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Makefile.am
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## Process this file with automake to produce Makefile.in
# $Id: Makefile.am,v 1.53 2020/05/21 15:31:46 mp Exp $
#
# AutoDock
#
# Copyright (C) 1989-2007, Garrett M. Morris, TSRI
# All Rights Reserved.
#
# AutoDock is a Trade Mark of The Scripps Research Institute.
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 2
# of the License, or (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
#
# Makefile.am to build AutoDock 4
#
# Autotools
EXTRA_DIST = AD4_PARM99.dat AD4_parameters.dat AD4.1_bound.dat AD4.1_extended.dat AD4.1_compact.dat paramdat2h.csh Tests
dist-hook:
rm -rf `find $(distdir)/Tests -name CVS -o -name '*.dlg'`
if WANT_OMP
bin_PROGRAMS = autodock4 autodock4.omp
else
bin_PROGRAMS = autodock4
endif
CLEANFILES = default_parameters.h
noinst_LIBRARIES =
# Define the AutoDock 4 source code files:
autodock4_SOURCES = \
main.cc
autodock4_SOURCES += \
alea.cc \
analysis.cc \
atom_parameter_manager.cc \
banner.cc \
bestpdb.cc \
calculateEnergies.cc \
call_glss.cc \
call_ls.cc \
center_ligand.cc \
changeState.cc \
check_header_float.cc \
check_header_int.cc \
check_header_line.cc \
cluster_analysis.cc \
clmode.cc \
cnv_state_to_coords.cc \
com.cc \
conformation_sampler.cc \
dimLibrary.cc\
distdepdiel.cc \
stateLibrary.cc \
readfield.cc \
readmap.cc \
readPDBQT.cc \
read_parameter_library.cc \
eval.cc \
gencau.cc \
getrms.cc \
get_atom_type.cc \
getInitialState.cc \
getpdbcrds.cc \
gs.cc \
initautodock.cc \
input_state.cc \
investigate.cc \
linpack.cc \
ls.cc \
mapping.cc \
mingw_getrusage.cc \
minmeanmax.cc \
mkNewState.cc \
mkTorTree.cc \
mkRandomState.cc \
nonbonds.cc \
openfile.cc \
output_state.cc \
parse_dpf_line.cc \
parse_param_line.cc \
parse_PDBQT_line.cc \
parse_trj_line.cc \
parsetypes.cc \
print_2x.cc \
print_atomic_energies.cc \
print_avsfld.cc \
writePDBQT.cc \
print_rem.cc \
printdate.cc \
printEnergies.cc \
printhms.cc \
prClusterHist.cc \
prInitialState.cc \
prTorConList.cc \
pso.cc \
qmultiply.cc \
qtransform.cc \
quicksort.cc \
ranlib.cc \
rep.cc \
scauchy.cc \
setflags.cc \
simanneal.cc \
sort_enrg.cc \
stack.cc \
stop.cc \
strindex.cc \
success.cc \
support.cc \
swap.cc \
targetfile.cc \
threadlog.cc \
timesys.cc \
timesyshms.cc \
torNorVec.cc \
torsion.cc \
trilinterp.cc \
usage.cc \
weedbonds.cc \
warn_bad_file.cc \
coliny.cc \
eintcal.cc \
eintcalPrint.cc \
intnbtable.cc \
nbe.cc \
PDBQT_tokens.h \
analysis.h \
atom_parameter_manager.h \
alea.h \
autocomm.h \
autoglobal.h \
banner.h \
bestpdb.h \
calculateEnergies.h \
call_glss.h \
call_ls.h \
center_ligand.h \
changeState.h \
check_header_float.h \
check_header_int.h \
check_header_line.h \
clmode.h \
cluster_analysis.h \
cnv_state_to_coords.h \
coliny.h \
conformation_sampler.h \
constants.h \
default_parameters.h \
dimLibrary.h \
distdepdiel.h \
dpftoken.h \
eintcal.h \
eintcalPrint.h \
