# Makefile for EGAD

OBJECT_DIR = ../lib/
EXECUTABLE_DIR = ../bin/
LIBRARY_DIR = ../lib/

# linux
CC = g++
CFLAGS = -Wall -O2 -g2  -IDEE
LFLAGS = -lm
MAKE = make

OBJECT_CC = $(CC) -c $(CFLAGS) -o $@
EXEC_CC = $(CC) $(CFLAGS) -o

OBJS = \
$(OBJECT_DIR)CHROMOSOME_to_lookupEnergy.o	\
$(OBJECT_DIR)sequence_CHROMOSOME_stuff.o	\
$(OBJECT_DIR)GA.o	\
$(OBJECT_DIR)GA_utilities.o	\
$(OBJECT_DIR)GENES_pdb.o	\
$(OBJECT_DIR)SASA.o	\
$(OBJECT_DIR)VARIABLE_POSITION.o	\
$(OBJECT_DIR)dihedral_cartesian.o	\
$(OBJECT_DIR)energy_functions.o	\
$(OBJECT_DIR)input_stuff.o	\
$(OBJECT_DIR)HQM_rotamers.o	\
$(OBJECT_DIR)lookup_table.o	\
$(OBJECT_DIR)moremath.o	\
$(OBJECT_DIR)output_stuff.o	\
$(OBJECT_DIR)pairwise_energy_calc.o	\
$(OBJECT_DIR)pdbATOM_utilities.o	\
$(OBJECT_DIR)read_forcefield.o	\
$(OBJECT_DIR)readpdbfile.o	\
$(OBJECT_DIR)lookup_table_disk_stuff.o	\
$(OBJECT_DIR)io.o	\
$(OBJECT_DIR)minimization.o	\
$(OBJECT_DIR)powell.o	\
$(OBJECT_DIR)general_GA.o	\
$(OBJECT_DIR)scmf.o	\
$(OBJECT_DIR)search_and_sort.o \
$(OBJECT_DIR)MC.o	\
$(OBJECT_DIR)dee_utilities.o	\
$(OBJECT_DIR)parallel_egad.o \
$(OBJECT_DIR)born_radius_sasa.o \
$(OBJECT_DIR)pK_calculate.o	\
$(OBJECT_DIR)energy_profile_table.o	\
$(OBJECT_DIR)complex_formation_energy.o	\
$(OBJECT_DIR)ligand_stuff.o \
$(OBJECT_DIR)rotamer_calc_foreman.o	\
$(OBJECT_DIR)rotamer_calc_master.o	\
$(OBJECT_DIR)scanning_mutagenesis.o	\
$(OBJECT_DIR)solubility.o	\
$(OBJECT_DIR)batch_jobs.o	\
$(OBJECT_DIR)multistate.o	\
$(OBJECT_DIR)multistate_objective_function.o	\
$(OBJECT_DIR)sequence_restraint.o	\
$(OBJECT_DIR)docking.o	\
$(OBJECT_DIR)somewhat_FASTER.o \
$(OBJECT_DIR)DeeControl.o \
$(OBJECT_DIR)ProteinDeeSpace.o

$(OBJECT_DIR):
	mkdir $@
$(LIBRARY_DIR):
	mkdir $@
$(EXECUTABLE_DIR):
	mkdir $@

# make library
$(LIBRARY_DIR)libEgadLib.a: $(OBJS)
	ar -r $(LIBRARY_DIR)libEgadLib.a $(OBJS)

$(LIBRARY_DIR)libDee.a: $(LIBRARY_DIR)libEgadLib.a
	(cd DEE ; $(MAKE) all)

all: $(EXECUTABLE_DIR)EGAD.exe

clean:
	-touch *.h 
	-touch *.cpp
	-touch DEE/*.h 
	-touch DEE/*.cpp
	-rm -f $(OBJECT_DIR)*.o
	-rm -f $(OBJECT_DIR)DEE/*.o
	-rm -f $(LIBRARY_DIR)*.a
	-rm -f $(LIBRARY_DIR)DEE/*.a
	-rm -f $(EXECUTABLE_DIR)EGAD.exe

# compile executable 
$(EXECUTABLE_DIR)EGAD.exe: $(LIBRARY_DIR)libEgadLib.a $(LIBRARY_DIR)libDee.a $(OBJECT_DIR)EGAD.o $(OBJECT_DIR)rotamer_calc_foreman.o $(OBJECT_DIR)DeeControl.o
	$(EXEC_CC) $(EXECUTABLE_DIR)EGAD.exe -L$(LIBRARY_DIR) $(OBJECT_DIR)EGAD.o -lEgadLib -lDee $(LFLAGS)

