gentoo resync : 03.09.2021

7 files changed, 127 insertions, 5 deletions

diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz
index 8c5226abd681..54ba54961282 100644
--- a/sci-chemistry/Manifest.gz
+++ b/sci-chemistry/Manifest.gz
diff --git a/sci-chemistry/dssp/Manifest b/sci-chemistry/dssp/Manifest
index e64b097b41a1..12dbd946b77f 100644
--- a/sci-chemistry/dssp/Manifest
+++ b/sci-chemistry/dssp/Manifest
@@ -1,5 +1,11 @@
+AUX 30-dssp 18 BLAKE2B 3d2b6cfc787c1bec902fca9be8b45bf821f87eb1a0603eab0b537f4ee97a33f61a7fc50aabe85a24d8d5ee48eda6d904db330ade9b71095623afb5df7d83b105 SHA512 a15df4c8b7599a2d6b2575fe02aeb11169ccbd26a70f328cc34b60aee08edabf3cff3d66e5a9c95d06e6630d212a18530ca81aa4004c92fcb461791897bce432
 AUX dssp-2.1.0-gentoo.patch 1513 BLAKE2B aabdcfff1083d7552392c35897eb8a84b07323c89dfdce014f4401b2e82e727e9fbc77dd3f7e6d5efda61a6e64fad905873516e5336f21627bda1f2f39caf5c2 SHA512 7d192019811a6892031c74e14ef9fc7461e77c050a164698f8c72cff08f81a0e6da202e0915b631a5cd6d910a6114a736c706d47b1fd6474ff77c3700efcd9f9
 AUX dssp-2.2.1-boost-1.65-tr1-removal.patch 2126 BLAKE2B dc59d21a6be26ee96b636c13645163478999d5122f09d3a72963843be773210ea225e374941bd057ef6f083a13fb77980bd4390174df2a0c715f0386da7232e0 SHA512 8f84c6e163888d6a8192683a6555f7d6003634854f5cde0f6f962744e531165c7e0b2b08c55cbfb9c396d167c44317dd2e7a8290e4defd2c8def0a6511fbbd6c
 DIST dssp-2.2.1.tgz 47141 BLAKE2B 34d8b2db8797a8c23763766c0214337f03584c4be52c1bc820a0df0db6a5f78ac0229aafdd47a60b8fd6f4832abf0399663c53f9e898c75f08ecbe22b141c8da SHA512 4a273714d6b3230daea166caa7f4117d5ccb225bea0cf1bc2eb61539b6cc8e227d0ba19047d61f0ad0d1d6bc2efdec9c193bd44341e15ef0950acb4a22498811
+DIST dssp-3.0.11.tar.gz 168085 BLAKE2B e1c42fd22cfb2287f10b5deae48b56a4583d4a67737a3485dcbd160d1597a15c2d5105c3794c875d8001abede1c014efb4f7f5b7c250f867bdf9ed95a0860217 SHA512 a0cfe44e517ff1f909ef2928b62ae2c639c6bddfd8a0fb538883f647fd2771e00da68e0fd2521aa02ba3c6d1b0c9b784b7fe142392af3a3abf6ea89f1546bd9d
+DIST dssp-4.0.1_p20210831.tar.gz 121793 BLAKE2B 1e028b086b418772a93db350f8084d1786996ff6ea935d236b1431d8f4a07c0b33ebf374a4c4d5d4d243952f3f56e29a548ce09763863a1e0c529755fba6c211 SHA512 62f1ac781dd3d6f3436e6c155ae1a470d0baf6a6d9f6d6729034a7a5ef41550f76d0473c688d235279336306c9f3598377c056cddd6d00a89a826fbb04c1bfb3
 EBUILD dssp-2.2.1-r2.ebuild 962 BLAKE2B 4badf2ae8647aab9c5e359d9e0763d051388afe3bf5763c8eeb99cb21b30283d72ace619f1b65c5ee248c42f8264cb31c2c1c079f75eacda1568cc4352cec5e3 SHA512 4a599b6e7cd068175bd89f4ea948ad1267df783c240ab46d3c6109bf3f2853de714ecf1e5776722309688599f28af545287fe5cb98d8b7a5f46d319df953b926
-MISC metadata.xml 271 BLAKE2B a446884cbe7a6789e0bcd82759f57bf1ab7b29c5ab714057ffa821c90f799d1fa9f9310c187ee4c3a8ae2476f6ea9d15f368045779f1581e68d02802c61c884c SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92
+EBUILD dssp-2.2.1-r3.ebuild 882 BLAKE2B d95025d549b3114107e3e52292e6ae086141436c23bfcbfe3604c59c971fc360de84a621e3415d26a6b2faf5c51810e9e3e7441641af9967b38534178ace62a7 SHA512 29f0c7cf76f6029146668d08d992380147f698ae2bb00cee76777936217f27e329cfe25f41c58c07906b881d40385d134d51f34e14f80c0836c78cf50f1bf37a
+EBUILD dssp-3.0.11.ebuild 825 BLAKE2B 020ea517127ffc1167cbff3a9362e5ff255b25664769ef2ac8f7f3060e34e0bec29e965df46e65bab8943cbf5fb11175d70b1b9f9e7d71bdbf92a4c54a903367 SHA512 b81dbe1cb9f7b66c5268485dc262bb705b12d250e2ec778c80fddbc584a38e36b64cb93e92385c178fdeca0e593c45ce25aef16480bfa9eb230bdd2b8a82fa53
+EBUILD dssp-4.0.1_p20210831.ebuild 849 BLAKE2B 0d6089c63608b85c98f67136cfd275098272985f689ac0e6338c7ee6cd158a851901815d0dab988a2ab65ff63a1bfbcd689577daa98c2c91bc04c95f2a95420b SHA512 35d5e67754a7a7b3d3021c16d57d1b4e5c8a2316606b7ebed08bb543e647794d87b64e4ba04db3d86d34f13999e04af08b4df8cbe4d8d5843c1f3f26c491b0b0
