See PR pending https://github.com/openbabel/openbabel/pull/2969.patch
fix headers with system InChI / various changes to handle InChI option
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -144,6 +144,7 @@ option(OPENBABEL_USE_SYSTEM_INCHI
   "Use the system inchi library." OFF)
 if(OPENBABEL_USE_SYSTEM_INCHI)
   find_package(Inchi REQUIRED)
+  add_definitions(-DHAVE_SYSTEM_INCHI)
   if (NOT INCHI_FOUND)
     message(FATAL_ERROR "Inchi library not found.")
   endif()
--- a/include/openbabel/inchiformat.h
+++ b/include/openbabel/inchiformat.h
@@ -21,8 +21,13 @@ GNU General Public License for more details.
 #include <openbabel/obconversion.h>
 #include <openbabel/obmolecformat.h>
 
+#ifdef HAVE_SYSTEM_INCHI
+#include <inchi_api.h>
+#define CURRENT_VER "unknown" // bcf_s.h is not packaged
+#else
 #include "../inchi/inchi_api.h"
 #include "../inchi/bcf_s.h"  // for CURRENT_VER
+#endif
 #ifdef HAVE_SSTREAM
 #include <sstream>
 #else

--- a/include/CMakeLists.txt
+++ b/include/CMakeLists.txt
@@ -5,9 +5,13 @@ file(GLOB stereo_headers      openbabel/stereo/*.h)
 file(GLOB depict_headers      openbabel/depict/*.h)
 file(GLOB lbfgs_headers       LBFGS/*.h)
 
+if(WITH_INCHI)
 if(NOT OPENBABEL_USE_SYSTEM_INCHI)
 install(FILES inchi/inchi_api.h          DESTINATION include/inchi)
 endif(NOT OPENBABEL_USE_SYSTEM_INCHI)
+else(WITH_INCHI)
+list(FILTER openbabel_headers      EXCLUDE REGEX ".*inchiformat\\.h$")
+endif(WITH_INCHI)
 install(FILES chemdrawcdx.h        DESTINATION ${OB_INCLUDE_DIRS}/openbabel)
 install(FILES ${openbabel_headers} DESTINATION ${OB_INCLUDE_DIRS}/openbabel)
 install(FILES ${math_headers}      DESTINATION ${OB_INCLUDE_DIRS}/openbabel/math)
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -34,10 +34,15 @@ set(descriptors
   descriptors/cmpdfilter.cpp
   descriptors/groupcontrib.cpp
   descriptors/filters.cpp
-  descriptors/inchidescriptor.cpp
   descriptors/smartsdescriptors.cpp
 )
 
+if(WITH_INCHI)
+  set(descriptors ${descriptors}
+    descriptors/inchidescriptor.cpp
+  )
+endif()
+
 set(fingerprints
   fingerprints/finger2.cpp
   fingerprints/finger3.cpp

--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -142,15 +142,17 @@ endif()
 option(WITH_INCHI   "Build inchi support" ON)
 option(OPENBABEL_USE_SYSTEM_INCHI
   "Use the system inchi library." OFF)
-if(OPENBABEL_USE_SYSTEM_INCHI)
-  find_package(Inchi REQUIRED)
-  add_definitions(-DHAVE_SYSTEM_INCHI)
-  if (NOT INCHI_FOUND)
-    message(FATAL_ERROR "Inchi library not found.")
+if(WITH_INCHI)
+  if(OPENBABEL_USE_SYSTEM_INCHI)
+    find_package(Inchi REQUIRED)
+    add_definitions(-DHAVE_SYSTEM_INCHI)
+    if (NOT INCHI_FOUND)
+      message(FATAL_ERROR "Inchi library not found.")
+    endif()
+  else()
+    message(STATUS "Using included inchi library.")
+    set(INCHI_LIBRARY inchi)
   endif()
-else()
-  message(STATUS "Using included inchi library.")
-  set(INCHI_LIBRARY inchi)
 endif()
 
 if(WIN32)