.00 48.01 ? ? ? ? ? ? 61 ALA A CA 1
+ATOM 399 C C . ALA A 1 59 ? -2.205 25.512 -13.166 1.00 44.63 ? ? ? ? ? ? 61 ALA A C 1
+ATOM 400 O O . ALA A 1 59 ? -2.516 24.556 -12.458 1.00 43.62 ? ? ? ? ? ? 61 ALA A O 1
+ATOM 401 C CB . ALA A 1 59 ? 0.153 26.320 -13.244 1.00 49.49 ? ? ? ? ? ? 61 ALA A CB 1
+ATOM 402 N N . TYR A 1 60 ? -2.667 25.686 -14.404 1.00 41.70 ? ? ? ? ? ? 62 TYR A N 1
+ATOM 403 C CA . TYR A 1 60 ? -3.493 24.707 -15.082 1.00 38.07 ? ? ? ? ? ? 62 TYR A CA 1
+ATOM 404 C C . TYR A 1 60 ? -2.627 24.044 -16.134 1.00 37.82 ? ? ? ? ? ? 62 TYR A C 1
+ATOM 405 O O . TYR A 1 60 ? -1.998 24.722 -16.954 1.00 38.91 ? ? ? ? ? ? 62 TYR A O 1
+ATOM 406 C CB . TYR A 1 60 ? -4.671 25.417 -15.716 1.00 36.81 ? ? ? ? ? ? 62 TYR A CB 1
+ATOM 407 C CG . TYR A 1 60 ? -5.719 24.566 -16.417 1.00 33.24 ? ? ? ? ? ? 62 TYR A CG 1
+ATOM 408 C CD1 . TYR A 1 60 ? -6.553 23.709 -15.702 1.00 30.81 ? ? ? ? ? ? 62 TYR A CD1 1
+ATOM 409 C CD2 . TYR A 1 60 ? -5.925 24.669 -17.795 1.00 32.16 ? ? ? ? ? ? 62 TYR A CD2 1
+ATOM 410 C CE1 . TYR A 1 60 ? -7.554 22.938 -16.349 1.00 26.98 ? ? ? ? ? ? 62 TYR A CE1 1
+ATOM 411 C CE2 . TYR A 1 60 ? -6.915 23.914 -18.446 1.00 29.38 ? ? ? ? ? ? 62 TYR A CE2 1
+ATOM 412 C CZ . TYR A 1 60 ? -7.728 23.053 -17.716 1.00 26.79 ? ? ? ? ? ? 62 TYR A CZ 1
+ATOM 413 O OH . TYR A 1 60 ? -8.701 22.329 -18.381 1.00 24.12 ? ? ? ? ? ? 62 TYR A OH 1
+ATOM 414 N N . ILE A 1 61 ? -2.579 22.717 -16.097 1.00 36.07 ? ? ? ? ? ? 63 ILE A N 1
+ATOM 415 C CA . ILE A 1 61 ? -1.662 21.980 -16.938 1.00 35.83 ? ? ? ? ? ? 63 ILE A CA 1
+ATOM 416 C C . ILE A 1 61 ? -2.384 20.971 -17.798 1.00 33.41 ? ? ? ? ? ? 63 ILE A C 1
+ATOM 417 O O . ILE A 1 61 ? -3.202 20.217 -17.298 1.00 31.94 ? ? ? ? ? ? 63 ILE A O 1
+ATOM 418 C CB . ILE A 1 61 ? -0.610 21.239 -16.097 1.00 37.09 ? ? ? ? ? ? 63 ILE A CB 1
+ATOM 419 C CG1 . ILE A 1 61 ? 0.153 22.208 -15.183 1.00 40.08 ? ? ? ? ? ? 63 ILE A CG1 1
+ATOM 420 C CG2 . ILE A 1 61 ? 0.358 20.461 -17.018 1.00 38.40 ? ? ? ? ? ? 63 ILE A CG2 1
+ATOM 421 C CD1 . ILE A 1 61 ? 0.912 21.521 -14.083 1.00 42.02 ? ? ? ? ? ? 63 ILE A CD1 1
+ATOM 422 N N . GLN A 1 62 ? -2.075 20.961 -19.094 1.00 32.65 ? ? ? ? ? ? 64 GLN A N 1
+ATOM 423 C CA . GLN A 1 62 ? -2.645 19.966 -20.035 1.00 31.02 ? ? ? ? ? ? 64 GLN A CA 1
+ATOM 424 C C . GLN A 1 62 ? -1.536 19.076 -20.577 1.00 31.29 ? ? ? ? ? ? 64 GLN A C 1
+ATOM 425 O O . GLN A 1 62 ? -0.503 19.573 -21.072 1.00 33.32 ? ? ? ? ? ? 64 GLN A O 1
+ATOM 426 C CB . GLN A 1 62 ? -3.321 20.649 -21.251 1.00 30.42 ? ? ? ? ? ? 64 GLN A CB 1
+ATOM 427 C CG . GLN A 1 62 ? -4.366 21.714 -20.928 1.00 29.89 ? ? ? ? ? ? 64 GLN A CG 1
+ATOM 428 C CD . GLN A 1 62 ? -5.024 22.308 -22.172 1.00 30.22 ? ? ? ? ? ? 64 GLN A CD 1
+ATOM 429 O OE1 . GLN A 1 62 ? -4.345 22.746 -23.129 1.00 31.89 ? ? ? ? ? ? 64 GLN A OE1 1
+ATOM 430 N NE2 . GLN A 1 62 ? -6.362 22.351 -22.155 1.00 28.53 ? ? ? ? ? ? 64 GLN A NE2 1
+ATOM 431 N N . THR A 1 63 ? -1.751 17.773 -20.518 1.00 29.70 ? ? ? ? ? ? 65 THR A N 1
+ATOM 432 C CA . THR A 1 63 ? -0.825 16.842 -21.142 1.00 29.95 ? ? ? ? ? ? 65 THR A CA 1
+ATOM 433 C C . THR A 1 63 ? -1.610 15.830 -21.967 1.00 28.22 ? ? ? ? ? ? 65 THR A C 1
+ATOM 434 O O . THR A 1 63 ? -2.852 15.745 -21.879 1.00 26.39 ? ? ? ? ? ? 65 THR A O 1
+ATOM 435 C CB . THR A 1 63 ? -0.010 16.071 -20.095 1.00 30.81 ? ? ? ? ? ? 65 THR A CB 1
+ATOM 436 O OG1 . THR A 1 63 ? -0.897 15.297 -19.248 1.00 30.42 ? ? ? ? ? ? 65 THR A OG1 1
+ATOM 437 C CG2 . THR A 1 63 ? 0.824 17.023 -19.275 1.00 33.74 ? ? ? ? ? ? 65 THR A CG2 1
+ATOM 438 N N . ARG A 1 64 ? -0.886 15.027 -22.737 1.00 28.10 ? ? ? ? ? ? 66 ARG A N 1
