From 2e7a7fc0ec4fbdb7f3ea7dcecd843bc48f843ce6 Mon Sep 17 00:00:00 2001
From: Jordan Dialpuri <44945647+Dialpuri@users.noreply.github.com>
Date: Fri, 6 Sep 2024 10:53:45 +0100
Subject: [PATCH] Reordered linking libraries

---
 CMakeLists.txt | 451 +++++++++++++++++++++++--------------------------
 1 file changed, 213 insertions(+), 238 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 72763566..e3817acb 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,10 +1,13 @@
 # New Build System CMake File - Jordan Dialpuri - 05/09/24
 
 cmake_minimum_required(VERSION 3.15)
-project(privateer VERSION 0.5 LANGUAGES C CXX)
+project(
+  privateer
+  VERSION 0.5
+  LANGUAGES C CXX)
 
-SET(PRIVATEER_CC_FLAGS "-O2 -w")
-SET(PRIVATEER_CXX_FLAGS "-O2 -w -I${CMAKE_INSTALL_PREFIX}/include")
+set(PRIVATEER_CC_FLAGS "-O2 -w")
+set(PRIVATEER_CXX_FLAGS "-O2 -w -I${CMAKE_INSTALL_PREFIX}/include")
 set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${PRIVATEER_CC_FLAGS}")
 set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${PRIVATEER_CXX_FLAGS} ")
 
@@ -25,35 +28,28 @@ set(WRK_DIR "${CMAKE_CURRENT_SOURCE_DIR}")
 include(FetchContent)
 # Download Clipper
 FetchContent_Declare(
-        clipper-dependencies
-        URL http://www.ysbl.york.ac.uk/jsd523/clipper-2.1.20201109.tar.gz
-)
+  clipper-dependencies
+  URL http://www.ysbl.york.ac.uk/jsd523/clipper-2.1.20201109.tar.gz)
 
 # Download MMDB
-FetchContent_Declare(
-        mmdb2-dependencies
-        URL http://www.ysbl.york.ac.uk/jsd523/mmdb2-2.0.22.tar.gz
-)
+FetchContent_Declare(mmdb2-dependencies
+                     URL http://www.ysbl.york.ac.uk/jsd523/mmdb2-2.0.22.tar.gz)
 
 # Download FFTW
-FetchContent_Declare(
-        fftw-dependencies
-        URL http://www.fftw.org/fftw-2.1.5.tar.gz
-)
+FetchContent_Declare(fftw-dependencies
+                     URL http://www.fftw.org/fftw-2.1.5.tar.gz)
 
 # Download CCP4
-FetchContent_Declare(
-        ccp4-dependencies
-        URL http://www.ysbl.york.ac.uk/jsd523/libccp4-8.0.0.tar.gz
-)
+FetchContent_Declare(ccp4-dependencies
+                     URL http://www.ysbl.york.ac.uk/jsd523/libccp4-8.0.0.tar.gz)
 
 # Download Gemmi
-FetchContent_Declare(
-        gemmi-dependencies
-        URL http://www.ysbl.york.ac.uk/jsd523/gemmi-0.6.5.tar.gz
-)
+FetchContent_Declare(gemmi-dependencies
+                     URL http://www.ysbl.york.ac.uk/jsd523/gemmi-0.6.5.tar.gz)
 
-FetchContent_MakeAvailable(clipper-dependencies mmdb2-dependencies fftw-dependencies ccp4-dependencies gemmi-dependencies)
+FetchContent_MakeAvailable(
+  clipper-dependencies mmdb2-dependencies fftw-dependencies ccp4-dependencies
+  gemmi-dependencies)
 
 add_subdirectory(${WRK_DIR}/clipper/minimol)
 add_subdirectory(${WRK_DIR}/clipper/core)
@@ -72,236 +68,215 @@ add_subdirectory(${WRK_DIR}/gemmi)
 
 set(PRIVATEER_SOURCE ${PRIVATEER_SOURCE_DIR}/cpp/privateer.cpp)
 
