diff --git a/.azure-pipelines/linux_build.yml b/.azure-pipelines/linux_build.yml
index 45a9290ab..901ffc994 100644
--- a/.azure-pipelines/linux_build.yml
+++ b/.azure-pipelines/linux_build.yml
@@ -22,7 +22,7 @@ steps:
     -DRDK_BUILD_PYTHON_WRAPPERS=ON \
     -DRDK_USE_BOOST_REGEX=ON \
     -DRDK_BUILD_COORDGEN_SUPPORT=ON \
-    -DRDK_OPTIMIZE_NATIVE=ON \
+    -DRDK_OPTIMIZE_POPCNT=ON \
     -DRDK_BUILD_TEST_GZIP=ON \
     -DRDK_BUILD_FREESASA_SUPPORT=ON \
     -DRDK_BUILD_AVALON_SUPPORT=ON \
diff --git a/.azure-pipelines/linux_build_java.yml b/.azure-pipelines/linux_build_java.yml
index 2cf39a594..64064f936 100644
--- a/.azure-pipelines/linux_build_java.yml
+++ b/.azure-pipelines/linux_build_java.yml
@@ -23,7 +23,7 @@ steps:
     -DRDK_BUILD_PYTHON_WRAPPERS=OFF \
     -DRDK_USE_BOOST_REGEX=OFF \
     -DRDK_BUILD_COORDGEN_SUPPORT=ON \
-    -DRDK_OPTIMIZE_NATIVE=ON \
+    -DRDK_OPTIMIZE_POPCNT=ON \
     -DRDK_BUILD_TEST_GZIP=OFF \
     -DRDK_BUILD_FREESASA_SUPPORT=ON \
     -DRDK_BUILD_AVALON_SUPPORT=ON \
diff --git a/.azure-pipelines/mac_build.yml b/.azure-pipelines/mac_build.yml
index e6af3f686..63fe3d0b7 100644
--- a/.azure-pipelines/mac_build.yml
+++ b/.azure-pipelines/mac_build.yml
@@ -36,7 +36,7 @@ steps:
     -DRDK_BUILD_PYTHON_WRAPPERS=ON \
     -DRDK_USE_BOOST_REGEX=ON \
     -DRDK_BUILD_COORDGEN_SUPPORT=ON \
-    -DRDK_OPTIMIZE_NATIVE=ON \
+    -DRDK_OPTIMIZE_POPCNT=ON \
     -DRDK_BUILD_TEST_GZIP=ON \
     -DRDK_BUILD_FREESASA_SUPPORT=ON \
     -DRDK_BUILD_AVALON_SUPPORT=ON \
diff --git a/.azure-pipelines/mac_build_java.yml b/.azure-pipelines/mac_build_java.yml
index 58437f04d..b46d320e4 100644
--- a/.azure-pipelines/mac_build_java.yml
+++ b/.azure-pipelines/mac_build_java.yml
@@ -36,7 +36,7 @@ steps:
     -DRDK_BUILD_PYTHON_WRAPPERS=OFF \
     -DRDK_USE_BOOST_REGEX=OFF \
     -DRDK_BUILD_COORDGEN_SUPPORT=ON \
-    -DRDK_OPTIMIZE_NATIVE=ON \
+    -DRDK_OPTIMIZE_POPCNT=ON \
     -DRDK_BUILD_TEST_GZIP=OFF \
     -DRDK_BUILD_FREESASA_SUPPORT=ON \
     -DRDK_BUILD_AVALON_SUPPORT=ON \
diff --git a/.azure-pipelines/vs_build.yml b/.azure-pipelines/vs_build.yml
index d2b154d1b..4aec23472 100644
--- a/.azure-pipelines/vs_build.yml
+++ b/.azure-pipelines/vs_build.yml
@@ -22,7 +22,7 @@ steps:
     -DRDK_BUILD_PYTHON_WRAPPERS=ON ^
     -DRDK_USE_BOOST_REGEX=ON ^
     -DRDK_BUILD_COORDGEN_SUPPORT=ON ^
-    -DRDK_OPTIMIZE_NATIVE=ON ^
+    -DRDK_OPTIMIZE_POPCNT=ON ^
     -DRDK_BUILD_TEST_GZIP=ON ^
     -DRDK_BUILD_FREESASA_SUPPORT=OFF ^
     -DRDK_BUILD_AVALON_SUPPORT=ON ^
diff --git a/.azure-pipelines/vs_build_dll.yml b/.azure-pipelines/vs_build_dll.yml
index 63e649642..f58ed0236 100644
--- a/.azure-pipelines/vs_build_dll.yml
+++ b/.azure-pipelines/vs_build_dll.yml
@@ -22,7 +22,7 @@ steps:
     -DRDK_BUILD_CPP_TESTS=ON ^
     -DRDK_USE_BOOST_REGEX=ON ^
     -DRDK_BUILD_COORDGEN_SUPPORT=ON ^
-    -DRDK_OPTIMIZE_NATIVE=ON ^
+    -DRDK_OPTIMIZE_POPCNT=ON ^
     -DRDK_BUILD_TEST_GZIP=ON ^
     -DRDK_BUILD_FREESASA_SUPPORT=OFF ^
     -DRDK_BUILD_AVALON_SUPPORT=ON ^
diff --git a/CMakeLists.txt b/CMakeLists.txt
index c32496337..a0e804758 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -45,7 +45,7 @@ option(RDK_USE_FLEXBISON "use flex/bison, if available, to build the SMILES/SMAR
 option(RDK_TEST_COVERAGE "Use G(L)COV to compute test coverage" OFF)
 option(RDK_USE_BOOST_SERIALIZATION "Use the boost serialization library if available" ON)
 option(RDK_BUILD_TEST_GZIP "Build the gzip'd stream test" OFF)
-option(RDK_OPTIMIZE_NATIVE "Use native features while compiling." ON)
+option(RDK_OPTIMIZE_POPCNT "Use SSE4.2 popcount instruction while compiling." ON)
 option(RDK_USE_STRICT_ROTOR_DEFINITION "Use the most strict rotatable bond definition" ON)
 option(RDK_BUILD_DESCRIPTORS3D "Build the 3D descriptors calculators, requires Eigen3 to be installed" ON)
 option(RDK_BUILD_FREESASA_SUPPORT "build the rdkit freesasa wrapper" OFF )
@@ -58,7 +58,7 @@ option(RDK_USE_BOOST_REGEX "use boost::regex instead of std::regex (needed for s
 option(RDK_USE_BOOST_IOSTREAMS "use boost::iostreams" ON)
 option(RDK_BUILD_MINIMAL_LIB "build the minimal RDKit wrapper (for the JS bindings)" OFF)
 if(NOT MSVC)
-  if(RDK_OPTIMIZE_NATIVE)
+  if(RDK_OPTIMIZE_POPCNT)
       set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -mpopcnt")
   endif()
 endif()
diff --git a/Code/DataStructs/CMakeLists.txt b/Code/DataStructs/CMakeLists.txt
index f03156199..741c82cf2 100644
--- a/Code/DataStructs/CMakeLists.txt
+++ b/Code/DataStructs/CMakeLists.txt
@@ -1,4 +1,4 @@
-if(RDK_OPTIMIZE_NATIVE)
+if(RDK_OPTIMIZE_POPCNT)
   ADD_DEFINITIONS("-DUSE_BUILTIN_POPCOUNT")
 endif()
 