+ATOM 439 C CA . ARG A 1 64 ? -1.516 13.903 -23.389 1.00 26.73 ? ? ? ? ? ? 66 ARG A CA 1
+ATOM 440 C C . ARG A 1 64 ? -2.410 13.108 -22.409 1.00 25.08 ? ? ? ? ? ? 66 ARG A C 1
+ATOM 441 O O . ARG A 1 64 ? -3.376 12.454 -22.828 1.00 23.73 ? ? ? ? ? ? 66 ARG A O 1
+ATOM 442 C CB . ARG A 1 64 ? -0.460 13.014 -24.044 1.00 27.91 ? ? ? ? ? ? 66 ARG A CB 1
+ATOM 443 C CG . ARG A 1 64 ? -1.032 11.692 -24.648 1.00 29.01 ? ? ? ? ? ? 66 ARG A CG 1
+ATOM 444 C CD . ARG A 1 64 ? -0.213 11.224 -25.909 1.00 33.87 ? ? ? ? ? ? 66 ARG A CD 1
+ATOM 445 N NE . ARG A 1 64 ? 1.113 10.719 -25.542 1.00 39.87 ? ? ? ? ? ? 66 ARG A NE 1
+ATOM 446 C CZ . ARG A 1 64 ? 1.273 9.451 -25.149 1.00 45.46 ? ? ? ? ? ? 66 ARG A CZ 1
+ATOM 447 N NH1 . ARG A 1 64 ? 2.466 9.006 -24.775 1.00 48.49 ? ? ? ? ? ? 66 ARG A NH1 1
+ATOM 448 N NH2 . ARG A 1 64 ? 0.208 8.625 -25.112 1.00 45.95 ? ? ? ? ? ? 66 ARG A NH2 1
+ATOM 449 N N . HIS A 1 65 ? -2.111 13.173 -21.107 1.00 24.86 ? ? ? ? ? ? 67 HIS A N 1
+ATOM 450 C CA . HIS A 1 65 ? -2.841 12.331 -20.131 1.00 24.10 ? ? ? ? ? ? 67 HIS A CA 1
+ATOM 451 C C . HIS A 1 65 ? -4.020 13.013 -19.469 1.00 23.34 ? ? ? ? ? ? 67 HIS A C 1
+ATOM 452 O O . HIS A 1 65 ? -4.610 12.431 -18.508 1.00 22.91 ? ? ? ? ? ? 67 HIS A O 1
+ATOM 453 C CB . HIS A 1 65 ? -1.918 11.730 -19.064 1.00 24.80 ? ? ? ? ? ? 67 HIS A CB 1
+ATOM 454 C CG . HIS A 1 65 ? -0.816 10.907 -19.640 1.00 27.48 ? ? ? ? ? ? 67 HIS A CG 1
+ATOM 455 N ND1 . HIS A 1 65 ? -0.956 10.191 -20.818 1.00 28.09 ? ? ? ? ? ? 67 HIS A ND1 1
+ATOM 456 C CD2 . HIS A 1 65 ? 0.447 10.682 -19.209 1.00 30.60 ? ? ? ? ? ? 67 HIS A CD2 1
+ATOM 457 C CE1 . HIS A 1 65 ? 0.181 9.571 -21.091 1.00 30.69 ? ? ? ? ? ? 67 HIS A CE1 1
+ATOM 458 N NE2 . HIS A 1 65 ? 1.041 9.835 -20.121 1.00 32.56 ? ? ? ? ? ? 67 HIS A NE2 1
+ATOM 459 N N . GLY A 1 66 ? -4.357 14.217 -19.977 1.00 23.45 ? ? ? ? ? ? 68 GLY A N 1
+ATOM 460 C CA . GLY A 1 66 ? -5.543 14.957 -19.528 1.00 23.05 ? ? ? ? ? ? 68 GLY A CA 1
+ATOM 461 C C . GLY A 1 66 ? -5.125 16.212 -18.813 1.00 23.58 ? ? ? ? ? ? 68 GLY A C 1
+ATOM 462 O O . GLY A 1 66 ? -3.974 16.630 -18.952 1.00 24.68 ? ? ? ? ? ? 68 GLY A O 1
+ATOM 463 N N . VAL A 1 67 ? -6.046 16.822 -18.054 1.00 23.73 ? ? ? ? ? ? 69 VAL A N 1
+ATOM 464 C CA . VAL A 1 67 ? -5.685 18.035 -17.310 1.00 25.29 ? ? ? ? ? ? 69 VAL A CA 1
+ATOM 465 C C . VAL A 1 67 ? -5.378 17.774 -15.842 1.00 27.38 ? ? ? ? ? ? 69 VAL A C 1
+ATOM 466 O O . VAL A 1 67 ? -5.799 16.787 -15.265 1.00 26.03 ? ? ? ? ? ? 69 VAL A O 1
+ATOM 467 C CB . VAL A 1 67 ? -6.706 19.173 -17.463 1.00 24.18 ? ? ? ? ? ? 69 VAL A CB 1
+ATOM 468 C CG1 . VAL A 1 67 ? -7.328 19.087 -18.796 1.00 23.47 ? ? ? ? ? ? 69 VAL A CG1 1
+ATOM 469 C CG2 . VAL A 1 67 ? -7.792 19.078 -16.407 1.00 23.38 ? ? ? ? ? ? 69 VAL A CG2 1
+ATOM 470 N N . ILE A 1 68 ? -4.609 18.685 -15.274 1.00 31.58 ? ? ? ? ? ? 70 ILE A N 1
+ATOM 471 C CA . ILE A 1 68 ? -4.257 18.667 -13.875 1.00 35.85 ? ? ? ? ? ? 70 ILE A CA 1
+ATOM 472 C C . ILE A 1 68 ? -3.894 20.103 -13.437 1.00 40.48 ? ? ? ? ? ? 70 ILE A C 1
+ATOM 473 O O . ILE A 1 68 ? -3.442 20.943 -14.252 1.00 41.26 ? ? ? ? ? ? 70 ILE A O 1
+ATOM 474 C CB . ILE A 1 68 ? -3.137 17.660 -13.591 1.00 35.31 ? ? ? ? ? ? 70 ILE A CB 1
+ATOM 475 C CG1 . ILE A 1 68 ? -3.062 17.400 -12.099 1.00 34.94 ? ? ? ? ? ? 70 ILE A CG1 1
+ATOM 476 C CG2 . ILE A 1 68 ? -1.813 18.148 -14.144 1.00 36.89 ? ? ? ? ? ? 70 ILE A CG2 1
+ATOM 477 C CD1 . ILE A 1 68 ? -2.514 16.052 -11.774 1.00 34.03 ? ? ? ? ? ? 70 ILE A CD1 1
+ATOM 478 N N . GLU A 1 69 ? -4.123 20.367 -12.150 1.00 45.39 ? ? ? ? ? ? 71 GLU A N 1
+ATOM 479 C CA . GLU A 1 69 ? -3.959 21.684 -11.556 1.00 51.34 ? ? ? ? ? ? 71 GLU A CA 1
