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Makefile.pre-autoconf
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# $Id: Makefile.pre-autoconf,v 1.7 2008/06/27 04:11:46 garrett Exp $
#
# AutoDock
#
# Copyright (C) 1989-2007, Garrett M. Morris
# 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 to build AutoDock 4
#
# NOTE: Must be run in the $(AUTODOCK_DEV) directory
#
# Copyright (C) 1994-2006, Garrett Matthew Morris, TSRI
#
#
# Edit this Makefile to reflect your machine architecture and OS
#
# Specifically, change these variables:
# LIB, CSTD, CFLAGS, OPT, LINT, LINTFLAGS, LINK, WARN, & CC
#
# 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
# Define the destination directory for the executables:
EXE = . # Change this to the directory path holding binaries for your platform
# Define the object files:
OBJS = \
analysis.o \
atom_parameter_manager.o \
banner.o \
bestpdb.o \
calculateEnergies.o \
call_glss.o \
call_gs.o \
call_ls.o \
changeState.o \
check_header_float.o \
check_header_int.o \
check_header_line.o \
cluster_analysis.o \
clmode.o \
cmdmode.o \
cnv_state_to_coords.o \
com.o \
conformation_sampler.o \
distdepdiel.o \
stateLibrary.o \
readfield.o \
readmap.o \
readPDBQT.o \
read_parameter_library.o \
eval.o \
gencau.o \
getrms.o \
get_atom_type.o \
getInitialState.o \
getpdbcrds.o \
gs.o \
initautodock.o \
input_state.o \
investigate.o \
linpack.o \
ls.o \
mapping.o \
minmeanmax.o \
mkNewState.o \
mkTorTree.o \
mkRandomState.o \
nonbonds.o \
openfile.o \
output_state.o \
parse_com_line.o \
parse_dpf_line.o \
parse_param_line.o \
parse_PDBQT_line.o \
parse_trj_line.o \
parsetypes.o \
print_2x.o \
print_atomic_energies.o \
print_avsfld.o \
writePDBQT.o \
print_rem.o \
printdate.o \
printEnergies.o \
printhms.o \
prClusterHist.o \
prInitialState.o \
prTorConList.o \
qmultiply.o \
qtransform.o \
quicksort.o \
ranlib.o \
rep.o \
scauchy.o \
set_cmd_io_std.o \
setflags.o \
simanneal.o \
sort_enrg.o \
stack.o \
stop.o \
strindex.o \
success.o \
summarizegrids.o \
support.o \
swap.o \
timesys.o \
timesyshms.o \
torNorVec.o \
torsion.o \
usage.o \
weedbonds.o \
warn_bad_file.o \
coliny.o
OBJS_LSFIT = \
analysis.o \
atom_parameter_manager.o \
banner.o \
bestpdb.o \
calculateEnergies.o \
call_glss.o \
call_gs.o \
call_ls.o \
changeState.o \
check_header_float.o \
check_header_int.o \
check_header_line.o \
cluster_analysis.o \
clmode.o \
cmdmode.o \
com.o \
conformation_sampler.o \
distdepdiel.o \
stateLibrary.o \
readfield.o \
readmap.o \
readPDBQT.o \
read_parameter_library.o \
eval.o \
gencau.o \
getrms.o \
get_atom_type.o \
getInitialState.o \
getpdbcrds.o \
gs.o \
initautodock.o \
input_state.o \
investigate.o \
linpack.o \
ls.o \
mapping.o \
minmeanmax.o \
mkNewState.o \
mkTorTree.o \
mkRandomState.o \
nonbonds.o \
openfile.o \
output_state.o \
parse_com_line.o \
parse_dpf_line.o \
parse_param_line.o \
parse_PDBQT_line.o \
parse_trj_line.o \
parsetypes.o \
print_2x.o \
print_atomic_energies.o \
print_avsfld.o \
writePDBQT.o \
print_rem.o \
printdate.o \
printEnergies.o \
printhms.o \
prClusterHist.o \
prInitialState.o \
prTorConList.o \
qmultiply.o \
qtransform.o \
quicksort.o \
ranlib.o \
rep.o \
scauchy.o \
set_cmd_io_std.o \
setflags.o \
simanneal.o \
sort_enrg.o \
stack.o \
stop.o \
strindex.o \
success.o \
summarizegrids.o \
support.o \
swap.o \
timesys.o \
timesyshms.o \
torNorVec.o \
torsion.o \
usage.o \
weedbonds.o \
warn_bad_file.o \
coliny.o
OBJNOSQRT = \
eintcal.o \
eintcalPrint.o \
intnbtable.o \
nbe.o
OBJSQRT = \
eintcal.sqrt.o \
eintcalPrint.sqrt.o \
intnbtable.sqrt.o \
nbe.sqrt.o
OBJNOMINPT = \
trilinterp.o
OBJMINPT = \
trilinterp.MINPT.o
# Define lint files:
LNS = \
analysis.ln \
atom_parameter_manager.ln \
banner.ln \
bestpdb.ln \
changeState.ln \
