diff options
Diffstat (limited to 'sci-chemistry/dssp')
| -rw-r--r-- | sci-chemistry/dssp/Manifest | 7 | ||||
| -rw-r--r-- | sci-chemistry/dssp/dssp-2.2.1-r1.ebuild | 45 | ||||
| -rw-r--r-- | sci-chemistry/dssp/files/dssp-2.1.0-gentoo.patch | 60 | ||||
| -rw-r--r-- | sci-chemistry/dssp/files/dssp-2.2.1-boost-1.65-tr1-removal.patch | 82 | ||||
| -rw-r--r-- | sci-chemistry/dssp/metadata.xml | 8 |
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> |