Cleanup Makefiles. Molby_command (on Mac) build target is restored.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@426 a2be9bc6-48de-4e38-9406-05402d4bc13c

diff --git a/Makefile b/Makefile
index b62e8f2..aa68840 100755 (executable)
--- a/Makefile
+++ b/Makefile
@@ -1,25 +1,29 @@
 ifeq ($(TARGET_PLATFORM),MAC)
- WXCONFIG_PREFIX = $(HOME)/Development/wxMac/osx-build/
- CPP_EXTRA_FLAGS = -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -arch ppc -arch i386 -DUSE_RUBY=1 -g -I$(PWD)/../../fftw-3.3.2/osx-build/include
+ WX_DIR = $(PWD)/../../wxWidgets-3.0.0
+ WX_LIB_DIR = $(WX_DIR)/osx-build/lib
+ WX_ARCH_DIR = $(WX_LIB_DIR)/wx/include/osx_cocoa-unicode-static-3.0
+ WX_CPPFLAGS = -isystem $(WX_ARCH_DIR) -isystem $(WX_DIR)/include -D_FILE_OFFSET_BITS=64 -D__WXMAC__ -D__WXOSX__ -D__WXOSX_COCOA__
+ WX_LDFLAGS = -L$(WX_LIB_DIR)  -framework IOKit -framework Carbon -framework Cocoa -framework AudioToolbox -framework System -framework OpenGL -framework QuickTime -lwx_osx_cocoau-3.0 -lwx_osx_cocoau_gl-3.0 -framework WebKit -lwxregexu-3.0 -lwxtiff-3.0 -lwxjpeg-3.0 -lwxpng-3.0 -lz -lpthread -liconv 
+ CPP_EXTRA_FLAGS = -isysroot /Developer/SDKs/MacOSX10.5.sdk -mmacosx-version-min=10.5 -arch ppc -arch i386 -DUSE_RUBY=1 -g -isystem $(PWD)/../../fftw-3.3.2/osx-build/include
  LD_EXTRA_FLAGS = -framework Accelerate -framework GLUT -L$(PWD)/../../fftw-3.3.2/osx-build/lib -lfftw3
- RUBY_DIR = $(HOME)/Development/ruby-1.8.7-static
- RUBY_CFLAGS = -I$(RUBY_DIR)
- RUBY_LDFLAGS = -L$(RUBY_DIR) -lruby-static
+ RUBY_DIR = $(PWD)/../../ruby-1.8.7-p160
+ RUBY_CFLAGS = -isystem $(RUBY_DIR)/osx-build/include
+ RUBY_LDFLAGS = -L$(RUBY_DIR)/osx-build/lib -lruby-static
  EXECUTABLE = Molby
  EXE_SUFFIX =
 endif
 
 ifeq ($(TARGET_PLATFORM),MSW)
  WX_DIR = $(PWD)/../../wxWidgets-3.0.0
- WX_LIB_DIR = $(WX_DIR)/msw-build-3/lib
+ WX_LIB_DIR = $(WX_DIR)/msw-build/lib
  WX_ARCH_DIR = $(WX_LIB_DIR)/wx/include/msw-unicode-static-3.0
- WX_CPPFLAGS = -I$(WX_ARCH_DIR) -I$(WX_DIR)/include -D_LARGEFIILE_SOURCE=unknown -D__WXMSW__
+ WX_CPPFLAGS = -isystem $(WX_ARCH_DIR) -isystem $(WX_DIR)/include -D_LARGEFIILE_SOURCE=unknown -D__WXMSW__
  WX_LDFLAGS = -L$(WX_LIB_DIR) -Wl,--subsystem,windows -mwindows -lwx_mswu_gl-3.0 -lopengl32 -lglu32 -lwx_mswu-3.0 -lwxregexu-3.0 -lwxexpat-3.0 -lwxtiff-3.0 -lwxjpeg-3.0 -lwxpng-3.0 -lwxzlib-3.0 -lrpcrt4 -loleaut32 -lole32 -luuid -lwinspool -lwinmm -lshell32 -lcomctl32 -lcomdlg32 -ladvapi32 -lwsock32 -lgdi32
- CPP_EXTRA_FLAGS = -O2 -I$(PWD)/../../CLAPACK-3.1.1.1-mingw/INCLUDE -I$(PWD)/../../fftw-3.3.2/msw-build-3/include
- LD_EXTRA_FLAGS = -L$(PWD)/../../CLAPACK-3.1.1.1-mingw/lib -L$(PWD)/../../fftw-3.3.2/msw-build-3/lib -llapackMinGW -lblasMinGW -lf2c_nomain -lfftw3
+ CPP_EXTRA_FLAGS = -isystem $(PWD)/../../CLAPACK-3.1.1.1-mingw/INCLUDE -isystem $(PWD)/../../fftw-3.3.2/msw-build/include
+ LD_EXTRA_FLAGS = -L$(PWD)/../../CLAPACK-3.1.1.1-mingw/lib -L$(PWD)/../../fftw-3.3.2/msw-build/lib -llapackMinGW -lblasMinGW -lf2c_nomain -lfftw3
  RUBY_DIR = $(PWD)/../../ruby-1.8.7-p160
- RUBY_CFLAGS = -I$(RUBY_DIR)/msw-build-3/include
- RUBY_LDFLAGS = -L$(RUBY_DIR)/msw-build-3/lib -lmsvcrt-ruby18-static -lws2_32
+ RUBY_CFLAGS = -isystem $(RUBY_DIR)/msw-build/include
+ RUBY_LDFLAGS = -L$(RUBY_DIR)/msw-build/lib -lmsvcrt-ruby18-static -lws2_32
  EXECUTABLE = _Molby.exe_
  FINAL_EXECUTABLE = Molby.exe
  EXE_SUFFIX = .exe
@@ -39,14 +43,30 @@ endif
 
