Fix build system, minor source code modifications for windows (mingw …

…compilers)

Makefile

@@ -1,21 +1,29 @@
 include config.h
 
-PROGS=antechamber acdoctor am1bcc antechamber_pvt atomtype bondtype charmmgen \
-		database espgen parmcal parmchk parmchk2 prepgen residuegen sqm teLeap \
-		tleap translate parmchk_pvt parmchk2_pvt
+ifeq ($(OS),Windows_NT)
+WRAPPER_SFX=.bat
+else
+WRAPPER_SFX=
+endif
+
+PROGS=antechamber$(WRAPPER_SFX) acdoctor$(SFX) am1bcc$(SFX) antechamber_pvt$(SFX) \
+		atomtype$(SFX) bondtype$(SFX) charmmgen$(SFX) database$(SFX) espgen$(SFX) \
+		parmcal$(SFX) parmchk$(WRAPPER_SFX) parmchk2$(WRAPPER_SFX) prepgen$(SFX) \
+		residuegen$(SFX) sqm$(SFX) teLeap$(SFX) tleap$(WRAPPER_SFX) translate$(SFX) \
+		parmchk_pvt$(SFX) parmchk2_pvt$(SFX)
 
 all: prep libs
 	$(MAKE) antechamber
 	$(MAKE) leap
 	$(MAKE) sqm
 
 install: all
-	mkdir -p $(PREFIX)/bin $(PREFIX)/share
-	cd bin && /bin/mv $(PROGS) $(PREFIX)/bin
+	$(MKDIR) -p $(PREFIX)/bin $(PREFIX)/share
+	cd bin && mv $(PROGS) $(PREFIX)/bin
 	cp -r share/amber/dat $(PREFIX)
 
 prep:
-	mkdir -p bin
+	$(MKDIR) -p bin
 
 antechamber::
 	cd antechamber && $(MAKE) install
@@ -33,12 +41,12 @@ libs::
 	cd arpack && $(MAKE) install
 
 clean:
-	-cd antechamber && $(MAKE) clean
-	-cd leap && $(MAKE) clean
-	-cd sqm && $(MAKE) clean
-	-cd lib && $(MAKE) clean
-	-cd cifparse && $(MAKE) clean
+	cd antechamber && $(MAKE) clean
+	cd leap && $(MAKE) clean
+	cd sqm && $(MAKE) clean
+	cd lib && $(MAKE) clean
+	cd cifparse && $(MAKE) clean
 
 uninstall:
 	cd $(PREFIX)/bin && rm -f $(PROGS)
-	rm -fr $(PREFIX)/dat
+	$(RM) -fr $(PREFIX)/dat

antechamber/Makefile

@@ -239,8 +239,13 @@ $(BINDIR)/antechamber_pvt$(SFX): antechamber.o
 	$(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) antechamber.o \
     -L$(LIBDIR) -lcifparse $(LM) -o $(BINDIR)/antechamber_pvt$(SFX)
 
+ifeq ($(OS),Windows_NT)
 $(BINDIR)/antechamber$(SFX):
-	/bin/cp -L antechamber $(BINDIR)
+	cp -L antechamber.bat $(BINDIR)
+else
+$(BINDIR)/antechamber$(SFX):
+	cp -L antechamber $(BINDIR)
+endif
 
 $(BINDIR)/atomtype$(SFX): atomtype.o
 	$(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) atomtype.o $(LM) -o $(BINDIR)/atomtype$(SFX)
@@ -272,14 +277,24 @@ $(BINDIR)/espgen$(SFX): espgen.o
 $(BINDIR)/parmcal$(SFX): parmcal.o
 	$(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) parmcal.o $(LM) -o $(BINDIR)/parmcal$(SFX)
 
+ifeq ($(OS),Windows_NT)
+$(BINDIR)/parmchk$(SFX):
+	cp -L parmchk.bat $(BINDIR)
+else
 $(BINDIR)/parmchk$(SFX):
-	/bin/cp -L parmchk $(BINDIR)
+	cp -L parmchk $(BINDIR)
+endif
 