energy.h \
eval.h \
gencau.h \
getInitialState.h \
get_atom_type.h \
getpdbcrds.h \
getrms.h \
globals.h \
grid.h \
gs.h \
hybrids.h \
initautodock.h \
input_state.h \
intnbtable.h \
investigate.h \
ls.h \
main.h \
mdist.h \
mingw_sysconf.h \
mingw_sys_times.h \
mkNewState.h \
mkRandomState.h \
mkTorTree.h \
nbe.h \
nonbonds.h \
openfile.h \
output_state.h \
parameters.h \
parse_PDBQT_line.h \
parse_dpf_line.h \
parse_param_line.h \
parse_trj_line.h \
parsetypes.h \
partokens.h \
prClusterHist.h \
prInitialState.h \
prTorConList.h \
printEnergies.h \
print_2x.h \
print_atomic_energies.h \
print_avsfld.h \
print_rem.h \
printdate.h \
printhms.h \
pso.h \
qmultiply.h \
qtransform.h \
quicksort.h \
ranlib.h \
readPDBQT.h \
read_parameter_library.h \
readfield.h \
readmap.h \
rep.h \
rep_constants.h \
setflags.h \
simanneal.h \
sort_enrg.h \
stateLibrary.h \
stack.h \
stop.h \
strindex.h \
structs.h \
success.h \
support.h \
swap.h \
targetfile.h \
threadlog.h \
timesys.h \
timesyshms.h \
torNorVec.h \
torsion.h \
trilinterp.h \
trjtokens.h \
typedefs.h \
usage.h \
version.h \
warn_bad_file.h \
weedbonds.h \
writePDBQT.h
if WANT_OMP
autodock4_omp_SOURCES = \
main.cc
autodock4_omp_SOURCES += \
alea.cc \
analysis.cc \
atom_parameter_manager.cc \
banner.cc \
bestpdb.cc \
calculateEnergies.cc \
call_glss.cc \
call_ls.cc \
center_ligand.cc \
changeState.cc \
check_header_float.cc \
check_header_int.cc \
check_header_line.cc \
cluster_analysis.cc \
clmode.cc \
cnv_state_to_coords.cc \
com.cc \
conformation_sampler.cc \
dimLibrary.cc\
distdepdiel.cc \
stateLibrary.cc \
readfield.cc \
readmap.cc \
readPDBQT.cc \
read_parameter_library.cc \
eval.cc \
gencau.cc \
getrms.cc \
get_atom_type.cc \
getInitialState.cc \
getpdbcrds.cc \
gs.cc \
initautodock.cc \
input_state.cc \
investigate.cc \
linpack.cc \
ls.cc \
mapping.cc \
mingw_getrusage.cc \
minmeanmax.cc \
mkNewState.cc \
mkTorTree.cc \
mkRandomState.cc \
nonbonds.cc \
openfile.cc \
output_state.cc \
parse_dpf_line.cc \
parse_param_line.cc \
parse_PDBQT_line.cc \
parse_trj_line.cc \
parsetypes.cc \
print_2x.cc \
print_atomic_energies.cc \
print_avsfld.cc \
writePDBQT.cc \
print_rem.cc \
printdate.cc \
printEnergies.cc \
printhms.cc \
prClusterHist.cc \
prInitialState.cc \
prTorConList.cc \
pso.cc \
qmultiply.cc \
qtransform.cc \
quicksort.cc \
ranlib.cc \
rep.cc \
scauchy.cc \
setflags.cc \
simanneal.cc \
sort_enrg.cc \
stack.cc \
stop.cc \
strindex.cc \
success.cc \
support.cc \
swap.cc \
targetfile.cc \
threadlog.cc \
timesys.cc \
timesyshms.cc \
torNorVec.cc \
torsion.cc \
trilinterp.cc \
usage.cc \
weedbonds.cc \
warn_bad_file.cc \
coliny.cc \
eintcal.cc \
eintcalPrint.cc \
intnbtable.cc \
nbe.cc \
PDBQT_tokens.h \
analysis.h \
atom_parameter_manager.h \
alea.h \
autocomm.h \
autoglobal.h \
banner.h \
bestpdb.h \
calculateEnergies.h \
call_glss.h \
call_ls.h \
center_ligand.h \
changeState.h \
check_header_float.h \
check_header_int.h \