check_header_float.ln \
check_header_int.ln \
check_header_line.ln \
cluster_analysis.ln \
clmode.ln \
cmdmode.ln \
conformation_sampler.ln \
cnv_state_to_coords.ln \
stateLibrary.ln \
readfield.ln \
readmap.ln \
readPDBQT.ln \
read_parameter_library.ln \
getrms.ln \
get_atom_type.ln \
getInitialState.ln \
getpdbcrds.ln \
initautodock.ln \
input_state.ln \
investigate.ln \
main.ln \
mkNewState.ln \
mkTorTree.ln \
mkRandomState.o \
nonbonds.ln \
openfile.ln \
output_state.ln \
parse_com_line.ln \
parse_dpf_line.ln \
parse_param_line.ln \
parse_PDBQT_line.ln \
parse_trj_line.ln \
parsetypes.ln \
print_2x.ln \
print_atomic_energies.ln \
print_avsfld.ln \
writePDBQT.ln \
print_rem.ln \
printdate.ln \
printEnergies.ln \
printhms.ln \
prClusterHist.ln \
prInitialState.ln \
prTorConList.ln \
qmultiply.ln \
qtransform.ln \
quicksort.ln \
set_cmd_io_std.ln \
setflags.ln \
simanneal.ln \
sort_enrg.ln \
stack.ln \
stop.ln \
strindex.ln \
success.ln \
summarizegrids.ln \
swap.ln \
timesys.ln \
timesyshms.ln \
torNorVec.ln \
torsion.ln \
trilinterp.ln \
usage.ln \
weedbonds.ln \
warn_bad_file.ln
LNSNOSQRT = \
eintcal.ln \
eintcalPrint.ln \
intnbtable.ln \
nbe.ln
LNSSQRT = \
eintcal.sqrt.ln \
eintcalPrint.sqrt.ln \
intnbtable.sqrt.ln \
nbe.sqrt.ln
# Libraries
ADLIB = libad.a
ARFLAGS = r # SGI, Sun, Alpha, Linux, Darwin, MacOSX
# RANLIB = file # SGI
RANLIB = ranlib # Linux, Darwin, MacOSX
RANLIBFLAGS = # Linux, SGI, MacOSX
# C++ compiler
CC = g++ # HP, Gnu, Cygwin, Linux, Darwin, MacOSX
# CC = g++-4.0 -arch i386 # MacOSX -- Cross-compiling for Intel on PowerPC
# CC = g++-3.3 -arch ppc # MacOSX -- Cross-compiling for PowerPC on Intel
# CC = CC # SGI
# CC = cxx # Alpha
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 = $(DBUG) $(PROF) $(WARN) -I/opt/sfw/include # Sun Soliaris 8
# CSTD = $(DBUG) $(PROF) $(WARN) -std # Convex
# CSTD = -std -verbose $(PROF) $(DBUG) $(WARN) # Alpha. Not sarah
# CSTD = -std arm -verbose $(PROF) $(DBUG) $(WARN) # Alpha. sarah
# CSTD = -DHPPA -D_HPUX_SOURCE -ansi $(PROF) $(DBUG) $(WARN) # HP
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 -DQUATERNION_MUTATION # As above, but treat quaternion genes properly when doing mutations--note, this is slow!
# 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
# OPTLEVEL = -O3 -ftree-vectorize # Agressive optimization + GCC vectorization
OPTLEVEL = -O3 # Agressive optimization
# OPTLEVEL = -O3 -ffast-math # Agressive optimization, for Intel Itanium, ia64Linux2
# OPTLEVEL = -fast # Agressive optimization for the G5 on MacOSX
# OPTLEVEL = -O2 # High optimization
# OPTLEVEL = -O1 # Do optimizations that can be done quickly; default. Recommended for unit testing
# OPTLEVEL = -O0 # Do not optimize
OPT_SGI_IPNUM = # Alpha, HP, Sun, Convex, SGI, Cygwin, Linux, MacOSX
# OPT_SGI_IPNUM = -Ofast=ip19 # SGI, 'uname -a' says 'IP19'
# OPT_SGI_IPNUM = -Ofast=ip21 # SGI, 'uname -a' says 'IP21'
# OPT_SGI_IPNUM = -Ofast=ip25 # SGI, 'uname -a' says 'IP25' PowerChallenge is R10000, IP25
# OPT_SGI_IPNUM = -Ofast=ip27 # SGI, 'uname -a' says 'IP27'
# OPT_SGI_IPNUM = -Ofast=ip30 # SGI, 'uname -a' says 'IP30'
# OPT_SGI_IPNUM = `uname -m | sed 's/IP/-Ofast=ip/'` # SGI, dynamic
OPT_SGI_R000 = # Alpha, HP, Sun, Convex, SGI, Cygwin, Linux, MacOSX
# OPT_SGI_R000 = -r4000 -mips2 # SGI, 'hinv' says MIPS Processor is R4000
# OPT_SGI_R000 = -r8000 -mips4 # SGI, 'hinv' says MIPS Processor is R8000
# OPT_SGI_R000 = -r10000 -mips4 # SGI, 'hinv' says MIPS Processor is R10000
# OPT_SGI_R000 = -r12000 -mips4 # SGI, 'hinv' says MIPS Processor is R12000
# OPT_SGI_R000 = -r14000 -mips4 # SGI, 'hinv' says MIPS Processor is R14000
# OPT_SGI_R000 = `hinv | grep '^CPU:' | awk '{print $3}' | sed 's/R/-r/'` -mips4 # SGI, dynamic, -mips4 (works with -r8000 to -r14000, not -r4000)