 $(BINDIR)/parmchk_pvt$(SFX): parmchk.o
 	$(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) parmchk.o $(LM) -o $(BINDIR)/parmchk_pvt$(SFX)
 
+ifeq ($(OS),Windows_NT)
+$(BINDIR)/parmchk2$(SFX):
+	cp -L parmchk2.bat $(BINDIR)
+else
 $(BINDIR)/parmchk2$(SFX):
-	/bin/cp -L parmchk2 $(BINDIR)
+	cp -L parmchk2 $(BINDIR)
+endif
 
 $(BINDIR)/parmchk2_pvt$(SFX): parmchk2.o
 	$(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) parmchk2.o $(LM) -o $(BINDIR)/parmchk2_pvt$(SFX)

antechamber/antechamber.bat

@@ -0,0 +1,3 @@
+:: Point AMBERHOME to the location that has dat/leap
+set AMBERHOME=%~dp0\..
+%~dp0\antechamber_pvt %*

antechamber/common.c

@@ -21,8 +21,8 @@ size_t build_path(char *path, const char *subdir, const char *fname,
 	char *quote = NULL;
     size_t c = 1;
     path[0] = '\0';
-	if (for_system && index(amberhome, ' ') != NULL) {
-		if (index(amberhome, '"') == NULL)
+	if (for_system && strchr(amberhome, ' ') != NULL) {
+		if (strchr(amberhome, '"') == NULL)
 			quote = "\"";
 		else
 			quote = "'";

antechamber/parmchk.bat

@@ -0,0 +1,3 @@
+:: Point AMBERHOME to the location that has dat/leap
+set AMBERHOME=%~dp0\..
+%~dp0\parmchk_pvt %*

antechamber/parmchk2.bat

@@ -0,0 +1,3 @@
+:: Point AMBERHOME to the location that has dat/leap
+set AMBERHOME=%~dp0\..
+%~dp0\parmchk_pvt %*

arpack/Makefile

@@ -30,8 +30,8 @@ $(LIBDIR)/libarpack.a: $(ARPACKLIB)
 	mv libarpack.a $(LIBDIR)
 
 clean:
-	-/bin/rm -f *.o _*.f
+	$(RM) -f *.o _*.f
 
 uninstall:
-	-rm -f $(LIBDIR)/libarpack.a
+	$(RM) -f $(LIBDIR)/libarpack.a
 

cifparse/Makefile

@@ -12,7 +12,7 @@ CIFOBS=	\
 	cifparse.o
 
 libcifparse.a: $(CIFOBS)
-	/bin/rm -f libcifparse.a
+	rm -f libcifparse.a
 	$(AR) libcifparse.a $(CIFOBS)
 	-ranlib libcifparse.a
 
@@ -22,7 +22,7 @@ cifp.tab.c:  cifparse.y lex.cif.c
 	$(YACC) -v -d cifparse.y
 	sed 's/yy/cifp/g' < y.tab.c > cifp.tab.c
 	sed 's/yy/cifp/g' < y.tab.h > cifp.tab.h
-	/bin/rm -f y.tab.c y.tab.h
+	$(RM) -f y.tab.c y.tab.h
 
 cifp.tab.o: cifp.tab.c
 	$(CC) -c -D$(LEX) $(CNOOPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) cifp.tab.c
@@ -34,11 +34,11 @@ install:  libcifparse.a
 	mv libcifparse.a $(LIBDIR)
 
 clean:
-	/bin/rm -f *.o libcifparse.a y.output
-	/bin/rm -f lex.cif.c cifp.tab.c cifp.tab.h
+	$(RM) -f *.o libcifparse.a y.output
+	$(RM) -f lex.cif.c cifp.tab.c cifp.tab.h
 
 uninstall: clean
-	/bin/rm -f $(LIBDIR)/libcifparse.a
+	$(RM) -f $(LIBDIR)/libcifparse.a
 
 lex.cif.o:	\
 	cifp.tab.h

configure

@@ -2,7 +2,9 @@
 from __future__ import with_statement
 
 import os, sys
+from distutils.spawn import find_executable
 from optparse import OptionParser
+on_win = bool(sys.platform == 'win32')
 
 CONFIG_H = """\
 #  Amber configuration file, created with: %(command)s
@@ -32,8 +34,7 @@ FLIBSF= -L../lib -larpack -llapack -lblas
 #  (3)  Modify any of the following if you need to change, e.g. to use gcc
 #        rather than cc, etc.
 
