Adding metadata

9 files changed, 0 insertions, 344 deletions

diff --git a/sci-chemistry/dssp/Manifest b/sci-chemistry/dssp/Manifest
deleted file mode 100644
index 86e5cc65df76..000000000000
--- a/sci-chemistry/dssp/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-DIST dssp-2.2.1.tgz 47141 BLAKE2B 34d8b2db8797a8c23763766c0214337f03584c4be52c1bc820a0df0db6a5f78ac0229aafdd47a60b8fd6f4832abf0399663c53f9e898c75f08ecbe22b141c8da SHA512 4a273714d6b3230daea166caa7f4117d5ccb225bea0cf1bc2eb61539b6cc8e227d0ba19047d61f0ad0d1d6bc2efdec9c193bd44341e15ef0950acb4a22498811
-DIST dssp-4.5.6.tar.gz 223229 BLAKE2B a5f60e1ea8d8ff8c9e63b9e68464ba81a705bbe2d87ebeaab7f13c9c2c05557b5d5aacf832f0f5f85e66ef653751cb9d53a07d6667fcbd8a7e6aae21a2d753f7 SHA512 06e1d74f5a39673560bd174032523018f063c8c6f2aaad21c4800334d39f81e5b8f68c78a184a14ff33897d9e6bde9810d7efd5f4c769a85705302bc480afdf4
-DIST dssp-4.5.8.tar.gz 225240 BLAKE2B 57602edf8981646716a2f882eff027f67a0e25128d50f5c2c4df53ef37682937879b0e42f41fcc5ea0741e203ccbe91d68e7f9c7022a2672f38f5f50101c5400 SHA512 981ac33060284a548d259fd854bcfb9a8ad10b5867379946ed4288e018ab3f7ea28ef8f3270d1a3db3e43c76d761ca920df6b7bf40e10fe40de37917b3d9e174
-DIST dssp-4.6.1.tar.gz 247855 BLAKE2B a35500bddfb91156e1cc29f95365ad327581f982310d923862f3e32b60af15f71bfca0cf278cd75c111b03d2ae06f7ecb27b33eee4091eeb2725fc77f0cb3a28 SHA512 3152e40ad7086ced6a9b27ad7459ae5c18dc2092aab7fdda12fd06ea6823437f1aa0e211218f85b6a3b2f81cd2614aab0d940b806ab4c2fe907a18352b6b2c30
diff --git a/sci-chemistry/dssp/dssp-2.2.1-r3.ebuild b/sci-chemistry/dssp/dssp-2.2.1-r3.ebuild
deleted file mode 100644
index 2aa55a52cf95..000000000000
--- a/sci-chemistry/dssp/dssp-2.2.1-r3.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit toolchain-funcs
-
-DESCRIPTION="The protein secondary structure standard"
-HOMEPAGE="https://swift.cmbi.umcn.nl/gv/dssp/"
-SRC_URI="ftp://ftp.cmbi.ru.nl/pub/molbio/software/dssp-2/${P}.tgz"
-
-LICENSE="Boost-1.0"
-SLOT="0"
-KEYWORDS="amd64 ~x86"
-
-RDEPEND="dev-libs/boost:=[bzip2,zlib]"
-DEPEND="${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_DIR = "${EPREFIX}/usr/$(get_libdir)"
-		BOOST_INC_DIR = "${EPREFIX}/usr/include"
-	EOF
-}
-
-src_install() {
-	dobin mkdssp
-	dosym mkdssp /usr/bin/dssp
-	doman doc/mkdssp.1
-	dodoc README.txt changelog
-
-	doenvd "${FILESDIR}"/30-${PN}
-}
diff --git a/sci-chemistry/dssp/dssp-4.5.6.ebuild b/sci-chemistry/dssp/dssp-4.5.6.ebuild
deleted file mode 100644
index cae362ee3d3d..000000000000
--- a/sci-chemistry/dssp/dssp-4.5.6.ebuild
+++ /dev/null
@@ -1,49 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-inherit cmake
-
-DESCRIPTION="The protein secondary structure standard"
-HOMEPAGE="https://swift.cmbi.umcn.nl/gv/dssp/ https://github.com/PDB-REDO/dssp"
-SRC_URI="https://github.com/PDB-REDO/${PN}/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD-2"
-SLOT="0"
-KEYWORDS="amd64 ~x86"
-# doc disabled as it only generates a PDF from the manpage for now
-# https://github.com/PDB-REDO/dssp/issues/64
-IUSE="test"
-RESTRICT="!test? ( test )"
-
-CDEPEND="
-	dev-libs/boost:=[zlib]
-	>=dev-libs/libmcfp-1.4.2
-	>=sci-libs/libcifpp-9:=
-"
-BDEPEND="${CDEPEND}
-	dev-cpp/catch:0
-"
-#	doc? (
-#		|| ( app-text/pandoc-bin[pandoc-symlink] app-text/pandoc )
-#		dev-python/weasyprint
-#	)
-RDEPEND="${CDEPEND}"
-
-#src_prepare() {
-#	# wkhtmltopdf is not available on Gentoo
-#	sed -i -e \
-#		's/-t html/-t html --pdf-engine=weasyprint/' \
-#		CMakeLists.txt
-#	cmake_src_prepare
-#}
-
-src_configure() {
-	local mycmakeargs=(
-		-DINSTALL_LIBRARY=YES
-		#-DBUILD_DOCUMENTATION=$(usex doc)
-		-DBUILD_DOCUMENTATION=NO
-		-DBUILD_TESTING=$(usex test)
-	)
-	cmake_src_configure
-}
diff --git a/sci-chemistry/dssp/dssp-4.5.8.ebuild b/sci-chemistry/dssp/dssp-4.5.8.ebuild