+ATOM 480 C C . GLU A 1 69 ? -2.832 21.594 -10.527 1.00 55.11 ? ? ? ? ? ? 71 GLU A C 1
+ATOM 481 O O . GLU A 1 69 ? -2.859 20.721 -9.664 1.00 55.41 ? ? ? ? ? ? 71 GLU A O 1
+ATOM 482 C CB . GLU A 1 69 ? -5.285 22.073 -10.896 1.00 50.78 ? ? ? ? ? ? 71 GLU A CB 1
+ATOM 483 C CG . GLU A 1 69 ? -5.358 23.453 -10.275 1.00 56.29 ? ? ? ? ? ? 71 GLU A CG 1
+ATOM 484 C CD . GLU A 1 69 ? -6.733 23.756 -9.687 1.00 59.81 ? ? ? ? ? ? 71 GLU A CD 1
+ATOM 485 O OE1 . GLU A 1 69 ? -6.805 24.062 -8.476 1.00 61.66 ? ? ? ? ? ? 71 GLU A OE1 1
+ATOM 486 O OE2 . GLU A 1 69 ? -7.742 23.685 -10.439 1.00 59.40 ? ? ? ? ? ? 71 GLU A OE2 1
+ATOM 487 N N . SER A 1 70 ? -1.830 22.463 -10.633 1.00 60.26 ? ? ? ? ? ? 72 SER A N 1
+ATOM 488 C CA . SER A 1 70 ? -0.785 22.528 -9.618 1.00 65.19 ? ? ? ? ? ? 72 SER A CA 1
+ATOM 489 C C . SER A 1 70 ? -1.191 23.554 -8.582 1.00 67.72 ? ? ? ? ? ? 72 SER A C 1
+ATOM 490 O O . SER A 1 70 ? -1.586 24.664 -8.933 1.00 68.67 ? ? ? ? ? ? 72 SER A O 1
+ATOM 491 C CB . SER A 1 70 ? 0.566 22.885 -10.232 1.00 66.81 ? ? ? ? ? ? 72 SER A CB 1
+ATOM 492 O OG . SER A 1 70 ? 0.520 24.141 -10.869 1.00 69.19 ? ? ? ? ? ? 72 SER A OG 1
+ATOM 493 N N . GLU A 1 71 ? -1.109 23.173 -7.312 1.00 70.07 ? ? ? ? ? ? 73 GLU A N 1
+ATOM 494 C CA . GLU A 1 71 ? -1.494 24.038 -6.212 1.00 72.36 ? ? ? ? ? ? 73 GLU A CA 1
+ATOM 495 C C . GLU A 1 71 ? -0.236 24.266 -5.347 1.00 75.16 ? ? ? ? ? ? 73 GLU A C 1
+ATOM 496 O O . GLU A 1 71 ? -0.249 24.010 -4.173 1.00 77.08 ? ? ? ? ? ? 73 GLU A O 1
+ATOM 497 C CB . GLU A 1 71 ? -2.606 23.360 -5.394 1.00 71.07 ? ? ? ? ? ? 73 GLU A CB 1
+ATOM 498 C CG . GLU A 1 71 ? -3.410 22.310 -6.167 1.00 69.29 ? ? ? ? ? ? 73 GLU A CG 1
+ATOM 499 C CD . GLU A 1 71 ? -4.836 22.110 -5.652 1.00 67.49 ? ? ? ? ? ? 73 GLU A CD 1
+ATOM 500 O OE1 . GLU A 1 71 ? -5.627 23.072 -5.780 1.00 67.26 ? ? ? ? ? ? 73 GLU A OE1 1
+ATOM 501 O OE2 . GLU A 1 71 ? -5.169 20.998 -5.157 1.00 64.72 ? ? ? ? ? ? 73 GLU A OE2 1
+ATOM 502 N N . GLY A 1 72 ? 0.917 24.600 -5.926 1.00 75.64 ? ? ? ? ? ? 74 GLY A N 1
+ATOM 503 C CA . GLY A 1 72 ? 2.179 24.627 -5.145 1.00 76.28 ? ? ? ? ? ? 74 GLY A CA 1
+ATOM 504 C C . GLY A 1 72 ? 2.532 25.958 -4.485 1.00 77.39 ? ? ? ? ? ? 74 GLY A C 1
+ATOM 505 O O . GLY A 1 72 ? 1.761 26.914 -4.592 1.00 77.60 ? ? ? ? ? ? 74 GLY A O 1
+ATOM 506 N N . LYS A 1 74 ? 3.692 26.048 -3.818 1.00 78.11 ? ? ? ? ? ? 75 LYS A N 1
+ATOM 507 C CA . LYS A 1 74 ? 4.129 27.336 -3.223 1.00 79.14 ? ? ? ? ? ? 75 LYS A CA 1
+ATOM 508 C C . LYS A 1 74 ? 4.479 28.474 -4.244 1.00 79.69 ? ? ? ? ? ? 75 LYS A C 1
+ATOM 509 O O . LYS A 1 74 ? 5.535 28.516 -4.903 1.00 79.72 ? ? ? ? ? ? 75 LYS A O 1
+ATOM 510 C CB . LYS A 1 74 ? 5.211 27.143 -2.149 1.00 79.82 ? ? ? ? ? ? 75 LYS A CB 1
+ATOM 511 C CG . LYS A 1 74 ? 6.646 27.001 -2.680 1.00 82.03 ? ? ? ? ? ? 75 LYS A CG 1
+ATOM 512 C CD . LYS A 1 74 ? 7.702 26.968 -1.556 1.00 83.81 ? ? ? ? ? ? 75 LYS A CD 1
+ATOM 513 C CE . LYS A 1 74 ? 9.130 26.847 -2.110 1.00 84.65 ? ? ? ? ? ? 75 LYS A CE 1
+ATOM 514 N NZ . LYS A 1 74 ? 10.106 26.489 -1.037 1.00 84.64 ? ? ? ? ? ? 75 LYS A NZ 1
diff --git a/modules/seq/base/doc/seq.rst b/modules/seq/base/doc/seq.rst
index 64ac6d3a7d974446f95657f30748d3ddc508f325..e84cfe6747c627a07f7c756eb26397ce95e1598d 100644
--- a/modules/seq/base/doc/seq.rst
+++ b/modules/seq/base/doc/seq.rst
@@ -54,7 +54,7 @@ methods, sequences can also be loaded from a string:
seq_string='''>sequence
abcdefghiklmnop'''
- s=io.LoadSequenceFromString(seq_string, 'fasta')
+ s=io.SequenceFromString(seq_string, 'fasta')
print s.name, s # will print "sequence abcdefghiklmnop"
Note that, in that case specifying the format is mandatory.