 CPP = g++
 CC = gcc
-CFLAGS = $(CPPFLAGS) $(CPP_EXTRA_FLAGS) $(RUBY_CFLAGS) $(WX_CPPFLAGS)
-LDFLAGS = $(WX_LDFLAGS) $(LD_EXTRA_FLAGS) $(RUBY_LDFLAGS)
-DESTPREFIX = build
+
+ifeq ($(MAKECMDGOALS),debug)
+ DEBUG = 1
+endif
+
+ifeq ($(DEBUG),1)
+ DESTPREFIX = build/debug
+ COPT = -O0 -g
+else
+ DESTPREFIX = build/release
+ COPT = -O2
+endif
 DESTDIR = $(PWD)/$(DESTPREFIX)
+CFLAGS = $(CPPFLAGS) $(COPT) $(CPP_EXTRA_FLAGS) $(RUBY_CFLAGS) $(WX_CPPFLAGS)
+LDFLAGS = $(WX_LDFLAGS) $(LD_EXTRA_FLAGS) $(RUBY_LDFLAGS)
 export CFLAGS
 export LDFLAGS
 export DESTDIR
 export CC
+export TARGET_PLATFORM
+
+release: all
+
+debug: all
 
 all: $(DESTPREFIX) $(DESTPREFIX)/$(PRODUCT)
 
@@ -56,7 +76,7 @@ $(DESTPREFIX) :
 amber11 : ../amber11/src/antechamber/*.[ch] ../amber11/src/sqm/*.f ../amber11/src/config.h
        make -f ../Makefile_amber11
 
-$(DESTPREFIX)/mopac-build/mopac/mopac606$(EXE_SUFFIX) : 
+mopac/mopac606$(EXE_SUFFIX) : 
        make -f ../Makefile_mopac606_nbo
 
 ifeq ($(TARGET_PLATFORM),MSW)
@@ -76,12 +96,12 @@ $(DESTPREFIX)/$(RESOURCE) : molby.rc
 endif
 
 depend: cleandep $(DESTPREFIX) $(OBJECTS:%.o=$(DESTPREFIX)/%.d) $(EXTRA_OBJECTS:%.o=$(DESTPREFIX)/%.d)
-       cat $(DESTPREFIX)/*.d > $(DESTPREFIX)/Makefile.depend
+       cat $(DESTPREFIX)/*.d > build/Makefile.depend
 
 cleandep:
-       rm -f $(DESTPREFIX)/Makefile.depend
+       rm -f build/Makefile.depend
 
--include $(DESTPREFIX)/Makefile.depend
+-include build/Makefile.depend
 
 $(DESTPREFIX)/%.d : ../wxSources/%.cpp
        $(CPP) -MM $< >$@ $(subst -arch ppc,,$(CFLAGS))
@@ -110,10 +130,10 @@ endif
 ifeq ($(TARGET_PLATFORM),MSW)
        sh ../record_build_date.sh
 endif
-       $(CC) -c $(DESTPREFIX)/buildInfo.c -o $(DESTPREFIX)/buildInfo.o
+       $(CC) -c buildInfo.c -o $(DESTPREFIX)/buildInfo.o $(CFLAGS)
        $(CPP) -o $@ $(DESTOBJECTS) $(DESTPREFIX)/buildInfo.o $(CFLAGS) $(LDFLAGS)
 
-$(DESTPREFIX)/$(PRODUCT) : $(DESTPREFIX)/$(EXECUTABLE) ../Scripts/*.rb amber11 $(DESTPREFIX)/mopac-build/mopac/mopac606$(EXE_SUFFIX)
+$(DESTPREFIX)/$(PRODUCT) : $(DESTPREFIX)/$(EXECUTABLE) ../Scripts/*.rb amber11 mopac/mopac606$(EXE_SUFFIX)
 ifeq ($(TARGET_PLATFORM),MAC)
        rm -rf $(DESTPREFIX)/$(PRODUCT)
        mkdir -p $(DESTPREFIX)/$(PRODUCT)/Contents/MacOS
@@ -122,7 +142,7 @@ ifeq ($(TARGET_PLATFORM),MAC)
        echo -n "APPL????" > $(DESTPREFIX)/$(PRODUCT)/Contents/PkgInfo
        cp -r ../Scripts $(DESTPREFIX)/$(PRODUCT)/Contents/Resources
        cp -r amber11 $(DESTPREFIX)/$(PRODUCT)/Contents/Resources
-       cp -r $(DESTPREFIX)/mopac-build/mopac $(DESTPREFIX)/$(PRODUCT)/Contents/Resources
+       cp -r mopac $(DESTPREFIX)/$(PRODUCT)/Contents/Resources
        mkdir -p $(DESTPREFIX)/$(PRODUCT)/Contents/Resources/Scripts/lib
        for i in $(RUBY_EXTLIB); do cp $(RUBY_DIR)/lib/$$i $(DESTPREFIX)/$(PRODUCT)/Contents/Resources/Scripts/lib; done
        cp $(DESTPREFIX)/$(EXECUTABLE) $(DESTPREFIX)/$(PRODUCT)/Contents/MacOS
@@ -134,13 +154,13 @@ ifeq ($(TARGET_PLATFORM),MSW)
        cp `which mingwm10.dll` $(DESTPREFIX)/$(PRODUCT_DIR)
        cp -r ../Scripts $(DESTPREFIX)/$(PRODUCT_DIR)
        cp -r amber11 $(DESTPREFIX)/$(PRODUCT_DIR)
-       cp -r $(DESTPREFIX)/mopac-build/mopac $(DESTPREFIX)/$(PRODUCT_DIR)
+       cp -r mopac $(DESTPREFIX)/$(PRODUCT_DIR)
        mkdir -p $(DESTPREFIX)/$(PRODUCT_DIR)/Scripts/lib
        for i in $(RUBY_EXTLIB); do cp $(RUBY_DIR)/lib/$$i $(DESTPREFIX)/$(PRODUCT_DIR)/Scripts/lib; done
 endif
 
