reinit the tree, so we can have metadata

5 files changed, 233 insertions, 0 deletions

diff --git a/sci-chemistry/autodock_vina/Manifest b/sci-chemistry/autodock_vina/Manifest
new file mode 100644
index 000000000000..5dbd7c90c62e
--- /dev/null
+++ b/sci-chemistry/autodock_vina/Manifest
@@ -0,0 +1,7 @@
+AUX 1.1.2-gentoo.patch 2448 SHA256 41a0f4091be44dc2a59a7f32fedc18fb6e8266740284c756f5b79f39a5080d57 SHA512 d8165d88f3e91064c74f1506a7f58473a74f6ebf993165827694d78170b29227dc378c61a7f096a3c49708b713583aca3d5714827d1fe43a5bb37f3d648d2613 WHIRLPOOL b169152e3e00b479a1cc7ef3dd6bcfa00dd2f9eb2b3f2ec0b584e2d894c515507ae1036fc3c009d2bd6f180afc086f3ffccd9570ffa34383f5846d3fa60a27d4
+AUX autodock_vina-1.1.2-boost-filesystem.patch 2936 SHA256 b7e6304fcee336bccd4f0244a24745f34f3bc7582f9f887fa885af99aa4f0947 SHA512 4226fb0d7196362a02afa4e0b0616146ef816a439dd63e1bffbfef183975fe7e6260318f919e9d9835d2d47973542b5340e93ad35b070467e42c0990f9a635f7 WHIRLPOOL 845159f7ea1caad30926b812867fe9e93377d27d83a486b504bf6d9876e2f13ca48855f803108c41b63da4070ec7ff23a65c64995ced0be8db1aa005c20cfe37
+DIST autodock_vina_1_1_2.tgz 67366 SHA256 b86412d316960b1e4e319401719daf57ff009229d91654d623c3cf09339f6776 SHA512 f704af322ebc192117c49d0cf8a3f217105beccb7b47d6361665470894ef7a9f91fc4b5f07cc9aff56e497bfa80953e40e39090c8394a095c61597756e333ae9 WHIRLPOOL b68f3bb81fe957fddb6674f71e0c63d1425eb5b4de0615258545ba8e241b347380c8745ee47bd2ee2257f29916191773440e3dd4e9ce857b83a947074eae8d45
+EBUILD autodock_vina-1.1.2.ebuild 932 SHA256 1b93b28ae1a083e18488a051203a3b5b6bf19e2f4ffad2e5e7350b1fa4f45164 SHA512 39f8acb795d17786a5112a4e70bf67c6ab594d25ab5eb4b739e2b0c70a9e0548265bcd5f36b6d4915b82b43a0f463187f8d9dc5aaa62f925c5172950a6bc26ee WHIRLPOOL a248e2bbd762f2af05afbc06f87af44280b725c66a584dd133f2e0d41aff764a6148a13d5441d3a3e078235c42df77a4079e4c28b083959794ddd6cb02835dd9
+MISC ChangeLog 2908 SHA256 1709392f8c6af9c9a333c7f41b8704a24b8faa024a576465512ce04ad527f9e7 SHA512 6adfb55110faf393f71a490f34d7c0c37494ede8192bfa05e683533f955cc82ae4c82ec2b65ad375d9d24219c4befac9fb86547e14187500f1f84cda46c35b8c WHIRLPOOL 42220c8bf5a5ab34c7bd8083c55741d2e85a1be69acf362fbbb5ca2dfc39f93e7cdb7c28bf7bf2c1b413cb5ef8134f2df26ce708d8f574f2d355b60825e43aeb
+MISC ChangeLog-2015 1914 SHA256 129b9a4a71807910a677edfa70f2bf88f46bd895a185febca45289ec0e9f71e7 SHA512 662b2f5038db3fe01bea84ad8a1ed40c95fbb5e4c28533ef8d665e06efd64f4fe40f0f5d7dc11497799aa72aae5557255b6913b122fbc3c78ab8e5875474de3c WHIRLPOOL 4a26d113831b76b817cf0dd195fbd388e3edf51e177e5e735e7158a7924d0089bf1e1815883a9ddb5c03d81412fe2898cde5e7528456339b6029f4ab3448cc33
+MISC metadata.xml 1234 SHA256 9c8715e6ffac3433885b0c5a5b778d19134e45b20bcf41ac4bbfeb0d6ad54cfa SHA512 b9b8753dacfaf0e511a90ad6fd1612fa3f11ac238654ccb6ad3a052026e366fc141776c6578923a024c77b8f2d6e37a9949822daa8d458902d383c1434eb6da9 WHIRLPOOL d808fedd3597aa5f4a71adbcfcde1d29d37f04442d9d7cbf5976c4e9023cbcae12d47c706a0dca1fe815bba4f7137ce0e4929b02400e778971c98b01a5da2bf4
diff --git a/sci-chemistry/autodock_vina/autodock_vina-1.1.2.ebuild b/sci-chemistry/autodock_vina/autodock_vina-1.1.2.ebuild
new file mode 100644
index 000000000000..bbff27f85e2f
--- /dev/null
+++ b/sci-chemistry/autodock_vina/autodock_vina-1.1.2.ebuild
@@ -0,0 +1,46 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+inherit eutils flag-o-matic versionator
+
+MY_P="${PN}_$(replace_all_version_separators _)"
+
+DESCRIPTION="Program for drug discovery, molecular docking and virtual screening"
+HOMEPAGE="http://vina.scripps.edu/"
+SRC_URI="http://vina.scripps.edu/download/${MY_P}.tgz"
+
+SLOT="0"
+KEYWORDS="amd64 x86"
+LICENSE="Apache-2.0"
+IUSE="debug"
+
+RDEPEND="dev-libs/boost[threads]"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}"/${MY_P}/build/linux/release
+
+src_prepare() {
+	cd "${WORKDIR}"/${MY_P} || die
+	epatch \
+		"${FILESDIR}"/${PV}-gentoo.patch \
+		"${FILESDIR}"/${P}-boost-filesystem.patch
+}
+
+src_compile() {
+	local c_options
+
+	use debug || c_options="-DNDEBUG"
+
+	append-cxxflags -DBOOST_FILESYSTEM_VERSION=3
+
+	emake \
+		BASE="${EPREFIX}"/usr/ \
+		GPP="$(tc-getCXX)" \
+		C_OPTIONS="${c_options}"
+}
+
+src_install() {
+	dobin vina{,_split}
+}
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&) {

