reinit the tree, so we can have metadata

5 files changed, 202 insertions, 0 deletions

diff --git a/sci-chemistry/dssp/Manifest b/sci-chemistry/dssp/Manifest
new file mode 100644
index 000000000000..c8f837aea7fe
--- /dev/null
+++ b/sci-chemistry/dssp/Manifest
@@ -0,0 +1,7 @@
+AUX dssp-2.1.0-gentoo.patch 1513 SHA256 76970f86426bcb1e5155117a784541a51e9489b70263a5f66761058c9251ad25 SHA512 7d192019811a6892031c74e14ef9fc7461e77c050a164698f8c72cff08f81a0e6da202e0915b631a5cd6d910a6114a736c706d47b1fd6474ff77c3700efcd9f9 WHIRLPOOL 0834a1d3eae75de760cb361d21a84c39f3c97cdcd11158c7775812506903a3e288720789c1d2880bb3966b29dadea16d81fd66604c1a7559be399153712a5c33
+AUX dssp-2.2.1-boost-1.65-tr1-removal.patch 2126 SHA256 d59a4d7c5c9f1ca1cae2073b554d28edfb36128265dc8dc07fc55b07c3024857 SHA512 8f84c6e163888d6a8192683a6555f7d6003634854f5cde0f6f962744e531165c7e0b2b08c55cbfb9c396d167c44317dd2e7a8290e4defd2c8def0a6511fbbd6c WHIRLPOOL 919ef00d60d9a621e752e6fcc6125318d20e3a424e1b8afdba50f37d28fa695ed61765b99e0fe997ef6ff2df6cd6bbfb5747fe74eae4ab52e63df530e636b5eb
+DIST dssp-2.2.1.tgz 47141 SHA256 5fb5e7c085de16c05981e3a72869c8b082911a0b46e6dcc6dbd669c9f267e8e1 SHA512 4a273714d6b3230daea166caa7f4117d5ccb225bea0cf1bc2eb61539b6cc8e227d0ba19047d61f0ad0d1d6bc2efdec9c193bd44341e15ef0950acb4a22498811 WHIRLPOOL abdb6777ccc06b062e3f20226c555348cd221d9c3e14d2adb9aeb85f14f84db8841c2fbbc4a487f5fa021da6616cddf2e96fde787d7670c419926d24d24944bd
+EBUILD dssp-2.2.1-r1.ebuild 962 SHA256 9045f91f7cfdeee3dccd3c02815e84762f91c9f95e430817c66051c88d23f85b SHA512 9488695b51ddfea2127b3b7e02e36095f494ba20f14eeb81b5ab9b6dd4a47bdaae6b517a6f27ad49af75202080f6fa511ea8efdd3aca8a7eee6fe8b7b31ec501 WHIRLPOOL 16f20d85b7f5ef8f803ad326f11719b1db8f541404d194ff3eb9afa8040692ea0ebd5c5a22adf887052261524ec6dd3c7e9114677754fafb813912fb2b5f9cac
+MISC ChangeLog 2958 SHA256 bd7a62613a65a005bcd36e23332edfad48515bfa1d34306e0e59e5e83ad3de8b SHA512 1847b40deee64d21d550aadf8650d0f50bb756a4068387392772e7d6f33532827e6a662d3c2b46722a9565a479116190f11c9f3c251d7d198f379346a631da41 WHIRLPOOL bafe24db0f788d1d3fb207912571dcc680f2b7ab2f0894d6c89e43b801f646fb31a4ff16cfb7c3f9de190e8c32ab8871defd19220218d89e496605a57e8faa30
+MISC ChangeLog-2015 2819 SHA256 a422307fec099c15ed41519c373f1f36deff9f2fbe570c2869fa7bf9d62dd9d3 SHA512 81ab13649c11ef7800dae3b85c03a67b9c27f1793a9f4f18c8ec66ce2c3d4294f1647ace9201bb51c44f8799ea2b84ec215d81e8868c9dc3700f1ef90cdb7043 WHIRLPOOL bcf46f6e4e3b7b0d06e04cc76e501eec75ea0483eeef86ec7299b4b4251170231a8eae73f9f4e58174d3d1b558745590e399a0217245309697760f1c55c3984d
+MISC metadata.xml 271 SHA256 70036ea85140f86ed670bc2791c9de861c4b6164755ee36a2560d1c812ec13f6 SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 WHIRLPOOL 1ccb964819c99258af550a41c6712ba8ebdecbec1c821106de2f22c37b1c981cd4f324856a8014b08bd186bcd2a7fa45a7e772cc15705d1a39016b5229e77269