-# include_directories(
-#         ${CMAKE_CURRENT_SOURCE_DIR}
-#         ${WRK_DIR}/checkout/mmdb2
-#         ${WRK_DIR}/checkout/clipper
-#         ${WRK_DIR}/checkout/libccp4/ccp4
-#         ${WRK_DIR}/checkout/gemmi/include
-#         ${WRK_DIR}/checkout/ssm/ssm 
-#         ${WRK_DIR}/checkout/zlib
-#         ${WRK_DIR}/checkout/pybind11/include
-#         ${PRIVATEER_SOURCE_DIR}/cpp
-#         ${PRIVATEER_SOURCE_DIR}/cpp/pybind11
-#         ${Python_INCLUDE_DIRS}
-#         ${pybind11_INCLUDE_DIRS}
-# )
+# include_directories( ${CMAKE_CURRENT_SOURCE_DIR} ${WRK_DIR}/checkout/mmdb2
+# ${WRK_DIR}/checkout/clipper ${WRK_DIR}/checkout/libccp4/ccp4
+# ${WRK_DIR}/checkout/gemmi/include ${WRK_DIR}/checkout/ssm/ssm
+# ${WRK_DIR}/checkout/zlib ${WRK_DIR}/checkout/pybind11/include
+# ${PRIVATEER_SOURCE_DIR}/cpp ${PRIVATEER_SOURCE_DIR}/cpp/pybind11
+# ${Python_INCLUDE_DIRS} ${pybind11_INCLUDE_DIRS} )
 
 include_directories(
-        ${CMAKE_CURRENT_SOURCE_DIR}
-        ${clipper-dependencies_SOURCE_DIR}
-        ${gemmi-dependencies_SOURCE_DIR}/include
-        ${mmdb2-dependencies_SOURCE_DIR}
-        ${ccp4-dependencies_SOURCE_DIR}
-        ${PRIVATEER_SOURCE_DIR}/cpp
-        ${PRIVATEER_SOURCE_DIR}/cpp/pybind11
-)
+  ${CMAKE_CURRENT_SOURCE_DIR}
+  ${clipper-dependencies_SOURCE_DIR}
+  ${gemmi-dependencies_SOURCE_DIR}/include
+  ${mmdb2-dependencies_SOURCE_DIR}
+  ${ccp4-dependencies_SOURCE_DIR}
+  ${PRIVATEER_SOURCE_DIR}/cpp
+  ${PRIVATEER_SOURCE_DIR}/cpp/pybind11)
 link_directories(
-        ${CMAKE_BINARY_DIR}/mmdb2
-        ${CMAKE_BINARY_DIR}/clipper
-        ${CMAKE_BINARY_DIR}/ccp4
-        ${WRK_DIR}/src
-        ${CMAKE_BINARY_DIR}
-        ${PRIVATEER_SOURCE_DIR}/cpp
-        ${PRIVATEER_SOURCE_DIR}/cpp/pybind11
-        ${Python_LIBRARY_DIRS}
-)
-
-# link_directories(
-#         ${WRK_DIR}/mmdb2
-#         ${WRK_DIR}/clipper
-#         ${WRK_DIR}/ccp4
-#         ${WRK_DIR}/gemmi
-#         ${WRK_DIR}/src
-#         ${CMAKE_BINARY_DIR}
-#         ${PRIVATEER_SOURCE_DIR}/cpp
-#         ${PRIVATEER_SOURCE_DIR}/cpp/pybind11
-#         ${Python_LIBRARY_DIRS}
-# )
-
-# add_custom_target(copy_resources ALL
-#         COMMAND ${CMAKE_COMMAND} -E copy_directory
-#         ${CMAKE_SOURCE_DIR}/data
-#         ${CLIBDENV}/privateer_data
-#         COMMENT "Copying Privateer Data files to ${CLIBDENV}/privateer_data")
-
+  ${CMAKE_BINARY_DIR}/mmdb2
+  ${CMAKE_BINARY_DIR}/clipper
+  ${CMAKE_BINARY_DIR}/ccp4
+  ${WRK_DIR}/src
+  ${CMAKE_BINARY_DIR}
+  ${PRIVATEER_SOURCE_DIR}/cpp
+  ${PRIVATEER_SOURCE_DIR}/cpp/pybind11
+  ${Python_LIBRARY_DIRS})
+
+# link_directories( ${WRK_DIR}/mmdb2 ${WRK_DIR}/clipper ${WRK_DIR}/ccp4
+# ${WRK_DIR}/gemmi ${WRK_DIR}/src ${CMAKE_BINARY_DIR}
+# ${PRIVATEER_SOURCE_DIR}/cpp ${PRIVATEER_SOURCE_DIR}/cpp/pybind11
+# ${Python_LIBRARY_DIRS} )
+
+# add_custom_target(copy_resources ALL COMMAND ${CMAKE_COMMAND} -E
+# copy_directory ${CMAKE_SOURCE_DIR}/data ${CLIBDENV}/privateer_data COMMENT
+# "Copying Privateer Data files to ${CLIBDENV}/privateer_data")
 