OPT = $(OPTLEVEL) # Alpha, HP, Sun, Convex, Cygwin, Linux, MacOSX
# OPT = $(OPTLEVEL) -ffast-math # Gnu cc, fast-math is dangerous!
# OPT = $(OPTLEVEL) -n32 $(OPT_SGI_IPNUM) $(OPT_SGI_R000) -IPA $(LNO_OPT) # SGI
# OPT = $(OPTLEVEL) -n32 $(OPT_SGI_IPNUM) $(OPT_SGI_R000) -IPA $(LNO_OPT) -DUSE_INT_AS_LONG # SGI (long is 8bytes)
# OPT = $(OPTLEVEL) $(OPT_SGI_IPNUM) $(OPT_SGI_R000) $(LNO_OPT) # SGI, not new 32-bit
LNO_OPT = # SGI, no special optimization at link time; Sun, Cygwin, Linux, MacOSX
# LNO_OPT = -LNO:auto_dist=ON:gather_scatter=2 # SGI
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
# LINK = $(LINKOPT) -cord # Procedure rearranger on SGI
LIB = -lm # for all platforms
# LIB = -lSaturn # for profiling using MacOSX Saturn
LINT = lint # lint C code checking
LINTFLAGS = $(LIB) -c # SGI, Linux, MacOSX
# LINTFLAGS = $(LIB) -MA -c # Alpha
# LINTFLAGS = -DHPPA -D_HPUX_SOURCE $(LIB) -c # HP
# LINTFLAGS = -u -n -lm # Sun
DBUG = # Use assert code
# DBUG = -DNDEBUG # No debugging and no assert code
# DBUG = -g # dbx, or Gnu gdb
# DBUG = -g -DDEBUG # dbx + DEBUG-specific code
# DBUG = -g3 # dbx + optimization
# DBUG = -g3 -DDEBUG # dbx + optimization, + DEBUG-specific code
# DBUG = -DDEBUG # Just DEBUG-specific code
# DBUG = -DDEBUG2 # Just DEBUG2-specific code for tracking prop.selection
# DBUG = -DDEBUG3 # Just DEBUG3-specific code for print age of individuals
# DBUG = -g -DDEBUG -DDEBUG2 -DDEBUG3 # Debug everything
# DBUG = -DDEBUG_MUTATION # Use assert code, & print out information anywhere involving mutation
# DBUG = -g3 -DDEBUG_QUAT # Use assert code, & assert quaternions are 4D-normalised
# DBUG = -g3 -DDEBUG_QUAT -DDEBUG_QUAT_PRINT # Use assert code, & assert quaternions are 4D-normalised, and print out
# DBUG = -g3 -DDEBUG_QUAT -DDEBUG_QUAT_PRINT -DDEBUG # Use assert code, & assert quaternions are 4D-normalised, and use DEBUG-specific code, and print out
# DBUG = -g3 -DDEBUG_MUTATION # dbx + optimization; Use assert code, & print out information anywhere involving mutation
# DBUG = -g3 -DDEBUG_MUTATION -DDEBUG # dbx + optimization; Use assert code, & print out information anywhere involving mutation + all debug statements
# DBUG = -g3 -DDEBUG_MUTATION -DDEBUG -DDEBUG3 # dbx + optimization; Use assert code, & print out information anywhere involving mutation + all debug statements incl. 3
# DBUG = -DASSERTQUATOK # Uses the macro "assertQuatOK()" to ensure the magnitude is near unity
PROF = # No profiling
# PROF = -p # CC Profiling
# PROF = -pg # For GNU gcc & GNU g++ Profiling with GNU gprof
# WARN = # Default warning level
# WARN = -woff all # For no warnings
WARN = -Wall # All warnings, gcc -- Recommended for developers
# WARN = -fullwarn -ansiE -ansiW # For full warnings during compilation
# WARNING! "ifeq" is a GNU make extension, this may not work everywhere
ifeq ($(COLINY),yes)
ACRO_OS = -DDARWIN # Darwin, MacOSX
# ACRO_OS = -DLINUX # Linux
# ACRO_LINK = -L../acro/lib -lcoliny -lcolin -lpico -lutilib -lappspack -l3po -lg2c # Linux
ACRO_LINK = -L../acro/lib -lcoliny -lcolin -lpico -lutilib -lappspack -l3po -L/sw/lib -lg2c # Darwin, MacOSX (Fink needed)
ACRO_INCLUDES = -I../acro/include -DUSING_COLINY $(ACRO_FLAGS)
ACRO_FLAGS = -DDEBUGGING -DUNIX -DMULTITASK -DANSI_HDRS -DANSI_NAMESPACES $(ACRO_OS)
LIB = $(ACRO_LINK)
