sci-chemistry/rosetta: removed unmaintained package

Package-Manager: Portage-3.0.8, Repoman-3.0.1
Signed-off-by: Horea Christian <chr@chymera.eu>

16 files changed, 0 insertions, 585 deletions

diff --git a/sci-chemistry/rosetta/Manifest b/sci-chemistry/rosetta/Manifest
deleted file mode 100644
index cf6a0a086..000000000
--- a/sci-chemistry/rosetta/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST patch_rosetta3.4_to_CSROSETTA3_ver1.3.txt 1187168 SHA256 071b11f6934ed308fa1f4594ee5500353d72b951c5d795fcbf4792d96e3f53c3 SHA512 7f59e0c41ad3f0a044d23bd3a4e877910aaec8a70478e1ffdf8474d77b0f4a7a5b39ca217180f888d69d1fbd5879dba80ff23b9dba4bc2fb7017a00a344916bf WHIRLPOOL 4bf39a527476e670f7459b4a03394ac800d204e45ddd7eca6d52cb36f04217b5e0ba3374a5166a55c6142939c82bd3b42055b40a320274c73bcead6e0ec120f0
-DIST rosetta3.4_source.tgz 89734375 SHA256 5ad2d06f7e4e08ef7e87c91bfe7c6d5687601f609892203c75b1abe465954e19 SHA512 d887e3660a8baecc91609463e5d64a86a48c76c72394b211cc388bf6eb49d5696a531eb1cfe19342c3bf9d399b49f1b0fb0a9682a0e166ab6594acc050a5f31e WHIRLPOOL f28706d46335da74934a4339c24c71b084fc8b2a2a2177f16a959ee2b9ea23710598b41c136ba4e18699ae7ddacb327f02a58620782554777651d50281e97fd2
diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-boinc.patch b/sci-chemistry/rosetta/files/rosetta-3.4-boinc.patch
deleted file mode 100644
index 1f6da965c..000000000
--- a/sci-chemistry/rosetta/files/rosetta-3.4-boinc.patch
+++ /dev/null
@@ -1,53 +0,0 @@
---- src/protocols/boinc/boinc_shmem.hh	2009-02-03 22:47:07.000000000 +0100
-+++ src/protocols/boinc/boinc_shmem.hh.new	2009-04-09 14:59:15.000000000 +0200
-@@ -18,7 +18,7 @@
- #include <core/types.hh>
- 
- #ifdef BOINC
--#include "boinc_api.h"
-+#include "boinc/boinc_api.h"
- #endif
- 
- namespace protocols {
---- src/protocols/boinc/boinc.hh	2009-02-03 22:47:07.000000000 +0100
-+++ src/protocols/boinc/boinc.hh.new	2009-04-09 15:00:57.000000000 +0200
-@@ -20,11 +20,11 @@
- #include <boinc_win.h>
- #include <str_util.h>
- #endif
--#include <boinc_api.h>
--#include <diagnostics.h>
--#include <error_numbers.h>
-+#include <boinc/boinc_api.h>
-+#include <boinc/diagnostics.h>
-+#include <boinc/error_numbers.h>
- #ifdef BOINC_GRAPHICS
--#include <graphics2.h>
--#include <util.h>
--#include <shmem.h>
-+#include <boinc/graphics2.h>
-+#include <boinc/util.h>
-+#include <boinc/shmem.h>
- 
---- src/utility/exit.cc	2009-02-03 22:47:28.000000000 +0100
-+++ src/utility/exit.cc.new	2009-04-09 16:23:18.000000000 +0200
-@@ -23,7 +23,7 @@
- // Boinc headers
- #ifdef BOINC
- #include <utility/io/izstream.hh>
--#include <boinc_api.h>
-+#include <boinc/boinc_api.h>
- #include <string>
- #endif
- 
---- src/utility/boinc/boinc_util.cc	2009-02-03 22:47:30.000000000 +0100
-+++ src/utility/boinc/boinc_util.cc.new	2009-04-09 16:25:16.000000000 +0200
-@@ -20,7 +20,7 @@
- //#ifdef _WIN32
- //#include <boinc_win.h>
- //#endif
--#include <boinc_api.h>
-+#include <boinc/boinc_api.h>
- 
- // C++ headers
- #include <iostream>
diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-boost.patch b/sci-chemistry/rosetta/files/rosetta-3.4-boost.patch
deleted file mode 100644
index 7c1e1ffc2..000000000
--- a/sci-chemistry/rosetta/files/rosetta-3.4-boost.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- tools/build/basic.settings | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/tools/build/basic.settings b/tools/build/basic.settings
-index ecf3237..356cd61 100644
---- a/tools/build/basic.settings
-+++ b/tools/build/basic.settings
-@@ -610,7 +610,7 @@ settings = {
-     "gcc, boost_thread" : {
-         "appends" : {
-             "defines" : [ "MULTI_THREADED" ],
--            "libraries"     : [ "pthread", "boost_thread" ],
-+            "libraries"     : [ "pthread", "boost_thread", "boost_system" ],
- 	    "library_path"  : [ "/usr/local/lib", "/opt/boost/lib" ],
-             "flags"         : {
-                 "compile"   : [ "pthread" ],
diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-boost157.patch b/sci-chemistry/rosetta/files/rosetta-3.4-boost157.patch
deleted file mode 100644
index c2d7594b6..000000000
--- a/sci-chemistry/rosetta/files/rosetta-3.4-boost157.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- src/protocols/moves/StructureRestrictor.cc | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/src/protocols/moves/StructureRestrictor.cc b/src/protocols/moves/StructureRestrictor.cc
