diff --git a/CMakeLists.txt b/CMakeLists.txt
index e438e4cb4542b2d8c0006c7c733341ba15143e73..4a46dc9b45b8d0cb4b1e0f5c87eb8dfa7811ce82 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -12,6 +12,15 @@ 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(USE_RPATH "embed rpath upon make install"
@@ -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)
@@ -178,8 +215,14 @@ if (ENABLE_STATIC)
find_package(Boost ${_BOOST_MIN_VERSION}
COMPONENTS filesystem system iostreams regex REQUIRED)
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)
@@ -217,6 +260,10 @@ 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)
@@ -231,6 +278,7 @@ 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"
@@ -242,4 +290,5 @@ 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}")
+ " 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/OST.cmake b/cmake_support/OST.cmake
index 6d3fff7edfd000415a2166ecb8768563779cc891..06e352919217f98e380ab796e085c3e1f77d36b7 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 ${_ARG_HEADER_OUTPUT_DIR})
else()
@@ -177,8 +179,11 @@ macro(module)
list(APPEND _ABS_SOURCE_NAMES "${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}
@@ -194,25 +199,6 @@ 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}_static ${ZLIB_LIBRARIES} ${_ARG_LINK})
- endif()
if (APPLE)
set_target_properties(${_LIB_NAME} PROPERTIES
LINK_FLAGS "-Wl,-rpath,@@loader_path"
@@ -222,7 +208,11 @@ 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 +220,10 @@ 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("${_LIB_NAME}" PROPERTIES HEADER_ONLY 1
@@ -302,13 +296,23 @@ macro(executable)
if (_ARG_LINK)
target_link_libraries(${_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 ${_ARG_NAME} DESTINATION bin)
endmacro()
@@ -338,11 +342,13 @@ macro(executable_libexec)
target_link_libraries(${_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 ${LIBEXEC_PATH})
endmacro()
@@ -472,6 +478,9 @@ macro(pymod)
if (NOT _ARG_NAME)
message(FATAL_ERROR "invalid use of pymod(): a name must be provided")
endif()
+ if (ENABLE_STATIC)
+ return()
+ endif()
if (_ARG_OUTPUT_DIR)
set(PYMOD_DIR "openstructure/${_ARG_OUTPUT_DIR}")
else()
@@ -499,14 +508,18 @@ 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}" "${LIB_STAGE_PATH}")
@@ -582,7 +595,6 @@ macro(pymod)
add_dependencies("_${_LIB_NAME}" "_${dep}")
endforeach()
endif()
-
endmacro()
add_custom_target(check)
@@ -845,7 +857,7 @@ 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/modules/base/pymod/CMakeLists.txt b/modules/base/pymod/CMakeLists.txt
index 0e9213ba1cb9795b86e212c36d4e0fa8cc20fe92..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 xmlrunner.py testutils.py)
+if (NOT ENABLE_STATIC)
+ pymod(NAME base OUTPUT_DIR ost
+ CPP ${OST_BASE_PYMOD_SOURCES}
+ PY __init__.py settings.py stutil.py table.py xmlrunner.py testutils.py)
+endif()
diff --git a/modules/config/CMakeLists.txt b/modules/config/CMakeLists.txt
index 617aa51c5b87a2dc03b95d7a92730b097b31d371..1e637d14470c6aa77af76cdd6c58e5ad5561c180 100644
--- a/modules/config/CMakeLists.txt
+++ b/modules/config/CMakeLists.txt
@@ -21,7 +21,6 @@ if (USE_NUMPY)
else()
set(numpy_support 0)
endif()
-
if (PROFILE)
set(profiling_enabled 1)
else()
@@ -62,6 +61,11 @@ if (_DEBIAN_STYLE_LIBEXEC)
else()
set(debian_style_libexec 0)
endif()
+if (ENABLE_INFO)
+ set(info_enabled 1)
+else()
+ set(info_enabled 0)
+endif()
set(config_hh_generator "CMake")
set(CONFIG_HH_FILE "${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/pymod/CMakeLists.txt b/modules/conop/pymod/CMakeLists.txt
index 650939bfd9aea21dac1925adadf6866f4db37e65..c1bf89d0e29cda36f4b4bcb9b0b357449aaa8ad7 100644
--- a/modules/conop/pymod/CMakeLists.txt
+++ b/modules/conop/pymod/CMakeLists.txt
@@ -8,4 +8,6 @@ set(OST_CONOP_PYMOD_SOURCES
export_ring_finder.cc
)
-pymod(NAME conop CPP ${OST_CONOP_PYMOD_SOURCES} PY __init__.py cleanup.py)
+if (NOT ENABLE_STATIC)
+ pymod(NAME conop CPP ${OST_CONOP_PYMOD_SOURCES} PY __init__.py cleanup.py)
+endif()
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/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/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/rule_based_builder.cc b/modules/conop/src/rule_based_builder.cc
index 35709c287d61181fa0beb5c5920a48ce7e8326b3..33d33c667faebb47593eebe53f28285c448b1956 100644
--- a/modules/conop/src/rule_based_builder.cc
+++ b/modules/conop/src/rule_based_builder.cc
@@ -237,12 +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/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_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/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/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 ${OST_IMG_ALG_PYMOD_SOURCES}
+ PY __init__.py)
+endif()
diff --git a/modules/img/alg/src/CMakeLists.txt b/modules/img/alg/src/CMakeLists.txt
index 5dc212da9f112a9eed2dafc53eb187254a550a95..a49b80125f11de0531412e7fd2929577669aa647 100644
--- a/modules/img/alg/src/CMakeLists.txt
