# PLEASE adhere to the alphabetical ordering in this Makefile!
# Also indentation by a single tab

MOSTLYCLEANFILES =
lib_LTLIBRARIES =
noinst_LTLIBRARIES =
pyexec_LTLIBRARIES =
BUILT_SOURCES =
bin_PROGRAMS =
EXTRA_DIST =

include Actions/Makefile.am
include Analysis/Makefile.am
include Atom/Makefile.am
include Element/Makefile.am
include Filling/Makefile.am
include Fragmentation/Makefile.am
include Graph/Makefile.am
include Helpers/Makefile.am

if CONDJOBMARKET
include Jobs/Makefile.am
endif

include LinkedCell/Makefile.am
include Parameters/Makefile.am
include Parser/Makefile.am
include RandomNumbers/Makefile.am
include Shapes/Makefile.am
include UIElements/Makefile.am

AM_LDFLAGS = -ldl ${BOOST_LDFLAGS} ${CodePatterns_LDFLAGS}
AM_CPPFLAGS = ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS}

BONDSOURCE = \
	Bond/bond.cpp \
	Bond/bond_observable.cpp \
	Bond/BondInfo.cpp \
	Bond/GraphEdge.cpp

BONDHEADER = \
	Bond/bond.hpp \
	Bond/bond_observable.hpp \
	Bond/BondInfo.hpp \
	Bond/GraphEdge.hpp

DESCRIPTORSOURCE = \
	Descriptors/AtomDescriptor.cpp \
  Descriptors/AtomIdDescriptor.cpp \
  Descriptors/AtomOfMoleculeDescriptor.cpp \
  Descriptors/AtomOfMoleculeSelectionDescriptor.cpp \
  Descriptors/AtomOrderDescriptor.cpp \
  Descriptors/AtomSelectionDescriptor.cpp \
  Descriptors/AtomShapeDescriptor.cpp \
  Descriptors/AtomTypeDescriptor.cpp \
  Descriptors/AtomsWithinDistanceOfDescriptor.cpp \
  Descriptors/MoleculeDescriptor.cpp \
  Descriptors/MoleculeFormulaDescriptor.cpp \
  Descriptors/MoleculeIdDescriptor.cpp \
  Descriptors/MoleculeNameDescriptor.cpp \
  Descriptors/MoleculeOfAtomSelectionDescriptor.cpp \
  Descriptors/MoleculeOrderDescriptor.cpp \
  Descriptors/MoleculePtrDescriptor.cpp \
  Descriptors/MoleculeSelectionDescriptor.cpp
				   

DESCRIPTORHEADER = \
	Descriptors/AtomDescriptor.hpp \
  Descriptors/AtomIdDescriptor.hpp \
  Descriptors/AtomOfMoleculeDescriptor.hpp \
  Descriptors/AtomOfMoleculeSelectionDescriptor.hpp \
  Descriptors/AtomOrderDescriptor.hpp \
  Descriptors/AtomSelectionDescriptor.hpp \
  Descriptors/AtomShapeDescriptor.hpp \
  Descriptors/AtomTypeDescriptor.hpp \
  Descriptors/AtomsWithinDistanceOfDescriptor.hpp \
  Descriptors/DescriptorBase.hpp \
  Descriptors/MoleculeDescriptor.hpp \
  Descriptors/MoleculeFormulaDescriptor.hpp \
  Descriptors/MoleculeIdDescriptor.hpp \
  Descriptors/MoleculeNameDescriptor.hpp \
  Descriptors/MoleculeOfAtomSelectionDescriptor.hpp \
  Descriptors/MoleculeOrderDescriptor.hpp \
  Descriptors/MoleculePtrDescriptor.hpp \
  Descriptors/MoleculeSelectionDescriptor.hpp \
  Descriptors/SelectiveIterator.hpp
  