 ifeq ($(TARGET_PLATFORM),MSW)
-setup: $(DESTPREFIX)/$(PRODUCT_DIR)/$(FINAL_EXECUTABLE)
+setup: build/release/$(PRODUCT_DIR)/$(FINAL_EXECUTABLE)
        /c/Program\ Files\ \(x86\)/Inno\ Setup\ 5/iscc molby.iss
 endif
 

diff --git a/Makefile_mopac606_nbo b/Makefile_mopac606_nbo
index 5ba6e55..6636ab8 100644 (file)
--- a/Makefile_mopac606_nbo
+++ b/Makefile_mopac606_nbo
@@ -1,4 +1,4 @@
-#  Usage: make -f Makefile_mopac606_nbo (in XXXX_build directory)
+#  Usage: make -f ../Makefile_mopac606_nbo (in XXXX_build directory)
 #  Copy source files to ./build/mopac-build and build mopac606 executable there
 
 ifeq ($(TARGET_PLATFORM),)
@@ -23,13 +23,14 @@ export FLDFLAGS
 
 OPWD = $(PWD)
 MOPDIR = $(OPWD)/../mopac606_nbo/src
+BUILDDIR = build/mopac-build
 
-build/mopac-build/mopac/mopac606$(EXE_SUFFIX) : build/mopac-build/mopac606$(EXE_SUFFIX)
-       (mkdir -p build/mopac-build/mopac; cp -p build/mopac-build/mopac606$(EXE_SUFFIX) build/mopac-build/mopac)
+mopac/mopac606$(EXE_SUFFIX) : $(BUILDDIR)/mopac606$(EXE_SUFFIX)
+       (mkdir -p mopac; cp -p $(BUILDDIR)/mopac606$(EXE_SUFFIX) mopac)
 
-build/mopac-build/mopac606$(EXE_SUFFIX) : $(MOPDIR)/*.f $(MOPDIR)/SIZES $(MOPDIR)/mopnbo.f.in
-       (cd ../mopac606_nbo/src; mkdir -p $(OPWD)/build/mopac-build; cp -p * $(OPWD)/build/mopac-build/)
-       (cd build/mopac-build && $(MAKE))
+$(BUILDDIR)/mopac606$(EXE_SUFFIX) : $(MOPDIR)/*.f $(MOPDIR)/SIZES $(MOPDIR)/mopnbo.f.in
+       (cd ../mopac606_nbo/src; mkdir -p $(OPWD)/$(BUILDDIR); cp -p * $(OPWD)/$(BUILDDIR)/)
+       (cd $(BUILDDIR) && $(MAKE))
 
 clean :
-       rm -rf build/mopac-build
+       rm -rf $(BUILDDIR)

diff --git a/MolLib/Ruby_bind/ruby_bind.c b/MolLib/Ruby_bind/ruby_bind.c
index 44ebb9f..2cd793e 100644 (file)
--- a/MolLib/Ruby_bind/ruby_bind.c
+++ b/MolLib/Ruby_bind/ruby_bind.c
@@ -314,6 +314,7 @@ s_Kernel_StopSound(VALUE self)
 static VALUE
 s_Kernel_ExportToClipboard(VALUE self, VALUE sval)
 {
+#if !defined(__CMDMAC__)
        const char *s = StringValuePtr(sval);
        char *ns;
 #if __WXMSW__
@@ -347,6 +348,7 @@ s_Kernel_ExportToClipboard(VALUE self, VALUE sval)
 #endif
        if (MoleculeCallback_writeToPasteboard("TEXT", ns, strlen(ns) + 1))
                rb_raise(rb_eMolbyError, "Cannot export string to clipboard");
+#endif
        return Qnil;
 }
 

diff --git a/amber11/src/Makefile b/amber11/src/Makefile
index e951471..3c1aad8 100644 (file)
--- a/amber11/src/Makefile
+++ b/amber11/src/Makefile
@@ -9,7 +9,10 @@ export AMBERHOME=$(PWD:/src=)
 endif
 
 ifeq ($(TARGET_PLATFORM),)
-ifeq ($(findstring darwin,$(OSTYPE)),darwin)
+ifeq ($(OSTYPE),)
+OSTYPE=`uname | tr A-Z a-z`
+endif
+ifeq (($findstring darwin $(OSTYPE)),darwin)
 export TARGET_PLATFORM=MAC
 else
 export TARGET_PLATFORM=MSW
@@ -21,6 +24,7 @@ include $(CONFIG_FILE)
 install: serial
 
 serial: configured_serial
+       @echo "TARGET_PLATFORM=${TARGET_PLATFORM}, OSTYPE=$(OSTYPE) FINDSTRING=$(FINDSTRING)"
        @echo "Starting installation of ${AMBERTOOLS} at `date`".
        mkdir -p $(LIBDIR)
 #      utility routines and libraries:

diff --git a/msw-build/molby.iss b/msw-build/molby.iss
index 9666f3e..f62c191 100755 (executable)
--- a/msw-build/molby.iss
+++ b/msw-build/molby.iss
@@ -7,20 +7,20 @@ UninstallDisplayIcon = {app}\Molby.exe
 OutputBaseFileName = SetupMolby
 