-SHELL=/bin/sh
-
+SHELL=%(shell)s
 #  Set the C compiler, etc. 
 
 #  The configure script should be fine, but if you need to hand-edit,
@@ -73,6 +74,8 @@ YACC=  %(yacc)s
 AR=    ar rv
 M4=    m4
 RANLIB=ranlib
+MKDIR = %(mkdir)s
+RM    = %(rm)s
 
 #  Set the C-preprocessor.  Code for a small preprocessor is in
 #    ucpp-1.3;  it gets installed as $(BINDIR)/ucpp;
@@ -96,7 +99,7 @@ C9XCOMPLEX=skip
 #  For Windows/cygwin, set SFX to ".exe"; for Unix/Linux leave it empty:
 #  Set OBJSFX to ".obj" instead of ".o" on Windows:
 
-SFX=
+SFX=%(sfx)s
 OSFX=.o
 MV=mv
 RM=rm
@@ -112,7 +115,7 @@ AMBERFFLAGS=$(AMBERBUILDFLAGS)
 FREEFORMAT_FLAG= -ffree-form
 LM=-lm
 FPP=cpp -traditional -P
-FPPFLAGS= -DBINTRAJ -DEMIL  $(CUSTOMBUILDFLAGS) $(AMBERBUILDFLAGS)
+FPPFLAGS= -cpp -DBINTRAJ -DEMIL  $(CUSTOMBUILDFLAGS) $(AMBERBUILDFLAGS)
 AMBERFPPFLAGS=$(AMBERBUILDFLAGS)
 FCREAL8=-fdefault-real-8
 NOFORTRANMAIN=-lgfortran -w
@@ -140,15 +143,21 @@ def which(prog):
 
 # Get the working directory
 cwd = os.path.abspath(os.path.dirname(sys.argv[0]))
-options = dict(basedir=cwd, cc='gcc', cxx='g++', copt='-O3', cxxopt='-O3',
-               fc='gfortran', fcopt='-O3', mathlib='')
+options = dict(basedir=cwd,  copt='-O3', cxxopt='-O3', fcopt='-O3', mathlib='')
 
 parser = OptionParser()
 parser.add_option('--prefix', dest='prefix', default='/usr/local',
                   help='Directory to install programs and files to.')
 parser.add_option('--yacc', dest='yacc', default=None,
                   help='Which YACC implementation to use. Looks for byacc '
                   'first then looks for bison or yacc if not given')
+parser.add_option('--cc', dest='cc', default='gcc',
+                   help='Path to C compiler (default=gcc)')
+parser.add_option('--cxx', dest='cxx', default='g++',
+                   help='Path to C++ compiler (default=g++)')
+parser.add_option('--fc', dest='fc', default='gfortran',
+                   help='Path to fortran compiler (default=gfortran)')
+
 
 opt, arg = parser.parse_args()
 
@@ -165,9 +174,19 @@ else:
 if myyacc is None:
     sys.exit('Could not find a YACC-compatible parser generator!')
 
+options['cc'] = opt.cc
+options['cxx'] = opt.cxx
+options['fc'] = opt.fc
 options['prefix'] = os.path.abspath(opt.prefix)
 options['yacc'] = myyacc
 options['command'] = ' '.join(sys.argv)
+options['mkdir'] = find_executable('mkdir')
+options['rm'] = find_executable('rm')
+options['sfx'] = '.exe' if on_win else ''
+if on_win:
+    options['shell'] = 'C:/Windows/System32/cmd.exe'
+else:
+    options['shell'] = '/bin/sh'
 
 if myyacc.endswith('bison'):
     options['yacc'] += ' -y'

lapack/Makefile

@@ -58,10 +58,10 @@ skip:
 	@echo "skipping compilation of LAPACK"
 