-index 1e1f1d4..da69796 100644
---- a/src/protocols/moves/StructureRestrictor.cc
-+++ b/src/protocols/moves/StructureRestrictor.cc
-@@ -40,7 +40,7 @@
- 
- using namespace std;
- using namespace boost;
--using namespace core;
-+using namespace boost::core;
-   using namespace pose;
-   using namespace protocols::jd2;
- 
diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-fix-scons-warnings.patch b/sci-chemistry/rosetta/files/rosetta-3.4-fix-scons-warnings.patch
deleted file mode 100644
index 321d0a784..000000000
--- a/sci-chemistry/rosetta/files/rosetta-3.4-fix-scons-warnings.patch
+++ /dev/null
@@ -1,82 +0,0 @@
---- src/SConscript.src	2009-02-03 22:44:31.000000000 +0100
-+++ src/SConscript.src.new	2009-04-07 16:25:30.000000000 +0200
-@@ -85,7 +85,7 @@
- 
- # Transform the modified settings into SCons Environment variables.
- # Gives priority to project settings over global settings.
--env = build.environment.Copy()
-+env = build.environment.Clone()
- env.Prepend(**actual.symbols())
- 
- 
---- tools/build/setup.py	2009-02-03 22:44:32.000000000 +0100
-+++ tools/build/setup.py.new	2009-04-07 16:43:42.000000000 +0200
-@@ -42,21 +42,21 @@
-     # Read in the options from the .settings files (1st pass)
-     # This has to be done in two passes, because some legal values
-     # (version numbers) are dependent on the other values
--    options.AddOptions(
-+    options.AddVariables(
-         # Options for the build.  Modifiable on the command-line.
--        EnumOption("cxx", "Select the C++ compiler to build with",
-+        EnumVariable("cxx", "Select the C++ compiler to build with",
-                    defaults.cxx, supported.cxx),
--        EnumOption("os", "Select the operating system to build for",
-+        EnumVariable("os", "Select the operating system to build for",
-                    defaults.os, supported.os),
--        EnumOption("arch", "Select the processor architecture to build for",
-+        EnumVariable("arch", "Select the processor architecture to build for",
-                    defaults.arch, supported.arch),
--        EnumOption("mode", "Select the optimization mode",
-+        EnumVariable("mode", "Select the optimization mode",
-                    defaults.mode, supported.mode),
--        ListOption("cat", "Select the build category",
-+        ListVariable("cat", "Select the build category",
-                    defaults.cat, supported.cat),
--        ListOption("extras", "Select any extras",
-+        ListVariable("extras", "Select any extras",
-                    defaults.extras, supported.extras),
--        ListOption("log", "Log debugging output",
-+        ListVariable("log", "Log debugging output",
-                    defaults.log, supported.log),
-     )
- 
---- tools/build/setup.py	2009-04-07 16:44:26.000000000 +0200
-+++ tools/build/setup.py.new	2009-04-07 16:46:45.000000000 +0200
-@@ -37,7 +37,7 @@
- 
-     # Incorporate options in site and user options
-     option_files = [ "%s.options" % (name) for name in ("site", "user") ]
--    options = Options(option_files)
-+    options = Variables(option_files)
- 
-     # Read in the options from the .settings files (1st pass)
-     # This has to be done in two passes, because some legal values
-@@ -68,12 +68,12 @@
-     cxx  = env["cxx"]
-     os   = env["os"]
-     arch = env["arch"]
--    options.AddOptions(
--        EnumOption("cxx_ver", "Select the C++ compiler version",
-+    options.AddVariables(
-+        EnumVariable("cxx_ver", "Select the C++ compiler version",
-                    defaults.cxx_ver, supported.cxx[cxx]),
--        EnumOption("os_ver", "Select the operating system version",
-+        EnumVariable("os_ver", "Select the operating system version",
-                    defaults.os_ver, supported.os[os]),
--        EnumOption("arch_size", "Select the architecture bit-size",
-+        EnumVariable("arch_size", "Select the architecture bit-size",
-                    defaults.arch_size, supported.arch[arch]),
-         )
- 
---- src/SConscript.apps	2009-02-03 22:44:31.000000000 +0100
-+++ src/SConscript.apps.new	2009-04-07 16:48:06.000000000 +0200
-@@ -92,7 +92,7 @@
- 
- # Transform the modified settings into SCons Environment variables.
