basic R support

gf712 · gf712 · commit a0dbe0c254ec · 2019-03-04T16:07:48.000Z
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -52,10 +52,7 @@ include(CheckCompilerFeatures)
 
 add_subdirectory(src/prostruct)
 
-IF(ENABLE_INTERFACE)
-    find_package(SWIG 3.0 REQUIRED)
-    find_package(PythonLibs 3.6 REQUIRED)
-    find_package(Numpy 1.7 REQUIRED)
+IF(${ENABLE_PYTHON} OR ${ENABLE_R})
     add_subdirectory(src/interface)
 ENDIF()
 
diff --git a/README.md b/README.md
@@ -22,7 +22,7 @@ C++:
 ```cpp
 #include <prostruct/prostruct.h>
 
-auto pdb = PDB<float>("test.pdb");
+auto pdb = PDB<float>("mypdb.pdb");
 auto ks = pdb.compute_kabsch_sander() // arma::Mat<float>
 ```
 
@@ -34,6 +34,16 @@ pdb = prostruct.PDB_float("mypdb.pdb")
 ks = pdb.compute_kabsch_sander() # numpy array
 ```
 
+R:
+```R
+dyn.load(paste("prostruct", .Platform$dynlib.ext, sep=""))
+source("prostruct.R")
+cacheMetaData(1)
+
+pdb <- PDB_float("mypdb.pdb")
+ks = pdb$compute_kabsch_sander() # R matrix
+```
+
 ## Build with CMake
 
 Currently ProStruct is only available from source.
diff --git a/cmake/FindR.cmake b/cmake/FindR.cmake
@@ -0,0 +1,67 @@
+# CMake module to find R
+# - Try to find R
+# Once done, this will define
+#
+#  R_FOUND - system has R
+#  R_INCLUDE_DIRS - the R include directories
+#  R_LIBRARIES - link these to use R
+#  R_ROOT_DIR - As reported by R
+# Autor: Omar Andres Zapata Mesa 31/05/2013
+
+if(${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
+  set(CMAKE_FIND_APPBUNDLE "LAST")
+endif()
+
+find_program(R_EXECUTABLE NAMES R R.exe)
+
+#---searching R installtion unsing R executable
+if(R_EXECUTABLE)
+  execute_process(COMMAND ${R_EXECUTABLE} RHOME
+                  OUTPUT_VARIABLE R_ROOT_DIR
+                  OUTPUT_STRIP_TRAILING_WHITESPACE)
+
+  find_path(R_INCLUDE_DIR R.h
+            HINTS ${R_ROOT_DIR}
+            PATHS /usr/local/lib /usr/local/lib64 /usr/share
+            PATH_SUFFIXES include R/include
+            DOC "Path to file R.h")
+
+  find_library(R_LIBRARY R
+            HINTS ${R_ROOT_DIR}/lib
+            DOC "R library (example libR.a, libR.dylib, etc.).")
+endif()
+
+#---setting include dirs and libraries
+set(R_LIBRARIES ${R_LIBRARY})
+set(R_INCLUDE_DIRS ${R_INCLUDE_DIR})
+foreach(_cpt ${R_FIND_COMPONENTS})
+  execute_process(COMMAND echo "cat(find.package('${_cpt}'))"
+                  COMMAND ${R_EXECUTABLE} --vanilla --slave
+                  RESULT_VARIABLE _rc
+                  ERROR_QUIET
+                  OUTPUT_VARIABLE _cpt_path
+                  OUTPUT_STRIP_TRAILING_WHITESPACE)
+  if(NOT _rc)
+    set(R_${_cpt}_FOUND 1)
+  endif()
+
+  find_library(R_${_cpt}_LIBRARY
+               lib${_cpt}.so lib${_cpt}.dylib
+               HINTS ${_cpt_path}/lib)
+  if(R_${_cpt}_LIBRARY)
+    mark_as_advanced(R_${_cpt}_LIBRARY)
+    list(APPEND R_LIBRARIES ${R_${_cpt}_LIBRARY})
+  endif()
+
+  find_path(R_${_cpt}_INCLUDE_DIR ${_cpt}.h HINTS  ${_cpt_path} PATH_SUFFIXES include R/include)
+  if(R_${_cpt}_INCLUDE_DIR)
+    mark_as_advanced(R_${_cpt}_INCLUDE_DIR)
+    list(APPEND R_INCLUDE_DIRS ${R_${_cpt}_INCLUDE_DIR})
+  endif()
+
+endforeach()
+
+# Handle the QUIETLY and REQUIRED arguments and set R_FOUND to TRUE if all listed variables are TRUE
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(R HANDLE_COMPONENTS REQUIRED_VARS R_EXECUTABLE R_INCLUDE_DIR R_LIBRARY)