 uninstall:
-	rm -f $(LIBDIR)/liblapack.a
+	$(RM) -f $(LIBDIR)/liblapack.a
 
 clean:
-	-/bin/rm -f *.o
+	$(RM) -f *.o
 
 dlamch.o:  dlamch.f
 	$(FC) -c $(FNOOPTFLAGS) $(FFLAGS) -o $@ $<

leap/Makefile

@@ -1,18 +1,25 @@
 include ../config.h
 
+ifeq ($(OS),Windows_NT)
+TLEAP_WRAPPER=tleap.bat
+else
+TLEAP_WRAPPER=tleap
+endif
+
+
 install:
 	@echo "Compiling basic programs"
 	cd src/leap && $(MAKE) installteLeap
 	@echo "Copying shell script" 
-	cp tleap $(BINDIR)/tleap
-	chmod +x $(BINDIR)/tleap
+	cp $(TLEAP_WRAPPER) $(BINDIR)/$(TLEAP_WRAPPER)
+	chmod +x $(BINDIR)/$(TLEAP_WRAPPER)
 	$(MAKE) $(MAKE_XLEAP)
 
 uninstall:
 	cd src/leap && $(MAKE) uninstallteLeap
-	-rm -f $(BINDIR)/tleap
+	$(RM) -f $(BINDIR)/tleap
 	-cd src/leap && $(MAKE) uninstall
-	-rm -f $(BINDIR)/xleap
+	$(RM) -f $(BINDIR)/xleap
 
 install_xleap:
 	cd src/Wc && $(MAKE)

leap/src/Xmu/Makefile

@@ -126,4 +126,4 @@ libXmu.a:  $(OBJS)
 	$(RANLIB) $@
 
 clean:
-	/bin/rm -f *.o *.a
+	$(RM) -f *.o *.a

leap/src/Xpm/Makefile

@@ -14,4 +14,4 @@ libXpm.a:  $(OBJS)
 	$(RANLIB) $@
 
 clean:
-	/bin/rm -f *.o *.a
+	$(RM) -f *.o *.a

leap/src/Xraw/Makefile

@@ -14,4 +14,4 @@ libXaw.a:  $(OBJS)
 	$(RANLIB) $@
 
 clean:
-	/bin/rm -f *.o *.a
+	$(RM) -f *.o *.a

leap/src/leap/Makefile

@@ -172,15 +172,15 @@ install: all
 	mv XaLeap_wcl $(DATDIR)
 
 uninstall:
-	-rm -f $(BINDIR)/teLeap$(SFX)
-	-rm -f $(BINDIR)/xaLeap$(SFX)
-	-rm -f $(DATDIR)/XaLeap_wcl
+	$(RM) -f $(BINDIR)/teLeap$(SFX)
+	$(RM) -f $(BINDIR)/xaLeap$(SFX)
+	$(RM) -f $(DATDIR)/XaLeap_wcl
 
 installteLeap: t
 	mv teLeap$(SFX) $(BINDIR)
 
 uninstallteLeap:
-	-rm -f $(BINDIR)/teLeap$(SFX)
+	$(RM) -f $(BINDIR)/teLeap$(SFX)
 
 teLeap$(SFX): $(TLEAP_OBJ)
 	$(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) \
@@ -209,15 +209,15 @@ utilLib2Pdb$(SFX): $(UL2P_OBJ)
 	$(CC) $(CFLAGS) $(AMBERCFLAGS) -o $@ $(UL2P_OBJ) $(LM)
 
 clean::
-	-rm -f *.o $(PROGS) *\~
-	-rm -f XaLeap_wcl
-	-rm -f *.gprof
-	-rm -f helptext.c parser.c
+	$(RM) -f *.o $(PROGS) *\~
+	$(RM) -f XaLeap_wcl
+	$(RM) -f *.gprof
+	$(RM) -f helptext.c parser.c
 
 parser.c:       parser.y parser.h
 	$(YACC) parser.y
 	@echo "(The warning 'conflicts: 6 shift/reduce' is normal)"
-	/bin/rm -f parser.c
+	$(RM) -f parser.c
 	mv y.tab.c parser.c
 
 helptext.c: helptext.text utilMakeHelp$(SFX)