 [Files]
-Source: "build\Molby\Molby.exe"; DestDir: {app}
-Source: "build\Molby\mingwm10.dll"; DestDir: {app}
-Source: "build\Molby\amber11\bin\*"; DestDir: {app}\amber11\bin
-Source: "build\Molby\amber11\dat\antechamber\*"; DestDir: {app}\amber11\dat\antechamber
-Source: "build\Molby\amber11\dat\leap\parm\*"; DestDir: {app}\amber11\dat\leap\parm
-Source: "build\Molby\Scripts\*"; DestDir: {app}\Scripts
-Source: "build\Molby\Scripts\mbsf\*"; DestDir: {app}\Scripts\mbsf
-Source: "build\Molby\Scripts\mbsf\alicyclic\*"; DestDir: {app}\Scripts\mbsf\alicyclic
-Source: "build\Molby\Scripts\mbsf\aromatic\*"; DestDir: {app}\Scripts\mbsf\aromatic
-Source: "build\Molby\Scripts\mbsf\heterocyclic\*"; DestDir: {app}\Scripts\mbsf\heterocyclic
-Source: "build\Molby\Scripts\mbsf\solvents\*"; DestDir: {app}\Scripts\mbsf\solvents
-Source: "build\Molby\Scripts\lib\*"; DestDir: {app}\Scripts\lib
-Source: "build\Molby\Scripts\basis_sets\*"; DestDir: {app}\Scripts\basis_sets
-Source: "build\Molby\mopac\*"; DestDir: {app}\mopac
+Source: "build\release\Molby\Molby.exe"; DestDir: {app}
+Source: "build\release\Molby\mingwm10.dll"; DestDir: {app}
+Source: "build\release\Molby\amber11\bin\*"; DestDir: {app}\amber11\bin
+Source: "build\release\Molby\amber11\dat\antechamber\*"; DestDir: {app}\amber11\dat\antechamber
+Source: "build\release\Molby\amber11\dat\leap\parm\*"; DestDir: {app}\amber11\dat\leap\parm
+Source: "build\release\Molby\Scripts\*"; DestDir: {app}\Scripts
+Source: "build\release\Molby\Scripts\mbsf\*"; DestDir: {app}\Scripts\mbsf
+Source: "build\release\Molby\Scripts\mbsf\alicyclic\*"; DestDir: {app}\Scripts\mbsf\alicyclic
+Source: "build\release\Molby\Scripts\mbsf\aromatic\*"; DestDir: {app}\Scripts\mbsf\aromatic
+Source: "build\release\Molby\Scripts\mbsf\heterocyclic\*"; DestDir: {app}\Scripts\mbsf\heterocyclic
+Source: "build\release\Molby\Scripts\mbsf\solvents\*"; DestDir: {app}\Scripts\mbsf\solvents
+Source: "build\release\Molby\Scripts\lib\*"; DestDir: {app}\Scripts\lib
+Source: "build\release\Molby\Scripts\basis_sets\*"; DestDir: {app}\Scripts\basis_sets
+Source: "build\release\Molby\mopac\*"; DestDir: {app}\mopac
 
 [Icons]
 Name: "{group}\Molby"; Filename: "{app}\Molby.exe"

diff --git a/record_build_date.sh b/record_build_date.sh
index e9fd2cd..54e4dda 100644 (file)
--- a/record_build_date.sh
+++ b/record_build_date.sh
@@ -2,7 +2,7 @@
 #  Usage: sh ../record_build_date.sh [--with-svn-status]
 LAST_BUILD=`date '+%Y-%m-%d %H:%M:%S %Z'`
 echo "last_build = \"$LAST_BUILD\"" > buildInfo.txt
-echo "char *gLastBuildString = \"$LAST_BUILD\";" > build/buildInfo.c
+echo "char *gLastBuildString = \"$LAST_BUILD\";" > buildInfo.c
 if [ "$1" = "--with-svn-status" ]; then
   REVISION_INFO=`(cd ..; svn status -v . --depth=empty | awk '{print $1}')`
   echo $REVISION_INFO > ../revisionInfo.txt
@@ -12,4 +12,4 @@ else
     REVISION_INFO=0
   fi
 fi
-echo "int gRevisionNumber = $REVISION_INFO;" >> build/buildInfo.c
+echo "int gRevisionNumber = $REVISION_INFO;" >> buildInfo.c