diff --git a/modules/seq/base/pymod/CMakeLists.txt b/modules/seq/base/pymod/CMakeLists.txt
index af105daed127eca4d4bd3d0fb7e11656d6e5e05a..f2aac4ea51cb0cd57fed4d304199db0a420158fb 100644
--- a/modules/seq/base/pymod/CMakeLists.txt
+++ b/modules/seq/base/pymod/CMakeLists.txt
@@ -3,4 +3,6 @@ set(OST_SEQ_PYMOD_SOURCES
wrap_seq.cc
)
-pymod(NAME seq CPP ${OST_SEQ_PYMOD_SOURCES} PY __init__.py)
+if (NOT ENABLE_STATIC)
+ pymod(NAME seq CPP ${OST_SEQ_PYMOD_SOURCES} PY __init__.py)
+endif()
diff --git a/modules/seq/base/pymod/export_sequence.cc b/modules/seq/base/pymod/export_sequence.cc
index 38a0e34ff3c211e649294c2d4f72b05b8f06e429..269ce3a7cb584704d5074505180d653ffe93539c 100644
--- a/modules/seq/base/pymod/export_sequence.cc
+++ b/modules/seq/base/pymod/export_sequence.cc
@@ -25,7 +25,10 @@
#include <ost/export_helper/pair_to_tuple_conv.hh>
#include <ost/generic_property.hh>
#include <ost/export_helper/generic_property_def.hh>
+#include <ost/config.hh>
+#if(OST_INFO_ENABLED)
#include <ost/info/info.hh>
+#endif
#include <ost/mol/mol.hh>
#include <ost/seq/sequence_handle.hh>
#include <ost/seq/alignment_handle.hh>
@@ -38,7 +41,6 @@
using namespace ost;
using namespace ost::seq;
using namespace boost::python;
-namespace {
void (SequenceHandle::*attach_one)(const mol::EntityView&)=&SequenceHandle::AttachView;
void (SequenceHandle::*attach_two)(const mol::EntityView&,
@@ -255,6 +257,8 @@ void const_seq_handle_def(O& bp_class)
.add_property("last_non_gap", &C::GetLastNonGap)
.def("GetAttachedView", &C::GetAttachedView)
.def("GetGaplessString", &C::GetGaplessString)
+ .add_property("role", make_function(&C::GetRole,
+ return_value_policy<copy_const_reference>()))
.def("GetString", &C::GetString,
return_value_policy<copy_const_reference>())
.def("GetName", &C::GetName,
@@ -276,7 +280,6 @@ void const_seq_handle_def(O& bp_class)
;
}
-}
void export_sequence()
{
@@ -298,6 +301,9 @@ void export_sequence()
make_function(&SequenceHandle::GetString,
return_value_policy<copy_const_reference>()),
&SequenceHandle::SetString)
+ .add_property("role", make_function(&SequenceHandle::GetRole,
+ return_value_policy<copy_const_reference>()),
+ &SequenceHandle::SetRole)
.def("SetName", &SequenceHandle::SetName)
.add_property("name",
make_function(&SequenceHandle::GetName,
@@ -311,7 +317,8 @@ void export_sequence()
implicitly_convertible<SequenceHandle, ConstSequenceHandle>();
- def("CreateSequence", &CreateSequence);
+ def("CreateSequence", &CreateSequence,
+ (arg("name"), arg("seq"), arg("role")="UNKNOWN"));
/*class_<SequenceHandleList>("SequenceHandleList", init<>())
.def(vector_indexing_suite<SequenceHandleList>())
;*/
@@ -339,6 +346,7 @@ void export_sequence()
.def("GetResidue", &AlignmentHandle::GetResidue)
.def("AddSequence", &AlignmentHandle::AddSequence)
.def("FindSequence", &AlignmentHandle::FindSequence)
+ .def("FindSequenceIndex", &AlignmentHandle::FindSequenceIndex)
.def("Copy", &AlignmentHandle::Copy)
.def("ToString", &AlignmentHandle::ToString)
.def("GetLength", &AlignmentHandle::GetLength)
@@ -346,6 +354,9 @@ void export_sequence()
.def("GetSequences", &AlignmentHandle::GetSequences)
.def("GetCoverage", &AlignmentHandle::GetCoverage)
.def("AttachView", attach_view_a)
+ .def("SetSequenceRole", &AlignmentHandle::SetSequenceRole)
+ .def("GetSequenceRole", &AlignmentHandle::GetSequenceRole,
+ return_value_policy<copy_const_reference>())
.def("AttachView", attach_view_b)
.def("Cut", &AlignmentHandle::Cut)
.def("MakeRegion", &AlignmentHandle::MakeRegion)
@@ -404,13 +415,15 @@ void export_sequence()
def("CreateSequenceList", &CreateSequenceList);
def("SequenceFromChain", seq_from_chain_a);
def("SequenceFromChain", seq_from_chain_b);
+#if(OST_INFO_ENABLED)
def("SequenceToInfo", &SequenceToInfo);
+ def("SequenceListToInfo", &SequenceListToInfo);
+ def("SequenceFromInfo", &SequenceFromInfo);
+ def("SequenceListFromInfo", &SequenceListFromInfo);
+#endif
def("ViewsFromSequences", &ViewsFromSequences, (arg("seq1"), arg("seq2")));
def("ViewsFromAlignment", &ViewsFromAlignment,
(arg("aln"), arg("index1")=0, arg("index2")=1));
- def("SequenceListToInfo", &SequenceListToInfo);
- def("SequenceFromInfo", &SequenceFromInfo);
def("CreateAlignment", &CreateAlignment);
def("AlignmentFromSequenceList", &AlignmentFromSequenceList);
- def("SequenceListFromInfo", &SequenceListFromInfo);
}
diff --git a/modules/seq/base/src/CMakeLists.txt b/modules/seq/base/src/CMakeLists.txt
index 6a22a5ad2a575ca7f633a6bde5c00ae31d1ed2b9..8ef75076e739e4cf90e01e97f5e9582f22cd67cf 100644
--- a/modules/seq/base/src/CMakeLists.txt
+++ b/modules/seq/base/src/CMakeLists.txt
@@ -29,8 +29,13 @@ alignment_handle.cc
sequence_op.cc
views_from_sequences.cc
)
-module(NAME seq SOURCES ${OST_SEQ_SOURCES}
- HEADERS ${OST_SEQ_IMPL_HEADERS} IN_DIR impl
- ${OST_SEQ_HEADERS}
- DEPENDS_ON ost_info ost_mol)
+if (ENABLE_INFO)
+ set(INFO_DEPS ost_info)
+endif()
+
+
+module(NAME seq SOURCES ${OST_SEQ_SOURCES}
+ HEADERS ${OST_SEQ_IMPL_HEADERS} IN_DIR impl