ACRO = acro
COLINYLIB = libcoliny.a # Using Coliny
else
COLINYLIB = # Not using Coliny
endif
# Uncomment this section with "###" if cross-compiling on MacOSX (Intel and PowerPC)
# This section remains the same for either type of cross-compilation.
### HOST_CC="gcc-4.0"
### HOST_CXX="g++-4.0"
### RANLIB=ranlib
### AR=ar
### AS=$CC
### LD=ld
### STRIP="strip -x -S"
### CROSS_COMPILE=1
#
# Makefile targets
#
autodock4 : main.o $(ADLIB)
@echo $(EXE)' on '`date`', by $(USER) using '`hostname` >> LATEST_MAKE
@echo 'Flags: '$(CC) $(LINK) -DNOSQRT -L. -lad $(LIB) >> LATEST_MAKE
@echo " "
@echo Making autodock4
@echo " "
$(CC) $(LINK) -DNOSQRT -o $@ main.o -L. -lad $(LIB)
autodock4sqrt : main.o $(ADLIB)
@echo $(EXE)' on '`date`', by $(USER) using '`hostname` >> LATEST_MAKE
@echo 'Flags: '$(CC) $(LINK) -L. -lad $(LIB) >> LATEST_MAKE
@echo " "
@echo Making autodock4sqrt
@echo " "
$(CC) $(CFLAGS) -o $@ main.o -L. -lad $(LIB)
autodock4minpt : main.o $(ADLIB)
@echo $(EXE)' on '`date`', by $(USER) using '`hostname` >> LATEST_MAKE
@echo 'Flags: '$(CC) $(LINK) -DNOSQRT -L. -lad $(LIB) >> LATEST_MAKE
@echo " "
@echo Making autodock4minpt
@echo " "
$(CC) $(CFLAGS) -DNOSQRT -o $@ main.o -L. -lad $(LIB)
autodock4alt : $(OBJS) $(OBJNOSQRT) $(OBJNOMINPT)
@echo $(EXE)' on '`date`', by $(USER) using '`hostname` >> LATEST_MAKE
@echo 'Flags: '$(CC) $(LINK) -DNOSQRT $(OBJS) $(OBJNOSQRT) $(OBJNOMINPT) $(LIB) >> LATEST_MAKE
@echo " "
@echo Making autodock4alt
@echo " "
$(CC) $(LINK) -DNOSQRT -o $@ $(OBJS) $(OBJNOSQRT) $(OBJNOMINPT) $(LIB)
install :
@echo " "
@echo Moving autodock4 to $(AUTODOCK_BIN)
@echo " "
mv autodock4 $(AUTODOCK_BIN)
autodock4.html :
@echo " "
@echo "Creating a colour-coded HTML report of the AutoDock source code"
@echo " "
enscript -E --color -Whtml --toc -p$@ *.h *.cc
$(ADLIB) : $(OBJS) $(OBJNOSQRT) $(OBJNOMINPT)
@echo " "
@echo Making the AutoDock library
@echo " "
@echo "Running ar"
$(AR) $(ARFLAGS) $(ADLIB) $(?:.cc=.o)
@echo "Running ranlib"
$(RANLIB) $(RANLIBFLAGS) $(ADLIB)
test : autodock4 Tests/test_autodock4.py
@echo " "
@echo "Running the unit tests on autodock4"
@echo " "
cd Tests ; python ./test_autodock4.py
OFILES= eigen.o matvec.o rot.o rotate.o rotlsqfit.o
lsfit: lsfit.o $(OFILES)
gcc $(CFLAGS) lsfit.o $(OFILES) -lm -o lsfit
testdriver: testdriver.o $(OFILES)
gcc $(CFLAGS) testdriver.o $(OFILES) -lm -o testdriver
lsfitclean:
rm -f $(OFILES) lsfit.o lsfit testdriver.o testdriver
autodock4lsfit : main.o cnv_state_to_coords_lsfit.o $(OBJS_LSFIT) $(OFILES)
echo $(EXE)' on '`date`', by $(USER) using '`hostname` >> LATEST_MAKE
echo 'Flags: '$(CC) $(LINK) -DNOSQRT -L. -lad $(LIB) >> LATEST_MAKE
@echo " "
@echo Making autodock4lsfit
@echo " "
$(CC) $(LINK) -DNOSQRT -o $@ main.o -L. -lad $(LIB)
#$(COLINYLIB) : $(OBJS) $(OBJNOSQRT) $(OBJNOMINPT)
# @echo " "
# @echo Making the Coliny library
# @echo " "
# $(AR) $(ARFLAGS) $(COLINYLIB) $(?:.cc=.o)
# $(RANLIB) $(RANLIBFLAGS) $(COLINYLIB)
###
### competing 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))
lcheck : $(LNS) $(LNSNOSQRT)
$(LINT) $(LIB) $(LNS) $(LNSNOSQRT)
lchecksqrt : $(LNS) $(LNSSQRT)
$(LINT) $(LIB) $(LNS) $(LNSSQRT)
dualmap : dualmap.c
$(CC) $(CFLAGS) -lm dualmap.c -o $@
.SUFFIXES: .cc .c .i
.cc.i:
$(CC) $(CFLAGS) -E $< > $*.i
.c.i:
$(CC) $(CFLAGS) -E $< > $*.i
#
# Object dependencies:
#
analysis.o : analysis.cc analysis.h constants.h getpdbcrds.h stateLibrary.h cnv_state_to_coords.h sort_enrg.h cluster_analysis.h prClusterHist.h getrms.h eintcal.h trilinterp.h print_rem.h strindex.h print_avsfld.h
$(CC) $(CFLAGS) -c analysis.cc
#analysis.o : analysis.cc analysis.h constants.h getpdbcrds.h stateLibrary.h cnv_state_to_coords.h sort_enrg.h cluster_analysis.h prClusterHist.h getrms.h eintcal.h trilinterp.h print_rem.h strindex.h print_avsfld.h
# $(CC) $(CFLAGS) -DEINTCALPRINT -c analysis.cc # Use this to print out detailed nonbond energy breakdown for each cluster
atom_parameter_manager.o : atom_parameter_manager.cc atom_parameter_manager.h structs.h
$(CC) $(CFLAGS) -c atom_parameter_manager.cc
banner.o : banner.cc banner.h
$(CC) $(CFLAGS) -c banner.cc
bestpdb.o : bestpdb.cc bestpdb.h constants.h print_rem.h strindex.h print_avsfld.h
$(CC) $(CFLAGS) -c bestpdb.cc
calculateEnergies.o : calculateEnergies.cc calculateEnergies.h constants.h autoglobal.h autocomm.h structs.h
$(CC) $(CFLAGS) -c calculateEnergies.cc
call_glss.o : call_glss.cc support.h rep.h eval.h ranlib.h call_glss.h
$(CC) $(CFLAGS) -c call_glss.cc
call_gs.o : call_gs.cc support.h rep.h eval.h ranlib.h call_gs.h autocomm.h timesyshms.h
$(CC) $(CFLAGS) -c call_gs.cc
call_ls.o : call_ls.cc support.h rep.h eval.h ranlib.h call_ls.h
$(CC) $(CFLAGS) -c call_ls.cc
changeState.o : changeState.cc changeState.h constants.h qmultiply.h
$(CC) $(CFLAGS) -c changeState.cc
check_header_float.o : check_header_float.cc check_header_float.h
$(CC) $(CFLAGS) -c check_header_float.cc
check_header_int.o : check_header_int.cc check_header_int.h constants.h print_2x.h stop.h
$(CC) $(CFLAGS) -c check_header_int.cc
check_header_line.o : check_header_line.cc check_header_line.h constants.h
$(CC) $(CFLAGS) -c check_header_line.cc
clmode.o : clmode.cc clmode.h constants.h openfile.h strindex.h readPDBQT.h get_atom_type.h getpdbcrds.h sort_enrg.h cluster_analysis.h prClusterHist.h bestpdb.h success.h
$(CC) $(CFLAGS) -c clmode.cc
cluster_analysis.o : cluster_analysis.cc cluster_analysis.h constants.h getrms.h
$(CC) $(CFLAGS) -c cluster_analysis.cc
cmdmode.o : cmdmode.cc cmdtokens.h trjtokens.h cmdmode.h constants.h set_cmd_io_std.h print_2x.h parse_com_line.h strindex.h print_avsfld.h success.h openfile.h readPDBQT.h get_atom_type.h timesys.h eintcal.h trilinterp.h qmultiply.h cnv_state_to_coords.h parse_trj_line.h input_state.h autocomm.h
$(CC) $(CFLAGS) -c -DEINTCALPRINT cmdmode.cc
cnv_state_to_coords.o : cnv_state_to_coords.cc cnv_state_to_coords.h constants.h torsion.h qtransform.h stateLibrary.h
$(CC) $(CFLAGS) -c cnv_state_to_coords.cc
cnv_state_to_coords_lsfit.o : cnv_state_to_coords.cc cnv_state_to_coords.h constants.h torsion.h qtransform.h stateLibrary.h rotlsqfit.c rotate.c rot.c eigen.c matvec.c useful.h q.h mymacs.h graph.h frac.h
$(CC) $(CFLAGS) -DLSQFIT -c cnv_state_to_coords.cc
com.o : com.cc ranlib.h
$(CC) $(CFLAGS) -c com.cc
conformation_sampler.o : conformation_sampler.cc conformation_sampler.h rep_constants.h
$(CC) $(CFLAGS) -c conformation_sampler.cc
distdepdiel.o : distdepdiel.cc distdepdiel.h
$(CC) $(CFLAGS) -c distdepdiel.cc