diff --git a/xcode-build/Molby.xcodeproj/project.pbxproj b/xcode-build/Molby.xcodeproj/project.pbxproj
index 0a062d3..088474d 100644 (file)
--- a/xcode-build/Molby.xcodeproj/project.pbxproj
+++ b/xcode-build/Molby.xcodeproj/project.pbxproj
@@ -28,6 +28,29 @@
                E420BE22188574F600A2B983 /* ProgressFrame.cpp in Sources */ = {isa = PBXBuildFile; fileRef = E420BE1D188574F600A2B983 /* ProgressFrame.cpp */; };
                E420BE23188574F600A2B983 /* RubyDialogFrame.cpp in Sources */ = {isa = PBXBuildFile; fileRef = E420BE1F188574F600A2B983 /* RubyDialogFrame.cpp */; };
                E420BE24188574F600A2B983 /* wxKillAddition.cpp in Sources */ = {isa = PBXBuildFile; fileRef = E420BE21188574F600A2B983 /* wxKillAddition.cpp */; };
+               E49BFBFA1886E72000188237 /* MyVersion.c in Sources */ = {isa = PBXBuildFile; fileRef = E420BE18188574D700A2B983 /* MyVersion.c */; };
+               E49BFBFB1886E74600188237 /* IntGroup.c in Sources */ = {isa = PBXBuildFile; fileRef = E4FC777D183E4F3F0064FB2E /* IntGroup.c */; };
+               E49BFBFF1886E74600188237 /* MainViewCommon.c in Sources */ = {isa = PBXBuildFile; fileRef = E4FC7781183E4F3F0064FB2E /* MainViewCommon.c */; };
+               E49BFC001886E74600188237 /* Missing.c in Sources */ = {isa = PBXBuildFile; fileRef = E4FC7790183E4F3F0064FB2E /* Missing.c */; };
+               E49BFC021886E74600188237 /* MolAction.c in Sources */ = {isa = PBXBuildFile; fileRef = E4FC7792183E4F3F0064FB2E /* MolAction.c */; };
+               E49BFC041886E74600188237 /* Molecule.c in Sources */ = {isa = PBXBuildFile; fileRef = E4FC7794183E4F3F0064FB2E /* Molecule.c */; };
+               E49BFC071886E74600188237 /* Object.c in Sources */ = {isa = PBXBuildFile; fileRef = E4FC7797183E4F3F0064FB2E /* Object.c */; };
+               E49BFC091886E74600188237 /* Dcd.c in Sources */ = {isa = PBXBuildFile; fileRef = E4FC777B183E4F3F0064FB2E /* Dcd.c */; };
+               E49BFC0B1886E74600188237 /* Parameter.c in Sources */ = {isa = PBXBuildFile; fileRef = E4FC7799183E4F3F0064FB2E /* Parameter.c */; };
+               E49BFC0D1886E74600188237 /* Trackball.c in Sources */ = {isa = PBXBuildFile; fileRef = E4FC77A4183E4F3F0064FB2E /* Trackball.c */; };
+               E49BFC0F1886E74600188237 /* Types.c in Sources */ = {isa = PBXBuildFile; fileRef = E4FC77A6183E4F3F0064FB2E /* Types.c */; };
+               E49BFC111886E74600188237 /* cmdtool_stubs.c in Sources */ = {isa = PBXBuildFile; fileRef = E4FC777A183E4F3F0064FB2E /* cmdtool_stubs.c */; };
+               E49BFC121886E75700188237 /* MDCore.c in Sources */ = {isa = PBXBuildFile; fileRef = E4FC7784183E4F3F0064FB2E /* MDCore.c */; };
+               E49BFC131886E75C00188237 /* MDEwald.c in Sources */ = {isa = PBXBuildFile; fileRef = E4FC7786183E4F3F0064FB2E /* MDEwald.c */; };
+               E49BFC141886E75D00188237 /* MDForce.c in Sources */ = {isa = PBXBuildFile; fileRef = E4FC7788183E4F3F0064FB2E /* MDForce.c */; };
+               E49BFC151886E75D00188237 /* MDGraphite.c in Sources */ = {isa = PBXBuildFile; fileRef = E4FC778A183E4F3F0064FB2E /* MDGraphite.c */; };
+               E49BFC161886E75E00188237 /* MDPressure.c in Sources */ = {isa = PBXBuildFile; fileRef = E4FC778C183E4F3F0064FB2E /* MDPressure.c */; };
+               E49BFC171886E75F00188237 /* MDSurface.c in Sources */ = {isa = PBXBuildFile; fileRef = E4FC778E183E4F3F0064FB2E /* MDSurface.c */; };
+               E49BFC191886E76F00188237 /* ruby_bind.c in Sources */ = {isa = PBXBuildFile; fileRef = E4FC779F183E4F3F0064FB2E /* ruby_bind.c */; };
+               E49BFC1B1886E77000188237 /* ruby_md.c in Sources */ = {isa = PBXBuildFile; fileRef = E4FC77A2183E4F3F0064FB2E /* ruby_md.c */; };
+               E49BFC1C1886E77100188237 /* ruby_types.c in Sources */ = {isa = PBXBuildFile; fileRef = E4FC77A3183E4F3F0064FB2E /* ruby_types.c */; };
+               E49BFC1F1886E78600188237 /* buildInfo.c in Sources */ = {isa = PBXBuildFile; fileRef = E4FC7CA5183F94D30064FB2E /* buildInfo.c */; };
+               E49BFC2C1886E88A00188237 /* Accelerate.framework in Frameworks */ = {isa = PBXBuildFile; fileRef = E4FC7810183E50DC0064FB2E /* Accelerate.framework */; };
                E4FC77A9183E4F3F0064FB2E /* Dcd.c in Sources */ = {isa = PBXBuildFile; fileRef = E4FC777B183E4F3F0064FB2E /* Dcd.c */; };
                E4FC77AA183E4F3F0064FB2E /* IntGroup.c in Sources */ = {isa = PBXBuildFile; fileRef = E4FC777D183E4F3F0064FB2E /* IntGroup.c */; };
                E4FC77AB183E4F3F0064FB2E /* MainView.c in Sources */ = {isa = PBXBuildFile; fileRef = E4FC777F183E4F3F0064FB2E /* MainView.c */; };