+ ${OST_SEQ_HEADERS}
+ DEPENDS_ON ost_mol ${INFO_DEPS})
\ No newline at end of file
diff --git a/modules/seq/base/src/alignment_handle.cc b/modules/seq/base/src/alignment_handle.cc
index 3e4ed4256f05bcef1128cdccef5585a3b1d8e582..47a4fd0dd371747b35761519f15c696751fa3a4a 100644
--- a/modules/seq/base/src/alignment_handle.cc
+++ b/modules/seq/base/src/alignment_handle.cc
@@ -166,6 +166,11 @@ ConstSequenceHandle AlignmentHandle::FindSequence(const String& name) const
return ConstSequenceHandle(impl_->FindSequence(name));
}
+int AlignmentHandle::FindSequenceIndex(const String& name) const
+{
+ this->CheckValidity();
+ return impl_->FindSequenceIndex(name);
+}
void AlignmentHandle::Cut(int start, int end)
{
@@ -308,4 +313,20 @@ mol::EntityViewPair AlignmentHandle::GetMatchingBackboneViews(int idx0, int idx1
return mol::EntityViewPair(v1, v2);
}
+
+const String& AlignmentHandle::GetSequenceRole(int seq_index)
+{
+ this->CheckValidity();
+ return impl_->GetSequence(seq_index)->GetRole();
+
+}
+
+void AlignmentHandle::SetSequenceRole(int seq_index, const String& role)
+{
+ this->CheckValidity();
+ impl_->GetSequence(seq_index)->SetRole(role);
+
+}
+
+
}}
diff --git a/modules/seq/base/src/alignment_handle.hh b/modules/seq/base/src/alignment_handle.hh
index 9a109215b7236dd7ccd3b7a9acf9ea838df48532..9990e170570d4c19f4c0f4a9eaf5129ea1b2f60f 100644
--- a/modules/seq/base/src/alignment_handle.hh
+++ b/modules/seq/base/src/alignment_handle.hh
@@ -97,7 +97,9 @@ public:
/// If several sequences have the same name, the first matching sequence will
/// be returned.
ConstSequenceHandle FindSequence(const String& name) const;
-
+
+ int FindSequenceIndex(const String& name) const;
+
/// \brief attach view to given sequence
/// \sa SequenceHandle::AttachView(const mol::EntityView&)
void AttachView(int seq_index, const mol::EntityView& view);
@@ -168,6 +170,10 @@ public:
/// between 0 (no coverage) and 1 (full coverage)
Real GetCoverage(int seq_index) const;
+
+ const String& GetSequenceRole(int seq_index);
+
+ void SetSequenceRole(int seq_index, const String& role);
private:
void CheckValidity() const;
impl::SequenceListImplPtr impl_;
diff --git a/modules/seq/base/src/impl/sequence_impl.cc b/modules/seq/base/src/impl/sequence_impl.cc
index df8cabe0aa3c87481ddc562d29c9829969ac5396..733eaf1b8e17f765581a4cb1e527beb2bf3483ef 100644
--- a/modules/seq/base/src/impl/sequence_impl.cc
+++ b/modules/seq/base/src/impl/sequence_impl.cc
@@ -21,8 +21,11 @@
*/
#include <boost/format.hpp>
-
+#include <ost/config.hh>
+#if(OST_INFO_ENABLED)
#include <ost/info/info.hh>
+#endif
+
#include <ost/integrity_error.hh>
#include <ost/mol/chain_view.hh>
@@ -52,11 +55,12 @@ bool SequenceImpl::IsSequenceStringSane(const String& seq_string)
}
SequenceImplPtr SequenceImpl::FromString(const String& seq_name,
- const String& seq_string)
+ const String& seq_string,
+ const String& role)
{
if (SequenceImpl::IsSequenceStringSane(seq_string)) {
- return SequenceImplPtr(new SequenceImpl(seq_name, seq_string));
+ return SequenceImplPtr(new SequenceImpl(seq_name, seq_string, role));
}
throw InvalidSequence();
}
@@ -99,15 +103,15 @@ void SequenceImpl::SetString(const String& seq)
}
SequenceImpl::SequenceImpl(const String& seq_name,
- const String& seq_string)
- : seq_name_(seq_name), seq_string_(seq_string), offset_(0)
+ const String& seq_string, const String& role)
+ : seq_name_(seq_name), seq_string_(seq_string), seq_role_(role), offset_(0)
{
this->ShiftsFromSequence();
}
SequenceImplPtr SequenceImpl::Copy() const
{
- SequenceImplPtr new_seq(new SequenceImpl(seq_name_, seq_string_));
+ SequenceImplPtr new_seq(new SequenceImpl(seq_name_, seq_string_, seq_role_));
new_seq->offset_=offset_;
new_seq->shifts_=shifts_;
new_seq->attached_view_=attached_view_;
@@ -280,6 +284,7 @@ bool SequenceImpl::HasAttachedView() const
return attached_view_.IsValid();
}
+#if(OST_INFO_ENABLED)
void SequenceImplToInfo(const SequenceImplPtr& sequence, info::InfoGroup& group)
{
group.SetTextData(sequence->GetString());
@@ -300,6 +305,7 @@ SequenceImplPtr SequenceImplFromInfo(const info::InfoGroup& group)
sequence->SetOffset(offset);
return sequence;
}
+#endif
int SequenceImpl::GetFirstNonGap() const
{
diff --git a/modules/seq/base/src/impl/sequence_impl.hh b/modules/seq/base/src/impl/sequence_impl.hh
index beae61e03033f4820f36b2c062b6368cf155dd0e..fecad2ca921599ecd85c58ee33e6c184bdbd5a52 100644
--- a/modules/seq/base/src/impl/sequence_impl.hh
+++ b/modules/seq/base/src/impl/sequence_impl.hh
@@ -27,7 +27,10 @@
#include <boost/shared_ptr.hpp>
#include <ost/generic_property.hh>
+#include <ost/config.hh>
+#if(OST_INFO_ENABLED)
#include <ost/info/info_fw.hh>
+#endif
#include <ost/mol/residue_prop.hh>
#include <ost/mol/entity_view.hh>
#include <ost/mol/residue_view.hh>
@@ -47,7 +50,8 @@ class DLLEXPORT_OST_SEQ SequenceImpl : public GenericPropContainerImpl {
public:
/// \brief Construct new sequence object from sequence_string.