DESCRIPTORIMPLHEADER = \
	Descriptors/AtomDescriptor_impl.hpp \
  Descriptors/AtomIdDescriptor_impl.hpp \
  Descriptors/AtomOfMoleculeDescriptor_impl.hpp \
  Descriptors/AtomOfMoleculeSelectionDescriptor_impl.hpp \
  Descriptors/AtomOrderDescriptor_impl.hpp \
  Descriptors/AtomSelectionDescriptor_impl.hpp \
  Descriptors/AtomShapeDescriptor_impl.hpp \
  Descriptors/AtomTypeDescriptor_impl.hpp \
  Descriptors/AtomsWithinDistanceOfDescriptor_impl.hpp \
  Descriptors/DescriptorBase_impl.hpp \
  Descriptors/MoleculeDescriptor_impl.hpp \
  Descriptors/MoleculeFormulaDescriptor_impl.hpp \
  Descriptors/MoleculeIdDescriptor_impl.hpp \
  Descriptors/MoleculeNameDescriptor_impl.hpp \
  Descriptors/MoleculeOfAtomSelectionDescriptor_impl.hpp \
  Descriptors/MoleculeOrderDescriptor_impl.hpp \
  Descriptors/MoleculePtrDescriptor_impl.hpp \
  Descriptors/MoleculeSelectionDescriptor_impl.hpp \
  Descriptors/SelectiveIterator_impl.hpp

DYNAMICSSOURCE = \
	Dynamics/MinimiseConstrainedPotential.cpp

DYNAMICSHEADER = \
	Dynamics/LinearInterpolationBetweenSteps.hpp \
	Dynamics/MinimiseConstrainedPotential.hpp \
	Dynamics/OutputTemperature.hpp \
	Dynamics/VerletForceIntegration.hpp

THERMOSTATSOURCE = \
  Thermostats/Berendsen.cpp \
  Thermostats/GaussianThermostat.cpp \
  Thermostats/Langevin.cpp \
  Thermostats/NoseHoover.cpp \
  Thermostats/NoThermostat.cpp \
  Thermostats/Thermostat.cpp \
  Thermostats/ThermoStatContainer.cpp \
  Thermostats/Woodcock.cpp

THERMOSTATHEADER = \
  Thermostats/Berendsen.hpp \
  Thermostats/GaussianThermostat.hpp \
  Thermostats/Langevin.hpp \
  Thermostats/NoseHoover.hpp \
  Thermostats/NoThermostat.hpp \
  Thermostats/Thermostat.hpp \
  Thermostats/ThermoStatContainer.hpp \
  Thermostats/Woodcock.hpp

TESSELATIONSOURCE = \
  Tesselation/ApproximateShapeArea.cpp \
  Tesselation/ApproximateShapeVolume.cpp \
  Tesselation/boundary.cpp \
  Tesselation/BoundaryLineSet.cpp \
  Tesselation/BoundaryPointSet.cpp \
  Tesselation/BoundaryPolygonSet.cpp \
  Tesselation/BoundaryTriangleSet.cpp \
  Tesselation/CandidateForTesselation.cpp \
  Tesselation/ellipsoid.cpp \
  Tesselation/tesselation.cpp \
  Tesselation/tesselationhelpers.cpp \
  Tesselation/triangleintersectionlist.cpp
  
TESSELATIONHEADER = \
  Tesselation/ApproximateShapeArea.hpp \
  Tesselation/ApproximateShapeVolume.hpp \
  Tesselation/boundary.hpp \
  Tesselation/BoundaryLineSet.hpp \
  Tesselation/BoundaryMaps.hpp \
  Tesselation/BoundaryPointSet.hpp \
  Tesselation/BoundaryPolygonSet.hpp \
  Tesselation/BoundaryTriangleSet.hpp \
  Tesselation/CandidateForTesselation.hpp \
  Tesselation/ellipsoid.hpp \
  Tesselation/tesselation.hpp \
  Tesselation/tesselationhelpers.hpp \
  Tesselation/triangleintersectionlist.hpp

MOLECUILDERSOURCE = \
  ${BONDSOURCE} \
  ${DESCRIPTORSOURCE} \
  ${DYNAMICSSOURCE} \
  ${THERMOSTATSOURCE} \
  ${TESSELATIONSOURCE} \
  AtomIdSet.cpp \
  Box.cpp \
  Box_BoundaryConditions.cpp \
  config.cpp \
  Formula.cpp \
  MoleculeLeafClass.cpp \
  moleculelist.cpp \
  molecule.cpp \
  molecule_geometry.cpp \
  molecule_graph.cpp \
  UIElements/UIFactory.cpp \
  version.c \
  World.cpp \
  WorldTime.cpp

