gentoo resync : 22.04.2018

16 files changed, 474 insertions, 447 deletions

diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz
index 6514084e97f4..6d67d7fc607c 100644
--- a/sci-chemistry/Manifest.gz
+++ b/sci-chemistry/Manifest.gz
diff --git a/sci-chemistry/ball/Manifest b/sci-chemistry/ball/Manifest
index c31e5573eae0..1c087ccb3314 100644
--- a/sci-chemistry/ball/Manifest
+++ b/sci-chemistry/ball/Manifest
@@ -1,13 +1,4 @@
-AUX ball-1.4.1-BondOrder.xml.patch 1675 BLAKE2B e2a36d281239fc5524b106a926060dd5631b5f10505561dad5c3479f75329fa213610119cd3456c06fbc765ecc3ea4b47812a377447e2fef06df56cf64c2a54a SHA512 77e04209bebff5057ad549d1c1d7b638391fb063efb8635a72b46287a4c4975c2d0940267bce9002f3c9dc0f6fab7e21a3099506f57a44e0a325149ee134b2e0
-AUX ball-1.4.1-missing-signed.patch 985 BLAKE2B 230f5a89086431483206253cd6da74e39c62b653b97d505ebbe7a237541bae239d1e8f4056c592d151266845ed9b60dc78845ff7abf02fc1b86e1ac1739be703 SHA512 ea50bbceb38e80416e4f49a247816ccaf1318c45676669388f681eca5be525b5ed6d472c1b20afe37d3d95ae5334d90831269c77bce922207b515e8c5a46f20a
-AUX ball-1.4.1-multilib.patch 1585 BLAKE2B 4b61cf04883ef98de4471584376796c5d6534e78ec6da7b181bdc139794e730c8d57dcd04cf9e37e0d57af2734a5bdf6194053b0283160912046a929e82fd41e SHA512 5eebfdce5fba25967c252d0c83f6187079efc55c9481045d6c9e111930e1bb2bed31666b913eb12f46a723aa875559b54f658460efd7be10bbbe4c7cd2982341
-AUX ball-1.4.2-Fix-compilation-of-sipModularWidget.patch 1565 BLAKE2B 853823ab0a5b174bad52290f933257ab9a3e8227855bf6a7769c11d008bcdc56914825ce9addb10b24d0c9c67fbf2be3b7f88997dd96bf2a76e50657f4e873eb SHA512 15cc7b8583b5dfcefa152dac0fcf300ad2369f147dc4bb4061fd06586eea403a67442389b2eecca93144b02f73c0eb252794604b87348e63dddcaa03d2775882
-AUX ball-1.4.2-PDBFile-Fix-compilation-with-gcc-4.8.patch 1011 BLAKE2B aa08be283cd17947e93c09f5020b08b5fa3f35fe9b94b138fb2df329e5f2bfecd204ffa5dab836a3a201cc415b2e074b29906822a943dcdf4676edc3b48069d4 SHA512 f99d0b42b6798b0f97aeb93f9aedf9dfd68c62f948dabab4cc1e7b6a4251b10ec8b4e109936f86456f77b1faecad5eff05bb40200d55490c7f82787b3f6951a1
-AUX ball-1.4.2-QT4_EXTRACT_OPTIONS-CMake-macro-changed-in-CMake-2.8.patch 1470 BLAKE2B db660cfc8414d913dd2473396d20622da9bc9629cd90843dcad4f2f004177f0b2c1d42ecbf95540d677e779f948223e0fbbf20126e34c8b72adfb541a0b1dc41 SHA512 18cd445e4867878f73d74afef1ae74d02bb3a118fdeb379beb2463cef501a79eacfa9c5d487fa2656993f652cc0a7432c7d139a2df101416cc6d7139dc4af034
-AUX ball-1.4.2-fix-python-bindings.patch 643 BLAKE2B 2d5d9a437d90ac52cc865d96419739d1ad5948cd5893fdc988b1530f6ce3bb9ea8cbdf11d1c4b0aa0bfd2352ebbc03b8ce1bffe3e1785f35c142f49f2845cabb SHA512 af1d61a2f4b6b1a0e567e0257e575ffe75f62bb0d0a49379bc08861d0c5bb9dee458a254966a88ecb62eefcd3c6fbb9426b734265627bf7a936111df0f7e61ef
-AUX ball-1.4.2-std-namespace-isnan.patch 716 BLAKE2B 86a5edd70115ba20cb34a4665840a7013d25e4b32cba6a31133a1c7429f7c56be7eba44450725c865e5657e66f5243bd9b8f385ab1650f4d7f9b817c863d73d4 SHA512 2fb87783e7d97d12c4841e9e475eb8d99c2a20b0e162f37394182236a6c1ca3c24c0193110671c296dbb2ae244aab720680b17b0862c3da54ab65061f49be9d2
