reinit the tree, so we can have metadata

2 files changed, 151 insertions, 0 deletions

diff --git a/sci-chemistry/autodock_vina/files/1.1.2-gentoo.patch b/sci-chemistry/autodock_vina/files/1.1.2-gentoo.patch
new file mode 100644
index 000000000000..61ae8bec36f5
--- /dev/null
+++ b/sci-chemistry/autodock_vina/files/1.1.2-gentoo.patch
@@ -0,0 +1,72 @@
+ build/linux/debug/Makefile   |    2 +-
+ build/linux/release/Makefile |    2 +-
+ build/makefile_common        |   14 +++++++-------
+ 3 files changed, 9 insertions(+), 9 deletions(-)
+
+diff --git a/build/linux/debug/Makefile b/build/linux/debug/Makefile
+index 6a41cfc..8097fb9 100644
+--- a/build/linux/debug/Makefile
++++ b/build/linux/debug/Makefile
+@@ -1,7 +1,7 @@
+ BASE=/usr/local
+ BOOST_VERSION=1_41
+ BOOST_INCLUDE = $(BASE)/include
+-C_PLATFORM=-static -pthread
++C_PLATFORM=-pthread
+ GPP=/usr/local/bin/g++
+ C_OPTIONS= -g
+ BOOST_LIB_VERSION=
+diff --git a/build/linux/release/Makefile b/build/linux/release/Makefile
+index 1de1063..ded8133 100644
+--- a/build/linux/release/Makefile
++++ b/build/linux/release/Makefile
+@@ -1,7 +1,7 @@
+ BASE=/usr/local
+ BOOST_VERSION=1_41
+ BOOST_INCLUDE = $(BASE)/include
+-C_PLATFORM=-static -pthread
++C_PLATFORM=-pthread
+ GPP=/usr/local/bin/g++
+ C_OPTIONS= -O3 -DNDEBUG
+ BOOST_LIB_VERSION=
+diff --git a/build/makefile_common b/build/makefile_common
+index a940329..96336e8 100644
+--- a/build/makefile_common
++++ b/build/makefile_common
+@@ -2,29 +2,29 @@ LIBOBJ = cache.o coords.o current_weights.o everything.o grid.o szv_grid.o manif
+ MAINOBJ = main.o
+ SPLITOBJ = split.o
+ 
+-INCFLAGS = -I $(BOOST_INCLUDE)
++INCFLAGS = -I$(BOOST_INCLUDE)
+ 
+ # -pedantic fails on Mac with Boost 1.41 (syntax problems in their headers)
+ #CC = ${GPP} ${C_PLATFORM} -ansi -pedantic -Wno-long-long ${C_OPTIONS} $(INCFLAGS)
+ CC = ${GPP} ${C_PLATFORM} -ansi -Wno-long-long ${C_OPTIONS} $(INCFLAGS)
+ 
+-LDFLAGS = -L$(BASE)/lib -L.
++LDFLAGS += -L.
+ 
+-LIBS = -l boost_system${BOOST_LIB_VERSION} -l boost_thread${BOOST_LIB_VERSION} -l boost_serialization${BOOST_LIB_VERSION} -l boost_filesystem${BOOST_LIB_VERSION} -l boost_program_options${BOOST_LIB_VERSION}#-l pthread
++LIBS = -lboost_system -lboost_thread -lboost_serialization -lboost_filesystem -lboost_program_options -lpthread
+ 
+ .SUFFIXES: .cpp .o
+ 
+ %.o : ../../../src/lib/%.cpp 
+-	$(CC) $(CFLAGS) -o $@ -c $< 
++	$(CC) $(CXXFLAGS) -o $@ -c $< 
+ 
+ %.o : ../../../src/design/%.cpp 
+-	$(CC) $(CFLAGS) -I ../../../src/lib -o $@ -c $< 
++	$(CC) $(CXXFLAGS) -I ../../../src/lib -o $@ -c $< 
+ 	
+ %.o : ../../../src/main/%.cpp 
+-	$(CC) $(CFLAGS) -I ../../../src/lib -o $@ -c $< 
++	$(CC) $(CXXFLAGS) -I ../../../src/lib -o $@ -c $< 
+ 
+ %.o : ../../../src/split/%.cpp 
+-	$(CC) $(CFLAGS) -I ../../../src/lib -o $@ -c $< 
++	$(CC) $(CXXFLAGS) -I ../../../src/lib -o $@ -c $< 
+ 
+ all: vina vina_split
+ 
diff --git a/sci-chemistry/autodock_vina/files/autodock_vina-1.1.2-boost-filesystem.patch b/sci-chemistry/autodock_vina/files/autodock_vina-1.1.2-boost-filesystem.patch
new file mode 100644
index 000000000000..298aaa9ab993
--- /dev/null
+++ b/sci-chemistry/autodock_vina/files/autodock_vina-1.1.2-boost-filesystem.patch
@@ -0,0 +1,79 @@
+ src/main/main.cpp   | 10 +++++++++-
+ src/split/split.cpp | 11 ++++++++++-
+ 2 files changed, 19 insertions(+), 2 deletions(-)
+
+diff --git a/src/main/main.cpp b/src/main/main.cpp
+index f49c8f5..b566aa2 100644
+--- a/src/main/main.cpp
++++ b/src/main/main.cpp
+@@ -47,7 +47,7 @@
+ using boost::filesystem::path;