 find_package(Threads REQUIRED)
 
-# file(COPY ${PRIVATEERDATA}/glycomics/privateer_glycomics_database.json 
-#     DESTINATION ${CLIBDENV})
-
-# file(COPY ${PRIVATEERDATA}/linkage_torsions/privateer_torsion_database.json 
-#     DESTINATION ${CLIBDENV})
-
-add_library(privateer_lib STATIC
-            ${PRIVATEER_SOURCE_DIR}/cpp/third-party/gemmi_compilation_unit.cpp
-            ${PRIVATEER_SOURCE_DIR}/cpp/privateer-error.h
-            ${PRIVATEER_SOURCE_DIR}/cpp/privateer-json.h
-            ${PRIVATEER_SOURCE_DIR}/cpp/clipper-glyco.cpp
-            ${PRIVATEER_SOURCE_DIR}/cpp/privateer-db.cpp
-            ${PRIVATEER_SOURCE_DIR}/cpp/privateer-blobs.cpp
-            ${PRIVATEER_SOURCE_DIR}/cpp/privateer-composition.cpp
-            ${PRIVATEER_SOURCE_DIR}/cpp/privateer-dbquery.cpp
-            ${PRIVATEER_SOURCE_DIR}/cpp/privateer-cryo_em.cpp
-            ${PRIVATEER_SOURCE_DIR}/cpp/privateer-xray.cpp
-            ${PRIVATEER_SOURCE_DIR}/cpp/privateer-modelling.cpp
-            ${PRIVATEER_SOURCE_DIR}/cpp/privateer-interactions.cpp
-            ${PRIVATEER_SOURCE_DIR}/cpp/privateer-lib.cpp
-            ${PRIVATEER_SOURCE_DIR}/cpp/pybind11/privateer-pybind11.cpp
-            ${PRIVATEER_SOURCE_DIR}/cpp/pybind11/privateer-ccp4mg.cpp
-            ${PRIVATEER_SOURCE_DIR}/cpp/pybind11/privateer-restraints.cpp
-            ${PRIVATEER_SOURCE_DIR}/cpp/pybind11/privateer-pyanalysis.cpp
-            ${PRIVATEER_SOURCE_DIR}/cpp/pybind11/privateer-pymodelling.cpp
-            ${PRIVATEER_SOURCE_DIR}/cpp/clipper-glyco_data.cpp
-            )
-
-target_link_directories(privateer_lib
-    PUBLIC
-    ${CMAKE_BINARY_DIR}/clipper/mmdb
-    ${CMAKE_BINARY_DIR}/clipper/cif
-    ${CMAKE_BINARY_DIR}/clipper/ccp4
-    ${CMAKE_BINARY_DIR}/clipper/minimol
-    ${CMAKE_BINARY_DIR}/clipper/core
-    ${CMAKE_BINARY_DIR}/clipper/contrib
-    ${CMAKE_BINARY_DIR}/fftw
