Implementation of enhanced stereochemistry

CMakeLists.txt

@@ -2,13 +2,22 @@ cmake_minimum_required(VERSION 3.21 FATAL_ERROR)
 
 project(InChI C CXX)
 
+option(COVERAGE "Enable coverage reporting" OFF)
+
+if(COVERAGE)
+    message(STATUS "Building with code coverage enabled")
+    if(CMAKE_CXX_COMPILER_ID MATCHES "GNU|Clang")
+        add_compile_options(--coverage -O0 -g)
+        add_link_options(--coverage)
+    else()
+        message(WARNING "Coverage only supported with GCC or Clang")
+    endif()
+endif()
+
 set(CMAKE_C_STANDARD 99)
 set(CMAKE_CXX_STANDARD 11)
 set(CMAKE_POSITION_INDEPENDENT_CODE ON)
 
-# set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fsanitize=address")
-# set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=address")
-
 include(FetchContent)
 FetchContent_Declare(
     googletest
@@ -26,3 +35,11 @@ add_subdirectory(INCHI-1-SRC/INCHI_EXE/inchi-1/src)
 add_subdirectory(INCHI-1-SRC/INCHI_API/libinchi/src)
 add_subdirectory(INCHI-1-TEST/tests/test_unit)
 
+if(COVERAGE)
+    add_custom_target(coverage
+        COMMAND ${CMAKE_CTEST_COMMAND} --output-on-failure
+        COMMAND find . -name '*.gcno' -exec gcov -b -c {} +
+        WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
+        COMMENT "Running tests and generating .gcov coverage reports"
+    )
+endif()

INCHI-1-SRC/INCHI_API/libinchi/src/CMakeLists.txt

@@ -5,11 +5,18 @@ project(LibInChI_API VERSION 1.7)
 add_library(libinchi_compiler_flags INTERFACE)
 target_compile_features(libinchi_compiler_flags INTERFACE c_std_11)
 
-set(gcc_like_cxx "$<COMPILE_LANG_AND_ID:C,ARMClang,AppleClang,Clang,GNU,LCC>")
-set(msvc_cxx "$<COMPILE_LANG_AND_ID:C,MSVC>")
+# set(gcc_like_cxx "$<COMPILE_LANG_AND_ID:C,ARMClang,AppleClang,Clang,GNU,LCC>")
+# set(msvc_cxx "$<COMPILE_LANG_AND_ID:C,MSVC>")
 target_compile_options(libinchi_compiler_flags INTERFACE
-	"$<${gcc_like_cxx}:$<BUILD_INTERFACE:-g;-O1;-c;-fno-strict-aliasing;-Wno-all>>"
-	"$<${msvc_cxx}:$<BUILD_INTERFACE:-W3;-MT;-O2>>"
+	# "$<$<CONFIG:Release>:<${gcc_like_cxx}:$<BUILD_INTERFACE:-g;-O1;-c;-fno-strict-aliasing;-Wno-all>>"
+	# "$<$<CONFIG:Release>:<${msvc_cxx}:$<BUILD_INTERFACE:-W3;-MT;-O2>>"
+	# "$<$<CONFIG:Debug>:<${gcc_like_cxx}:$<BUILD_INTERFACE:-g;-O0;-fsanitize=address;-c;-fno-strict-aliasing;-Wno-all>>"
+	# "$<$<CONFIG:Debug>:<${msvc_cxx}:$<BUILD_INTERFACE:-W3;-MT;-g;-O0;-fsanitize=address>>"
+
+    "$<$<AND:$<CONFIG:Release>,$<COMPILE_LANG_AND_ID:C,ARMClang,AppleClang,Clang,GNU,LCC>>:-g;-O1;-c;-fno-strict-aliasing;-Wno-all>"
+    "$<$<AND:$<CONFIG:Release>,$<COMPILE_LANG_AND_ID:C,MSVC>>:-W3;-MT;-O2>"
+    "$<$<AND:$<CONFIG:Debug>,$<COMPILE_LANG_AND_ID:C,ARMClang,AppleClang,Clang,GNU,LCC>>:-g;-O0;-fsanitize=address;-c;-fno-strict-aliasing;-Wno-all>"
+    "$<$<AND:$<CONFIG:Debug>,$<COMPILE_LANG_AND_ID:C,MSVC>>:-W3;-MT;-g;-O0>"
 )
 