+mark_as_advanced(R_FOUND R_EXECUTABLE R_INCLUDE_DIR R_LIBRARY)
diff --git a/src/interface/CMakeLists.txt b/src/interface/CMakeLists.txt
@@ -1,29 +1,67 @@
 cmake_minimum_required(VERSION 3.13)
 
-set(TARGET_NAME prostruct_interface)
+find_package(SWIG 3.0 REQUIRED)
+
+set(PYTHON_TARGET_NAME prostruct_python_interface)
+set(R_TARGET_NAME prostruct_r_interface)
+
 cmake_policy(SET CMP0078 NEW)
 
 if(${CMAKE_VERSION} GREATER "3.14.0")
-    cmake_policy(SET CMP0086 NEW)
+    cmake_policy(SET CMP0086 OLD)
 endif()
 
 include(${SWIG_USE_FILE})
 include_directories(swig)
 include_directories(${PROJECT_SOURCE_DIR}/src)
-file(GLOB_RECURSE SWIG_FILES ${PROJECT_SOURCE_DIR}/src/interface/python/*.i)
 
-set_property(SOURCE ${SWIG_FILES} PROPERTY CPLUSPLUS ON)
 #set(CMAKE_SWIG_OUTDIR ${CMAKE_BINARY_DIR}/src/interface/python)
-set(CMAKE_SWIG_FLAGS "-builtin")
-swig_add_library(${TARGET_NAME}
-        LANGUAGE python SOURCES ${SWIG_FILES})
-target_include_directories(${TARGET_NAME} PUBLIC ${PYTHON_INCLUDE_DIRS} PUBLIC ${PROJECT_SOURCE_DIR}/src)
+if (ENABLE_PYTHON)
+    find_package(PythonLibs 3.6 REQUIRED)
+    find_package(Numpy 1.7 REQUIRED)
+	file(GLOB_RECURSE SWIG_FILES ${PROJECT_SOURCE_DIR}/src/interface/python/*.i)
+	set_property(SOURCE ${SWIG_FILES} PROPERTY CPLUSPLUS ON)
 
-if (APPLE)
-    target_link_libraries(${TARGET_NAME} PUBLIC "-undefined dynamic_lookup")
+	set(CMAKE_SWIG_FLAGS "-builtin")
+	swig_add_library(${PYTHON_TARGET_NAME}
+        	LANGUAGE python SOURCES ${SWIG_FILES}
+        	OUTFILE_DIR "${CMAKE_BINARY_DIR}/src/interface/python"
+        	OUTPUT_DIR "${CMAKE_BINARY_DIR}/src/interface/python")
+	target_include_directories(${PYTHON_TARGET_NAME} 
+			PUBLIC ${PYTHON_INCLUDE_DIRS} 
+			PUBLIC ${PROJECT_SOURCE_DIR}/src)
+	if (APPLE)
+    	target_link_libraries(${PYTHON_TARGET_NAME} PUBLIC "-undefined dynamic_lookup")
+	endif()
+	target_link_libraries(${PYTHON_TARGET_NAME} PUBLIC prostruct ${ARMADILLO_LIBRARIES})
+	target_include_directories(${PYTHON_TARGET_NAME} PUBLIC ${NUMPY_INCLUDE_DIRS})
+	set_target_properties(${PYTHON_TARGET_NAME} PROPERTIES SWIG_DEPENDS prostruct)
+	set_target_properties(${PYTHON_TARGET_NAME} PROPERTIES 
+						  OUTPUT_NAME prostruct
+						  LIBRARY_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/src/interface/python")
+endif()
+if (ENABLE_R)
+	find_package(R REQUIRED)
+	find_package(Rcpp REQUIRED)
+	find_package(Boost REQUIRED)
+	file(GLOB_RECURSE SWIG_FILES ${PROJECT_SOURCE_DIR}/src/interface/r/*.i)
+	set_property(SOURCE ${SWIG_FILES} PROPERTY CPLUSPLUS ON)
+	set(CMAKE_SWIG_FLAGS "")
+	swig_add_library(${R_TARGET_NAME}
+        	LANGUAGE r SOURCES ${SWIG_FILES}
+        	OUTFILE_DIR "${CMAKE_BINARY_DIR}/src/interface/r"
+        	OUTPUT_DIR "${CMAKE_BINARY_DIR}/src/interface/r")	
+	target_include_directories(${R_TARGET_NAME} 
+			PUBLIC ${R_INCLUDE_DIR}
+			PUBLIC ${RCPP_INCLUDE_DIR}
+			PUBLIC ${PROJECT_SOURCE_DIR}/src
+			PUBLIC ${Boost_INCLUDE_DIRS})
+	if (APPLE)
+    	target_link_libraries(${R_TARGET_NAME} PUBLIC "-undefined dynamic_lookup")
+	endif()
+	target_link_libraries(${R_TARGET_NAME} PUBLIC prostruct ${ARMADILLO_LIBRARIES} ${R_LIBRARIES})
+	set_target_properties(${R_TARGET_NAME} PROPERTIES SWIG_DEPENDS prostruct)
+	set_target_properties(${R_TARGET_NAME} PROPERTIES
+						  OUTPUT_NAME prostruct
+						  LIBRARY_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/src/interface/r")
 endif()
-