stateLibrary.o : stateLibrary.cc stateLibrary.h constants.h
$(CC) $(CFLAGS) -c stateLibrary.cc
eintcal.o : eintcal.cc eintcal.h constants.h
$(CC) $(CFLAGS) -DNOSQRT -DBOUNDED -c eintcal.cc -o eintcal.o
eintcalPrint.o : eintcal.cc eintcal.h constants.h
$(CC) $(CFLAGS) -DNOSQRT -DBOUNDED -DEINTCALPRINT -c eintcal.cc -o eintcalPrint.o
eval.o : eval.cc eval.h structs.h constants.h autocomm.h
$(CC) $(CFLAGS) $(ACRO_INCLUDES) -c eval.cc
gencau.o : gencau.cc ranlib.h
$(CC) $(CFLAGS) -c gencau.cc
getInitialState.o : getInitialState.cc getInitialState.h constants.h qmultiply.h stateLibrary.h initautodock.h trilinterp.h eintcal.h cnv_state_to_coords.h prInitialState.h timesys.h autocomm.h
$(CC) $(CFLAGS) -c getInitialState.cc
get_atom_type.o : get_atom_type.cc get_atom_type.h constants.h
$(CC) $(CFLAGS) -c get_atom_type.cc
getpdbcrds.o : getpdbcrds.cc getpdbcrds.h constants.h openfile.h
$(CC) $(CFLAGS) -c getpdbcrds.cc
getrms.o : getrms.cc getrms.h constants.h autocomm.h
$(CC) $(CFLAGS) -c getrms.cc
gs.o : gs.cc gs.h ranlib.h eval.h rep.h support.h writePDBQT.h
$(CC) $(CFLAGS) -DCHECK_ISNAN -c gs.cc -o gs.o
initautodock.o : initautodock.cc initautodock.h constants.h qmultiply.h cnv_state_to_coords.h print_2x.h autocomm.h
$(CC) $(CFLAGS) -c initautodock.cc
input_state.o : input_state.cc input_state.h constants.h qmultiply.h
$(CC) $(CFLAGS) -c input_state.cc
investigate.o : investigate.cc investigate.h constants.h changeState.h mkRandomState.h cnv_state_to_coords.h getrms.h trilinterp.h eintcal.h getpdbcrds.h stateLibrary.h
$(CC) $(CFLAGS) -c investigate.cc
intnbtable.o : intnbtable.cc intnbtable.h constants.h
$(CC) $(CFLAGS) -DNOSQRT -c intnbtable.cc
linpack.o : linpack.cc
$(CC) $(CFLAGS) -c linpack.cc
ls.o : ls.cc ls.h support.h ranlib.h
$(CC) $(CFLAGS) -c ls.cc
main.o : main.cc hybrids.h ranlib.h gs.h ls.h rep.h support.h main.h constants.h autocomm.h dpftoken.h structs.h autoglobal.h autocomm.h coliny.h parse_param_line.cc partokens.h eintcal.cc eintcal.h atom_parameter_manager.cc atom_parameter_manager.h read_parameter_library.h calculateEnergies.cc calculateEnergies.h
$(CC) $(CFLAGS) $(ACRO_INCLUDES) -c -DEINTCALPRINT -DWRITEPDBQSTATE main.cc
mapping.o : mapping.cc support.h
$(CC) $(CFLAGS) -c mapping.cc
minmeanmax.o : minmeanmax.cc rep.h support.h
$(CC) $(CFLAGS) -c minmeanmax.cc
mkNewState.o : mkNewState.cc mkNewState.h constants.h
$(CC) $(CFLAGS) -c mkNewState.cc
mkTorTree.o : mkTorTree.cc PDBQT_tokens.h mkTorTree.h constants.h
$(CC) $(CFLAGS) -c mkTorTree.cc
mkRandomState.o : mkRandomState.cc mkRandomState.h constants.h
$(CC) $(CFLAGS) -c mkRandomState.cc
nbe.o : nbe.cc nbe.h constants.h
$(CC) $(CFLAGS) -DNOSQRT -c nbe.cc
nonbonds.o : nonbonds.cc nonbonds.h constants.h mdist.h
$(CC) $(CFLAGS) -c nonbonds.cc
openfile.o : openfile.cc openfile.h constants.h autocomm.h
$(CC) $(CFLAGS) -c openfile.cc
output_state.o : output_state.cc output_state.h constants.h
$(CC) $(CFLAGS) -c output_state.cc
parse_com_line.o : parse_com_line.cc cmdtokens.h parse_com_line.h constants.h
$(CC) $(CFLAGS) -c parse_com_line.cc
parse_dpf_line.o : parse_dpf_line.cc parse_dpf_line.h constants.h dpftoken.h
$(CC) $(CFLAGS) $(ACRO_INCLUDES) -c parse_dpf_line.cc