static SequenceImplPtr FromString(const String& seq_name,
- const String& sequence_string);
+ const String& sequence_string,
+ const String& role="UNKNOWN");
/// \brief Get residue index corresponding to given sequence position
/// \param pos zero-based index
@@ -102,7 +106,8 @@ public:
///
/// If you want to check whether the sequence String does only contain
/// valid characters use \c CreateSequence instead.
- SequenceImpl(const String& seq_name, const String& sequence_string);
+ SequenceImpl(const String& seq_name, const String& sequence_string,
+ const String& role);
/// \brief get one letter code of residue at position
char GetOneLetterCode(int position) const;
@@ -145,7 +150,15 @@ public:
{
return seq_string_[index];
}
+ const String& GetRole() const
+ {
+ return seq_role_;
+ }
+ void SetRole(const String& role)
+ {
+ seq_role_=role;
+ }
private:
/// \brief Recalculates gap shifts from sequence.
@@ -166,6 +179,7 @@ private:
} Shift;
String seq_name_;
String seq_string_;
+ String seq_role_;
std::list<Shift> shifts_;
bool editing_;
int offset_;
@@ -175,14 +189,15 @@ private:
/// \internal
typedef std::vector<SequenceImplPtr> SequenceList;
+#if(OST_INFO_ENABLED)
/// \internal
-void DLLEXPORT_OST_SEQ SequenceImplToInfo(const SequenceImplPtr& sequence,
- info::InfoGroup& group);
-/// \internal
-SequenceImplPtr DLLEXPORT_OST_SEQ
+SequenceImplPtr DLLEXPORT_OST_SEQ SequenceImplFromInfo(const info::InfoGroup& group);
/// \internal
-SequenceImplFromInfo(const info::InfoGroup& group);
+void DLLEXPORT_OST_SEQ SequenceImplToInfo(const SequenceImplPtr& sequence,
+ info::InfoGroup& group);
+#endif
+
}}} //ns
#endif
diff --git a/modules/seq/base/src/impl/sequence_list_impl.cc b/modules/seq/base/src/impl/sequence_list_impl.cc
index f0ef01531e91cedb69c0039d78edfc9673e6c1fb..6580aac92bf8032f3b40de53a28a3df23670565f 100644
--- a/modules/seq/base/src/impl/sequence_list_impl.cc
+++ b/modules/seq/base/src/impl/sequence_list_impl.cc
@@ -18,7 +18,10 @@
//------------------------------------------------------------------------------
#include <limits>
+#include <ost/config.hh>
+#if(OST_INFO_ENABLED)
#include <ost/info/info.hh>
+#endif
#include <ost/seq/impl/sequence_list_impl.hh>
namespace ost { namespace seq { namespace impl {
@@ -58,6 +61,18 @@ SequenceImplPtr SequenceListImpl::FindSequence(const String& name) const
return SequenceImplPtr();
}
+
+int SequenceListImpl::FindSequenceIndex(const String& name) const
+{
+ for (size_t i=0; i<list_.size(); ++i) {
+ if (list_[i]->GetName()==name) {
+ return int(i);
+ }
+ }
+ return -1;
+}
+
+
String SequenceListImpl::ToString(int width) const
{
std::stringstream buffer;
@@ -142,6 +157,7 @@ SequenceListImplPtr SequenceListImpl::Copy() const
return new_ali;
}
+#if(OST_INFO_ENABLED)
void SequenceListImplToInfo(const SequenceListImplPtr& seq_list,
info::InfoGroup& group)
{
@@ -163,6 +179,7 @@ SequenceListImplPtr SequenceListImplFromInfo(info::InfoGroup& group)
}
return seq_list;
}
+#endif
SequenceListImplPtr SequenceListImpl::Slice(int first, int n) const
{
diff --git a/modules/seq/base/src/impl/sequence_list_impl.hh b/modules/seq/base/src/impl/sequence_list_impl.hh
index 7be941f730778218dfda4d7a54b1dead9f8c45f0..cb69e41ead9bfbc91975b3ce5062bde00b836eef 100644
--- a/modules/seq/base/src/impl/sequence_list_impl.hh
+++ b/modules/seq/base/src/impl/sequence_list_impl.hh
@@ -65,6 +65,8 @@ public:
SequenceImplPtr FindSequence(const String& name) const;
+ int FindSequenceIndex(const String& name) const;
+
String ToString(int width=80) const;
SequenceListImplPtr Slice(int first, int n) const;
@@ -92,6 +94,7 @@ private:
std::vector<SequenceImplPtr> list_;
};
+#if(OST_INFO_ENABLED)
/// \brief export sequence list impl to info
/// \internal
void DLLEXPORT_OST_SEQ
@@ -102,6 +105,7 @@ SequenceListImplToInfo(const SequenceListImplPtr& seq_list,
/// \internal
SequenceListImplPtr DLLEXPORT_OST_SEQ
SequenceListImplFromInfo(info::InfoGroup& group);
+#endif
}}}
diff --git a/modules/seq/base/src/sequence_handle.cc b/modules/seq/base/src/sequence_handle.cc
index acd2b13e7b44d2baa53ec57c64b8cc3d4a7b3f60..627ebdc36ee0501a7ff5fcf2926af7c199dae592 100644
--- a/modules/seq/base/src/sequence_handle.cc
+++ b/modules/seq/base/src/sequence_handle.cc
@@ -59,6 +59,25 @@ char ConstSequenceHandle::operator[](int index) const
+const String& ConstSequenceHandle::GetRole() const
+{
+ this->CheckValidity();
+ return Impl()->GetRole();
+}
+
+
+const String& SequenceHandle::GetRole() const
+{
+ this->CheckValidity();
+ return Impl()->GetRole();
+}
+
+void SequenceHandle::SetRole(const String& role) const
+{
+ this->CheckValidity();
+ Impl()->SetRole(role);
+}
+