- # Gives priority to project settings over global settings.
--env = build.environment.Copy()
-+env = build.environment.Clone()
- env.Prepend(**actual.symbols())
- if "static" not in build.options.extras:
-   env["RPATH"] = build.toplevel + "/build/src/" + build.platform
diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-fix-valgrind.patch b/sci-chemistry/rosetta/files/rosetta-3.4-fix-valgrind.patch
deleted file mode 100644
index bc98773c1..000000000
--- a/sci-chemistry/rosetta/files/rosetta-3.4-fix-valgrind.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- tools/build/options.settings	2009-02-03 22:44:32.000000000 +0100
-+++ tools/build/options.settings.new	2009-04-07 18:12:00.000000000 +0200
-@@ -76,7 +76,7 @@
-         # Build so that valgrind can follow the memory use.
-         # Valgrind normally works fine with most executables but not
-         # with static builds, which we are doing.
--        "valgrind",
-+        "shared",
- 
-         # Build using static linking.
-         "static",
diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-gcc4.7.patch b/sci-chemistry/rosetta/files/rosetta-3.4-gcc4.7.patch
deleted file mode 100644
index d0893c183..000000000
--- a/sci-chemistry/rosetta/files/rosetta-3.4-gcc4.7.patch
+++ /dev/null
@@ -1,32 +0,0 @@
- tools/build/options.settings | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/tools/build/options.settings b/tools/build/options.settings
-index 30fb65e..f79ef5b 100644
---- a/tools/build/options.settings
-+++ b/tools/build/options.settings
-@@ -9,7 +9,7 @@
- options = {
- 
-     "cxx" : {
--        "gcc"     : [ "3.3", "3.4", "4.0", "4.1", "4.2", "4.3","4.4","4.5", "4.6", "*" ],
-+        "gcc"     : [ "3.3", "3.4", "4.0", "4.1", "4.2", "4.3","4.4","4.5", "4.6", "4.7", "*" ],
-         "icc"     : [ "8.0", "8.1", "9.0", "9.1", "10.0", "10.1", "11.1", "*" ], #PBHACK
-         "msvc"    : [ "7.0", "7.1", "8.0", "8.1", "*" ],
-         "xlc"     : [ "7.0", "8.0", "9.0", "XL", "*" ],
- src/protocols/jd2/SingleFileBuffer.cc | 2 ++
- 1 file changed, 2 insertions(+)
-
-diff --git a/src/protocols/jd2/SingleFileBuffer.cc b/src/protocols/jd2/SingleFileBuffer.cc
-index aa78d91..61ca823 100644
---- a/src/protocols/jd2/SingleFileBuffer.cc
-+++ b/src/protocols/jd2/SingleFileBuffer.cc
-@@ -28,6 +28,8 @@
- #include <ctime>      // for clock()
- #endif
- 
-+#include <unistd.h>
-+
- namespace protocols {
- namespace jd2 {
- using namespace core;
diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-gcc4.78.patch b/sci-chemistry/rosetta/files/rosetta-3.4-gcc4.78.patch
deleted file mode 100644
index 882534bfd..000000000
--- a/sci-chemistry/rosetta/files/rosetta-3.4-gcc4.78.patch
+++ /dev/null
@@ -1,32 +0,0 @@
- tools/build/options.settings | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/tools/build/options.settings b/tools/build/options.settings
-index 30fb65e..f79ef5b 100644
---- a/tools/build/options.settings
