## Makefile to build AutoDock from Object files.## NOTE: Must be run in the $(AUTODOCK_DEV) directory.## Copyright (C) 1994-1999,  Garrett Matthew Morris,  TSRI.### Edit this Makefile to reflect your machine architecture.## Specifically, change these variables:# LIB, CSTD, CFLAGS, OPT, OLIMIT, LINT, LINTFLAGS, LINK, WARN, & CC.## If you need to use debugging or profiling, these should also be # modified appropriately:# DBUG & PROF### Edit the line defining "EXE" to your binaries directory for # your machine architecture.## Define the destination directory for the executables:#EXE = .			# Default destination## Define the object files:#OBJS = \    analysis.o \    banner.o \    bestpdb.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 \    stateLibrary.o \    readfield.o \    readmap.o \    readPDBQ.o \    dpftypes.o \    eval.o \    evaluate_energy.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_pdbq_line.o \    parse_trj_line.o \    print_2x.o \    print_atomic_energies.o \    print_avsfld.o \    writeMolAsPDBQ.o \    writePDBQ.o \    writePDBQState.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 \    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.oOBJNOSQRT = \    eintcal.o \    eintcalPrint.o \    intnbtable.o \    nbe.oOBJSQRT = \    eintcal.sqrt.o \    eintcalPrint.sqrt.o \    intnbtable.sqrt.o \    nbe.sqrt.oOBJNOMINPT = \    trilinterp.oOBJMINPT = \    trilinterp.MINPT.oADLIB = libad.aARFLAGS = r# Define lint files:LNS = \    analysis.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 \    cnv_state_to_coords.ln \    stateLibrary.ln \    readfield.ln \    readmap.ln \    readPDBQ.ln \    dpftypes.ln \    evaluate_energy.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_pdbq_line.ln \    parse_trj_line.ln \    print_2x.ln \    print_atomic_energies.ln \    print_avsfld.ln \    writeMolAsPDBQ.ln \    writePDBQ.ln \    writePDBQState.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 \    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.lnLNSNOSQRT = \    eintcal.ln \    eintcalPrint.ln \    intnbtable.ln \    nbe.lnLNSSQRT = \    eintcal.sqrt.ln \    eintcalPrint.sqrt.ln \    intnbtable.sqrt.ln \    nbe.sqrt.ln## Abbreviations of machine architectures:## SGI    = Silicon Graphics Inc., sgi4D.# Alpha  = Compaq/Digital Equipment Corp., Alpha.# Sun    = Sun Microsystems, sun4.# HP     = Hewlett Packard Precision Architecture, hppa.# Convex = Convex, c2.### C++ compiler## AutoDock 3.0 Makefile GNU Linux -- STARTCC        = g++LIB       = -lmCSTD      = -DHPPA $(PROF) $(DBUG) $(WARN)CFLAGS    = $(OPT)OPTLEVEL  = -g -O3OPT       = $(CSTD) $(OPTLEVEL)OLIMIT    = $(OPT)LINKOPT   = $(OPT)LINK      = $(LINKOPT)LINT      = lintLINTFLAGS = -DHPPA $(LIB) -cDBUG      = -DNDEBUG # No debugging and no assert codePROF      = # No profilingWARN      = # Default warning level# AutoDock 3.0 Makefile GNU Linux -- ENDautodock3 : main.o $(ADLIB)	echo $(EXE)'  on  '`date`', using '`hostname` >> LATEST_MAKE	echo 'Flags: '$(CC) $(LINK) -DNOSQRT -L. -lad $(LIB) >> LATEST_MAKE	$(CC) $(LINK) -DNOSQRT -o $@ main.o -L. -lad $(LIB)autodock3sqrt : main.o $(ADLIB)	$(CC) $(OPT) $(CFLAGS) -o $@ main.o -L. -lad $(LIB)autodock3minpt : main.o $(ADLIB)	echo $(EXE)'  on  '`date`', using '`hostname` >> LATEST_MAKE	$(CC) $(OPT) -DNOSQRT -o $@ main.o -L. -lad $(LIB)autodock3alt : $(OBJS) $(OBJNOSQRT) $(OBJNOMINPT)	echo $(EXE)'  on  '`date`', using '`hostname` >> LATEST_MAKE	$(CC) $(LINK) -DNOSQRT -o $@ $(OBJS) $(OBJNOSQRT) $(OBJNOMINPT) $(LIB)$(ADLIB) : $(OBJS) $(OBJNOSQRT) $(OBJNOMINPT)	$(AR) $(ARFLAGS) $(ADLIB) $(?:.cc=.o)lcheck : $(LNS) $(LNSNOSQRT)	$(LINT) $(LIB) $(LNS) $(LNSNOSQRT)lchecksqrt : $(LNS) $(LNSSQRT)	$(LINT) $(LIB) $(LNS) $(LNSSQRT)dualmap : dualmap.c	$(CC) $(OPT) $(CFLAGS) -lm dualmap.c -o $@## 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.ccbanner.o : banner.cc banner.h	$(CC) $(CFLAGS) -c banner.ccbestpdb.o : bestpdb.cc bestpdb.h constants.h print_rem.h strindex.h print_avsfld.h	$(CC) $(CFLAGS) -c bestpdb.cccall_glss.o : call_glss.cc support.h rep.h eval.h ranlib.h call_glss.h	$(CC) $(CFLAGS) -c call_glss.cccall_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.cccall_ls.o : call_ls.cc support.h rep.h eval.h ranlib.h call_ls.h	$(CC) $(CFLAGS) -c call_ls.ccchangeState.o : changeState.cc changeState.h constants.h qmultiply.h	$(CC) $(CFLAGS) -c changeState.cccheck_header_float.o : check_header_float.cc check_header_float.h	$(CC) $(CFLAGS) -c check_header_float.cccheck_header_int.o : check_header_int.cc check_header_int.h constants.h print_2x.h stop.h	$(CC) $(CFLAGS) -c check_header_int.cccheck_header_line.o : check_header_line.cc check_header_line.h constants.h	$(CC) $(CFLAGS) -c check_header_line.ccclmode.o : clmode.cc clmode.h constants.h openfile.h strindex.h readPDBQ.h get_atom_type.h getpdbcrds.h sort_enrg.h cluster_analysis.h prClusterHist.h bestpdb.h success.h	$(CC) $(CFLAGS) -c clmode.cccluster_analysis.o : cluster_analysis.cc cluster_analysis.h constants.h getrms.h	$(CC) $(CFLAGS) -c cluster_analysis.cccmdmode.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 readPDBQ.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.cccnv_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.cccom.o : com.cc ranlib.h	$(CC) $(CFLAGS) -c com.ccstateLibrary.o : stateLibrary.cc stateLibrary.h constants.h	$(CC) $(CFLAGS) -c stateLibrary.ccreadPDBQ.o : readPDBQ.cc  readPDBQ.h constants.h openfile.h stop.h readPDBQ.h get_atom_type.h print_2x.h mkTorTree.h nonbonds.h weedbonds.h torNorVec.h success.h autocomm.h	$(CC) $(OLIMIT) -c readPDBQ.ccdpftypes.o : dpftypes.cc dpftypes.h constants.h dpftoken.h stop.h	$(CC) $(CFLAGS) -c dpftypes.cceintcal.o : eintcal.cc eintcal.h constants.h	$(CC) $(CFLAGS) -DNOSQRT -DBOUNDED -c eintcal.cc -o eintcal.oeintcalPrint.o : eintcal.cc eintcal.h constants.h	$(CC) $(CFLAGS) -DNOSQRT -DBOUNDED -DEINTCALPRINT -c eintcal.cc -o eintcalPrint.oeval.o : eval.cc eval.h structs.h constants.h autocomm.h 	$(CC) $(CFLAGS) -c eval.ccevaluate_energy.o : evaluate_energy.cc evaluate_energy.h constants.h trilinterp.h eintcal.h	$(CC) $(CFLAGS) -c evaluate_energy.ccgencau.o : gencau.cc ranlib.h	$(CC) $(CFLAGS) -c gencau.ccgetInitialState.