void ConstSequenceHandle::CheckValidity() const
{
@@ -78,9 +97,10 @@ impl::SequenceImplPtr& ConstSequenceHandle::Impl() const
}
-SequenceHandle CreateSequence(const String& name, const String& seq)
+SequenceHandle CreateSequence(const String& name, const String& seq,
+ const String& role)
{
- return SequenceHandle(impl::SequenceImpl::FromString(name, seq));
+ return SequenceHandle(impl::SequenceImpl::FromString(name, seq, role));
}
@@ -206,6 +226,8 @@ void SequenceHandle::AttachView(const mol::EntityView& view,
Impl()->AttachView(view, chain_name);
}
+#if(OST_INFO_ENABLED)
+
/// \brief export sequence to info
void SequenceToInfo(const ConstSequenceHandle& sequence,
info::InfoGroup& group)
@@ -218,6 +240,9 @@ SequenceHandle SequenceFromInfo(info::InfoGroup& group)
{
return SequenceHandle(impl::SequenceImplFromInfo(group));
}
+#endif
+
+
std::ostream& operator<<(std::ostream& os, const ConstSequenceHandle& sequence)
{
diff --git a/modules/seq/base/src/sequence_handle.hh b/modules/seq/base/src/sequence_handle.hh
index 1c2cee610fbe20e92b9e446bf4af894d710fb433..937387c797bc42f28b0fe902f1e9af256d6fa416 100644
--- a/modules/seq/base/src/sequence_handle.hh
+++ b/modules/seq/base/src/sequence_handle.hh
@@ -25,7 +25,10 @@
#include <ost/base.hh>
#include <ost/generic_property.hh>
+#include <ost/config.hh>
+#if(OST_INFO_ENABLED)
#include <ost/info/info_fw.hh>
+#endif
#include <ost/seq/module_config.hh>
#include <ost/mol/residue_view.hh>
@@ -119,6 +122,8 @@ public:
/// \sa SequenceHandle::AttachView(const mol::EntityView&, const String&)
bool HasAttachedView() const;
+ const String& GetRole() const;
+
bool operator==(const ConstSequenceHandle& rhs) const;
bool operator!=(const ConstSequenceHandle& rhs) const;
@@ -283,6 +288,10 @@ public:
/// \internal
SequenceHandle(const impl::SequenceImplPtr& impl);
+ const String& GetRole() const;
+
+ void SetRole(const String& role) const;
+
impl::SequenceImplPtr& Impl() const;
GenericPropContainerImpl* GpImpl();
@@ -294,14 +303,17 @@ private:
};
SequenceHandle DLLEXPORT_OST_SEQ CreateSequence(const String& name,
- const String& seq);
-
+ const String& seq,
+ const String& role="UNKNOWN");
+#if(OST_INFO_ENABLED)
/// \brief export sequence to info
void DLLEXPORT_OST_SEQ SequenceToInfo(const ConstSequenceHandle& sequence,
info::InfoGroup& group);
/// \brief create sequence from info
SequenceHandle DLLEXPORT_OST_SEQ SequenceFromInfo(info::InfoGroup& group);
+#endif
+
DLLEXPORT_OST_SEQ std::ostream& operator<<(std::ostream& os,
const ConstSequenceHandle& sequence);
diff --git a/modules/seq/base/src/sequence_list.cc b/modules/seq/base/src/sequence_list.cc
index eb45568fdbb639c1a14eab4732f076f9d500bcee..52474a3d71b40ccb2498bcc245f4564755fda048 100644
--- a/modules/seq/base/src/sequence_list.cc
+++ b/modules/seq/base/src/sequence_list.cc
@@ -22,7 +22,10 @@
*/
#include <ost/invalid_handle.hh>
+#include <ost/config.hh>
+#if(OST_INFO_ENABLED)
#include <ost/info/info.hh>
+#endif
#include <ost/seq/impl/sequence_list_impl.hh>
#include <ost/seq/sequence_list.hh>
@@ -180,6 +183,7 @@ int SequenceList::GetMaxLength() const
return impl_->GetMaxLength();
}
+#if(OST_INFO_ENABLED)
/// \brief export sequence list to info
void SequenceListToInfo(const ConstSequenceList& seq_list,
info::InfoGroup& group)
@@ -192,6 +196,7 @@ SequenceList SequenceListFromInfo(info::InfoGroup& group)
{
return SequenceList(impl::SequenceListImplFromInfo(group));
}
+#endif
SequenceList::operator ConstSequenceList() const
{
diff --git a/modules/seq/base/src/sequence_list.hh b/modules/seq/base/src/sequence_list.hh
index 71067438d0404a0af7c41a6138b3fb09c403433f..2e6895c6e62b19b52e31aad3cebc1d9de8904cec 100644
--- a/modules/seq/base/src/sequence_list.hh
+++ b/modules/seq/base/src/sequence_list.hh
@@ -124,12 +124,14 @@ protected:
SequenceList DLLEXPORT_OST_SEQ CreateSequenceList();
ConstSequenceList DLLEXPORT_OST_SEQ CreateConstSequenceList();
+#if(OST_INFO_ENABLED)
/// \brief export sequence list to info
void DLLEXPORT_OST_SEQ SequenceListToInfo(const ConstSequenceList& seq_list,
info::InfoGroup& group);
/// \brief create sequence list object from info
SequenceList DLLEXPORT_OST_SEQ SequenceListFromInfo(info::InfoGroup& group);
+#endif
}}
#endif
diff --git a/modules/seq/base/tests/test_seq.py b/modules/seq/base/tests/test_seq.py
index 7cc73a5cedb9cad4044948f840693b63bc72b16b..bfd80d7bf70461211962f6b36c2c603584b4fe4c 100644
--- a/modules/seq/base/tests/test_seq.py
+++ b/modules/seq/base/tests/test_seq.py
@@ -174,6 +174,8 @@ class TestSeq(unittest.TestCase):
string_b=''.join([r.one_letter_code for r in b.residues])
self.assertEqual(string_a, 'BDFH')
self.assertEqual(string_b, 'BDFH')