deleted file mode 100644
index 24b75290b6b0..000000000000
--- a/sci-chemistry/dssp/dssp-4.5.8.ebuild
+++ /dev/null
@@ -1,49 +0,0 @@
-# Copyright 1999-2026 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-inherit cmake
-
-DESCRIPTION="The protein secondary structure standard"
-HOMEPAGE="https://swift.cmbi.umcn.nl/gv/dssp/ https://github.com/PDB-REDO/dssp"
-SRC_URI="https://github.com/PDB-REDO/${PN}/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD-2"
-SLOT="0"
-KEYWORDS="amd64 ~x86"
-# doc disabled as it only generates a PDF from the manpage for now
-# https://github.com/PDB-REDO/dssp/issues/64
-IUSE="test"
-RESTRICT="!test? ( test )"
-
-CDEPEND="
-	>=dev-libs/boost-1.84:=[zlib]
-	>=dev-libs/libmcfp-1.4.2
-	>=sci-libs/libcifpp-9.0.6:=
-"
-BDEPEND="${CDEPEND}
-	dev-cpp/catch:0
-"
-#	doc? (
-#		|| ( app-text/pandoc-bin[pandoc-symlink] app-text/pandoc )
-#		dev-python/weasyprint
-#	)
-RDEPEND="${CDEPEND}"
-
-#src_prepare() {
-#	# wkhtmltopdf is not available on Gentoo
-#	sed -i -e \
-#		's/-t html/-t html --pdf-engine=weasyprint/' \
-#		CMakeLists.txt
-#	cmake_src_prepare
-#}
-
-src_configure() {
-	local mycmakeargs=(
-		-DINSTALL_LIBRARY=YES
-		#-DBUILD_DOCUMENTATION=$(usex doc)
-		-DBUILD_DOCUMENTATION=NO
-		-DBUILD_TESTING=$(usex test)
-	)
-	cmake_src_configure
-}
diff --git a/sci-chemistry/dssp/dssp-4.6.1.ebuild b/sci-chemistry/dssp/dssp-4.6.1.ebuild
deleted file mode 100644
index 5ea3099341df..000000000000
--- a/sci-chemistry/dssp/dssp-4.6.1.ebuild
+++ /dev/null
@@ -1,49 +0,0 @@
-# Copyright 1999-2026 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-inherit cmake
-
-DESCRIPTION="The protein secondary structure standard"
-HOMEPAGE="https://swift.cmbi.umcn.nl/gv/dssp/ https://github.com/PDB-REDO/dssp"
-SRC_URI="https://github.com/PDB-REDO/${PN}/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-# doc disabled as it only generates a PDF from the manpage for now
-# https://github.com/PDB-REDO/dssp/issues/64
-IUSE="test"
-RESTRICT="!test? ( test )"
-
-CDEPEND="
-	>=dev-libs/boost-1.86:=[zlib]
-	>=dev-libs/libmcfp-1.4.2
-	>=sci-libs/libcifpp-9.0.6:=
-"
-BDEPEND="${CDEPEND}
-	dev-cpp/catch:0
-"
-#	doc? (
-#		|| ( app-text/pandoc-bin[pandoc-symlink] app-text/pandoc )
-#		dev-python/weasyprint
-#	)
-RDEPEND="${CDEPEND}"
-
-#src_prepare() {
-#	# wkhtmltopdf is not available on Gentoo
-#	sed -i -e \
-#		's/-t html/-t html --pdf-engine=weasyprint/' \
-#		CMakeLists.txt
-#	cmake_src_prepare
-#}
-
-src_configure() {
-	local mycmakeargs=(
-		-DINSTALL_LIBRARY=YES
-		#-DBUILD_DOCUMENTATION=$(usex doc)
-		-DBUILD_DOCUMENTATION=NO
-		-DBUILD_TESTING=$(usex test)
-	)
-	cmake_src_configure
-}
diff --git a/sci-chemistry/dssp/files/30-dssp b/sci-chemistry/dssp/files/30-dssp
deleted file mode 100644
index e0a5e0ce5626..000000000000
--- a/sci-chemistry/dssp/files/30-dssp
+++ /dev/null
@@ -1 +0,0 @@
-DSSP=/usr/bin/dssp
\ No newline at end of file
diff --git a/sci-chemistry/dssp/files/dssp-2.1.0-gentoo.patch b/sci-chemistry/dssp/files/dssp-2.1.0-gentoo.patch
deleted file mode 100644
index 15198feaea19..000000000000
--- a/sci-chemistry/dssp/files/dssp-2.1.0-gentoo.patch
+++ /dev/null
@@ -1,60 +0,0 @@
- 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
deleted file mode 100644
index 4eee6b567349..000000000000
--- a/sci-chemistry/dssp/files/dssp-2.2.1-boost-1.65-tr1-removal.patch
+++ /dev/null
@@ -1,82 +0,0 @@
---- 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
deleted file mode 100644
index e3c02bf1bb6f..000000000000
--- a/sci-chemistry/dssp/metadata.xml
+++ /dev/null
@@ -1,10 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>pacho@gentoo.org</email>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">PDB-REDO/dssp</remote-id>
-	</upstream>
-</pkgmetadata>