ROOT = /netapp/home/dkeedy/qFit


# Directories where we should search for #include'd files
CGAL_INCLUDE = $(ROOT)/CGAL-4.1/include
LOOPTK_INCLUDE = $(ROOT)/looptk-2.0.1/src/core $(ROOT)/looptk-2.0.1/src/utils
#CLIPPER_INCLUDE = $(ROOT)/clipper-2.1/clipper
CLIPPER_INCLUDE = $(ROOT)/clipper-2.1
CPLEX_INCLUDE = $(ROOT)/cplex/ILOG/CPLEX_Studio124/cplex/include $(ROOT)/cplex/ILOG/CPLEX_Studio124/concert/include
GSL_INCLUDE = $(ROOT)/gsl-1.15/include
#MKL_INCLUDE = /home/sw/intel/Compiler/11.1/072/mkl/include
#GLUT_INCLUDE = $(ROOT)/looptk_helper/freeglut-2.6.0/include
GLUI_INCLUDE = $(ROOT)/glui-2.36/src/include/GL
MMDB_INCLUDE = $(ROOT)/mmdb-1.23.2.2/include
GPP4_INCLUDE = $(ROOT)/gpp4-1.3.1/include
MY_INCLUDES = \
    $(CGAL_INCLUDE) \
    $(LOOPTK_INCLUDE) \
    $(CLIPPER_INCLUDE) \
    $(CPLEX_INCLUDE) \
    $(GPP4_INCLUDE) \
    $(GSL_INCLUDE) \
    $(MKL_INCLUDE) \
    $(GLUT_INCLUDE) \
    $(GLUI_INCLUDE) \
    $(MMDB_INCLUDE) \
    $(GPP4_INCLUDE)


# Directories where we should search for libraries
CGAL_LIBDIR = $(ROOT)/CGAL-4.1/cmake/platforms/debug/lib
CLIPPER_LIBDIR = $(ROOT)/clipper-2.1/lib
CPLEX_LIBDIR = $(ROOT)/cplex/ILOG/CPLEX_Studio124/concert/lib/x86-64_sles10_4.1/static_pic $(ROOT)/cplex/ILOG/CPLEX_Studio124/cplex/lib/x86-64_sles10_4.1/static_pic
#X_LIBDIR = /usr/X11R6/lib /usr/X11R6/lib/modules/extensions /usr/X11R6/lib64
#X_LIBDIR = ??? ??? ???
SYS_LIBDIR = /lib64
GSL_LIBDIR = $(ROOT)/gsl-1.15/lib
#MKL_LIBDIR = /home/sw/intel/Compiler/11.1/072/mkl/32
#GLUT_LIBDIR = $(ROOT)/looptk_helper/freeglut-2.6.0/lib
MMDB_LIBDIR = $(ROOT)/mmdb-1.23.2.2/lib
GPP4_LIBDIR = $(ROOT)/gpp4-1.3.1/lib
FFTW_LIBDIR = $(ROOT)/fftw-2.1.5/lib
MY_LIBDIRS = \
    $(CGAL_LIBDIR) \
    $(CLIPPER_LIBDIR) \
    $(CPLEX_LIBDIR) \
    $(X_LIBDIR) \
    $(SYS_LIBDIR) \
    $(GSL_LIBDIR) \
    $(MKL_LIBDIR) \
    $(GLUT_LIBDIR) \
    $(MMDB_LIBDIR) \
    $(GPP4_LIBDIR) \
    $(FFTW_LIBDIR)


# Libraries the program will need
SYS_LIBS = Xi Xext X11 xml2 
CLIPPER_LIBS = \
    clipper-minimol \
    clipper-mmdb \
    clipper-phs \
    clipper-cif \
    clipper-contrib \
    clipper-core \
    clipper-ccp4 \
    fftw \
    rfftw \
    mmdb \
    m
CPLEX_LIBS = ilocplex cplex concert
GLUT_LIBS = glut 
MMDB_LIBS = mmdb
#MKL_LIBS = mkl_lapack guide mkl_ia32 
#GSL_LIBS = gsl gslcblas
MY_LIBS = \
    $(SYS_LIBS) \
    $(CLIPPER_LIBS) \
    $(CPLEX_LIBS) \
    $(GLUT_LIBS) \
    $(MMDB_LIBS)
    # no $(MKL_LIBS) or $(GSL_LIBS) for some reason


# Flags for the compiler and linker
CXX = gcc
DEBUG_VAR = -g 
OPT_VAR = -O2 -msse2 -DMATH_DOUBLE -frounding-math -Wno-deprecated
CPPFLAGS = \
    $(DEBUG_VAR) \
    $(OPT_VAR) \
    $(CGAL_CXXFLAGS) \
    $(addprefix -I,$(MY_INCLUDES)) \
    -I/usr/include/libxml2


# Stuff the build targets use directly
LD_FLAGS = \
    -pthread \
    $(ROOT)/looptk-2.0.1/lib/looptk.a \
    $(CGAL_LIBDIR)/libCGAL.a \
    $(GSL_LIBDIR)/libgsl.a \
    $(GSL_LIBDIR)/libgslcblas.a \
    /usr/lib64/libboost_thread-mt.so \
    $(addprefix -L, $(MY_LIBDIRS)) \
    $(addprefix -l,$(MY_LIBS))
# /usr/lib64/libboost_thread-mt.so replaces
# /usr/lib64/libboost_thread.a above
OBJECTS = $(patsubst src/%.cpp, src/%.o, $(wildcard src/*.cpp)) 
EXECUTABLE = qFit


# Build targets
all: $(EXECUTABLE)
default: $(EXECUTABLE)
qFit : $(OBJECTS)
	$(CXX) -o bin/$@ $(OBJECTS) $(LD_FLAGS)
reDokkum_frag : $(OBJECTS)
	$(CXX) -o bin/$@ $(OBJECTS) $(LD_FLAGS)
docs:
	./scandoc -i ./default.pl *.h
	mv *.html $(DOC_DIR)
 
# Cleaning targets
clean :
	rm -f src/*.o #resolve
realclean : clean
	rm -f $(DOC_DIR)/*.html