-    ${CMAKE_BINARY_DIR}/rfftw
-    ${CMAKE_BINARY_DIR}/ccp4
-    ${CMAKE_BINARY_DIR}/mmdb2
-    ${CMAKE_BINARY_DIR}/gemmi
-)
+# file(COPY ${PRIVATEERDATA}/glycomics/privateer_glycomics_database.json
+# DESTINATION ${CLIBDENV})
+
+# file(COPY ${PRIVATEERDATA}/linkage_torsions/privateer_torsion_database.json
+# DESTINATION ${CLIBDENV})
+
+add_library(
+  privateer_lib STATIC
+  ${PRIVATEER_SOURCE_DIR}/cpp/third-party/gemmi_compilation_unit.cpp
+  ${PRIVATEER_SOURCE_DIR}/cpp/privateer-error.h
+  ${PRIVATEER_SOURCE_DIR}/cpp/privateer-json.h
+  ${PRIVATEER_SOURCE_DIR}/cpp/clipper-glyco.cpp
+  ${PRIVATEER_SOURCE_DIR}/cpp/privateer-db.cpp
+  ${PRIVATEER_SOURCE_DIR}/cpp/privateer-blobs.cpp
+  ${PRIVATEER_SOURCE_DIR}/cpp/privateer-composition.cpp
+  ${PRIVATEER_SOURCE_DIR}/cpp/privateer-dbquery.cpp
+  ${PRIVATEER_SOURCE_DIR}/cpp/privateer-cryo_em.cpp
+  ${PRIVATEER_SOURCE_DIR}/cpp/privateer-xray.cpp
+  ${PRIVATEER_SOURCE_DIR}/cpp/privateer-modelling.cpp
+  ${PRIVATEER_SOURCE_DIR}/cpp/privateer-interactions.cpp
+  ${PRIVATEER_SOURCE_DIR}/cpp/privateer-lib.cpp
+  ${PRIVATEER_SOURCE_DIR}/cpp/pybind11/privateer-pybind11.cpp
+  ${PRIVATEER_SOURCE_DIR}/cpp/pybind11/privateer-ccp4mg.cpp
+  ${PRIVATEER_SOURCE_DIR}/cpp/pybind11/privateer-restraints.cpp
+  ${PRIVATEER_SOURCE_DIR}/cpp/pybind11/privateer-pyanalysis.cpp
+  ${PRIVATEER_SOURCE_DIR}/cpp/pybind11/privateer-pymodelling.cpp
+  ${PRIVATEER_SOURCE_DIR}/cpp/clipper-glyco_data.cpp)
+
+target_link_directories(
+  privateer_lib
+  PUBLIC
+  ${CMAKE_BINARY_DIR}/clipper/mmdb
+  ${CMAKE_BINARY_DIR}/clipper/cif
+  ${CMAKE_BINARY_DIR}/clipper/ccp4
+  ${CMAKE_BINARY_DIR}/clipper/minimol
+  ${CMAKE_BINARY_DIR}/clipper/core
+  ${CMAKE_BINARY_DIR}/clipper/contrib
+  ${CMAKE_BINARY_DIR}/fftw
+  ${CMAKE_BINARY_DIR}/rfftw
+  ${CMAKE_BINARY_DIR}/ccp4
+  ${CMAKE_BINARY_DIR}/mmdb2
+  ${CMAKE_BINARY_DIR}/gemmi)
 