check_header_line.h \
clmode.h \
cluster_analysis.h \
cnv_state_to_coords.h \
coliny.h \
conformation_sampler.h \
constants.h \
default_parameters.h \
dimLibrary.h \
distdepdiel.h \
dpftoken.h \
eintcal.h \
eintcalPrint.h \
energy.h \
eval.h \
gencau.h \
getInitialState.h \
get_atom_type.h \
getpdbcrds.h \
getrms.h \
globals.h \
grid.h \
gs.h \
hybrids.h \
initautodock.h \
input_state.h \
intnbtable.h \
investigate.h \
ls.h \
main.h \
mdist.h \
mingw_sysconf.h \
mingw_sys_times.h \
mkNewState.h \
mkRandomState.h \
mkTorTree.h \
nbe.h \
nonbonds.h \
openfile.h \
output_state.h \
parameters.h \
parse_PDBQT_line.h \
parse_dpf_line.h \
parse_param_line.h \
parse_trj_line.h \
parsetypes.h \
partokens.h \
prClusterHist.h \
prInitialState.h \
prTorConList.h \
printEnergies.h \
print_2x.h \
print_atomic_energies.h \
print_avsfld.h \
print_rem.h \
printdate.h \
printhms.h \
pso.h \
qmultiply.h \
qtransform.h \
quicksort.h \
ranlib.h \
readPDBQT.h \
read_parameter_library.h \
readfield.h \
readmap.h \
rep.h \
rep_constants.h \
setflags.h \
simanneal.h \
sort_enrg.h \
stateLibrary.h \
stack.h \
stop.h \
strindex.h \
structs.h \
success.h \
support.h \
swap.h \
targetfile.h \
threadlog.h \
timesys.h \
timesyshms.h \
torNorVec.h \
torsion.h \
trilinterp.h \
trjtokens.h \
typedefs.h \
usage.h \
version.h \
warn_bad_file.h \
weedbonds.h \
writePDBQT.h
endif
BUILT_SOURCES = $(autodock4_SOURCES) default_parameters.h
AM_CXXFLAGS = -O3 # Agressive optimization
#AM_CXXFLAGS = -g # debug
# if gnu c++ compiler
AM_CXXFLAGS += -Wall # All warnings
AM_CXXFLAGS += -Wno-write-strings # increase compatibility with pre 4.x compilers for string handling
AM_LDFLAGS =
# M Pique May 2020 support for libzip, see targetfile.cc
if WANT_LIBZIP
AM_CXXFLAGS += -DHAVE_ZIP_H
AM_LDFLAGS += -lzip
endif
if WANT_OMP
# M Pique - I'm not sure which of these are really necessary
# could this be replaced by : AC_SUBST(AM_CXXFLAGS,"$OPENMP_CXXFLAGS")
autodock4_omp_CFLAGS = $(AM_CFLAGS) -fopenmp $(OPENMP_CXXFLAGS)
autodock4_omp_CPPFLAGS = $(AM_CPPFLAGS) $(OPENMP_CXXFLAGS)
autodock4_omp_LDFLAGS = $(AM_LDFLAGS) -fopenmp $(OPENMP_CXXFLAGS)
autodock4_omp_CXXFLAGS = $(AM_CXXFLAGS) $(autodock4_CXXFLAGS) -fopenmp $(OPENMP_CXXFLAGS)
autodock4_omp_LDADD = $(autodock4_LDADD)
endif
# M Pique - add ASSERTQUATOK if you want error checking in qmultiply.cc
# M Pique - add USE_DOUBLE to define Real as double instead of float, see typedefs.h
# M Pique - USE_INT_AS_FOURBYTELONG is for random number seeds only and is appropriate for
# all post-2005 computers, which treat "int" as four bytes.
# M Pique - add -g for debugging
# M Pique - add -O3 for optimization
AM_CPPFLAGS = \
-DUSE_DOUBLE \
-DUSE_INT_AS_FOURBYTELONG \
-O3
# -DUSE_8A_NBCUTOFF
# AM_LDFLAGS = -g # -g is MP debug
#autodock4_CXXFLAGS = -Wall -O3 # All warnings, Agressive optimization
#autodock4_CXXFLAGS = -Wall -O3 -ftree-vectorize # All warnings, Agressive optimization + GCC vectorization # MacOSX only?