-suite = unittest.TestLoader().loadTestsFromTestCase(TestSeq)
-unittest.TextTestRunner().run(suite)
+
+if __name__== '__main__':
+ from ost import testutils
+ testutils.RunTests()
diff --git a/scripts/CMakeLists.txt b/scripts/CMakeLists.txt
index f71f153277224ae97a8e7155b15e653ec504123d..0b6b429a45beebc7c2233d65218dba89fa86f32d 100644
--- a/scripts/CMakeLists.txt
+++ b/scripts/CMakeLists.txt
@@ -1,4 +1,5 @@
-set(SUBST_DICT BUILD_TYPE=${CMAKE_BUILD_TYPE} PYTHON_BINARY=${PYTHON_BINARY} LIBDIR=${LIB_DIR} LIBEXEC_PATH=${LIBEXEC_PATH})
+set(SUBST_DICT BUILD_TYPE=${CMAKE_BUILD_TYPE} PYTHON_BINARY=${PYTHON_BINARY}
+PYTHON_VERSION=${PYTHON_VERSION} LIBDIR=${LIB_DIR} LIBEXEC_PATH=${LIBEXEC_PATH})
message("${BUILD_TYPE}")
add_custom_target(ost_scripts ALL)
@@ -11,32 +12,34 @@ else()
add_dependencies(ost_scripts _ost_io)
endif()
-if(WIN32)
- script(NAME dng.bat INPUT dng.bat.in SUBSTITUTE ${SUBST_DICT}
- TARGET ost_scripts)
- script(NAME ost.bat INPUT ost.bat.in SUBSTITUTE ${SUBST_DICT}
- TARGET ost_scripts)
- script(NAME gipltng.bat INPUT gipltng.bat.in SUBSTITUTE ${SUBST_DICT})
-else()
- script(NAME ost_config INPUT ost_config.in SUBSTITUTE ${SUBST_DICT}
- TARGET ost_scripts OUTPUT_DIR ${LIBEXEC_PATH})
- script(NAME ost INPUT ost.in SUBSTITUTE ${SUBST_DICT}
- TARGET ost_scripts)
- if (ENABLE_GUI)
- script(NAME dng INPUT dng.in SUBSTITUTE ${SUBST_DICT}
+if (NOT ENABLE_STATIC)
+ if(WIN32)
+ script(NAME dng.bat INPUT dng.bat.in SUBSTITUTE ${SUBST_DICT}
+ TARGET ost_scripts)
+ script(NAME ost.bat INPUT ost.bat.in SUBSTITUTE ${SUBST_DICT}
TARGET ost_scripts)
+ script(NAME gipltng.bat INPUT gipltng.bat.in SUBSTITUTE ${SUBST_DICT})
+ else()
+ script(NAME ost_config INPUT ost_config.in SUBSTITUTE ${SUBST_DICT}
+ TARGET ost_scripts OUTPUT_DIR ${LIBEXEC_PATH})
+ script(NAME ost INPUT ost.in SUBSTITUTE ${SUBST_DICT}
+ TARGET ost_scripts)
+ if (ENABLE_GUI)
+ script(NAME dng INPUT dng.in SUBSTITUTE ${SUBST_DICT}
+ TARGET ost_scripts)
+ endif()
endif()
-endif()
-set(INIT_SCRIPTS
- init_cl.py
-)
+ set(INIT_SCRIPTS
+ init_cl.py
+ )
-if (ENABLE_GUI)
- list(APPEND INIT_SCRIPTS init.py)
-endif()
-copy_if_different("./" "${STAGE_DIR}/${LIB_DIR}/openstructure"
+ if (ENABLE_GUI)
+ list(APPEND INIT_SCRIPTS init.py)
+ endif()
+ copy_if_different("./" "${STAGE_DIR}/${LIB_DIR}/openstructure"
"${INIT_SCRIPTS}" "python init scripts" ost_scripts)
-install(FILES ${INIT_SCRIPTS} DESTINATION "${LIB_DIR}/openstructure")
+ install(FILES ${INIT_SCRIPTS} DESTINATION "${LIB_DIR}/openstructure")
+endif()
diff --git a/scripts/README.txt b/scripts/README.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5258171c4e6d10fd9d21b7c877ddc4db7691d2cc
--- /dev/null
+++ b/scripts/README.txt
@@ -0,0 +1,10 @@
+1. Setup the rpm build environment (See guides on the web)
+2. Checkout openstructure source in a fodler called 'openstructure-1.1d'
+3. Copy the compounds.chemlib into the folder
+4. Remove '.git' and '.gitignore' from the folder
+5. COmpress the source with 'tar -cJvf openstructuere.tar.xz openstructure-1.1d'
+6. Put the zipped source in '~/rpmbuild/SOURCES'
+7. Put the desktop file in '~/rpmbuild/SOURCES'
+8. Put the spec file in '~/rpmbuild/SPECS'
+9. Go the the 'SPECS' directory and build with 'rpmbuild -ba openstructure.spec'
+
diff --git a/scripts/ost_config.in b/scripts/ost_config.in
index b7b8b7c3ef001947e5310375c787e43e5d936aa6..faaae8e264e655496fe35471dc0bb685c6a6f59b 100644
--- a/scripts/ost_config.in
+++ b/scripts/ost_config.in
@@ -26,15 +26,13 @@ export DNG_BINDIR="$DNG_ROOT/bin"
export DNG_LIBDIR="$DNG_ROOT/@LIBDIR@"
export DNG_INITDIR="$DNG_LIBDIR/openstructure"
-export PATH="$DNG_BINDIR:$PATH"
-export DYLD_FRAMEWORK_PATH="$BIN_LIBDIR:${DYLD_FRAMEWORK_PATH}"
-export DYLD_LIBRARY_PATH="$BIN_LIBDIR:${DYLD_LIBRARY_PATH}"
-export LD_LIBRARY_PATH="$DNG_LIBDIR:$LD_LIBRARY_PATH"
-# set QT_PLUGIN_PATH PYTHONHOME and PYTHONPATH for bundle (commented except in linux bundles)
-# set QT_PLUGIN_PATH and pythonpath for bundle (commented except in linux bundles)
-#export QT_PLUGIN_PATH="$BIN_DIR/plugins"
-#export PYTHONPATH="$DNG_ROOT/@LIBDIR@/python2.6:$OST_ADDITIONAL_PYTHONPATH"
+export PATH="$DNG_BINDIR:${PATH}"
+export DYLD_FRAMEWORK_PATH="$DNG_LIBDIR:${DYLD_FRAMEWORK_PATH}"
+export DYLD_LIBRARY_PATH="$DNG_LIBDIR:${DYLD_LIBRARY_PATH}"
+export LD_LIBRARY_PATH="$DNG_LIBDIR:${LD_LIBRARY_PATH}"
+# set QT_PLUGIN_PATH and PYTHONPATH for bundle (commented except in linux bundles)
#export QT_PLUGIN_PATH="$BIN_DIR/plugins"
+#export PYTHONPATH="$DNG_ROOT/@LIBDIR@/python@PYTHON_VERSION@:$OST_ADDITIONAL_PYTHONPATH"
# retrieve absolute path to python executable
pyexec="@PYTHON_BINARY@"