 target_link_libraries(
-    privateer_lib
-    PUBLIC
-    clipper-contrib
-    clipper-mmdb
-    clipper-cif
-    clipper-ccp4
-    clipper-minimol
-    clipper-core
-    rfftw
-    fftw
-    ccp4
-    mmdb2
-    gemmi_cpp
-    Threads::Threads
-    pybind11::module
-)
+  privateer_lib
+  PUBLIC clipper-contrib
+         clipper-mmdb
+         clipper-cif
+         clipper-ccp4
+         clipper-minimol
+         clipper-core
+         rfftw
+         fftw
+         ccp4
+         mmdb2
+         gemmi_cpp
+         Threads::Threads
+         pybind11::module)
 
 add_executable(privateer_exec ${PRIVATEER_SOURCE_DIR}/cpp/privateer.cpp)
-               
-set_target_properties (privateer_exec  PROPERTIES OUTPUT_NAME privateer )
-
-pybind11_add_module(privateer_core          ${PRIVATEER_SOURCE_DIR}/cpp/pybind11/privateer-pybind11.cpp
-                                            ${PRIVATEER_SOURCE_DIR}/cpp/pybind11/privateer-ccp4mg.cpp
-                                            ${PRIVATEER_SOURCE_DIR}/cpp/pybind11/privateer-restraints.cpp
-                                            ${PRIVATEER_SOURCE_DIR}/cpp/pybind11/privateer-pyanalysis.cpp
-                                            ${PRIVATEER_SOURCE_DIR}/cpp/pybind11/privateer-pymodelling.cpp)
-
-pybind11_add_module(privateer_modelling     ${PRIVATEER_SOURCE_DIR}/cpp/pybind11/privateer-pybind11.cpp
-                                            ${PRIVATEER_SOURCE_DIR}/cpp/pybind11/privateer-ccp4mg.cpp
-                                            ${PRIVATEER_SOURCE_DIR}/cpp/pybind11/privateer-restraints.cpp
-                                            ${PRIVATEER_SOURCE_DIR}/cpp/pybind11/privateer-pyanalysis.cpp
-                                            ${PRIVATEER_SOURCE_DIR}/cpp/pybind11/privateer-pymodelling.cpp)
-
-
-target_link_directories(privateer_exec
-    PUBLIC
-    ${CMAKE_BINARY_DIR}/clipper/mmdb
-    ${CMAKE_BINARY_DIR}/clipper/cif
-    ${CMAKE_BINARY_DIR}/clipper/ccp4
-    ${CMAKE_BINARY_DIR}/clipper/minimol
-    ${CMAKE_BINARY_DIR}/clipper/core
-    ${CMAKE_BINARY_DIR}/clipper/contrib
-    ${CMAKE_BINARY_DIR}/fftw
-    ${CMAKE_BINARY_DIR}/rfftw
-    ${CMAKE_BINARY_DIR}/ccp4
-    ${CMAKE_BINARY_DIR}/mmdb2
-    ${CMAKE_BINARY_DIR}/gemmi
-    ${Python_LIBRARY_DIRS}
-)
-
 