parse_param_line.o : parse_param_line.cc partokens.h parse_param_line.h constants.h
$(CC) $(CFLAGS) -c parse_param_line.cc
parse_PDBQT_line.o : parse_PDBQT_line.cc PDBQT_tokens.h parse_PDBQT_line.h constants.h
$(CC) $(CFLAGS) -c parse_PDBQT_line.cc
parse_trj_line.o : parse_trj_line.cc trjtokens.h parse_trj_line.h constants.h
$(CC) $(CFLAGS) -c parse_trj_line.cc
parsetypes.o : parsetypes.cc parsetypes.h
$(CC) $(CFLAGS) -c parsetypes.cc
prClusterHist.o : prClusterHist.cc prClusterHist.h constants.h
$(CC) $(CFLAGS) -c prClusterHist.cc
prInitialState.o : prInitialState.cc prInitialState.h constants.h
$(CC) $(CFLAGS) -c prInitialState.cc
prTorConList.o : prTorConList.cc prTorConList.h constants.h autocomm.h
$(CC) $(CFLAGS) -c prTorConList.cc
print_2x.o : print_2x.cc print_2x.h
$(CC) $(CFLAGS) -c print_2x.cc
print_atomic_energies.o : print_atomic_energies.cc print_atomic_energies.h constants.h
$(CC) $(CFLAGS) -c print_atomic_energies.cc
print_avsfld.o : print_avsfld.cc print_avsfld.h
$(CC) $(CFLAGS) -c print_avsfld.cc
writePDBQT.o : writePDBQT.cc writePDBQT.h constants.h autocomm.h
$(CC) $(CFLAGS) -c writePDBQT.cc -o writePDBQT.o
print_rem.o : print_rem.cc print_rem.h
$(CC) $(CFLAGS) -c print_rem.cc
printdate.o : printdate.cc printdate.h
$(CC) $(CFLAGS) -c printdate.cc
printEnergies.o : printEnergies.cc printEnergies.h
$(CC) $(CFLAGS) -c printEnergies.cc
printhms.o : printhms.cc printhms.h
$(CC) $(CFLAGS) -c printhms.cc
qmultiply.o : qmultiply.cc qmultiply.h
$(CC) $(CFLAGS) -c qmultiply.cc
qtransform.o : qtransform.cc qtransform.h constants.h
$(CC) $(CFLAGS) -c qtransform.cc
quicksort.o : quicksort.cc quicksort.h
$(CC) $(CFLAGS) -c quicksort.cc
ranlib.o : ranlib.cc ranlib.h
$(CC) $(CFLAGS) -c ranlib.cc
readfield.o : readfield.cc readfield.h constants.h openfile.h stop.h
$(CC) $(CFLAGS) -c readfield.cc
readmap.o : readmap.cc readmap.h constants.h openfile.h warn_bad_file.h strindex.h print_2x.h check_header_line.h warn_bad_file.h check_header_float.h check_header_int.h timesys.h autocomm.h
$(CC) $(CFLAGS) -c readmap.cc
readPDBQT.o : readPDBQT.cc readPDBQT.h constants.h openfile.h stop.h get_atom_type.h print_2x.h mkTorTree.h nonbonds.cc nonbonds.h weedbonds.cc weedbonds.h torNorVec.cc torNorVec.h success.cc success.h autocomm.h parse_PDBQT_line.cc parse_PDBQT_line.h mdist.h atom_parameter_manager.cc atom_parameter_manager.h stack.cc stack.h
$(CC) $(CFLAGS) -c readPDBQT.cc
default_parameters.h : AD4.1_bound.dat paramdat2h.csh
rm -f $@
./paramdat2h.csh AD4.1_bound.dat > $@
read_parameter_library.o : read_parameter_library.cc autocomm.h default_parameters.h
$(CC) $(CFLAGS) -c read_parameter_library.cc
rep.o: rep.cc rep.h ranlib.h
$(CC) $(CFLAGS) -c rep.cc
scauchy.o : scauchy.cc ranlib.h
$(CC) $(CFLAGS) -c scauchy.cc
set_cmd_io_std.o : set_cmd_io_std.cc set_cmd_io_std.h
$(CC) $(CFLAGS) -c set_cmd_io_std.cc
setflags.o : setflags.cc setflags.h
$(CC) $(CFLAGS) -c setflags.cc
simanneal.o : simanneal.cc simanneal.h constants.h autocomm.h
$(CC) $(CFLAGS) -c simanneal.cc
sort_enrg.o : sort_enrg.cc sort_enrg.h constants.h
$(CC) $(CFLAGS) -c sort_enrg.cc
stack.o : stack.cc stack.h
$(CC) $(CFLAGS) -c stack.cc
stop.o : stop.cc stop.h constants.h
$(CC) $(CFLAGS) -c stop.cc
strindex.o : strindex.cc strindex.h
$(CC) $(CFLAGS) -c strindex.cc