 set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY "${PROJECT_BINARY_DIR}/lib/static")
@@ -165,8 +172,12 @@ string(REGEX REPLACE "/RTC(su|[1su])" "" CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAG
 set_target_properties(libinchi PROPERTIES PREFIX "")
 
 
+target_link_options(libinchi PRIVATE
+    "$<$<AND:$<CONFIG:Debug>,$<COMPILE_LANG_AND_ID:C,ARMClang,AppleClang,Clang,GNU,LCC>>:-fsanitize=address>"
+)
+
 if(UNIX AND NOT APPLE)
 	target_link_options(libinchi PRIVATE "LINKER:--version-script=${P_LIBINCHI_MAP}/libinchi.map,-z,relro")
 elseif(WIN32 AND NOT MSVC)
 	target_link_options(libinchi PRIVATE "LINKER:--version-script=${P_LIBINCHI_MAP}/libinchi.map")
-endif()
+endif()

INCHI-1-SRC/INCHI_BASE/src/ichi_io.c

@@ -1679,7 +1679,7 @@ int inchi_strbuf_addline(INCHI_IOS_STRING* buf,
 /****************************************************************************/
 /* djb-rwth: placed as a global variable to avoid function buffer issues */
 char it_buffer[32767];
-int _inchi_trace(char* format, ...)
+int _inchi_trace(const char* format, ...)
 {
     /*
     TCHAR buffer[32767];

INCHI-1-SRC/INCHI_BASE/src/ichidrp.h

@@ -187,6 +187,7 @@ typedef struct tagInputParms {
     int             bNoWarnings;            /* v. 1.06+ suppress warning messages                                   */
     int             bHideInChI;             /* v. 1.06+ Do not print InChI itself                                   */
 
+    int             bEnhancedStereo;
 
     /* */
     INCHI_MODE      bTautFlags;

INCHI-1-SRC/INCHI_BASE/src/ichimain.h

@@ -125,7 +125,7 @@ typedef struct tagINCHI_OUT_CTL
     int iCurTautMode;
 
     int num_components;
-    int  nNumRemovedProtons;
+    int nNumRemovedProtons;
     int nTag;
     int bTag1;
     int bTag2;

INCHI-1-SRC/INCHI_BASE/src/ichimake.c

@@ -608,22 +608,21 @@ int GetSp3RelRacAbs(const INChI* pINChI, INChI_Stereo* Stereo)
                 nRet = SP3_REL;
 #endif
             }
-            else
-                if (pINChI->nFlags & INCHI_FLAG_RAC_STEREO)
-                {
+            else if (pINChI->nFlags & INCHI_FLAG_RAC_STEREO)
+            {
 #if ( REL_RAC_STEREO_IGN_1_SC == 1 )
-                    if (1 < Stereo->nNumberOfStereoCenters)
-                    {
-                        nRet = SP3_REL;
-                    }
-#else
-                    nRet = SP3_RAC;
-#endif
-                }
-                else
+                if (1 < Stereo->nNumberOfStereoCenters)
                 {
-                    nRet = SP3_ABS;
+                    nRet = SP3_REL;
                 }
+#else
+                nRet = SP3_RAC;
+#endif
+            }
+            else
+            {
+                nRet = SP3_ABS;
+            }
         }
         else
 #if ( REL_RAC_STEREO_IGN_1_SC == 1 )