+++ b/modules/img/alg/src/CMakeLists.txt
@@ -94,7 +94,9 @@ line_average.hh
rscrosscorr.hh
)
+if(ENABLE_INFO)
include(${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/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/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/io/pymod/CMakeLists.txt b/modules/io/pymod/CMakeLists.txt
index 38f43cdfae0dae30f926ce679fbb0fcbeefe240b..007569fff38887504ed15d21231b2b5d4464b346 100644
--- a/modules/io/pymod/CMakeLists.txt
+++ b/modules/io/pymod/CMakeLists.txt
@@ -14,10 +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(_ost_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 5654e22a5508f22ad2072732a2d57b8d73b2e1ce..95ea418b344a21910a925f463151d34af4a8eb22 100644
--- a/modules/io/pymod/__init__.py
+++ b/modules/io/pymod/__init__.py
@@ -86,7 +86,7 @@ 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 return one or more entities. Several options
allow to customize the exact behaviour of the PDB import. For more information
@@ -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:
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/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/tests/CMakeLists.txt b/modules/io/tests/CMakeLists.txt
index c4b3486d52aeb26db1865488f61e42c750f9c67c..98f075bd9785c1c051f642e3be91dd2e125cc62f 100644
--- a/modules/io/tests/CMakeLists.txt
+++ b/modules/io/tests/CMakeLists.txt
@@ -19,6 +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_pdb.cc b/modules/io/tests/test_io_pdb.cc
index cb40a2c04a0a737da86f6c83ab2e8a014e1d378c..da9efce0dcd4974f738f28d48247d6e91b2ccc32 100644
--- a/modules/io/tests/test_io_pdb.cc
+++ b/modules/io/tests/test_io_pdb.cc
@@ -913,7 +913,7 @@ 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();
@@ -933,7 +933,7 @@ 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();
@@ -953,7 +953,7 @@ 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();
diff --git a/modules/io/tests/test_io_pdb.py b/modules/io/tests/test_io_pdb.py
index 873a91e155c3ea64b37623881f1ef8e4aeec177c..348fde1d929669405e612cb92d3a274ceb5636f1 100644
--- a/modules/io/tests/test_io_pdb.py
+++ b/modules/io/tests/test_io_pdb.py
@@ -11,8 +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__':
from ost import testutils
testutils.RunTests()
+
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 5ac7e71dba294b13d510a84e1c01d5d9b08654f3..004c475efdf99c095aa693c133f7a2af51e84248 100644
--- a/modules/mol/alg/pymod/CMakeLists.txt
+++ b/modules/mol/alg/pymod/CMakeLists.txt
@@ -20,7 +20,7 @@ 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/wrap_mol_alg.cc b/modules/mol/alg/pymod/wrap_mol_alg.cc
index 4e4ccc2f56d67b196549fb5648efd39b6b2430a8..20a78f90e3ede2920d09b7d1cadc70cfc1fe65df 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>
@@ -35,12 +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);
+}
+
}
@@ -56,12 +84,65 @@ BOOST_PYTHON_MODULE(_ost_mol_alg)
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));
+
+
+ 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 259f7f7dc860c7b8f787527cd44efc9321659a02..050d4822712f8789bfac97938e18c327334f7d92 100644
--- a/modules/mol/alg/src/CMakeLists.txt
+++ b/modules/mol/alg/src/CMakeLists.txt
@@ -40,8 +40,7 @@ if (ENABLE_IMG)
endif()
executable(NAME ldt SOURCES ldt.cc
- DEPENDS_ON ost_io ost_mol_alg STATIC)
-target_link_libraries(ldt ${BOOST_PROGRAM_OPTIONS})
+ DEPENDS_ON ost_mol ost_mol_alg ost_io STATIC)
module(NAME mol_alg SOURCES ${OST_MOL_ALG_SOURCES}
HEADERS ${OST_MOL_ALG_HEADERS}
@@ -54,3 +53,7 @@ copy_if_different("." "${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..4b81ed10b8a81e92b120a2fc51367803a9ed9be9 100644
--- a/modules/mol/alg/src/filter_clashes.cc
+++ b/modules/mol/alg/src/filter_clashes.cc
@@ -18,66 +18,445 @@
//------------------------------------------------------------------------------
#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)
+{
+ 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")
+ 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("BOND:" << " " << res.GetChain() << " " << res.GetName() << " " << res.GetNumber() << " " << bond_str << " " << min_length << " " << max_length << " " << blength << " " << zscore << " " << "PASS")
+ }
+ }
}
- 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")
+ 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("ANGLE:" << " " << res.GetChain() << " " << res.GetName() << " " << res.GetNumber() << " " << angle_str << " " << min_width << " " << max_width << " " << awidth << " " << zscore << " " << "PASS")
+ }
+ }
+ }
+ }
+ }
+
+ 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);
}
+ 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)
{
+ 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) {
@@ -86,7 +465,7 @@ EntityView FilterClashes(const EntityView& ent, Real tolerance,
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;
@@ -97,15 +476,22 @@ 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.