-AUX ball-1.4.2-struct-swap-attribute.patch 1997 BLAKE2B 93c59eca3ea8f49d8b7ec225c0ddb68ed476acd3c8ab1fba81dc183fa504489248033c52a027f04060ab2cd7e6a1badff646805c8c9a55a0651b5f567e7abcf0 SHA512 a8b7e2eaf094a97008fb69030549a4c4bb2eabaf3d06ee5191ae5512c3af73198f88c26dca5e0b63cc19d9e3b1e21c323494017f81339b4a30caf1ae8f0f98f0
-AUX ball-1.4.2-underlinking.patch 665 BLAKE2B d34df60aee08bccfe31aa208d912feee7446fd186b7f7b6db09cb213a7e90a8f1159ccabb8cb06457f4cc441c2c36774f12e0a44e08a5378158526af17cbcb24 SHA512 b122e4f6e87be39642355869a42730263ec9d5e66d9887af5e2c4040eef4fce1306a57b106731bba8136197eecc3f72ca99b863aead70f89825ae6724268c688
-DIST BALL-1.4.2.tar.xz 16080664 BLAKE2B 15faa5f1aed0701ab318ac965ece216be0ff653ab1e57b0a1f2c253cf97b1ac89800ab528c9d044da903b154e16d1dfde936bd1475d6b1903acfa867904a55a7 SHA512 c719af4ef2dc1076818d59b72350b704fbffea06bd44737519fb50d88da113ea509333d407f2330aa59bf1c4e6b81adfd3d28e05459f66d7c9707f8d85db7a87
-EBUILD ball-1.4.2-r2.ebuild 2037 BLAKE2B 55f985f97248c5581f802e370afb586f82b18efd312618aa425ce831b9f5b37f7f112722735535b1a8deb04e1eca4700cb32f630ec4aad5d5f4dc387236352ac SHA512 81f51cdb2e6d7d988aa7f180bf506804d8eb76e2e8a5a297ed50068afc536ece9b42b381123b1bfddc2f69c315aa3cbdba4fe7b60912d82907c0f5ed6ae02479
-MISC metadata.xml 1431 BLAKE2B 74b306217177742cba96db2095cdb43d118a1e76fb41ee847c147dbe73800535c563a9131c62bcc8bda91a5a6dd2bf83cd07a7449af07b97481c0ff6c22fe080 SHA512 c12eaa309bc4e2f6fb51415b943144974a23a92e0705dd7368e402c1be7244485b66bf2d1f0dc11a6b2b673be7189b2543b999924e5ecb94ca00ec9bd1ba32b2
+AUX ball-1.5.0-gnuinstalldirs.patch 14265 BLAKE2B abb1795e7e322e532d041d16e919b59bfa0430df2e06c3b179ae94e8462ed98369e32056c4cc63d181c2d5af59109a4a0b602cf1af47384350c6ef29871d4b0d SHA512 cdf71a863347c3b8716f7e54ded4df15e2615e3375adeaf4c3de1659d52ffde0e3bcd82f7eb26f6f27d03517d279fb4b19fd1c06f12e2191bf81d19d54161906
+DIST ball-1.5.0_pre20180419.tar.gz 37577697 BLAKE2B 44db256dad4703115ca381c4bc7f8393657d9d205b78c9ed55328769129dc38a2898d838bea2beb2e1e5e25184944a5724dd808917928f79c41b8216d98a6677 SHA512 a5cf9680468636c6b3de950f058d1bedb9c2d9ef7b5ba1af60e4b79fab3e6bae9cd814ec3238703075ae66c5a637d1ba8281ce7f11ac842133af91c000c983c3
+EBUILD ball-1.5.0_pre20180419.ebuild 2389 BLAKE2B 45982157a733cbcd4cf785a33071dffcf3f37211bf697876cc64e6e2d9602c44b6dbb0e58c752085c60a23b84cd971f2693ec4da6089e4300f4741aa37af4593 SHA512 5cd1d8d7c87af7720c5ccfbad4ca824fabadd9fbecf129d30ae179379d34c3b5218298c745fe36c77b0bfc0a8080eb330ac72df81bb936f2bd0b8d10ad29b55f
+MISC metadata.xml 1920 BLAKE2B 5c44bceae9d74d6e720184b0e2c1eb2fef57c96c05ae7224065e83b088dcf159cf51875390e651d906daa5cb08f714d3808783cccba0935c73dd6ae5b14bf8bc SHA512 8a4ab19d094b8d538cd2494e43572420fb3dd9fdc474056f18c10c6baa4bbb6fad8c89095df3914c9639d4396a7cddbab16ed9b0cd050521e92f1bf3ef162288