diff --git a/sci-chemistry/dssp/dssp-2.2.1-r1.ebuild b/sci-chemistry/dssp/dssp-2.2.1-r1.ebuild
new file mode 100644
index 000000000000..b660e9ef3c96
--- /dev/null
+++ b/sci-chemistry/dssp/dssp-2.2.1-r1.ebuild
@@ -0,0 +1,45 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit toolchain-funcs
+
+DESCRIPTION="The protein secondary structure standard"
+HOMEPAGE="http://swift.cmbi.ru.nl/gv/dssp/"
+SRC_URI="ftp://ftp.cmbi.ru.nl/pub/molbio/software/dssp-2/${P}.tgz"
+
+LICENSE="Boost-1.0"
+SLOT="0"
+KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND="dev-libs/boost:=[threads]"
+DEPEND="${RDEPEND}"
+
+PATCHES=(
+	"${FILESDIR}"/${PN}-2.1.0-gentoo.patch
+	"${FILESDIR}"/${PN}-2.2.1-boost-1.65-tr1-removal.patch
+)
+
+src_configure() {
+	tc-export CXX
+
+	cat >> make.config <<- EOF || die
+		BOOST_LIB_SUFFIX = -mt
+		BOOST_LIB_DIR = "${EPREFIX}/usr/$(get_libdir)"
+		BOOST_INC_DIR = "${EPREFIX}/usr/include"
+	EOF
+}
+
+src_install() {
+	dobin mkdssp
+	dosym mkdssp /usr/bin/dssp
+	doman doc/mkdssp.1
+	dodoc README.txt changelog
+
+	cat >> "${T}"/30-${PN} <<- EOF || die
+		DSSP="${EPREFIX}"/usr/bin/${PN}
+	EOF
+	doenvd "${T}"/30-${PN}
+}
diff --git a/sci-chemistry/dssp/files/dssp-2.1.0-gentoo.patch b/sci-chemistry/dssp/files/dssp-2.1.0-gentoo.patch
new file mode 100644
index 000000000000..15198feaea19
--- /dev/null
+++ b/sci-chemistry/dssp/files/dssp-2.1.0-gentoo.patch
@@ -0,0 +1,60 @@
+ makefile | 21 +++++++++++----------
+ 1 file changed, 11 insertions(+), 10 deletions(-)
+
+diff --git a/makefile b/makefile
+index d6f335e..68736c6 100644
+--- a/makefile
++++ b/makefile
+@@ -25,22 +25,23 @@ BOOST_LIBS			= thread filesystem program_options iostreams system
+ LIBS				= $(BOOST_LIBS:%=boost_%$(BOOST_LIB_SUFFIX)) z bz2
+ 
+ DEFINES				= USE_COMPRESSION LINUX VERSION='"$(VERSION)"'
+-CXX					= g++
++CXX					?= g++
+ 
+-CFLAGS				+= $(INC_DIR:%=-I%) -iquote src -g -Wall -Wno-multichar -pthread
+-LDOPTS				+= $(LIB_DIR:%=-L%) $(LIBS:%=-l%) -g -pthread
++CPPFLAGS				+= $(INC_DIR:%=-I%) -iquote src
++CXXFLAGS				+= -Wall -Wno-multichar -pthread
++LDOPTS				+= $(LIB_DIR:%=-L%) $(LIBS:%=-l%) -pthread
+ 
+ OBJ_DIR				= obj
+ 
+ ifeq ($(DEBUG),1)
+ OBJ_DIR				:= $(OBJ_DIR).dbg
+-CFLAGS				+= -g3
++CFLAGS				+=
+ else
+ DEFINES				+= NDEBUG
+-CFLAGS				+= -O3
++CFLAGS				+=
+ endif
+ 
+-CFLAGS				+= $(DEFINES:%=-D%)
++CPPFLAGS				+= $(DEFINES:%=-D%)
+ 
+ DIST_NAME			= dssp-$(VERSION)
+ 
+@@ -50,18 +51,18 @@ OBJECTS = $(OBJ_DIR)/mkdssp.o $(OBJ_DIR)/dssp.o $(OBJ_DIR)/primitives-3d.o $(OBJ
+ 
+ mkdssp: $(OBJECTS)
+ 	@ echo linking $@
+-	@ $(CXX) -static -o $@ $^ $(LDOPTS)
++	$(CXX) $(LDFLAGS) -o $@ $^ $(LDOPTS)
+ 
+ include $(OBJECTS:%.o=%.d)
+ 
+ $(OBJECTS:.o=.d):
+ 
+-$(OBJ_DIR):
++OBJ_DIR:
+ 	@ mkdir -p $(OBJ_DIR)
+ 
+-$(OBJ_DIR)/%.o: %.cpp | $(OBJ_DIR)
++$(OBJ_DIR)/%.o: %.cpp OBJ_DIR
+ 	@ echo compiling $@
+-	@ $(CXX) -MD -c -o $@ $< $(CFLAGS)