@@ -111,6 +134,7 @@
                E420BE1F188574F600A2B983 /* RubyDialogFrame.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = RubyDialogFrame.cpp; sourceTree = "<group>"; };
                E420BE20188574F600A2B983 /* RubyDialogFrame.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = RubyDialogFrame.h; sourceTree = "<group>"; };
                E420BE21188574F600A2B983 /* wxKillAddition.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = wxKillAddition.cpp; sourceTree = "<group>"; };
+               E49BFB761886E2E400188237 /* Molby_command */ = {isa = PBXFileReference; explicitFileType = "compiled.mach-o.executable"; includeInIndex = 0; path = Molby_command; sourceTree = BUILT_PRODUCTS_DIR; };
                E4FC777A183E4F3F0064FB2E /* cmdtool_stubs.c */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.c; name = cmdtool_stubs.c; path = ../MolLib/cmdtool_stubs.c; sourceTree = SOURCE_ROOT; };
                E4FC777B183E4F3F0064FB2E /* Dcd.c */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.c; name = Dcd.c; path = ../MolLib/Dcd.c; sourceTree = SOURCE_ROOT; };
                E4FC777C183E4F3F0064FB2E /* Dcd.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; name = Dcd.h; path = ../MolLib/Dcd.h; sourceTree = SOURCE_ROOT; };
@@ -158,8 +182,8 @@
                E4FC77C9183E4FCD0064FB2E /* style.css */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text.css; name = style.css; path = ../Documents/etc/style.css; sourceTree = SOURCE_ROOT; };
                E4FC77D4183E4FF20064FB2E /* molby_icon.icns */ = {isa = PBXFileReference; lastKnownFileType = image.icns; name = molby_icon.icns; path = ../bitmaps/molby_icon.icns; sourceTree = SOURCE_ROOT; };
                E4FC77D6183E4FFE0064FB2E /* Scripts */ = {isa = PBXFileReference; lastKnownFileType = folder; name = Scripts; path = ../Scripts; sourceTree = SOURCE_ROOT; };
-               E4FC77D8183E503E0064FB2E /* amber11 */ = {isa = PBXFileReference; lastKnownFileType = folder; path = amber11; sourceTree = "<group>"; };
-               E4FC7806183E50710064FB2E /* mopac */ = {isa = PBXFileReference; lastKnownFileType = folder; name = mopac; path = "build/mopac-build/mopac"; sourceTree = SOURCE_ROOT; };
+               E4FC77D8183E503E0064FB2E /* amber11 */ = {isa = PBXFileReference; lastKnownFileType = folder; path = amber11; sourceTree = SOURCE_ROOT; };
+               E4FC7806183E50710064FB2E /* mopac */ = {isa = PBXFileReference; lastKnownFileType = folder; path = mopac; sourceTree = SOURCE_ROOT; };
                E4FC7810183E50DC0064FB2E /* Accelerate.framework */ = {isa = PBXFileReference; lastKnownFileType = wrapper.framework; name = Accelerate.framework; path = /System/Library/Frameworks/Accelerate.framework; sourceTree = "<absolute>"; };
                E4FC7837183E50F00064FB2E /* AGL.framework */ = {isa = PBXFileReference; lastKnownFileType = wrapper.framework; name = AGL.framework; path = /System/Library/Frameworks/AGL.framework; sourceTree = "<absolute>"; };
                E4FC7845183E51180064FB2E /* Carbon.framework */ = {isa = PBXFileReference; lastKnownFileType = wrapper.framework; name = Carbon.framework; path = /System/Library/Frameworks/Carbon.framework; sourceTree = "<absolute>"; };
@@ -173,7 +197,7 @@
                E4FC7A16183E51570064FB2E /* Foundation.framework */ = {isa = PBXFileReference; lastKnownFileType = wrapper.framework; name = Foundation.framework; path = ../../../../../../System/Library/Frameworks/Foundation.framework; sourceTree = SOURCE_ROOT; };
                E4FC7B58183E53710064FB2E /* WebKit.framework */ = {isa = PBXFileReference; lastKnownFileType = wrapper.framework; name = WebKit.framework; path = /System/Library/Frameworks/WebKit.framework; sourceTree = "<absolute>"; };
                E4FC7C16183E54730064FB2E /* Molby-Info.plist */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text.plist.xml; path = "Molby-Info.plist"; sourceTree = SOURCE_ROOT; };
-               E4FC7CA5183F94D30064FB2E /* buildInfo.c */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.c; name = buildInfo.c; path = build/buildInfo.c; sourceTree = SOURCE_ROOT; };
+               E4FC7CA5183F94D30064FB2E /* buildInfo.c */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.c; path = buildInfo.c; sourceTree = SOURCE_ROOT; };
                E4FC7CAC183F953E0064FB2E /* AudioToolbox.framework */ = {isa = PBXFileReference; lastKnownFileType = wrapper.framework; name = AudioToolbox.framework; path = /System/Library/Frameworks/AudioToolbox.framework; sourceTree = "<absolute>"; };
 /* End PBXFileReference section */
 
