Correctly skip all structures where gemmi throws exceptions

steineggerlab · Jun 13, 2024 · 7cd8939 · 7cd8939
1 parent 8d2fe3a
commit 7cd8939
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Showing 3 changed files with 4 additions and 4 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -33,7 +33,6 @@ include_directories(lib)
 include_directories(lib/3di)
 include_directories(lib/pulchra)
 include_directories(lib/kerasify)
-include_directories(lib/gemmi)
 
 set(ENV{CARGO_NET_OFFLINE} true)
 add_subdirectory(lib/corrosion)

diff --git a/src/strucclustutils/CMakeLists.txt b/src/strucclustutils/CMakeLists.txt
@@ -20,7 +20,7 @@ set(strucclustutils_source_files
         PARENT_SCOPE
         )
 
-add_library(gemmiwrapper OBJECT
+add_library(gemmiwrapper
     GemmiWrapper.cpp
     GemmiWrapper.h
     )
@@ -34,4 +34,5 @@ set_property(TARGET gemmiwrapper APPEND PROPERTY COMPILE_DEFINITIONS ${DEF_TMP})
 set_property(TARGET gemmiwrapper APPEND PROPERTY INCLUDE_DIRECTORIES ${INCL_TMP})
 restore_exceptions(gemmiwrapper)
 target_link_libraries(gemmiwrapper foldcomp)
+target_include_directories(gemmiwrapper PRIVATE ../../lib/gemmi)
 target_include_directories(gemmiwrapper PRIVATE ../../lib/foldcomp/src)
diff --git a/src/strucclustutils/GemmiWrapper.cpp b/src/strucclustutils/GemmiWrapper.cpp
@@ -143,7 +143,7 @@ bool GemmiWrapper::load(const std::string& filename, Format format) {
                 st = gemmi::read_pdb(infile);
         }
         updateStructure((void*) &st, filename, entity_to_tax_id);
-    } catch (std::runtime_error& e) {
+    } catch (...) {
         return false;
     }
     return true;
@@ -240,7 +240,7 @@ bool GemmiWrapper::loadFromBuffer(const char * buffer, size_t bufferSize, const
                 return false;
         }
         updateStructure((void*) &st, name, entity_to_tax_id);
-    } catch (std::runtime_error& e) {
+    } catch (...) {
         return false;
     }
     return true;