+ 

+ path make_path(const std::string& str) {

+-	return path(str, boost::filesystem::native);

++	return path(str);

+ }

+ 

+ void doing(int verbosity, const std::string& str, tee& log) {

+@@ -661,7 +661,11 @@ Thank you!\n";
+ 					cpu, seed, verbosity, max_modes_sz, energy_range, log);

+ 	}

+ 	catch(file_error& e) {

++#if defined(BOOST_FILESYSTEM_VERSION) && BOOST_FILESYSTEM_VERSION >= 3

++		std::cerr << "\n\nError: could not open \"" << e.name.string() << "\" for " << (e.in ? "reading" : "writing") << ".\n";

++#else

+ 		std::cerr << "\n\nError: could not open \"" << e.name.native_file_string() << "\" for " << (e.in ? "reading" : "writing") << ".\n";

++#endif

+ 		return 1;

+ 	}

+ 	catch(boost::filesystem::filesystem_error& e) {

+@@ -673,7 +677,11 @@ Thank you!\n";
+ 		return 1;

+ 	}

+ 	catch(parse_error& e) {

++#if defined(BOOST_FILESYSTEM_VERSION) && BOOST_FILESYSTEM_VERSION >= 3

++		std::cerr << "\n\nParse error on line " << e.line << " in file \"" << e.file.string() << "\": " << e.reason << '\n';

++#else

+ 		std::cerr << "\n\nParse error on line " << e.line << " in file \"" << e.file.native_file_string() << "\": " << e.reason << '\n';

++#endif

+ 		return 1;

+ 	}

+ 	catch(std::bad_alloc&) {

+diff --git a/src/split/split.cpp b/src/split/split.cpp
+index 54c614b..bc5530e 100644
+--- a/src/split/split.cpp
++++ b/src/split/split.cpp
+@@ -38,7 +38,7 @@
+ using boost::filesystem::path;

+ 

+ path make_path(const std::string& str) {

+-	return path(str, boost::filesystem::native);

++	return path(str);

+ }

+ 

+ std::string default_prefix(const std::string& input_name, const std::string& add) {

+@@ -208,7 +208,12 @@ Thank you!\n";
+ 		write_multimodel_pdbqt(tmp, ligand_prefix, flex_prefix);

+ 	}

+ 	catch(file_error& e) {

++

++#if defined(BOOST_FILESYSTEM_VERSION) && BOOST_FILESYSTEM_VERSION >= 3

++		std::cerr << "\n\nError: could not open \"" << e.name.string() << "\" for " << (e.in ? "reading" : "writing") << ".\n";

++#else

+ 		std::cerr << "\n\nError: could not open \"" << e.name.native_file_string() << "\" for " << (e.in ? "reading" : "writing") << ".\n";

++#endif

+ 		return 1;

+ 	}

+ 	catch(boost::filesystem::filesystem_error& e) {

+@@ -220,7 +225,11 @@ Thank you!\n";
+ 		return 1;

+ 	}

+ 	catch(parse_error& e) {

++#if defined(BOOST_FILESYSTEM_VERSION) && BOOST_FILESYSTEM_VERSION >= 3

++		std::cerr << "\n\nParse error on line " << e.line << " in file \"" << e.file.string() << "\": " << e.reason << '\n';

++#else

+ 		std::cerr << "\n\nParse error on line " << e.line << " in file \"" << e.file.native_file_string() << "\": " << e.reason << '\n';

++#endif

+ 		return 1;

+ 	}

+ 	catch(std::bad_alloc&) {