--- trunk/OOPSE-3.0/make/Makefile.in	2005/04/29 19:16:27	2217
+++ trunk/OOPSE-3.0/make/Makefile.in	2005/12/02 15:38:25	2470
@@ -52,7 +52,9 @@ PackageLibs = \
 	selection \
 	restraints \
 	lattice \
-
+	openbabel\
+        antlr\
+        mdParser
 #packages containing applications
 Applications = \
 	applications/oopse \
@@ -61,6 +63,7 @@ Applications = \
 	applications/dynamicProps \
         applications/simpleBuilder\
 	applications/nanoRodBuilder \
+	applications/atom2mdin
 
 Samples = \
 	samples/argon \
@@ -91,6 +94,7 @@ Libraries = \
 	@MPI_LIB_DIR@ 
 
 Libraries = \
+	@LIBS@ \
 	@CGAL_LIBS@ \
 	@MPI_LIB@ \
 	@MPI_F90_LIB@ 
@@ -332,6 +336,7 @@ INSTALL                = @INSTALL@
 CppCompiler            = @CXX@
 Linker                 = @CXX@
 MakeDepend             = makedepend
+LN_S                   = @LN_S@
 INSTALL                = @INSTALL@
 InstallProgram         = @INSTALL_PROGRAM@
 InstallScript          = @INSTALL_SCRIPT@
@@ -416,6 +421,10 @@ endif
     InstallFiles             = $(Executable)
   endif 
   InstallCommand           = $(InstallProgram)
+  ifneq "$(words $(LinkTargets))" "0"
+    MyLinkSource = $(patsubst %, $(MyInstallDir)/%,$(Main)) 
+    MyLinkTargets = $(patsubst %, $(MyInstallDir)/%,$(LinkTargets))
+  endif
 endif
 
 ifneq "$(words $(ForcefieldFiles))" "0"
@@ -639,6 +648,7 @@ do_create = $(call extract_objs,$(1))$(call create_arc
 create_archive = $(shell  $(StaticArchiver) $(StaticArchiverOptions) $(2) $(call find_objs, $(1)))
 remove_objs = $(shell $(Delete) $(call find_objs, $(1)))
 do_create = $(call extract_objs,$(1))$(call create_archive,$(1),$(2))$(call remove_objs,$(1))  
+do_link = $(shell $(LN_S) $(1) $(2))
 
 $(CombinedStaticLib) : $(LibDir)/.stamp_UP
 	$(Print) create $@     	
@@ -798,7 +808,7 @@ _installall : _buildall _installdata
 install : $(InstallListLoop)
 	$(Print) Done Install
 
-_installall : _buildall _installdata
+_installall : _buildall _installdata _installlinks
 
 $(MyInstallDir) : 
 	$(MkDir) $@
@@ -807,6 +817,12 @@ endif	    
 	$(Print) $(InstallFiles) 
 ifneq "$(words $(InstallFiles))" "0"
 	$(InstallCommand) $(InstallFiles) $(MyInstallDir)
+endif	    
+
+_installlinks :  $(MyInstallDir)
+ifneq "$(words $(MyLinkTargets))" "0"
+	@cd $(MyInstallDir)
+	$(foreach thisLink,$(MyLinkTargets),$(call do_link,$(MyLinkSource),$(thisLink)))
 endif	    
 
 # make statistics
@@ -819,12 +835,12 @@ $(Executable).pure :
 	$(Print) Done statistics.
 
 # make pure
-$(Executable).pure :
-	$(Purify) $(PurifyOptions) $(CppCompiler) $(LinkOptions) $(LibDirs) \
-	$(LibList) $(ObjectFiles) -o $@
+#$(Executable).pure :
+#	$(Purify) $(PurifyOptions) $(CppCompiler) $(LinkOptions) $(LibDirs) \
+#	$(LibList) $(ObjectFiles) -o $@
+#
+#pure : $(Executable).pure
 
-pure : $(Executable).pure
-
 #make cvslog
 cvslog:
 	$(DEV_ROOT)/scripts/cvs2cl