+MISC metadata.xml 216 BLAKE2B 0fbfa16661345362ff89f87adc0bb42fc5f5c9145cdedb36f3f537b39af4023b91c4dfb0d8e83a4f9ac963141f594ba8ae678371c338d992a96e02c11fd84195 SHA512 628a69805356b7458edaa2297901224178b016477a937f77e692a78ce3e7a0b6d2d7b4c4b7e70d0185d7112e6a59a5131e07d8c950e90b9c8722471d7511afc6
diff --git a/sci-chemistry/dssp/dssp-2.2.1-r3.ebuild b/sci-chemistry/dssp/dssp-2.2.1-r3.ebuild
new file mode 100644
index 000000000000..8697005fc2cd
--- /dev/null
+++ b/sci-chemistry/dssp/dssp-2.2.1-r3.ebuild
@@ -0,0 +1,41 @@
+# Copyright 1999-2021 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/${P}.tgz"
+
+LICENSE="Boost-1.0"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND="dev-libs/boost:=[bzip2,zlib,threads(+)]"
+DEPEND="${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_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-${PN}
+}
diff --git a/sci-chemistry/dssp/dssp-3.0.11.ebuild b/sci-chemistry/dssp/dssp-3.0.11.ebuild
new file mode 100644
index 000000000000..b0771e31047d
--- /dev/null
+++ b/sci-chemistry/dssp/dssp-3.0.11.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+inherit autotools
+
+MY_PN="hssp"
+MY_P="${MY_PN}-${PV}"
+
+DESCRIPTION="The protein secondary structure standard"
+HOMEPAGE="https://swift.cmbi.umcn.nl/gv/dssp/ https://github.com/cmbi/hssp"
+SRC_URI="https://github.com/cmbi/${MY_PN}/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="Boost-1.0"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND="
+	dev-lang/perl:=
+	dev-libs/boost:=[bzip2,zlib,threads(+)]
+"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+	default
+
+	# Fix version
+	sed -i -e "s/3.0.10/${PV}/" configure.ac || die
+
+	sed -i -e '/-Werror/d' Makefile.am || die
+
+	eautoreconf
+}
+
+src_install() {
+	default
+	dosym mkdssp /usr/bin/dssp
+	doenvd "${FILESDIR}"/30-${PN}
+}
diff --git a/sci-chemistry/dssp/dssp-4.0.1_p20210831.ebuild b/sci-chemistry/dssp/dssp-4.0.1_p20210831.ebuild
new file mode 100644
index 000000000000..a5e5af9c7424
--- /dev/null
+++ b/sci-chemistry/dssp/dssp-4.0.1_p20210831.ebuild
@@ -0,0 +1,33 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+inherit cmake
+
+DESCRIPTION="The protein secondary structure standard"
+HOMEPAGE="https://swift.cmbi.umcn.nl/gv/dssp/ https://github.com/PDB-REDO/dssp"
+
+COMMIT="728cc7c6c8d95460d8db453cf7adb25a89ba15f6"
+SRC_URI="https://github.com/PDB-REDO/${PN}/archive/${COMMIT}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/${PN}-${COMMIT}"
+
+LICENSE="BSD-2"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+BDEPEND="
+	>=dev-libs/boost-1.70.0:=[bzip2,zlib,threads(+)]
+	>=sci-libs/libcifpp-1.1.1
+"
+DEPEND=""
+RDEPEND="${BDEPEND}"
+
+pkg_postinst() {
+	if has_version sci-chemistry/gromacs; then
+		ewarn "DSSP > 3.0.x is not compatible with gmx do_dssp:"
+		ewarn "https://gitlab.com/gromacs/gromacs/-/issues/4129"
+		ewarn
+		ewarn "Feel free to mask newer versions if needed."
+	fi
+}
diff --git a/sci-chemistry/dssp/files/30-dssp b/sci-chemistry/dssp/files/30-dssp
new file mode 100644
index 000000000000..e0a5e0ce5626
--- /dev/null
+++ b/sci-chemistry/dssp/files/30-dssp
@@ -0,0 +1 @@
+DSSP=/usr/bin/dssp
\ No newline at end of file
diff --git a/sci-chemistry/dssp/metadata.xml b/sci-chemistry/dssp/metadata.xml
index 8937bad0b175..020b40648ee8 100644
--- a/sci-chemistry/dssp/metadata.xml
+++ b/sci-chemistry/dssp/metadata.xml
@@ -1,8 +1,7 @@
 <?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>
+	<maintainer type="person">
+		<email>pacho@gentoo.org</email>
+	</maintainer>
 </pkgmetadata>