autodock4_CPPFLAGS = $(AM_CPPFLAGS)
autodock4_LDFLAGS = $(AM_LDFLAGS)
autodock4_LDADD = $(COLINY_LDFLAGS) -lm
if WANT_BIGSTACK
autodock4_LDFLAGS += -Wl,--stack,8388608 # Cygwin, big stacksize
endif
#
# If you need to use debugging or profiling, these should also be
# modified appropriately:
# DBUG & PROF
#
# If you want to use the Coliny solver library, uncomment the following:
# COLINY = yes
#
# Abbreviations:
#
# Alpha = Compaq/Digital Equipment Corp., Alpha
# Convex = Convex, c2
# Cygwin = Cygwin running on Microsoft Windows
# Darwin = Darwin
# HP = Hewlett Packard Precision Architecture, hppa
# Linux = Any platform that runs GNU/Linux, Linux
# MacOSX = Apple Mac OS X 10.0 & higher, MacOSX
# SGI = Silicon Graphics Inc., sgi4D
# Sun = Sun Microsystems, sun4
# CFLAGS = $(CSTD) $(OPT) -DUSE_8A_NBCUTOFF # SGI, HP, Alpha, Sun, Convex, Cygwin, Linux, MacOSX: Standard accuracy, but faster; no crossover in quaternion
# CFLAGS = $(CSTD) $(OPT) -DUSE_8A_NBCUTOFF # SGI, HP, Alpha, Sun, Convex, Linux, MacOSX: Standard accuracy, but faster
# CFLAGS = $(CSTD) $(OPT) -DUSE_8A_NBCUTOFF -DUSE_DOUBLE # SGI, HP, Alpha, Sun, Convex, Linux, MacOSX: Standard accuracy, but faster; also use Double precision throughout
# CFLAGS = $(CSTD) $(OPT) # SGI, HP, Alpha, Sun, Convex, Cygwin, Linux, MacOSX
# CSTD = $(DBUG) $(PROF) $(WARN) # SGI, Sun, Linux, MacOSX
# CSTD = $(DBUG) $(PROF) $(WARN) -DUSE_XCODE # Smaller memory footprint, good for Xcode
# CSTD = $(DBUG) $(PROF) $(WARN) # SGI, Sun, Linux, MacOSX
# CSTD = -std arm -verbose $(PROF) $(DBUG) $(WARN) # Alpha. sarah
# OPTLEVEL = -O3 -ftree-vectorize # Agressive optimization + GCC vectorization
# OPTLEVEL = -O3 -ffast-math # Agressive optimization, for Intel Itanium, ia64Linux2
# OPTLEVEL = -O3 # Agressive optimization
# OPTLEVEL = -O2 # High optimization
# OPTLEVEL = -O1 # Do optimizations that can be done quickly; default. Recommended for unit testing
# OPTLEVEL = -O0 # Do not optimize
# LINKOPT = $(CSTD) $(OPT) # All platforms except Cygwin and Sun
# LINKOPT = $(CSTD) $(OPT) -fno-stack-limit # Cygwin, 32MB stacksize
# LINKOPT = $(CSTD) $(OPT) -Wl,--stack=0x4000000 # Cygwin, 64MB stacksize
# LINKOPT = $(CSTD) $(OPT) -L/opt/sfw/lib # Sun
# LINK = $(LINKOPT) # Linking flags
# LIB = -lm # for all platforms
# DBUG = # Use assert code
# DBUG = -DNDEBUG # No debugging and no assert code
# DBUG = -g # dbx, or Gnu gdb
# DBUG = -g -DDEBUG # dbx + DEBUG-specific code
# DBUG = -g3 # dbx + optimization
# DBUG = -g3 -DDEBUG # dbx + optimization, + DEBUG-specific code
# DBUG = -DDEBUG # Just DEBUG-specific code
# DBUG = -DDEBUG2 # Just DEBUG2-specific code for tracking prop.selection
# DBUG = -DDEBUG3 # Just DEBUG3-specific code for print age of individuals
# DBUG = -g -DDEBUG -DDEBUG2 -DDEBUG3 # Debug everything
# DBUG = -g3 -DDEBUG_QUAT # Use assert code, & assert quaternions are 4D-normalised
# DBUG = -g3 -DDEBUG_QUAT -DDEBUG_QUAT_PRINT # Use assert code, & assert quaternions are 4D-normalised, and print out
# DBUG = -g3 -DDEBUG_QUAT -DDEBUG_QUAT_PRINT -DDEBUG # Use assert code, & assert quaternions are 4D-normalised, and use DEBUG-specific code, and print out
# DBUG = -g3 -DDEBUG_MUTATION # dbx + optimization; Use assert code, & print out information anywhere involving mutation
# DBUG = -g3 -DDEBUG_MUTATION -DDEBUG # dbx + optimization; Use assert code, & print out information anywhere involving mutation + all debug statements
# DBUG = -g3 -DDEBUG_MUTATION -DDEBUG -DDEBUG3 # dbx + optimization; Use assert code, & print out information anywhere involving mutation + all debug statements incl. 3
# DBUG = -DASSERTQUATOK # Uses the macro "assertQuatOK()" to ensure the quaternion magnitude is near unity
# PROF = # No profiling
# PROF = -p # CC Profiling
# PROF = -pg # For GNU gcc & GNU g++ Profiling with GNU gprof
# WARN = # Default warning level
# WARN = -woff all # For no warnings
# WARN = -Wall # All warnings, gcc -- Recommended for developers
# WARN = -fullwarn -ansiE -ansiW # For full warnings during compilation
### ifeq ($(COLINY),yes)
### COLINYLIB = libcoliny.a # Using Coliny
### else
#COLINY_LDADD = # Not using Coliny
### endif
#
# Makefile targets
#
autodock4.html :
@echo " "
@echo "Creating a colour-coded HTML report of the AutoDock source code"
@echo " "
enscript -E --color -Whtml --toc -p$@ *.h *.cc
check : test
if WANT_OMP
test : autodock4 autodock4.omp $(srcdir)/Tests/test_autodock4.py
else
test : autodock4 $(srcdir)/Tests/test_autodock4.py
endif
#if HAVE_PYTHON
@echo " "
@echo "Running the Python test_autodock4.py unit-tests on autodock4"
@echo " "