diff --git a/sci-chemistry/autodock_vina/metadata.xml b/sci-chemistry/autodock_vina/metadata.xml
new file mode 100644
index 000000000000..e255923b229e
--- /dev/null
+++ b/sci-chemistry/autodock_vina/metadata.xml
@@ -0,0 +1,29 @@
+<?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>
+  <longdescription>
+AutoDock Vina is a new open-source program for drug discovery, molecular
+docking and virtual screening, offering multi-core capability, high
+performance and enhanced accuracy and ease of use. [1]
+AutoDock Vina has been designed and implemented by Dr. Oleg Trott
+in the Molecular Graphics Lab at The Scripps Research Institute.
+If you used AutoDock Vina in your work, please cite:
+O. Trott, A. J. Olson, AutoDock Vina: improving the speed and accuracy
+of docking with a new scoring function, efficient optimization and
+multithreading
+Journal of Computational Chemistry 31 (2010) 455-461
+</longdescription>
+  <!--
+<use>
+  <flag name='flag'>Description of how USE='flag' affects this package</flag>
+  <flag name='userland_GNU'>Description of how USERLAND='GNU' affects this
+	  package</flag>
+  <flag name='aspell'>Uses <pkg>app-text/aspell</pkg> for spell checking.
+	  Requires an installed dictionary from <cat>app-dicts</cat></flag>
+</use>
+-->
+</pkgmetadata>