diff --git a/sci-chemistry/ball/ball-1.4.2-r2.ebuild b/sci-chemistry/ball/ball-1.4.2-r2.ebuild
deleted file mode 100644
index 89c96a194b67..000000000000
--- a/sci-chemistry/ball/ball-1.4.2-r2.ebuild
+++ /dev/null
@@ -1,83 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit cmake-utils python-single-r1
-
-DESCRIPTION="Biochemical Algorithms Library"
-HOMEPAGE="http://www.ball-project.org/"
-SRC_URI="http://www.ball-project.org/Downloads/v${PV}/BALL-${PV}.tar.xz"
-
-SLOT="0"
-LICENSE="LGPL-2 GPL-3"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="cuda mpi +python sql test +threads"
-
-REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
-
-RDEPEND="
-	dev-cpp/eigen:3
-	dev-libs/boost:=
-	dev-qt/qtcore:4
-	dev-qt/qtgui:4
-	dev-qt/qtopengl:4
-	dev-qt/qttest:4
-	media-libs/glew:0
-	sci-libs/fftw:3.0[threads?]
-	sci-libs/gsl
-	sci-libs/libsvm
-	sci-mathematics/lpsolve
-	virtual/opengl
-	x11-libs/libX11
-	cuda? ( dev-util/nvidia-cuda-toolkit )
-	mpi? ( virtual/mpi )
-	python? ( ${PYTHON_DEPS} )
-	sql? ( dev-qt/qtsql:4 )"
-DEPEND="${RDEPEND}
-	dev-python/sip
-	sys-devel/bison
-	virtual/yacc"
-
-S="${WORKDIR}"/BALL-${PV}
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-1.4.1-multilib.patch
-	"${FILESDIR}"/${PN}-1.4.1-missing-signed.patch
-	"${FILESDIR}"/${P}-PDBFile-Fix-compilation-with-gcc-4.8.patch
-	"${FILESDIR}"/${P}-QT4_EXTRACT_OPTIONS-CMake-macro-changed-in-CMake-2.8.patch
-	"${FILESDIR}"/${PN}-1.4.1-BondOrder.xml.patch
-	"${FILESDIR}"/${P}-Fix-compilation-of-sipModularWidget.patch
-	"${FILESDIR}"/${P}-underlinking.patch
-	"${FILESDIR}"/${P}-fix-python-bindings.patch
-	"${FILESDIR}"/${P}-std-namespace-isnan.patch
-	"${FILESDIR}"/${P}-struct-swap-attribute.patch
-)
-
-pkg_setup() {
-	use python && python-single-r1_pkg_setup
-}
-
-src_configure() {
-	local mycmakeargs=(
-		-DUSE_FFTW_THREADS=$(usex threads)
-		-DMT_ENABLE_CUDA=$(usex cuda)
-		-DMT_ENABLE_MPI=$(usex mpi)
-		-DBALL_HAS_QTSQL=$(usex sql)
-		-DBALL_PYTHON_SUPPORT=$(usex python)
-	)
-	cmake-utils_src_configure
-
-	local i
-	for i in "${S}"/data/*; do
-		ln -sf "${i}" "${BUILD_DIR}"/source/TEST/ || die
-		ln -sf "${i}" "${S}"/source/TEST/ || die
-	done
-}
-
-src_compile() {
-	cmake-utils_src_compile
-	use test && cmake-utils_src_make build_tests
-}
diff --git a/sci-chemistry/ball/ball-1.5.0_pre20180419.ebuild b/sci-chemistry/ball/ball-1.5.0_pre20180419.ebuild
new file mode 100644
index 000000000000..b4d49d1fb14b
--- /dev/null
+++ b/sci-chemistry/ball/ball-1.5.0_pre20180419.ebuild
@@ -0,0 +1,100 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+PYTHON_COMPAT=( python2_7 )
+COMMIT=e80b5e2021a72faa36bf9e35207998d4590f2cf4
+inherit cmake-utils python-single-r1
+
+DESCRIPTION="Biochemical Algorithms Library"
+HOMEPAGE="https://github.com/BALL-Project/ball"
+SRC_URI="https://github.com/BALL-Project/${PN}/archive/${COMMIT}.tar.gz -> ${P}.tar.gz"
+
+SLOT="0"