# compile objects
$(OBJECT_DIR)EGAD.o: EGAD.cpp egad.h
	$(OBJECT_CC) EGAD.cpp
$(OBJECT_DIR)CHROMOSOME_to_lookupEnergy.o: CHROMOSOME_to_lookupEnergy.cpp CHROMOSOME_to_lookupEnergy.h
	$(OBJECT_CC) CHROMOSOME_to_lookupEnergy.cpp
$(OBJECT_DIR)sequence_CHROMOSOME_stuff.o: sequence_CHROMOSOME_stuff.cpp sequence_CHROMOSOME_stuff.h
	$(OBJECT_CC) sequence_CHROMOSOME_stuff.cpp
$(OBJECT_DIR)GA.o: GA.cpp GA.h
	$(OBJECT_CC) GA.cpp
$(OBJECT_DIR)GA_utilities.o: GA_utilities.cpp GA_utilities.h
	$(OBJECT_CC) GA_utilities.cpp
$(OBJECT_DIR)GENES_pdb.o: GENES_pdb.cpp GENES_pdb.h
	$(OBJECT_CC) GENES_pdb.cpp
$(OBJECT_DIR)SASA.o: SASA.cpp SASA.h
	$(OBJECT_CC) SASA.cpp
$(OBJECT_DIR)VARIABLE_POSITION.o: VARIABLE_POSITION.cpp VARIABLE_POSITION.h
	$(OBJECT_CC) VARIABLE_POSITION.cpp
$(OBJECT_DIR)dihedral_cartesian.o: dihedral_cartesian.cpp dihedral_cartesian.h
	$(OBJECT_CC) dihedral_cartesian.cpp
$(OBJECT_DIR)energy_functions.o: energy_functions.cpp energy_functions.h
	$(OBJECT_CC) energy_functions.cpp
$(OBJECT_DIR)input_stuff.o: input_stuff.cpp input_stuff.h
	$(OBJECT_CC) input_stuff.cpp
$(OBJECT_DIR)lookup_table.o: lookup_table.cpp lookup_table.h
	$(OBJECT_CC) lookup_table.cpp
$(OBJECT_DIR)lookup_table_disk_stuff.o: lookup_table_disk_stuff.cpp lookup_table_disk_stuff.h
	$(OBJECT_CC) lookup_table_disk_stuff.cpp
$(OBJECT_DIR)io.o: io.cpp io.h
	$(OBJECT_CC) io.cpp
$(OBJECT_DIR)minimization.o: minimization.cpp minimization.h
	$(OBJECT_CC) minimization.cpp	
$(OBJECT_DIR)powell.o: powell.cpp powell.h
	$(OBJECT_CC) powell.cpp
$(OBJECT_DIR)general_GA.o: general_GA.cpp general_GA.h
	$(OBJECT_CC) general_GA.cpp
$(OBJECT_DIR)moremath.o: moremath.cpp moremath.h
	$(OBJECT_CC) moremath.cpp
$(OBJECT_DIR)output_stuff.o: output_stuff.cpp output_stuff.h
	$(OBJECT_CC) output_stuff.cpp
$(OBJECT_DIR)pairwise_energy_calc.o: pairwise_energy_calc.cpp pairwise_energy_calc.h
	$(OBJECT_CC) pairwise_energy_calc.cpp
$(OBJECT_DIR)pdbATOM_utilities.o: pdbATOM_utilities.cpp pdbATOM_utilities.h
	$(OBJECT_CC) pdbATOM_utilities.cpp
$(OBJECT_DIR)read_forcefield.o: read_forcefield.cpp read_forcefield.h
	$(OBJECT_CC) read_forcefield.cpp
$(OBJECT_DIR)readpdbfile.o: readpdbfile.cpp readpdbfile.h
	$(OBJECT_CC) readpdbfile.cpp
$(OBJECT_DIR)search_and_sort.o: search_and_sort.cpp search_and_sort.h