# for technical reasons, autodock must be run in the directory where the
# test files reside because it writes its logs into its current directory
# and expects to find AD4.1_bound.dat in that same directory.
# We create a run-time Testruns directory for this purpose.
# The name is different from Tests to allow "configure;make;make check" in the source dir.
outputdir=`pwd` ;\
umask 0 ;\
test -d $$outputdir/Testruns && chmod -fR a+w $$outputdir/Testruns;\
test -d $$outputdir/Testruns || mkdir $$outputdir/Testruns ;\
cp $(srcdir)/AD4.1_bound.dat $$outputdir/Testruns;\
cp $(srcdir)/AD4_parameters.dat $$outputdir/Testruns;\
cp $(srcdir)/Tests/*.py $$outputdir/Testruns;\
cp $(srcdir)/Tests/*.dpf $$outputdir/Testruns;\
cp $(srcdir)/Tests/*.pdbqt $$outputdir/Testruns;\
cp $(srcdir)/Tests/*.map* $$outputdir/Testruns;\
ln -f $(srcdir)/Tests/*.trg $$outputdir/Testruns;\
chmod -fR a+w $$outputdir/Testruns;
-cd Testruns; rm -f test_*.dlg ; \
python ./test_autodock4.py -d . -e ../autodock4$(EXEEXT) -o . ;
if WANT_OMP
@echo " "
@echo "Running the Python test_autodock4.py unit-tests on autodock4.omp"
@echo " "
-cd Testruns; rm -f test_*.dlg ; \
python ./test_autodock4.py -d . -e ../autodock4.omp$(EXEEXT) -o . ;
endif
#else
# @echo " "
# @echo "Python version 2.1 or higher needed for 'make check', but not found."
# @echo "Skipping AutoDock4 unit tests."
# @echo " "
#endif
#$(COLINYLIB) : $(OBJS) $(OBJNOSQRT) $(OBJNOMINPT)
# @echo " "
# @echo Making the Coliny library
# @echo " "
# $(AR) $(ARFLAGS) $(COLINYLIB) $(?:.cc=.o)
# $(RANLIB) $(RANLIBFLAGS) $(COLINYLIB)
###
### alternative from another CVS user
###
# coliny: $(ACRO)
### acro:
### @echo " "
### @echo Making the Coliny library
### @echo " "
### @(cd ../acro;\
### if [ ! -e Makefile ]; then\
### ./setup configure;\
### fi;\
### $(MAKE))
#
# Object dependencies:
#
gs.o : gs.cc gs.h ranlib.h eval.h rep.h support.h writePDBQT.h
$(CXXCOMPILE) -DCHECK_ISNAN -c $(srcdir)/gs.cc
# 2007-04-30 MP & GMM: this line is necessary to be able to compile read_parameter_library.o
read_parameter_library.o : default_parameters.h
default_parameters.h : AD4_parameters.dat AD4.1_bound.dat paramdat2h.csh
rm -f $@
csh $(srcdir)/paramdat2h.csh $(srcdir)/AD4_parameters.dat $(srcdir)/AD4.1_bound.dat > $@
#coliny.o : coliny.h
# $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(ACRO_INCLUDES) -c coliny.cc -o coliny.o
# see Autoconf manual 4.7.3 (p. 25) support for VPATH
# enabling multi-platform builds
srcdir = @srcdir@
VPATH = @srcdir@
# see Autoconf manual for how to extend 'make clean' to directories:
clean-local: clean-local-check
.PHONY: clean-local-check
clean-local-check:
-rm -rf Testruns
#
# EOF
#