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")
+
remove_sc=true;
if (always_remove_bb==true) {
remove_bb=true;
@@ -115,15 +501,18 @@ EntityView FilterClashes(const EntityView& ent, Real tolerance,
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")
+ }
}
}
+
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;
@@ -140,12 +529,11 @@ EntityView FilterClashes(const EntityView& ent, Real tolerance,
}
-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..5dbab61cfceb3d77794dbf465447980cdfa32e54 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=8.0;
+
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 +136,183 @@ 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;
+ if (vm.count("verbosity")) {
+ verbosity_level=vm["verbosity"].as<int>();
+ if (verbosity_level==0) {
+ Logger::Instance().PushVerbosityLevel(0);
+ } else if (verbosity_level==1) {
+ Logger::Instance().PushVerbosityLevel(3);
+ } else if (verbosity_level==2) {
+ Logger::Instance().PushVerbosityLevel(4);
+ } else {
+ std::cout << "Verbosity level " << verbosity_level << " is not available" << std::endl;
+ exit(-1);
+ }
+ }
+
+ if (verbosity_level>0) {
+ LOG_INFO("LDT INFO FORMAT: Chain1 Residue1 ResNum1 Atom1 Chain2 Residue2 ResNum2 Atom2 ModelDist TargetDist Difference Tolerance Status");
+ }
+
+ 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);
+ }
+ }
+ 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);
+ }
+ EntityView 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..83d842226ac03a401796a111dcdf3334365f8a61 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_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 << " " << "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/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/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 1c2649f70ea0230dc4c5021afd9f2a618af60dcd..134eb4e25691507a50039077bdf58099b57ae9ea 100644
--- a/modules/mol/base/src/CMakeLists.txt
+++ b/modules/mol/base/src/CMakeLists.txt
@@ -100,7 +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/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/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/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/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/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 5ec0f088fe1bca98b9486936faeb6041d48c236f..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>
@@ -412,13 +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/impl/sequence_impl.cc b/modules/seq/base/src/impl/sequence_impl.cc
index 2a0570b37e9795372f36983353b3ea7502692dc9..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>
@@ -281,6 +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());
@@ -301,6 +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 05ba042f0b1db1ac933760eff20302618f731b23..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>
@@ -186,14 +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 bd332872bb1c2b1d531d50a3aa820e7fb5f083ac..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 {
@@ -154,6 +157,7 @@ SequenceListImplPtr SequenceListImpl::Copy() const
return new_ali;
}
+#if(OST_INFO_ENABLED)
void SequenceListImplToInfo(const SequenceListImplPtr& seq_list,
info::InfoGroup& group)
{
@@ -175,6 +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 52443dcd64178222c688918aae9ee94dd27267f7..cb69e41ead9bfbc91975b3ce5062bde00b836eef 100644
--- a/modules/seq/base/src/impl/sequence_list_impl.hh
+++ b/modules/seq/base/src/impl/sequence_list_impl.hh
@@ -94,6 +94,7 @@ private:
std::vector<SequenceImplPtr> list_;
};
+#if(OST_INFO_ENABLED)
/// \brief export sequence list impl to info
/// \internal
void DLLEXPORT_OST_SEQ
@@ -104,6 +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 8f0d6cce7cae08564d50a81d9b09dc5923a00991..627ebdc36ee0501a7ff5fcf2926af7c199dae592 100644
--- a/modules/seq/base/src/sequence_handle.cc
+++ b/modules/seq/base/src/sequence_handle.cc
@@ -226,6 +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)
@@ -238,6 +240,8 @@ 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 103c6aeb43156039960cdfd3eed8b375fe7f672f..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>
@@ -302,13 +305,15 @@ private:
SequenceHandle DLLEXPORT_OST_SEQ CreateSequence(const String& name,
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/scripts/CMakeLists.txt b/scripts/CMakeLists.txt
index 734e377e86e68961beddc9c96b444c6bb9cec86b..0b6b429a45beebc7c2233d65218dba89fa86f32d 100644
--- a/scripts/CMakeLists.txt
+++ b/scripts/CMakeLists.txt
@@ -12,32 +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'
+