-+++ b/tools/build/options.settings
-@@ -9,7 +9,7 @@
- options = {
- 
-     "cxx" : {
--        "gcc"     : [ "3.3", "3.4", "4.0", "4.1", "4.2", "4.3","4.4","4.5", "4.6", "*" ],
-+        "gcc"     : [ "3.3", "3.4", "4.0", "4.1", "4.2", "4.3","4.4","4.5", "4.6", "4.7", "4.8", "*" ],
-         "icc"     : [ "8.0", "8.1", "9.0", "9.1", "10.0", "10.1", "11.1", "*" ], #PBHACK
-         "msvc"    : [ "7.0", "7.1", "8.0", "8.1", "*" ],
-         "xlc"     : [ "7.0", "8.0", "9.0", "XL", "*" ],
- src/protocols/jd2/SingleFileBuffer.cc | 2 ++
- 1 file changed, 2 insertions(+)
-
-diff --git a/src/protocols/jd2/SingleFileBuffer.cc b/src/protocols/jd2/SingleFileBuffer.cc
-index aa78d91..61ca823 100644
---- a/src/protocols/jd2/SingleFileBuffer.cc
-+++ b/src/protocols/jd2/SingleFileBuffer.cc
-@@ -28,6 +28,8 @@
- #include <ctime>      // for clock()
- #endif
- 
-+#include <unistd.h>
-+
- namespace protocols {
- namespace jd2 {
- using namespace core;
diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-gcc4.789.patch b/sci-chemistry/rosetta/files/rosetta-3.4-gcc4.789.patch
deleted file mode 100644
index e11532ac4..000000000
--- a/sci-chemistry/rosetta/files/rosetta-3.4-gcc4.789.patch
+++ /dev/null
@@ -1,32 +0,0 @@
- tools/build/options.settings | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/tools/build/options.settings b/tools/build/options.settings
-index 30fb65e..f79ef5b 100644
---- a/tools/build/options.settings
-+++ b/tools/build/options.settings
-@@ -9,7 +9,7 @@
- options = {
- 
-     "cxx" : {
--        "gcc"     : [ "3.3", "3.4", "4.0", "4.1", "4.2", "4.3","4.4","4.5", "4.6", "*" ],
-+        "gcc"     : [ "3.3", "3.4", "4.0", "4.1", "4.2", "4.3","4.4","4.5", "4.6", "4.7", "4.8", "4.9", "*" ],
-         "icc"     : [ "8.0", "8.1", "9.0", "9.1", "10.0", "10.1", "11.1", "*" ], #PBHACK
-         "msvc"    : [ "7.0", "7.1", "8.0", "8.1", "*" ],
-         "xlc"     : [ "7.0", "8.0", "9.0", "XL", "*" ],
- src/protocols/jd2/SingleFileBuffer.cc | 2 ++
- 1 file changed, 2 insertions(+)
-
-diff --git a/src/protocols/jd2/SingleFileBuffer.cc b/src/protocols/jd2/SingleFileBuffer.cc
-index aa78d91..61ca823 100644
---- a/src/protocols/jd2/SingleFileBuffer.cc
-+++ b/src/protocols/jd2/SingleFileBuffer.cc
-@@ -28,6 +28,8 @@
- #include <ctime>      // for clock()
- #endif
- 
-+#include <unistd.h>
-+
- namespace protocols {
- namespace jd2 {
- using namespace core;
diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-lange-fix.patch b/sci-chemistry/rosetta/files/rosetta-3.4-lange-fix.patch
deleted file mode 100644
index 17e85f882..000000000
--- a/sci-chemistry/rosetta/files/rosetta-3.4-lange-fix.patch
+++ /dev/null
@@ -1,22 +0,0 @@
- tools/build/setup.py | 8 +++++++-
- 1 file changed, 7 insertions(+), 1 deletion(-)
-
-diff --git a/tools/build/setup.py b/tools/build/setup.py
-index 4e57ff6..d8a2a08 100644
---- a/tools/build/setup.py
-+++ b/tools/build/setup.py
-@@ -354,7 +354,13 @@ what SCons will use to build the system.