@@ -37,4 +37,4 @@ rdkit_test(testMultiFPB testMultiFPB.cpp
 
 if(RDK_BUILD_PYTHON_WRAPPERS)
 add_subdirectory(Wrap)
-endif()
\ No newline at end of file
+endif()
diff --git a/Code/MinimalLib/docker/Dockerfile b/Code/MinimalLib/docker/Dockerfile
index c22834aec..bbe77637b 100644
--- a/Code/MinimalLib/docker/Dockerfile
+++ b/Code/MinimalLib/docker/Dockerfile
@@ -47,7 +47,7 @@ RUN echo "source /opt/emsdk/emsdk_env.sh" >> ~/.bashrc
 SHELL ["/bin/bash", "-c", "-l"]
 RUN emconfigure cmake -DBoost_INCLUDE_DIR=/opt/boost/include -DRDK_BUILD_MINIMAL_LIB=ON \
   -DRDK_BUILD_PYTHON_WRAPPERS=OFF -DRDK_BUILD_CPP_TESTS=OFF -DRDK_BUILD_INCHI_SUPPORT=ON \
-  -DRDK_USE_BOOST_SERIALIZATION=OFF -DRDK_OPTIMIZE_NATIVE=OFF -DRDK_BUILD_THREADSAFE_SSS=OFF \
+  -DRDK_USE_BOOST_SERIALIZATION=OFF -DRDK_OPTIMIZE_POPCNT=OFF -DRDK_BUILD_THREADSAFE_SSS=OFF \
   -DRDK_BUILD_DESCRIPTORS3D=OFF -DRDK_TEST_MULTITHREADED=OFF -DRDK_BUILD_COORDGEN_SUPPORT=OFF \
   -DRDK_BUILD_SLN_SUPPORT=OFF -DRDK_USE_BOOST_IOSTREAMS=OFF -DCMAKE_CXX_FLAGS="-s DISABLE_EXCEPTION_CATCHING=0" \
   -DCMAKE_C_FLAGS="-DCOMPILE_ANSI_ONLY"  ..
diff --git a/Code/PgSQL/rdkit/CMakeLists.txt b/Code/PgSQL/rdkit/CMakeLists.txt
index ee78d4f7c..c0c870c7b 100644
--- a/Code/PgSQL/rdkit/CMakeLists.txt
+++ b/Code/PgSQL/rdkit/CMakeLists.txt
@@ -10,9 +10,9 @@ endif(APPLE)
 
 find_package(PostgreSQL REQUIRED)
 
-if(RDK_OPTIMIZE_NATIVE)
+if(RDK_OPTIMIZE_POPCNT)
   add_definitions(-DUSE_BUILTIN_POPCOUNT)
-endif(RDK_OPTIMIZE_NATIVE)
+endif(RDK_OPTIMIZE_POPCNT)
 
 set(EXTENSION rdkit)
 if(NOT DEFINED Boost_INCLUDE_DIRS)
diff --git a/Code/RDGeneral/RDConfig.h.cmake b/Code/RDGeneral/RDConfig.h.cmake
index 123e043bb..5fc8beb1f 100644
--- a/Code/RDGeneral/RDConfig.h.cmake
+++ b/Code/RDGeneral/RDConfig.h.cmake
@@ -12,8 +12,8 @@
 #cmakedefine RDK_USE_BOOST_SERIALIZATION
 #cmakedefine RDK_USE_BOOST_IOSTREAMS
 
-#cmakedefine RDK_OPTIMIZE_NATIVE
-#ifdef RDK_OPTIMIZE_NATIVE
+#cmakedefine RDK_OPTIMIZE_POPCNT
+#ifdef RDK_OPTIMIZE_POPCNT
 #define USE_BUILTIN_POPCOUNT
 #endif