success.o : success.cc success.h constants.h autocomm.h
$(CC) $(CFLAGS) -c success.cc
summarizegrids.o : summarizegrids.cc summarizegrids.h constants.h autocomm.h
$(CC) $(CFLAGS) -c summarizegrids.cc
support.o : support.cc support.h eval.h
$(CC) $(CFLAGS) -c support.cc
swap.o : swap.cc swap.h
$(CC) $(CFLAGS) -c swap.cc
timesys.o : timesys.cc timesys.h
$(CC) $(CFLAGS) -c timesys.cc
timesyshms.o : timesyshms.cc timesyshms.h
$(CC) $(CFLAGS) -c timesyshms.cc
torNorVec.o : torNorVec.cc torNorVec.h constants.h
$(CC) $(CFLAGS) -c torNorVec.cc
torsion.o : torsion.cc torsion.h constants.h
$(CC) $(CFLAGS) -c torsion.cc
trilinterp.o : trilinterp.cc trilinterp.h constants.h
$(CC) $(CFLAGS) -c trilinterp.cc
trilinterp.MINPT.o : trilinterp.cc trilinterp.h constants.h
$(CC) $(CFLAGS) -DMINPT -c trilinterp.cc -o trilinterp.MINPT.o
usage.o : usage.cc usage.h constants.h
$(CC) $(CFLAGS) -c usage.cc
warn_bad_file.o : warn_bad_file.cc warn_bad_file.h constants.h
$(CC) $(CFLAGS) -c warn_bad_file.cc
weedbonds.o : weedbonds.cc weedbonds.h constants.h
$(CC) $(CFLAGS) -c weedbonds.cc
eintcal.sqrt.o : eintcal.cc eintcal.h constants.h
$(CC) $(CFLAGS) -c -DBOUNDED eintcal.cc -o eintcal.sqrt.o
eintcalPrint.sqrt.o : eintcal.cc eintcal.h constants.h
$(CC) $(CFLAGS) -c -DBOUNDED -DEINTCALPRINT eintcal.cc -o eintcalPrint.sqrt.o
intnbtable.sqrt.o : intnbtable.cc intnbtable.h constants.h
$(CC) $(CFLAGS) -c intnbtable.cc -o intnbtable.sqrt.o
nbe.sqrt.o : nbe.cc nbe.h constants.h
$(CC) $(CFLAGS) -c nbe.cc -o nbe.sqrt.o
coliny.o : coliny.h
$(CC) $(CFLAGS) $(ACRO_INCLUDES) -c coliny.cc -o coliny.o
#
# lcheck dependencies...
#
analysis.ln : analysis.cc
$(LINT) $(LINTFLAGS) $?
banner.ln : banner.cc
$(LINT) $(LINTFLAGS) $?
bestpdb.ln : bestpdb.cc
$(LINT) $(LINTFLAGS) $?
changeState.ln : changeState.cc
$(LINT) $(LINTFLAGS) $?
check_header_float.ln : check_header_float.cc
$(LINT) $(LINTFLAGS) $?
check_header_int.ln : check_header_int.cc
$(LINT) $(LINTFLAGS) $?
check_header_line.ln : check_header_line.cc
$(LINT) $(LINTFLAGS) $?
cluster_analysis.ln : cluster_analysis.cc
$(LINT) $(LINTFLAGS) $?
clmode.ln : clmode.cc
$(LINT) $(LINTFLAGS) $?
cmdmode.ln : cmdmode.cc
$(LINT) $(LINTFLAGS) $?
cnv_state_to_coords.ln : cnv_state_to_coords.cc
$(LINT) $(LINTFLAGS) $?
stateLibrary.ln : stateLibrary.cc
$(LINT) $(LINTFLAGS) $?
readfield.ln : readfield.cc
$(LINT) $(LINTFLAGS) $?
readmap.ln : readmap.cc
$(LINT) $(LINTFLAGS) $?
readPDBQT.ln : readPDBQT.cc
$(LINT) $(LINTFLAGS) $?
getrms.ln : getrms.cc
$(LINT) $(LINTFLAGS) $?
get_atom_type.ln : get_atom_type.cc
$(LINT) $(LINTFLAGS) $?
getInitialState.ln : getInitialState.cc
$(LINT) $(LINTFLAGS) $?
getpdbcrds.ln : getpdbcrds.cc
$(LINT) $(LINTFLAGS) $?
initautodock.ln : initautodock.cc
$(LINT) $(LINTFLAGS) $?
input_state.ln : input_state.cc
$(LINT) $(LINTFLAGS) $?
investigate.ln : investigate.cc
$(LINT) $(LINTFLAGS) $?
main.ln : main.cc
$(LINT) $(LINTFLAGS) $?
mkNewState.ln : mkNewState.cc
$(LINT) $(LINTFLAGS) $?
mkTorTree.ln : mkTorTree.cc
$(LINT) $(LINTFLAGS) $?
mkRandomState.ln : mkRandomState.cc
$(LINT) $(LINTFLAGS) $?
nonbonds.ln : nonbonds.cc
$(LINT) $(LINTFLAGS) $?
openfile.ln : openfile.cc
$(LINT) $(LINTFLAGS) $?
output_state.ln : output_state.cc
$(LINT) $(LINTFLAGS) $?