-             symbols = setting.appends.symbols()
-             if symbols.has_key("ENV"):
-                 for key, value in symbols["ENV"].items():
--                    env["ENV"][key] += value
-+                    if key == "PATH":
-+                        env["ENV"][key] = value
-+                    else:
-+                        try:
-+                            env["ENV"][key] += value
-+                        except:
-+                            print key, value
-                 del symbols["ENV"]
-             env.Append(**symbols)
-         if setting.prepends:
diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-platform.patch b/sci-chemistry/rosetta/files/rosetta-3.4-platform.patch
deleted file mode 100644
index 82f0ba63f..000000000
--- a/sci-chemistry/rosetta/files/rosetta-3.4-platform.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- ./tools/build/setup_platforms.py	2009-02-03 22:44:32.000000000 +0100
-+++ ./tools/build/setup_platforms.py.new	2009-04-07 16:16:44.000000000 +0200
-@@ -274,7 +274,7 @@
-     """
-     # Note that these are very different values, and need processing
-     if globals().has_key("platform"):
--        return platform.processor() or _uname()[4]
-+        return platform.machine() or _uname()[4]
-     else:
-         return _uname()[4]
- 
diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-unbundle.patch b/sci-chemistry/rosetta/files/rosetta-3.4-unbundle.patch
deleted file mode 100644
index ba810b162..000000000
--- a/sci-chemistry/rosetta/files/rosetta-3.4-unbundle.patch
+++ /dev/null
@@ -1,47 +0,0 @@
- src/core/pack/dunbrack/RotamericSingleResidueDunbrackLibrary.tmpl.hh   | 3 +--
- .../pack/dunbrack/SemiRotamericSingleResidueDunbrackLibrary.tmpl.hh    | 3 +--
- src/utility/io/zipstream.hpp                                           | 3 +--
- 3 files changed, 3 insertions(+), 6 deletions(-)
-
-diff --git a/src/core/pack/dunbrack/RotamericSingleResidueDunbrackLibrary.tmpl.hh b/src/core/pack/dunbrack/RotamericSingleResidueDunbrackLibrary.tmpl.hh
-index 0aa44a6..299e0c5 100644
---- a/src/core/pack/dunbrack/RotamericSingleResidueDunbrackLibrary.tmpl.hh
-+++ b/src/core/pack/dunbrack/RotamericSingleResidueDunbrackLibrary.tmpl.hh
-@@ -402,8 +402,7 @@
- #include <boost/function.hpp>
- #include <boost/pool/detail/mutex.hpp>
- #include <boost/pool/poolfwd.hpp>
--#include <zlib/zlib.h>
--#include <zlib/zutil.h>
-+#include <zlib.h>
- 
- namespace core {
- namespace pack {
-diff --git a/src/core/pack/dunbrack/SemiRotamericSingleResidueDunbrackLibrary.tmpl.hh b/src/core/pack/dunbrack/SemiRotamericSingleResidueDunbrackLibrary.tmpl.hh
-index 2396126..700e78d 100644
---- a/src/core/pack/dunbrack/SemiRotamericSingleResidueDunbrackLibrary.tmpl.hh
-+++ b/src/core/pack/dunbrack/SemiRotamericSingleResidueDunbrackLibrary.tmpl.hh
-@@ -405,8 +405,7 @@
- #include <boost/function.hpp>
- #include <boost/pool/detail/mutex.hpp>
- #include <boost/pool/poolfwd.hpp>
--#include <zlib/zlib.h>
--#include <zlib/zutil.h>
-+#include <zlib.h>
- 
- namespace core {
- namespace pack {
-diff --git a/src/utility/io/zipstream.hpp b/src/utility/io/zipstream.hpp
-index adaf88c..c7d36d0 100644
---- a/src/utility/io/zipstream.hpp
-+++ b/src/utility/io/zipstream.hpp
-@@ -43,8 +43,7 @@
- 
- 
- // Zlib headers
--#include <zlib/zlib.h>
--#include <zlib/zutil.h>
-+#include <zlib.h>
- 
- 
- 
diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-user-settings.patch b/sci-chemistry/rosetta/files/rosetta-3.4-user-settings.patch
deleted file mode 100644
index d7297cfc0..000000000
--- a/sci-chemistry/rosetta/files/rosetta-3.4-user-settings.patch
+++ /dev/null
@@ -1,29 +0,0 @@
- tools/build/user.settings | 8 +++++++-
- 1 file changed, 7 insertions(+), 1 deletion(-)
-
-diff --git a/tools/build/user.settings b/tools/build/user.settings
-index 27a001f..9696e3e 100644
---- a/tools/build/user.settings
-+++ b/tools/build/user.settings
-@@ -22,7 +22,7 @@
- # and select between them from the options.  For now there is only the
- # single "user" settings.