INCHI-1-SRC/INCHI_BASE/src/ichimake.h

@@ -208,6 +208,20 @@ const char *EquString( int EquVal );
                           INCHI_IOS_STRING *buf,
                           int nCtMode,
                           int *bOverflow );
+    int MakeEnhStereoString( INChI_Aux        *pAux,
+                             INCHI_IOS_STRING *strbuf,
+                             const char*      conf_stereo_string,
+                             int              **enh_stereo,
+                             int              nof_stereo_groups,
+                             int              nCtMode,
+                             int              *bOverflow );
+    int MakeSlayerString( ORIG_ATOM_DATA   *orig_inp_data,
+                          INCHI_SORT       *pINChISort,
+                          INCHI_IOS_STRING *strbuf,
+                          int              bOutType,
+                          int              num_components,
+                          int              nCtMode,
+                          int              *bOverflow );
     int MakeCRVString( ORIG_INFO *OrigInfo,
                        int nLenCT,
                        int bAddDelim,

INCHI-1-SRC/INCHI_BASE/src/ichiparm.c

@@ -122,7 +122,8 @@ int set_common_options_by_parg(const char* pArg,
     int* pbNPZz,
     int* pbNoWarnings,
     int* pbMergeHash,
-    int* pbHideInChI);
+    int* pbHideInChI,
+    int* pbEnhancedStereochemistry);
 
 
 /****************************************************************************
@@ -165,7 +166,8 @@ int set_common_options_by_parg(const char* pArg,
     int* pbNPZz,
     int* pbNoWarnings,
     int* pbMergeHash,
-    int* pbHideInChI
+    int* pbHideInChI,
+    int* pbEnhancedStereochemistry
 )
 {
     int got = 0;
@@ -266,6 +268,11 @@ int set_common_options_by_parg(const char* pArg,
         (*pbLooseTSACheck) = 1;
         got = 1;
     }
+    else if (!inchi_stricmp(pArg, "EnhancedStereochemistry"))
+    {
+        *pbEnhancedStereochemistry = 1;
+        got = 1;
+    }
 
 #ifndef USE_STDINCHI_API
     /* These options DO TURN OFF Std flag   */
@@ -643,6 +650,7 @@ int ReadCommandLineParms(int argc,
     int bAcidTautomerism = (DISCONNECT_SALTS == 1) ? (TEST_REMOVE_S_ATOMS == 1 ? 2 : 1) : 0;
     int bUnchargedAcidTaut = (CHARGED_SALTS_ONLY == 0);
     int bMergeSaltTGroups = (DISCONNECT_SALTS == 1);
+    int bEnhancedStereochemistry = 0;
 #if ( MIN_SB_RING_SIZE > 0 )
     int nMinDbRinSize = MIN_SB_RING_SIZE, mdbr = 0;
 #endif
@@ -795,7 +803,8 @@ int ReadCommandLineParms(int argc,
                 &bLargeMolecules, &bPolymers,
                 &bFoldPolymerSRU, &bFrameShiftScheme,
                 &bStereoAtZz, &bNPZz,
-                &bNoWarnings, &bMergeHash, &bHideInChI);
+                &bNoWarnings, &bMergeHash, &bHideInChI,
+                &bEnhancedStereochemistry);
             if (got)
             {
                 ;
@@ -1243,7 +1252,8 @@ int ReadCommandLineParms(int argc,
                 &bLargeMolecules, &bPolymers,
                 &bFoldPolymerSRU, &bFrameShiftScheme,
                 &bStereoAtZz, &bNPZz,
-                &bNoWarnings, &bMergeHash, &bHideInChI);
+                &bNoWarnings, &bMergeHash, &bHideInChI,
+                &bEnhancedStereochemistry);
 
             if (got)
             {
@@ -2120,6 +2130,8 @@ int ReadCommandLineParms(int argc,
 
     ip->bINChIOutputOptions2 = bINChIOutputOptions2;
 
+    ip->bEnhancedStereo = bEnhancedStereochemistry;
+
     return 0;
 }