MOLECUILDERHEADER = \
  ${BONDHEADER} \
  ${DESCRIPTORHEADER} \
  ${DESCRIPTORIMPLHEADER} \
  ${DYNAMICSHEADER} \
  ${THERMOSTATHEADER} \
  ${TESSELATIONHEADER} \
  AtomIdSet.hpp \
  Box.hpp \
  Box_BoundaryConditions.hpp \
  config.hpp \
  Formula.hpp \
  IdPool.hpp \
  IdPool_impl.hpp \
  IdPool_policy.hpp \
  MoleculeLeafClass.hpp \
  MoleculeListClass.hpp \
  molecule.hpp \
  types.hpp \
  UIElements/UIFactory.hpp \
  version.h \
  World.hpp \
  World_calculations.hpp \
  WorldTime.hpp

noinst_LTLIBRARIES += libMolecuilder.la
libMolecuilder_la_includedir = $(includedir)/MoleCuilder/

nobase_libMolecuilder_la_include_HEADERS = ${MOLECUILDERHEADER}

## Define the source file list for the "libexample-@MOLECUILDER_API_VERSION@.la"
## target.  Note that @MOLECUILDER_API_VERSION@ is not interpreted by Automake and
## will therefore be treated as if it were literally part of the target name,
## and the variable name derived from that.
## The file extension .cc is recognized by Automake, and makes it produce
## rules which invoke the C++ compiler to produce a libtool object file (.lo)
## from each source file.  Note that it is not necessary to list header files
## which are already listed elsewhere in a _HEADERS variable assignment.
libMolecuilder_la_SOURCES = ${MOLECUILDERSOURCE}

## Instruct libtool to include ABI version information in the generated shared
## library file (.so).  The library ABI version is defined in configure.ac, so
## that all version information is kept in one place.
#libMolecuilder_la_LDFLAGS = -version-info $(MOLECUILDER_SO_VERSION)

## The generated configuration header is installed in its own subdirectory of
## $(libdir).  The reason for this is that the configuration information put
## into this header file describes the target platform the installed library
## has been built for.  Thus the file must not be installed into a location
## intended for architecture-independent files, as defined by the Filesystem
## Hierarchy Standard (FHS).
## The nodist_ prefix instructs Automake to not generate rules for including
## the listed files in the distribution on 'make dist'.  Files that are listed
## in _HEADERS variables are normally included in the distribution, but the
## configuration header file is generated at configure time and should not be
## shipped with the source tarball.
libMolecuilder_la_libincludedir = $(libdir)/MoleCuilder/include
nodist_libMolecuilder_la_libinclude_HEADERS = $(top_builddir)/libmolecuilder_config.h

## Install the generated pkg-config file (.pc) into the expected location for
## architecture-dependent package configuration information.  Occasionally,
## pkg-config files are also used for architecture-independent data packages,
## in which case the correct install location would be $(datadir)/pkgconfig.
pkgconfigdir = $(libdir)/pkgconfig
pkgconfig_DATA = $(top_builddir)/MoleCuilder.pc


INCLUDES = \
	-I$(top_srcdir)/src/unittests \
	-I$(top_srcdir)/src/Actions \
	-I$(top_srcdir)/src/UIElements \
	-I$(top_srcdir)/LinearAlgebra/src

libmenu_a_SOURCES = ${UISOURCE} ${UIHEADER} 
noinst_LIBRARIES = libmenu.a
bin_PROGRAMS += molecuilder joiner analyzer 
EXTRA_PROGRAMS = unity


extrastuffdir = $(datadir)/@PACKAGE@/data
databasedir = $(extrastuffdir)/databases
database_DATA = \
	${top_srcdir}/data/databases/*.db

bondtabledir = $(extrastuffdir)/bondtables
bondtable_DATA = \
	${top_srcdir}/data/bondtables/*.dat

moleculedir = $(extrastuffdir)/molecules
molecule_DATA = \
	${top_srcdir}/data/molecules/*.pdb

if CONDPYTHON
pyexec_LTLIBRARIES += pyMoleCuilder.la
pyMoleCuilder_la_SOURCES = \
	cleanUp.cpp \
	cleanUp.hpp \
	Actions/Action_impl_python.hpp \
	Actions/GlobalListOfActions.hpp \
	Actions/ActionHistory.hpp \
	Actions/pyMoleCuilder.cpp
pyMoleCuilder_la_CPPFLAGS = ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS} -I$(PYTHON_INCLUDE_DIR)
pyMoleCuilder_la_LDFLAGS = -module -avoid-version -shared $(BOOST_PYTHON_LDFLAGS) 
pyMoleCuilder_la_LIBADD = \
	libMolecuilderUI.la \
	$(BOOST_PYTHON_LIBS) \
	${CodePatterns_LIBS} \
	-l$(PYTHON_LIB)
endif