- 
--#import os
-+import os
- settings = {
-     "user" : {
-         "prepends" : {
-@@ -38,6 +38,12 @@ settings = {
-             #"program_path"  : os.environ["PATH"].split(":"),
-         },
-         "overrides" : {
-+            "flags" : {
-+                  "compile" : [ GENTOO_CXXFLAGS ],
-+                  "link"    : [ GENTOO_LDFLAGS ],
-+            },
-+            "cc"     : os.environ["CC"],
-+            "cxx"     : os.environ["CXX"],
-         },
-         "removes" : {
-         },
diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-zlib.patch b/sci-chemistry/rosetta/files/rosetta-3.4-zlib.patch
deleted file mode 100644
index 18060add4..000000000
--- a/sci-chemistry/rosetta/files/rosetta-3.4-zlib.patch
+++ /dev/null
@@ -1,12 +0,0 @@
---- src/utility/io/zipstream.hpp	2009-02-03 22:47:27.000000000 +0100
-+++ src/utility/io/zipstream.hpp.new	2009-04-07 19:57:09.000000000 +0200
-@@ -36,8 +36,7 @@
- 
- 
- // Zlib headers
--#include <zlib/zlib.h>
--#include <zlib/zutil.h>
-+#include <zlib.h>
- 
- // C++ headers
- #include <algorithm>
diff --git a/sci-chemistry/rosetta/metadata.xml b/sci-chemistry/rosetta/metadata.xml
deleted file mode 100644
index dcf5c02f4..000000000
--- a/sci-chemistry/rosetta/metadata.xml
+++ /dev/null
@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-	<use>
-		<flag name="boinc">compile rosetta as a rosetta@home client</flag>
-		<flag name="boost">compile rosetta with boost supported code</flag>
-		<flag name="float">Build with floats rather than doubles</flag>
-		<flag name="lange">Apply patches from www.csrosetta.org</flag>
-	</use>
-	<upstream>
-		<bugs-to>mailto:general-support@mail.rosettacommons.org</bugs-to>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-chemistry/rosetta/rosetta-3.4.ebuild b/sci-chemistry/rosetta/rosetta-3.4.ebuild
deleted file mode 100644
index bf40276a7..000000000
--- a/sci-chemistry/rosetta/rosetta-3.4.ebuild
+++ /dev/null
@@ -1,171 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-# boinc support is BROKEN !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-
-EAPI=5
-
-inherit eutils multilib prefix scons-utils toolchain-funcs versionator
-
-#MY_P="${PN}$(get_major_version)_source"
-MY_P="${PN}${PV}_source"
-
-DESCRIPTION="Prediction of protein structures and protein-protein interactions"
-HOMEPAGE="http://www.rosettacommons.org/"
-SRC_URI="${MY_P}.tgz patch_rosetta3.4_to_CSROSETTA3_ver1.3.txt"
-
-LICENSE="|| ( rosetta-academic rosetta-commercial )"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="boinc +boost custom-cflags debug doc float +lange mpi +openmp X"
-
-REQUIRED_USE="?? ( mpi boinc )"
-
-RESTRICT="fetch"
-
-RDEPEND="
-	dev-db/cppdb
-	mpi? ( virtual/mpi )
-	boinc? ( sci-misc/boinc[X?] )
-	boost? ( dev-libs/boost )
-	sci-libs/rosetta-db"
-DEPEND="${RDEPEND}
-	dev-util/scons
-	doc? ( app-doc/doxygen )
-	X? ( media-libs/freeglut )"
-
-MYCONF=""
-
-S="${WORKDIR}/${PN}_source"
-
-pkg_nofetch() {
-	einfo "Go to ${HOMEPAGE} and get ${A}"
-	einfo "which must be placed in ${DISTDIR}"
-}
-
-src_prepare() {
-	local myCXXFLAGS