++	$(CXX) $(CPPFLAGS) $(CXXFLAGS) -MD -c -o $@ $<
+ 
+ clean:
+ 	install -d $(BIN_DIR) $(MAN_DIR)
diff --git a/sci-chemistry/dssp/files/dssp-2.2.1-boost-1.65-tr1-removal.patch b/sci-chemistry/dssp/files/dssp-2.2.1-boost-1.65-tr1-removal.patch
new file mode 100644
index 000000000000..4eee6b567349
--- /dev/null
+++ b/sci-chemistry/dssp/files/dssp-2.2.1-boost-1.65-tr1-removal.patch
@@ -0,0 +1,82 @@
+--- a/src/dssp.cpp
++++ b/src/dssp.cpp
+@@ -73,7 +73,7 @@
+ 
+ 	double alpha;
+ 	char chirality;
+-	tr1::tie(alpha,chirality) = residue.Alpha();
++	boost::tie(alpha,chirality) = residue.Alpha();
+ 	
+ 	uint32 bp[2] = {};
+ 	char bridgelabel[2] = { ' ', ' ' };
+--- a/src/primitives-3d.cpp
++++ b/src/primitives-3d.cpp
+@@ -153,7 +153,7 @@
+ 
+ // --------------------------------------------------------------------
+ 
+-tr1::tuple<double,MPoint> QuaternionToAngleAxis(MQuaternion q)
++boost::tuple<double,MPoint> QuaternionToAngleAxis(MQuaternion q)
+ {
+ 	if (q.R_component_1() > 1)
+ 		q = Normalize(q);
+@@ -169,7 +169,7 @@
+ 	
+ 	MPoint axis(q.R_component_2() / s, q.R_component_3() / s, q.R_component_4() / s);
+ 
+-	return tr1::make_tuple(angle, axis);
++	return boost::make_tuple(angle, axis);
+ }
+ 
+ MPoint CenterPoints(vector<MPoint>& points)
+--- a/src/primitives-3d.h
++++ b/src/primitives-3d.h
+@@ -9,7 +9,7 @@
+ 
+ #include <vector>
+ 
+-#include <boost/tr1/tuple.hpp>
++#include <boost/tuple/tuple.hpp>
+ #include <boost/math/quaternion.hpp>
+ 
+ typedef boost::math::quaternion<double> MQuaternion;
+@@ -64,7 +64,7 @@
+ 
+ MQuaternion Normalize(MQuaternion q);
+ 
+-std::tr1::tuple<double,MPoint> QuaternionToAngleAxis(MQuaternion q);
++boost::tuple<double,MPoint> QuaternionToAngleAxis(MQuaternion q);
+ MPoint Centroid(std::vector<MPoint>& points);
+ MPoint CenterPoints(std::vector<MPoint>& points);
+ MQuaternion AlignPoints(const std::vector<MPoint>& a, const std::vector<MPoint>& b);
+--- a/src/structure.cpp
++++ b/src/structure.cpp
+@@ -544,7 +544,7 @@
+ 	return result;
+ }
+ 
+-tr1::tuple<double,char> MResidue::Alpha() const
++boost::tuple<double,char> MResidue::Alpha() const
+ {
+ 	double alhpa = 360;
+ 	char chirality = ' ';
+@@ -558,7 +558,7 @@
+ 		else
+ 			chirality = '+';
+ 	}
+-	return tr1::make_tuple(alhpa, chirality);
++	return boost::make_tuple(alhpa, chirality);
+ }
+ 
+ double MResidue::Kappa() const
+--- a/src/structure.h
++++ b/src/structure.h
+@@ -168,7 +168,7 @@
+ 
+ 	double				Phi() const;
+ 	double				Psi() const;
+-	std::tr1::tuple<double,char>
++	boost::tuple<double,char>
+ 						Alpha() const;
+ 	double				Kappa() const;
+ 	double				TCO() const;
diff --git a/sci-chemistry/dssp/metadata.xml b/sci-chemistry/dssp/metadata.xml
new file mode 100644
index 000000000000..8937bad0b175
--- /dev/null
+++ b/sci-chemistry/dssp/metadata.xml
@@ -0,0 +1,8 @@
+<?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>
+</pkgmetadata>