molecuilder_CPPFLAGS = $(AM_CPPFLAGS)
#molecuilder_CXXFLAGS += -DNO_CACHING
molecuilder_LDFLAGS = $(AM_LDFLAGS) $(BOOST_FILESYSTEM_LDFLAGS) $(BOOST_PROGRAM_OPTIONS_LDFLAGS) $(BOOST_RANDOM_LDFLAGS) $(BOOST_SYSTEM_LDFLAGS) $(BOOST_THREAD_LDFLAGS)
molecuilder_SOURCES = \
	builder.cpp \
	builder_init.cpp \
	builder_init.hpp \
	cleanUp.cpp \
	cleanUp.hpp
molecuilder_LDADD = \
	libMolecuilderUI.la \
	$(top_builddir)/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la \
	${CodePatterns_LIBS} \
	$(BOOST_THREAD_LIBS) \
	$(BOOST_PROGRAM_OPTIONS_LIBS) \
	$(BOOST_RANDOM_LIBS) \
	$(BOOST_SYSTEM_LIBS) \
	$(BOOST_FILESYSTEM_LIBS)

#Stuff for building the GUI using Qt
if CONDQTGUI
bin_PROGRAMS += molecuildergui
molecuildergui_SOURCES = \
	builder.cpp \
	builder_init.cpp \
	builder_init.hpp \
	cleanUp.cpp \
	cleanUp.hpp
molecuildergui_CXXFLAGS = $(AM_CPPFLAGS) -DUSE_GUI_QT
molecuildergui_LDFLAGS = $(AM_LDFLAGS) $(BOOST_FILESYSTEM_LDFLAGS) $(BOOST_PROGRAM_OPTIONS_LDFLAGS) $(BOOST_SYSTEM_LDFLAGS) $(BOOST_THREAD_LDFLAGS)
molecuildergui_LDADD = \
	libMolecuilderQtUI.la \
	libMolecuilderUI.la \
	$(top_builddir)/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la \
	${CodePatterns_LIBS} \
	$(BOOST_THREAD_LIBS) \
	$(BOOST_PROGRAM_OPTIONS_LIBS) \
	$(BOOST_RANDOM_LIBS) \
	$(BOOST_SYSTEM_LIBS) \
	$(BOOST_FILESYSTEM_LIBS) \
	$(GUI_LIBS)
endif

joiner_SOURCES = Fragmentation/joiner.cpp Fragmentation/datacreator.cpp Fragmentation/datacreator.hpp
joiner_CXXFLAGS = $(AM_CPPFLAGS) 
joiner_LDFLAGS = $(AM_LDFLAGS) $(BOOST_THREAD_LDFLAGS)
joiner_LDADD = \
	libMolecuilderFragmentation.la \
	libMolecuilderHelpers.la \
	libMolecuilderElement.la \
	$(top_builddir)/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la \
	${CodePatterns_LIBS} \
	$(BOOST_THREAD_LIBS)

analyzer_SOURCES = Fragmentation/analyzer.cpp Fragmentation/datacreator.cpp Fragmentation/datacreator.hpp
analyzer_CXXFLAGS = $(AM_CPPFLAGS) 
analyzer_LDFLAGS = $(AM_LDFLAGS) $(BOOST_THREAD_LDFLAGS)
analyzer_LDADD = \
	libMolecuilderFragmentation.la \
	libMolecuilderHelpers.la \
	libMolecuilderElement.la \
	$(top_builddir)/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la \
	${CodePatterns_LIBS} \
	$(BOOST_THREAD_LIBS)

if CONDJOBMARKET
CONTROLLERSOURCE = \
        controller_MPQCCommandJob.cpp \
        ControllerOptions_MPQCCommandJob.cpp