+set_target_properties(privateer_exec PROPERTIES OUTPUT_NAME privateer)
+
+pybind11_add_module(
+  privateer_core
+  ${PRIVATEER_SOURCE_DIR}/cpp/pybind11/privateer-pybind11.cpp
+  ${PRIVATEER_SOURCE_DIR}/cpp/pybind11/privateer-ccp4mg.cpp
+  ${PRIVATEER_SOURCE_DIR}/cpp/pybind11/privateer-restraints.cpp
+  ${PRIVATEER_SOURCE_DIR}/cpp/pybind11/privateer-pyanalysis.cpp
+  ${PRIVATEER_SOURCE_DIR}/cpp/pybind11/privateer-pymodelling.cpp)
+
+pybind11_add_module(
+  privateer_modelling
+  ${PRIVATEER_SOURCE_DIR}/cpp/pybind11/privateer-pybind11.cpp
+  ${PRIVATEER_SOURCE_DIR}/cpp/pybind11/privateer-ccp4mg.cpp
+  ${PRIVATEER_SOURCE_DIR}/cpp/pybind11/privateer-restraints.cpp
+  ${PRIVATEER_SOURCE_DIR}/cpp/pybind11/privateer-pyanalysis.cpp
+  ${PRIVATEER_SOURCE_DIR}/cpp/pybind11/privateer-pymodelling.cpp)
+
+target_link_directories(
+  privateer_exec
+  PUBLIC
+  ${CMAKE_BINARY_DIR}/clipper/mmdb
+  ${CMAKE_BINARY_DIR}/clipper/cif
+  ${CMAKE_BINARY_DIR}/clipper/ccp4
+  ${CMAKE_BINARY_DIR}/clipper/minimol
+  ${CMAKE_BINARY_DIR}/clipper/core
+  ${CMAKE_BINARY_DIR}/clipper/contrib
+  ${CMAKE_BINARY_DIR}/fftw
+  ${CMAKE_BINARY_DIR}/rfftw
+  ${CMAKE_BINARY_DIR}/ccp4
+  ${CMAKE_BINARY_DIR}/mmdb2
+  ${CMAKE_BINARY_DIR}/gemmi
+  ${Python_LIBRARY_DIRS})
 
 target_link_libraries(
-    privateer_exec
-    privateer_lib
-    clipper-mmdb
-    clipper-cif
-    clipper-ccp4
-    clipper-minimol
-    clipper-core
-    clipper-contrib
-    rfftw
-    fftw
-    ccp4
-    mmdb2
-    gemmi_cpp
-    Threads::Threads
-    pybind11::module
-    ${Python_LIBRARIES}
-    )
-
-target_link_libraries ( privateer_core PRIVATE 
-                        privateer_lib 
-    clipper-mmdb
-    clipper-cif
-    clipper-ccp4
-    clipper-minimol
-    clipper-core
-    clipper-contrib
-    rfftw
-    fftw
-    ccp4
-    mmdb2
-    gemmi_cpp
-    Threads::Threads
-    ${Python_LIBRARIES}
-    pybind11::module
-        )
-
-target_link_libraries ( privateer_modelling PRIVATE
-                        privateer_lib 
-
-        clipper-mmdb
-        clipper-cif
-        clipper-ccp4
-        clipper-minimol
-        clipper-core
-        clipper-contrib
-        clipper-minimol
-        rfftw
-        fftw
-        ccp4
-        mmdb2
-        gemmi_cpp
-    Threads::Threads
-    ${Python_LIBRARIES}
-    pybind11::module    )
+  privateer_exec
+  privateer_lib
+  clipper-contrib
+  clipper-mmdb
+  clipper-cif
+  clipper-ccp4
+  clipper-minimol
+  clipper-core
+  rfftw
+  fftw
+  ccp4
+  mmdb2
+  gemmi_cpp
+  Threads::Threads
+  pybind11::module
+  ${Python_LIBRARIES})
 
-set(privateer_HEADERS
-  ${PRIVATEER_SOURCE_DIR}/cpp/pybind11/privateer-restraints.h
-  ${PRIVATEER_SOURCE_DIR}/cpp/privateer-xray.h
-  ${PRIVATEER_SOURCE_DIR}/cpp/privateer-blobs.h
-  ${PRIVATEER_SOURCE_DIR}/cpp/privateer-dbquery.h
-  ${PRIVATEER_SOURCE_DIR}/cpp/privateer-error.h
-  ${PRIVATEER_SOURCE_DIR}/cpp/clipper-glyco_data.h
-  ${PRIVATEER_SOURCE_DIR}/cpp/privateer-composition.h
-  ${PRIVATEER_SOURCE_DIR}/cpp/privateer-lib.h
-  ${PRIVATEER_SOURCE_DIR}/cpp/privateer-json.h
-  ${PRIVATEER_SOURCE_DIR}/cpp/clipper-glyco.h
-#   ${PRIVATEER_SOURCE_DIR}/cpp/privateer-parallelism.h
-  ${PRIVATEER_SOURCE_DIR}/cpp/privateer-cryo_em.h
-)
+target_link_libraries(
+  privateer_core
+  PRIVATE privateer_lib
+          clipper-contrib
+          clipper-mmdb
+          clipper-cif
+          clipper-ccp4
+          clipper-minimol
+          clipper-core
+          rfftw
+          fftw
+          ccp4
+          mmdb2
+          gemmi_cpp
+          Threads::Threads
+          ${Python_LIBRARIES}
+          pybind11::module)
 