	$(OBJECT_CC) search_and_sort.cpp
$(OBJECT_DIR)HQM_rotamers.o: HQM_rotamers.cpp HQM_rotamers.h
	$(OBJECT_CC) HQM_rotamers.cpp
$(OBJECT_DIR)scmf.o: scmf.cpp scmf.h
	$(OBJECT_CC) scmf.cpp
$(OBJECT_DIR)MC.o: MC.cpp MC.h
	$(OBJECT_CC) MC.cpp
$(OBJECT_DIR)dee_utilities.o: dee_utilities.cpp dee_utilities.h
	$(OBJECT_CC) dee_utilities.cpp
$(OBJECT_DIR)parallel_egad.o: parallel_egad.cpp parallel_egad.h
	$(OBJECT_CC) parallel_egad.cpp
$(OBJECT_DIR)born_radius_sasa.o: born_radius_sasa.cpp born_radius_sasa.h
	$(OBJECT_CC) born_radius_sasa.cpp  
$(OBJECT_DIR)pK_calculate.o: pK_calculate.cpp pK_calculate.h
	$(OBJECT_CC) pK_calculate.cpp	
$(OBJECT_DIR)energy_profile_table.o: energy_profile_table.cpp energy_profile_table.h
	$(OBJECT_CC) energy_profile_table.cpp	
$(OBJECT_DIR)complex_formation_energy.o: complex_formation_energy.cpp complex_formation_energy.h
	$(OBJECT_CC) complex_formation_energy.cpp
$(OBJECT_DIR)ligand_stuff.o: ligand_stuff.cpp ligand_stuff.h
	$(OBJECT_CC) ligand_stuff.cpp
$(OBJECT_DIR)rotamer_calc_foreman.o: rotamer_calc_foreman.cpp rotamer_calc_foreman.h
	$(OBJECT_CC) rotamer_calc_foreman.cpp
$(OBJECT_DIR)rotamer_calc_master.o: rotamer_calc_master.cpp rotamer_calc_master.h
	$(OBJECT_CC) rotamer_calc_master.cpp
$(OBJECT_DIR)solubility.o: solubility.cpp solubility.h
	$(OBJECT_CC) solubility.cpp
$(OBJECT_DIR)scanning_mutagenesis.o: scanning_mutagenesis.cpp scanning_mutagenesis.h	
	$(OBJECT_CC) scanning_mutagenesis.cpp
$(OBJECT_DIR)batch_jobs.o: batch_jobs.cpp batch_jobs.h
	$(OBJECT_CC) batch_jobs.cpp	
$(OBJECT_DIR)multistate.o: multistate.cpp multistate.h
	$(OBJECT_CC) multistate.cpp
$(OBJECT_DIR)multistate_objective_function.o: multistate_objective_function.cpp multistate_objective_function.h
	$(OBJECT_CC) multistate_objective_function.cpp
$(OBJECT_DIR)sequence_restraint.o: sequence_restraint.cpp sequence_restraint.h
	$(OBJECT_CC) sequence_restraint.cpp
$(OBJECT_DIR)docking.o: docking.cpp docking.h
	$(OBJECT_CC) docking.cpp
$(OBJECT_DIR)somewhat_FASTER.o: somewhat_FASTER.cpp somewhat_FASTER.h
	$(OBJECT_CC) somewhat_FASTER.cpp
$(OBJECT_DIR)DeeControl.o: DeeControl.cpp DeeControl.h
	$(OBJECT_CC) DeeControl.cpp
$(OBJECT_DIR)ProteinDeeSpace.o: ProteinDeeSpace.cpp ProteinDeeSpace.h \
				structure_types.h
	$(OBJECT_CC) ProteinDeeSpace.cpp