CONTROLLERHEADER = \
        controller_MPQCCommandJob.hpp \
        ControllerOptions_MPQCCommandJob.hpp


noinst_LTLIBRARIES += libFragmentationAutomationController.la
libFragmentationAutomationController_la_includedir = $(includedir)/MoleCuilder/JobMarket
nobase_libFragmentationAutomationController_la_include_HEADERS = $(CONTROLLERHEADER)
libFragmentationAutomationController_la_SOURCES = $(CONTROLLERSOURCE)
 libFragmentationAutomationController_la_CPPFLAGS = $(AM_CPPFLAGS) $(JobMarket_CFLAGS)
libFragmentationAutomationController_la_LIBADD = \
	${JobMarket_Controller_LIBS} \
	$(JobMarket_LIBS)

bin_PROGRAMS += Controller PoolWorker Server

Controller_SOURCES = controller.cpp controller_AddOn_MPQCCommandJob.cpp
Controller_LDFLAGS = $(AM_LDFLAGS) $(BOOST_PROGRAM_OPTIONS_LDFLAGS) ${CodePatterns_LDFLAGS}
Controller_CXXFLAGS = $(AM_CPPFLAGS) $(JobMarket_CFLAGS)
Controller_LDADD = \
	libFragmentationAutomationController.la \
	libMolecuilderJobs.la \
	libMolecuilderFragmentation.la \
	libMolecuilderHelpers.la \
	$(JobMarket_Controller_LIBS) \
	$(top_builddir)/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la \
	$(BOOST_PROGRAM_OPTIONS_LIBS) \
	${CodePatterns_LIBS}

PoolWorker_SOURCES = poolworker.cpp 
PoolWorker_LDFLAGS = $(AM_LDFLAGS) ${CodePatterns_LDFLAGS}
PoolWorker_CXXFLAGS = $(AM_CPPFLAGS) $(JobMarket_CFLAGS)
PoolWorker_LDADD = \
	libMolecuilderJobs.la \
	${JobMarket_PoolWorker_LIBS} \
	$(top_builddir)/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la \
	${CodePatterns_LIBS}

Server_SOURCES = Server.cpp 
Server_LDFLAGS = $(AM_LDFLAGS) ${CodePatterns_LDFLAGS}
Server_CXXFLAGS = $(AM_CPPFLAGS) $(JobMarket_CFLAGS)
Server_LDADD = \
	libMolecuilderJobs.la \
	${JobMarket_Server_LIBS} \
	$(top_builddir)/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la \
	${CodePatterns_LIBS}
endif

unity_SOURCES = unity.cpp
unity_CXXFLAGS = $(AM_CPPFLAGS) 
unity_LDFLAGS = $(AM_LDFLAGS) $(BOOST_FILESYSTEM_LDFLAGS) $(BOOST_PROGRAM_OPTIONS_LDFLAGS) $(BOOST_RANDOM_LDFLAGS) $(BOOST_SYSTEM_LDFLAGS) $(BOOST_THREAD_LDFLAGS)
unity_LDADD = \
	${CodePatterns_LIBS} \
	$(BOOST_THREAD_LIBS) \
	$(BOOST_PROGRAM_OPTIONS_LIBS) \
	$(BOOST_RANDOM_LIBS) \
	$(BOOST_SYSTEM_LIBS) \
	$(BOOST_FILESYSTEM_LIBS)


FORCE:
$(srcdir)/.git-version: FORCE
	@if (test -d $(top_srcdir)/.git && cd $(srcdir) \
	     && { git describe --dirty --always || git describe; } ) > .git-version-t 2>/dev/null \
	  && ! diff .git-version-t $(srcdir)/.git-version >/dev/null 2>&1; then \
	  mv -f .git-version-t $(srcdir)/.git-version; \
	else \
	  rm -f .git-version-t; \
	fi

EXTRA_DIST += \
	$(srcdir)/.git-version \
	$(bondtable_DATA) \
	$(database_DATA) \
	$(molecule_DATA)

$(srcdir)/version.c: $(srcdir)/.git-version
	echo "const char *MOLECUILDERVERSION = \"$(PACKAGE_NAME) version "`cat $(srcdir)/.git-version`"\";" > $@


unity.cpp: ${MOLECUILDERSOURCE} ${MOLECUILDERHEADER}
	list='$(MOLECUILDERSOURCE)'; for file in $$list; do \
  	echo "#include \"$(srcdir)/$$file\"" >> unity.cpp; \
	done; \
	subdirs='$(SUBDIRS)';for directory in $$subdirs; do\
		olddir=$$PWD;\
		cd $$directory && make unity.cpp;\
		cd $$olddir;\
		echo "#include \"$$directory/unity.cpp\"" >> unity.cpp;\
	done;\
	echo "#include \"$(srcdir)/builder.cpp\"" >> unity.cpp;
	echo "#include \"$(srcdir)/version.c\"" >> unity.cpp;

MOSTLYCLEANFILES += unity.cpp