-# set_target_properties(privateer_core PROPERTIES LINK_FLAGS "-undefined dynamic_lookup")
-# set_target_properties(privateer_modelling PROPERTIES LINK_FLAGS "-undefined dynamic_lookup")
+target_link_libraries(
+  privateer_modelling
+  PRIVATE privateer_lib
+          clipper-contrib
+          clipper-mmdb
+          clipper-cif
+          clipper-ccp4
+          clipper-minimol
+          clipper-core
+          clipper-minimol
+          rfftw
+          fftw
+          ccp4
+          mmdb2
+          gemmi_cpp
+          Threads::Threads
+          ${Python_LIBRARIES}
+          pybind11::module)
 
-# set_target_properties(privateer_exec PROPERTIES PUBLIC_HEADER "${privateer_HEADERS}")
+set(privateer_HEADERS
+    ${PRIVATEER_SOURCE_DIR}/cpp/pybind11/privateer-restraints.h
+    ${PRIVATEER_SOURCE_DIR}/cpp/privateer-xray.h
+    ${PRIVATEER_SOURCE_DIR}/cpp/privateer-blobs.h
+    ${PRIVATEER_SOURCE_DIR}/cpp/privateer-dbquery.h
+    ${PRIVATEER_SOURCE_DIR}/cpp/privateer-error.h
+    ${PRIVATEER_SOURCE_DIR}/cpp/clipper-glyco_data.h
+    ${PRIVATEER_SOURCE_DIR}/cpp/privateer-composition.h
+    ${PRIVATEER_SOURCE_DIR}/cpp/privateer-lib.h
+    ${PRIVATEER_SOURCE_DIR}/cpp/privateer-json.h
+    ${PRIVATEER_SOURCE_DIR}/cpp/clipper-glyco.h
+    # ${PRIVATEER_SOURCE_DIR}/cpp/privateer-parallelism.h
+    ${PRIVATEER_SOURCE_DIR}/cpp/privateer-cryo_em.h)
+
+# set_target_properties(privateer_core PROPERTIES LINK_FLAGS "-undefined
+# dynamic_lookup") set_target_properties(privateer_modelling PROPERTIES
+# LINK_FLAGS "-undefined dynamic_lookup")
+
+# set_target_properties(privateer_exec PROPERTIES PUBLIC_HEADER
+# "${privateer_HEADERS}")
 set(PRIVATEER_SOURCE ${PRIVATEER_SOURCE_DIR}/cpp/privateer.cpp)
 
-install ( TARGETS privateer_lib LIBRARY DESTINATION privateer)
-install ( TARGETS privateer_exec DESTINATION ${CMAKE_SOURCE_DIR})
-install ( TARGETS privateer_core LIBRARY DESTINATION privateer )
-install ( TARGETS privateer_modelling LIBRARY DESTINATION privateer)
+install(TARGETS privateer_lib LIBRARY DESTINATION privateer)
+install(TARGETS privateer_exec DESTINATION ${CMAKE_SOURCE_DIR})
+install(TARGETS privateer_core LIBRARY DESTINATION privateer)
+install(TARGETS privateer_modelling LIBRARY DESTINATION privateer)