# header dependencies
CHROMOSOME_to_lookupEnergy.h: structure_types.h moremath.h energy_functions.h pairwise_energy_calc.h
sequence_CHROMOSOME_stuff: structure_types.h
GA.h: structure_types.h GA_utilities.h CHROMOSOME_to_lookupEnergy.h search_and_sort.h HQM_rotamers.h io.h output_stuff.h
GA_utilities.h: structure_types.h moremath.h CHROMOSOME_to_lookupEnergy.h
HQM_rotamers.h: structure_types.h moremath.h GA_utilities.h CHROMOSOME_to_lookupEnergy.h
GENES_pdb.h: structure_types.h dihedral_cartesian.h pdbATOM_utilities.h search_and_sort.h
SASA.h: structure_types.h moremath.h
VARIABLE_POSITION.h: structure_types.h moremath.h search_and_sort.h energy_functions.h pdbATOM_utilities.h
dihedral_cartesian.h: structure_types.h moremath.h
energy_functions.h: structure_types.h moremath.h SASA.h dihedral_cartesian.h pdbATOM_utilities.h
input_stuff.h: structure_types.h readpdbfile.h read_forcefield.h VARIABLE_POSITION.h energy_functions.h pairwise_energy_calc.h io.h lookup_table_disk_stuff.h GA_utilities.h lookup_table.h pdbATOM_utilities.h
lookup_table.h: structure_types.h moremath.h energy_functions.h pairwise_energy_calc.h dihedral_cartesian.h GENES_pdb.h SASA.h lookup_table_disk_stuff.h sequence_CHROMOSOME_stuff.h sequence_restraint.h
io.h: structure_types.h
minimization.h: structure_types.h dihedral_cartesian.h pdbATOM_utilities.h GENES_pdb.h search_and_sort.h energy_functions.h pairwise_energy_calc.h io.h GA_utilities.h
powell.h: structure_types.h io.h moremath.h
general_GA.h: structure_types.h io.h powell.h moremath.h
lookup_table_disk_stuff.h: structure_types.h moremath.h pairwise_energy_calc.h io.h
moremath.h: structure_types.h io.h
output_stuff.h: structure_types.h pdbATOM_utilities.h energy_functions.h search_and_sort.h GENES_pdb.h pairwise_energy_calc.h io.h lookup_table_disk_stuff.h energy_profile_table.h sequence_CHROMOSOME_stuff.h
pairwise_energy_calc.h: structure_types.h moremath.h energy_functions.h
pdbATOM_utilities.h: structure_types.h moremath.h dihedral_cartesian.h search_and_sort.h
read_forcefield.h: structure_types.h moremath.h dihedral_cartesian.h search_and_sort.h energy_functions.h SASA.h io.h
readpdbfile.h: output_stuff.h structure_types.h moremath.h pdbATOM_utilities.h GENES_pdb.h VARIABLE_POSITION.h dihedral_cartesian.h GA_utilities.h io.h
search_and_sort.h: structure_types.h
scmf.h: structure_types.h HQM_rotamers.h moremath.h MC.h GENES_pdb.h
MC.h: structure_types.h GA_utilities.h CHROMOSOME_to_lookupEnergy.h search_and_sort.h HQM_rotamers.h output_stuff.h GA.h
dee_utilities.h: structure_types.h moremath.h
parallel_egad.h: structure_types.h moremath.h io.h
born_radius_sasa.h: structure_types.h energy_functions.h
pK_calculate.h: structure_types.h scmf.h	
energy_profile_table.h: structure_types.h io.h pdbATOM_utilities.h energy_functions.h
complex_formation_energy.h:  structure_types.h io.h pdbATOM_utilities.h energy_functions.h output_stuff.h moremath.h
ligand_stuff.h: structure_types.h io.h read_forcefield.h
rotamer_calc_foreman.h: structure_types.h io.h MC.h scmf.h DeeControl.h lookup_table.h output_stuff.h
rotamer_calc_master.h: structure_types.h io.h energy_functions.h
batch_jobs.h: structure_types.h io.h
multistate.h: structure_types.h GA_utilities.h energy_functions.h rotamer_calc_master.h sequence_CHROMOSOME_stuff.h sequence_restraint.h multistate_objective_function.h
multistate_objective_function.h: structure_types.h io.h moremath.h energy_functions.h
sequence_restraint.h: structure_types.h io.h GA_utilities.h sequence_CHROMOSOME_stuff.h
docking.h: structure_types.h io.h moremath.h powell.h CHROMOSOME_to_lookupEnergy.h
somewhat_FASTER.h: structure_types.h io.h moremath.h CHROMOSOME_to_lookupEnergy.h MC.h HQM_rotamers.h GA_utilities.h
solubility.h: structure_types.h GA_utilities.h moremath.h 
scanning_mutagenesis.h: structure_types.h GENES_pdb.h energy_functions.h io.h
DeeControl.h:
ProteinDeeSpace.h: DEE/DeeSpace.h
egad.h: structure_types.h CHROMOSOME_to_lookupEnergy.h GA.h GA_utilities.h GENES_pdb.h SASA.h VARIABLE_POSITION.h \
		dihedral_cartesian.h energy_functions.h input_stuff.h lookup_table.h moremath.h output_stuff.h \
		pairwise_energy_calc.h pdbATOM_utilities.h read_forcefield.h readpdbfile.h search_and_sort.h \
		HQM_rotamers.h minimization.h io.h scmf.h MC.h dee_utilities.h parallel_egad.h general_GA.h \
		born_radius_sasa.h pK_calculate.h energy_profile_table.h complex_formation_energy.h ligand_stuff.h 	\
		rotamer_calc_foreman.h rotamer_calc_master.h solubility.h DeeControl.h batch_jobs.h multistate.h  \
		sequence_restraint.h docking.h