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.ccget_atom_type.o : get_atom_type.cc get_atom_type.h constants.h	$(CC) $(CFLAGS) -c get_atom_type.ccgetpdbcrds.o : getpdbcrds.cc getpdbcrds.h constants.h openfile.h	$(CC) $(CFLAGS) -c getpdbcrds.ccgetrms.o : getrms.cc getrms.h constants.h autocomm.h	$(CC) $(CFLAGS) -c getrms.ccgs.o : gs.cc gs.h ranlib.h eval.h rep.h support.h writePDBQ.h	$(CC) $(CFLAGS) -DCHECK_ISNAN -c gs.cc -o gs.oinitautodock.o : initautodock.cc initautodock.h constants.h qmultiply.h cnv_state_to_coords.h print_2x.h autocomm.h	$(CC) $(CFLAGS) -c initautodock.ccinput_state.o : input_state.cc input_state.h constants.h qmultiply.h	$(CC) $(CFLAGS) -c input_state.ccinvestigate.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.ccintnbtable.o : intnbtable.cc intnbtable.h constants.h	$(CC) $(OLIMIT) -DNOSQRT -c intnbtable.cclinpack.o : linpack.cc	$(CC) $(CFLAGS) -c linpack.ccls.o : ls.cc ls.h support.h ranlib.h	$(CC) $(CFLAGS) -c ls.ccmain.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	$(CC) $(OLIMIT) -c -DWRITEPDBQSTATE main.ccmapping.o : mapping.cc support.h	$(CC) $(CFLAGS) -c mapping.ccminmeanmax.o : minmeanmax.cc  rep.h support.h	$(CC) $(CFLAGS) -c minmeanmax.ccmkNewState.o : mkNewState.cc mkNewState.h constants.h	$(CC) $(CFLAGS) -c mkNewState.ccmkTorTree.o : mkTorTree.cc pdbqtokens.h mkTorTree.h constants.h	$(CC) $(CFLAGS) -c mkTorTree.ccmkRandomState.o : mkRandomState.cc mkRandomState.h constants.h	$(CC) $(CFLAGS) -c mkRandomState.ccnbe.o : nbe.cc nbe.h constants.h	$(CC) $(OLIMIT) -DNOSQRT -c nbe.ccnonbonds.o : nonbonds.cc nonbonds.h constants.h	$(CC) $(CFLAGS) -c nonbonds.ccopenfile.o : openfile.cc openfile.h constants.h autocomm.h	$(CC) $(CFLAGS) -c openfile.ccoutput_state.o : output_state.cc output_state.h constants.h	$(CC) $(CFLAGS) -c output_state.ccparse_com_line.o : parse_com_line.cc cmdtokens.h parse_com_line.h constants.h	$(CC) $(CFLAGS) -c parse_com_line.ccparse_dpf_line.o : parse_dpf_line.cc parse_dpf_line.h constants.h dpftoken.h	$(CC) $(CFLAGS) -c parse_dpf_line.ccparse_pdbq_line.o : parse_pdbq_line.cc pdbqtokens.h  parse_pdbq_line.h constants.h	$(CC) $(CFLAGS) -c parse_pdbq_line.ccparse_trj_line.o : parse_trj_line.cc trjtokens.h parse_trj_line.h constants.h	$(CC) $(CFLAGS) -c parse_trj_line.ccprClusterHist.o : prClusterHist.cc prClusterHist.h constants.h	$(CC) $(CFLAGS) -c prClusterHist.ccprInitialState.o : prInitialState.cc prInitialState.h constants.h	$(CC) $(CFLAGS) -c prInitialState.ccprTorConList.o : prTorConList.cc prTorConList.h constants.h autocomm.h	$(CC) $(CFLAGS) -c prTorConList.ccprint_2x.o : print_2x.cc print_2x.h	$(CC) $(CFLAGS) -c print_2x.ccprint_atomic_energies.o : print_atomic_energies.cc print_atomic_energies.h constants.h	$(CC) $(CFLAGS) -c print_atomic_energies.ccprint_avsfld.o : print_avsfld.cc print_avsfld.h