-target_link_libraries(${TARGET_NAME} PUBLIC prostruct ${ARMADILLO_LIBRARIES})
-target_include_directories(${TARGET_NAME} PUBLIC ${NUMPY_INCLUDE_DIRS})
-set_target_properties(${TARGET_NAME} PROPERTIES SWIG_DEPENDS prostruct)
-set_target_properties(${TARGET_NAME} PROPERTIES OUTPUT_NAME prostruct)
diff --git a/src/interface/python/typemaps.i b/src/interface/python/typemaps.i
@@ -37,8 +37,6 @@
 ARMA_COL_OUT(float, NPY_FLOAT);
 ARMA_COL_OUT(double, NPY_DOUBLE);
 ARMA_COL_OUT(arma::uword, NPY_ULONGLONG);
-ARMA_COL_OUT(unsigned long long, NPY_ULONGLONG);
-
 
 ARMA_MAT_OUT(float, NPY_FLOAT);
 ARMA_MAT_OUT(double, NPY_DOUBLE);
diff --git a/src/interface/r/typemaps.i b/src/interface/r/typemaps.i
@@ -0,0 +1,56 @@
+%{
+	#include <boost/smart_ptr/shared_ptr.hpp>
+%}
+
+
+
+%define ARMA_COL_OUT(TYPE, R_TYPESXP, R_CAST_TYPE, R_TYPE, R_TYPE_STRING)
+%typemap(out) arma::Col<TYPE>
+{
+   	Rf_protect($result = Rf_allocVector(R_TYPESXP, $1.size()));  
+   	printf("TEST");
+   	fflush(stdout);
+   	for (arma::uword i=0; i< $1.size(); ++i) 
+   	{     
+   		R_TYPE($result)[i] = static_cast<R_CAST_TYPE>($1(i));
+	}
+	Rf_unprotect(1);
+}
+
+%typemap("rtype") arma::Col<TYPE> R_TYPE_STRING
+
+%typemap("scoerceout") arma::Col<TYPE>
+%{ %}
+
+%enddef
+
+%define ARMA_MAT_OUT(TYPE, R_TYPESXP, R_CAST_TYPE, R_TYPE)
+%typemap(out) arma::Mat<TYPE>
+{
+   	Rf_protect($result = Rf_allocMatrix(R_TYPESXP, $1.n_cols, $1.n_rows));    
+   	for (arma::uword i=0; i < $1.n_rows; ++i) 
+   	{
+   		for (arma::uword j=0; j < $1.n_cols; ++j) 
+   		{
+   			R_TYPE($result)[i*$1.n_cols+j] = static_cast<R_CAST_TYPE>($1(i, j));   
+   		}
+	}
+	Rf_unprotect(1);
+}
+
+%typemap("rtype") arma::Mat<TYPE> "matrix"
+
+%typemap("scoerceout") arma::Mat<TYPE>
+%{ %}
+
+%enddef
+
+ARMA_COL_OUT(float, REALSXP, float, REAL, "numeric");
+ARMA_COL_OUT(double, REALSXP, float, REAL, "numeric");
+ARMA_COL_OUT(arma::uword, INTSXP, int, INTEGER, "integer");
+
+ARMA_MAT_OUT(float, REALSXP, float, REAL);
+ARMA_MAT_OUT(double, REALSXP, float, REAL);
+ARMA_MAT_OUT(arma::uword, INTSXP, int, INTEGER);
+
+%include "prostruct.i"
diff --git a/src/interface/swig/prostruct.i b/src/interface/swig/prostruct.i
@@ -10,6 +10,8 @@
     $action 
   } catch (const std::exception& e) { 
     SWIG_exception(SWIG_RuntimeError, e.what()); 
+  } catch (const char* e) { 
+    SWIG_exception(SWIG_RuntimeError, e); 
   } catch (const std::string& e) { 
     SWIG_exception(SWIG_RuntimeError, e.c_str()); 
   } 
@@ -22,12 +24,32 @@
 %template() std::vector<std::string>;
 #endif
 
+#ifdef SWIGPYTHON
 %include <std_shared_ptr.i>
+#else 
+%include <boost_shared_ptr.i>
+#endif
+
+//#ifdef SWIGPYTHON
+%define ADD_SHARED_PTR(class_name)
+%shared_ptr(class_name)
+%enddef
+// #else 
+// %define ADD_SHARED_PTR(class_name)
+// %boost_shared_ptr(class_name)
+// %enddef
+// #endif
+
+ADD_SHARED_PTR(prostruct::Residue<float>)
+ADD_SHARED_PTR(prostruct::Residue<double>)
+ADD_SHARED_PTR(prostruct::Chain<float>)
+ADD_SHARED_PTR(prostruct::Chain<double>)
+
+//%shared_ptr(prostruct::Residue<float>)
+//%shared_ptr(prostruct::Residue<double>)
+//%shared_ptr(prostruct::Chain<float>)
+//%shared_ptr(prostruct::Chain<double>)
 
-%shared_ptr(prostruct::Residue<float>)
-%shared_ptr(prostruct::Residue<double>)
-%shared_ptr(prostruct::Chain<float>)
-%shared_ptr(prostruct::Chain<double>)
 //%shared_ptr(prostruct::PDB)
 
 %include "prostruct/pdb/PDB.h"