@@ -198,6 +222,14 @@
                        );
                        runOnlyForDeploymentPostprocessing = 0;
                };
+               E49BFB741886E2E400188237 /* Frameworks */ = {
+                       isa = PBXFrameworksBuildPhase;
+                       buildActionMask = 2147483647;
+                       files = (
+                               E49BFC2C1886E88A00188237 /* Accelerate.framework in Frameworks */,
+                       );
+                       runOnlyForDeploymentPostprocessing = 0;
+               };
 /* End PBXFrameworksBuildPhase section */
 
 /* Begin PBXGroup section */
@@ -205,6 +237,7 @@
                        isa = PBXGroup;
                        children = (
                                8D1107320486CEB800E47090 /* Molby.app */,
+                               E49BFB761886E2E400188237 /* Molby_command */,
                        );
                        name = Products;
                        sourceTree = "<group>";
@@ -427,6 +460,22 @@
                        productReference = 8D1107320486CEB800E47090 /* Molby.app */;
                        productType = "com.apple.product-type.application";
                };
+               E49BFB751886E2E400188237 /* Molby_command */ = {
+                       isa = PBXNativeTarget;
+                       buildConfigurationList = E49BFB7A1886E30200188237 /* Build configuration list for PBXNativeTarget "Molby_command" */;
+                       buildPhases = (
+                               E49BFB731886E2E400188237 /* Sources */,
+                               E49BFB741886E2E400188237 /* Frameworks */,
+                       );
+                       buildRules = (
+                       );
+                       dependencies = (
+                       );
+                       name = Molby_command;
+                       productName = Molby_command;
+                       productReference = E49BFB761886E2E400188237 /* Molby_command */;
+                       productType = "com.apple.product-type.tool";
+               };
 /* End PBXNativeTarget section */
 
 /* Begin PBXProject section */
@@ -447,6 +496,7 @@
                        projectRoot = "";
                        targets = (
                                8D1107260486CEB800E47090 /* Molby */,
+                               E49BFB751886E2E400188237 /* Molby_command */,
                        );
                };
 /* End PBXProject section */
@@ -532,6 +582,35 @@
                        );
                        runOnlyForDeploymentPostprocessing = 0;
                };
+               E49BFB731886E2E400188237 /* Sources */ = {
+                       isa = PBXSourcesBuildPhase;
+                       buildActionMask = 2147483647;
+                       files = (
+                               E49BFBFA1886E72000188237 /* MyVersion.c in Sources */,
+                               E49BFBFB1886E74600188237 /* IntGroup.c in Sources */,
+                               E49BFBFF1886E74600188237 /* MainViewCommon.c in Sources */,
+                               E49BFC001886E74600188237 /* Missing.c in Sources */,
+                               E49BFC021886E74600188237 /* MolAction.c in Sources */,
+                               E49BFC041886E74600188237 /* Molecule.c in Sources */,
+                               E49BFC071886E74600188237 /* Object.c in Sources */,
+                               E49BFC091886E74600188237 /* Dcd.c in Sources */,
+                               E49BFC0B1886E74600188237 /* Parameter.c in Sources */,
+                               E49BFC0D1886E74600188237 /* Trackball.c in Sources */,
+                               E49BFC0F1886E74600188237 /* Types.c in Sources */,
+                               E49BFC111886E74600188237 /* cmdtool_stubs.c in Sources */,
+                               E49BFC121886E75700188237 /* MDCore.c in Sources */,
+                               E49BFC131886E75C00188237 /* MDEwald.c in Sources */,
+                               E49BFC141886E75D00188237 /* MDForce.c in Sources */,
+                               E49BFC151886E75D00188237 /* MDGraphite.c in Sources */,
+                               E49BFC161886E75E00188237 /* MDPressure.c in Sources */,
+                               E49BFC171886E75F00188237 /* MDSurface.c in Sources */,
+                               E49BFC191886E76F00188237 /* ruby_bind.c in Sources */,
+                               E49BFC1B1886E77000188237 /* ruby_md.c in Sources */,
+                               E49BFC1C1886E77100188237 /* ruby_types.c in Sources */,
+                               E49BFC1F1886E78600188237 /* buildInfo.c in Sources */,
+                       );
+                       runOnlyForDeploymentPostprocessing = 0;
+               };
 /* End PBXSourcesBuildPhase section */
 