+LICENSE="LGPL-2 fftw? ( GPL-3 ) openbabel? ( GPL-3 )"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="cuda doc +fftw +gui lpsolve mpi openbabel +python svm test threads webengine"
+
+REQUIRED_USE="
+	python? ( ${PYTHON_REQUIRED_USE} )
+	threads? ( fftw )
+	webengine? ( gui )
+"
+
+RDEPEND="
+	dev-cpp/eigen:3
+	dev-libs/boost:=
+	dev-qt/qtcore:5
+	dev-qt/qtnetwork:5
+	dev-qt/qtxml:5
+	media-libs/glew:0=
+	virtual/opengl
+	x11-libs/libX11
+	cuda? ( dev-util/nvidia-cuda-toolkit )
+	fftw? ( sci-libs/fftw:3.0=[threads?] )
+	gui? (
+		dev-qt/qtgui:5
+		dev-qt/qtopengl:5
+		dev-qt/qtprintsupport:5
+		dev-qt/qttest:5
+		dev-qt/qtwidgets:5
+	)
+	lpsolve? ( sci-mathematics/lpsolve )
+	mpi? ( virtual/mpi )
+	openbabel? ( sci-chemistry/openbabel:= )
+	python? ( ${PYTHON_DEPS} )
+	svm? ( sci-libs/libsvm:= )
+	webengine? (
+		dev-qt/qtwebchannel:5
+		dev-qt/qtwebengine:5[widgets]
+	)
+"
+DEPEND="${RDEPEND}
+	sys-devel/bison
+	virtual/yacc
+	doc? ( app-doc/doxygen[dot] )
+	gui? ( dev-qt/linguist-tools:5 )
+	python? ( dev-python/sip )
+"
+
+S="${WORKDIR}"/${PN}-${COMMIT}
+
+PATCHES=( "${FILESDIR}"/${PN}-1.5.0-gnuinstalldirs.patch )
+
+RESTRICT="test"
+
+pkg_setup() {
+	use python && python-single-r1_pkg_setup
+}
+
+src_configure() {
+	local mycmakeargs=(
+		-DUPDATE_TRANSLATIONS=ON
+		-DCMAKE_DISABLE_FIND_PACKAGE_LATEX=ON
+		-DCMAKE_INSTALL_DOCDIR=/usr/share/doc/${PF}
+		-DUSE_CUDA=$(usex cuda)
+		-DCMAKE_DISABLE_FIND_PACKAGE_Doxygen=$(usex !doc)
+		-DCMAKE_DISABLE_FIND_PACKAGE_FFTW=$(usex !fftw)
+		-DUSE_LPSOLVE=$(usex lpsolve)
+		-DUSE_MPI=$(usex mpi)
+		-DREQUIRE_MPI=$(usex mpi)
+		-DCMAKE_DISABLE_FIND_PACKAGE_OpenBabel2=$(usex !openbabel)
+		-DBALL_PYTHON_SUPPORT=$(usex python)
+		-DBALL_HAS_VIEW=$(usex gui)
+		-DUSE_LIBSVM=$(usex svm)
+		-DUSE_FFTW_THREADS=$(usex threads)
+		-DUSE_QTWEBENGINE=$(usex webengine)
+	)
+
+	if use fftw || use openbabel; then
+		mycmakeargs+=( -DBALL_LICENSE=GPL )
+	fi
+
+	cmake-utils_src_configure
+}
+
+src_compile() {
+	cmake-utils_src_compile
+	use test && cmake-utils_src_make build_tests
+}
diff --git a/sci-chemistry/ball/files/ball-1.4.1-BondOrder.xml.patch b/sci-chemistry/ball/files/ball-1.4.1-BondOrder.xml.patch
deleted file mode 100644
index 51e592806999..000000000000
--- a/sci-chemistry/ball/files/ball-1.4.1-BondOrder.xml.patch
+++ /dev/null
@@ -1,30 +0,0 @@
- source/STRUCTURE/assignBondOrderProcessor.C | 2 +-
- source/TEST/AssignBondOrderProcessor_test.C | 2 +-
- 2 files changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/source/STRUCTURE/assignBondOrderProcessor.C b/source/STRUCTURE/assignBondOrderProcessor.C
-index f8acc4f..035fffc 100644
---- a/source/STRUCTURE/assignBondOrderProcessor.C
-+++ b/source/STRUCTURE/assignBondOrderProcessor.C
-@@ -100,7 +100,7 @@ namespace BALL
- 	const bool  AssignBondOrderProcessor::Default::KEKULIZE_RINGS = true;
- 
- 	const char* AssignBondOrderProcessor::Option::INIFile = "iniFile";
--	const String  AssignBondOrderProcessor::Default::INIFile = "/bond_lengths/BondOrder.xml";