-	local myLDFLAGS
-
-	use custom-cflags || \
-		export CXXFLAGS="-O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -pipe"
-
-	export LD_LIBRARY_PATH=""
-	use lange && \
-		epatch \
-			"${DISTDIR}"/patch_${PN}${PV}_to_CSROSETTA3_ver1.3.txt \
-			"${FILESDIR}"/${P}-lange-fix.patch
-
-	epatch \
-		"${FILESDIR}"/${P}-platform.patch \
-		"${FILESDIR}"/${P}-user-settings.patch \
-		"${FILESDIR}"/${P}-fix-valgrind.patch \
-		"${FILESDIR}"/${P}-boinc.patch \
-		"${FILESDIR}"/${P}-boost.patch \
-		"${FILESDIR}"/${P}-boost157.patch \
-		"${FILESDIR}"/${P}-gcc4.789.patch
-
-	eprefixify tools/build/*
-
-	rm bin/* external/{dbio,scons-local,lib} -rfv || die
-
-	find external/boost_1_46_1 -name "*.hpp" -delete || die
-
-	for i in ${CXXFLAGS}; do
-		myCXXFLAGS="${myCXXFLAGS} \"${i/-/}\","
-	done
-
-	for i in ${LDFLAGS}; do
-		myLDFLAGS="${myLDFLAGS} \"${i/-/}\","
-	done
-
-	sed \
-		-e "s:GENTOO_CXXFLAGS:${myCXXFLAGS}:g" \
-		-e "s:GENTOO_LDFLAGS:${myCXXFLAGS} ${myLDFLAGS}:g" \
-		-e "s:GENTOO_LIBDIR:$(get_libdir):g" \
-		-e "/program_path/s:#::g" \
-		-i tools/build/user.settings || die
-
-	tc-export CC CXX
-
-	if use mpi; then
-		sed \
-			-e 's:mpiCC:mpicxx:g' \
-			-i tools/build/basic.settings || die
-		sed \
-			-e "/cxx/d" \
-			-i tools/build/user.settings || die
-	fi
-}
-
-src_configure() {
-	local myextras=""
-	local mymode=""
-	local mycxx=""
-
-	use boinc && EXTRAS="boinc"
-	use boost && EXTRAS=$(my_list_append "${EXTRAS}" "boost")
-	use boost && EXTRAS=$(my_list_append "${EXTRAS}" "boost_thread")
-	use float && EXTRAS=$(my_list_append "${EXTRAS}" "rosetta_float")
-	use openmp && EXTRAS=$(my_list_append "${EXTRAS}" "omp")
-	use X && EXTRAS=$(my_list_append "${EXTRAS}" "graphics")
-	use mpi && EXTRAS=$(my_list_append "${EXTRAS}" "mpi")
-
-	COMPILER=$(expr match "$(tc-getCC)" '.*\([a-z]cc\)')
-	mycxx="cxx=${COMPILER}"
-
-	test -n "${EXTRAS}" && myextras="extras=${EXTRAS}"
-
-	if use debug; then
-		mymode="debug"
-	else
-		mymode="release"
-	fi
-
-	MYCONF="mode=${mymode} ${myextras} ${mycxx}"
-}
-
-src_compile() {
-	einfo "running 'scons bin cat=src ${MYCONF}' ..."
-	escons bin cat=src ${MYCONF}
-
-	if use doc; then
-		einfo "running 'scons ${MYCONF} cat=doc' ..."
-		scons ${MYCONF} cat=doc || die "scons failed to build documentation"
-	fi
-}
-
-src_install() {
-	dolib.so build/src/release/linux/*/*/*/*/*/${EXTRAS//,/-}/*.so*
-
-	use doc && dohtml build/doc/rosetta++/docs/*
-
-	cd bin || die
-	for BIN in *; do
-		newbin ${BIN} ${BIN%%.*} || die "could not install rosetta program files"
-	done
-
-	if [[ -e "${ED}"/usr/bin/cluster ]]; then
-		mv "${ED}"/usr/bin/cluster{,-${PN}} || die
-	fi
-
-	if [[ -e "${ED}"/usr/bin/benchmark ]]; then
-		mv "${ED}"/usr/bin/benchmark{,-${PN}} || die
-	fi
-}
-
-my_filter_option() {
-	local value="$1"
-	local exp="$2"
-	local result=`echo ${value} | sed -e s/${exp}//g`
-	echo "${result}"
-	return 0;
-}
-
-my_list_append() {
-	local old_value="$1"
-	local new_value="$2"
-	test -n "${old_value}" && old_value="${old_value},"
-	echo "${old_value}${new_value}"
-	return 0;
-}