 /* Begin XCBuildConfiguration section */
@@ -551,17 +630,17 @@
                                GCC_REUSE_STRINGS = NO;
                                GCC_SYMBOLS_PRIVATE_EXTERN = YES;
                                HEADER_SEARCH_PATHS = (
-                                       "$(PROJECT_DIR)/../../fftw-3.3.2/osx-build-3/include",
+                                       "$(PROJECT_DIR)/../../fftw-3.3.2/osx-build/include",
                                        "$(PROJECT_DIR)/../../wxWidgets-3.0.0/include",
                                        "$(PROJECT_DIR)/../../wxWidgets-3.0.0/osx-build/lib/wx/include/osx_cocoa-unicode-static-3.0",
-                                       "$(PROJECT_DIR)/../../ruby-1.8.7-p160/osx-build-3/include",
+                                       "$(PROJECT_DIR)/../../ruby-1.8.7-p160/osx-build/include",
                                );
                                INFOPLIST_FILE = "Molby-Info.plist";
                                INSTALL_PATH = "$(HOME)/Applications";
                                LIBRARY_SEARCH_PATHS = (
-                                       "$(PROJECT_DIR)/../../fftw-3.3.2/osx-build-3/lib",
+                                       "$(PROJECT_DIR)/../../fftw-3.3.2/osx-build/lib",
                                        "$(PROJECT_DIR)/../../wxWidgets-3.0.0/osx-build/lib",
-                                       "$(PROJECT_DIR)/../../ruby-1.8.7-p160/osx-build-3/lib",
+                                       "$(PROJECT_DIR)/../../ruby-1.8.7-p160/osx-build/lib",
                                );
                                OTHER_CFLAGS = (
                                        "-D_FILE_OFFSET_BITS=64",
@@ -604,17 +683,17 @@
                                GCC_REUSE_STRINGS = NO;
                                GCC_SYMBOLS_PRIVATE_EXTERN = YES;
                                HEADER_SEARCH_PATHS = (
-                                       "$(PROJECT_DIR)/../../fftw-3.3.2/osx-build-3/include",
+                                       "$(PROJECT_DIR)/../../fftw-3.3.2/osx-build/include",
                                        "$(PROJECT_DIR)/../../wxWidgets-3.0.0/include",
                                        "$(PROJECT_DIR)/../../wxWidgets-3.0.0/osx-build/lib/wx/include/osx_cocoa-unicode-static-3.0",
-                                       "$(PROJECT_DIR)/../../ruby-1.8.7-p160/osx-build-3/include",
+                                       "$(PROJECT_DIR)/../../ruby-1.8.7-p160/osx-build/include",
                                );
                                INFOPLIST_FILE = "Molby-Info.plist";
                                INSTALL_PATH = "$(HOME)/Applications";
                                LIBRARY_SEARCH_PATHS = (
-                                       "$(PROJECT_DIR)/../../fftw-3.3.2/osx-build-3/lib",
+                                       "$(PROJECT_DIR)/../../fftw-3.3.2/osx-build/lib",
                                        "$(PROJECT_DIR)/../../wxWidgets-3.0.0/osx-build/lib",
-                                       "$(PROJECT_DIR)/../../ruby-1.8.7-p160/osx-build-3/lib",
+                                       "$(PROJECT_DIR)/../../ruby-1.8.7-p160/osx-build/lib",
                                );
                                OTHER_CFLAGS = (
                                        "-D_FILE_OFFSET_BITS=64",
@@ -649,6 +728,7 @@
                                        i386,
                                );
                                GCC_C_LANGUAGE_STANDARD = gnu99;
+                               GCC_MODEL_TUNING = G5;
                                GCC_OPTIMIZATION_LEVEL = 0;
                                GCC_WARN_ABOUT_RETURN_TYPE = YES;
                                GCC_WARN_UNUSED_VARIABLE = YES;
@@ -666,6 +746,8 @@
                                        i386,
                                );
                                GCC_C_LANGUAGE_STANDARD = gnu99;
+                               GCC_MODEL_TUNING = G5;
+                               GCC_OPTIMIZATION_LEVEL = 2;
                                GCC_WARN_ABOUT_RETURN_TYPE = YES;
                                GCC_WARN_UNUSED_VARIABLE = YES;
                                PREBINDING = NO;
@@ -673,6 +755,57 @@
                        };
                        name = Release;
                };
+               E49BFB781886E2E400188237 /* Debug */ = {
+                       isa = XCBuildConfiguration;
+                       buildSettings = {
+                               ALWAYS_SEARCH_USER_PATHS = NO;
+                               COPY_PHASE_STRIP = NO;
+                               GCC_VERSION = 4.2;
+                               HEADER_SEARCH_PATHS = (
+                                       "$(PROJECT_DIR)/../../fftw-3.3.2/osx-build/include",
+                                       "$(PROJECT_DIR)/../../ruby-1.8.7-p160/osx-build/include",
+                               );
+                               INSTALL_PATH = /usr/local/bin;
+                               LIBRARY_SEARCH_PATHS = (
+                                       "$(PROJECT_DIR)/../../fftw-3.3.2/osx-build/lib",
+                                       "$(PROJECT_DIR)/../../ruby-1.8.7-p160/osx-build/lib",
+                               );
+                               OTHER_CFLAGS = "-D__CMDMAC__=1";
+                               OTHER_LDFLAGS = (
+                                       "-lfftw3",
+                                       "-lruby-static",
+                               );
+                               PREBINDING = NO;
+                               PRODUCT_NAME = Molby_command;
+                       };
+                       name = Debug;
+               };
+               E49BFB791886E2E400188237 /* Release */ = {
+                       isa = XCBuildConfiguration;
+                       buildSettings = {
+                               ALWAYS_SEARCH_USER_PATHS = NO;
+                               COPY_PHASE_STRIP = YES;
+                               DEBUG_INFORMATION_FORMAT = "dwarf-with-dsym";
+                               GCC_VERSION = 4.2;
+                               HEADER_SEARCH_PATHS = (
+                                       "$(PROJECT_DIR)/../../fftw-3.3.2/osx-build/include",
+                                       "$(PROJECT_DIR)/../../ruby-1.8.7-p160/osx-build/include",
+                               );
+                               INSTALL_PATH = /usr/local/bin;
+                               LIBRARY_SEARCH_PATHS = (
+                                       "$(PROJECT_DIR)/../../fftw-3.3.2/osx-build/lib",
+                                       "$(PROJECT_DIR)/../../ruby-1.8.7-p160/osx-build/lib",
+                               );
+                               OTHER_CFLAGS = "-D__CMDMAC__=1";
+                               OTHER_LDFLAGS = (
+                                       "-lfftw3",
+                                       "-lruby-static",
+                               );
+                               PREBINDING = NO;
+                               PRODUCT_NAME = Molby_command;
+                       };
+                       name = Release;
+               };
 /* End XCBuildConfiguration section */
 
 /* Begin XCConfigurationList section */
@@ -694,6 +827,15 @@
                        defaultConfigurationIsVisible = 0;
                        defaultConfigurationName = Release;
                };
+               E49BFB7A1886E30200188237 /* Build configuration list for PBXNativeTarget "Molby_command" */ = {
+                       isa = XCConfigurationList;
+                       buildConfigurations = (
+                               E49BFB781886E2E400188237 /* Debug */,
+                               E49BFB791886E2E400188237 /* Release */,
+                       );
+                       defaultConfigurationIsVisible = 0;
+                       defaultConfigurationName = Release;
+               };
 /* End XCConfigurationList section */
        };
        rootObject = 29B97313FDCFA39411CA2CEA /* Project object */;