-+	const String  AssignBondOrderProcessor::Default::INIFile = "bond_lengths/BondOrder.xml";
- 
- 	const char* AssignBondOrderProcessor::Option::MAX_BOND_ORDER = "max_bond_order";
- 	const int  AssignBondOrderProcessor::Default::MAX_BOND_ORDER = 3;
-diff --git a/source/TEST/AssignBondOrderProcessor_test.C b/source/TEST/AssignBondOrderProcessor_test.C
-index 6dfafcc..3405ef5 100644
---- a/source/TEST/AssignBondOrderProcessor_test.C
-+++ b/source/TEST/AssignBondOrderProcessor_test.C
-@@ -1834,7 +1834,7 @@ CHECK(Option::INIFile)
- 	// There is really not much we can test here, so we just execute the processor
- 	// to have a chance of catching bugs with valgrind if they sneak in
- 	AssignBondOrderProcessor abop;
--	abop.options.set(AssignBondOrderProcessor::Option::INIFile, "/bond_lengths/BondOrderGAFF.xml");
-+	abop.options.set(AssignBondOrderProcessor::Option::INIFile, "bond_lengths/BondOrderGAFF.xml");
- 
- 	System sys40;
- 	MOL2File mol40(BALL_TEST_DATA_PATH(AssignBondOrderProcessor_test_C4_input.mol2), std::ios::in);
diff --git a/sci-chemistry/ball/files/ball-1.4.1-missing-signed.patch b/sci-chemistry/ball/files/ball-1.4.1-missing-signed.patch
deleted file mode 100644
index 6868871b3dc4..000000000000
--- a/sci-chemistry/ball/files/ball-1.4.1-missing-signed.patch
+++ /dev/null
@@ -1,26 +0,0 @@
-Index: ball/include/BALL/DATATYPE/hashGrid.h
-===================================================================
---- ball.orig/include/BALL/DATATYPE/hashGrid.h	2011-12-09 13:49:26.000000000 +0100
-+++ ball/include/BALL/DATATYPE/hashGrid.h	2011-12-09 13:51:09.000000000 +0100
-@@ -37,7 +37,7 @@
- {
- 	namespace __private
- 	{
--		extern const char BALL_EXPORT neighbour_table_[27][3];
-+		extern const signed char BALL_EXPORT neighbour_table_[27][3];
- 	}
- 
- 	template <typename Item> class HashGrid3;
-Index: ball/source/DATATYPE/hashGrid.C
-===================================================================
---- ball.orig/source/DATATYPE/hashGrid.C	2011-12-09 13:49:26.000000000 +0100
-+++ ball/source/DATATYPE/hashGrid.C	2011-12-09 13:50:49.000000000 +0100
-@@ -9,7 +9,7 @@
- {
- 	namespace __private
- 	{
--		const char neighbour_table_[27][3] =
-+		const signed char neighbour_table_[27][3] =
- 		{
- 			{ 0,  0,  0 }, { 0,  0, -1 }, { 0,  0,  1 },
- 			{ 0, -1, -1 }, { 0, -1,  0 }, { 0, -1,  1 },
diff --git a/sci-chemistry/ball/files/ball-1.4.1-multilib.patch b/sci-chemistry/ball/files/ball-1.4.1-multilib.patch
deleted file mode 100644
index 317c4029c678..000000000000
--- a/sci-chemistry/ball/files/ball-1.4.1-multilib.patch
+++ /dev/null
@@ -1,39 +0,0 @@
-From 5b8f4e58b4e54bcdfa6f287e01f91d9dfd4e5a14 Mon Sep 17 00:00:00 2001
-From: Justin Lecher <jlec@gentoo.org>
-Date: Sun, 25 Mar 2012 14:12:21 +0200
-Subject: [PATCH] Correct path for multilib installation.
-
-Libraries should go into lib64 not lib on native 64bit. Therefore we can use the LIBDIR detected by cmake.
----
- CMakeLists.txt |    8 ++++----
- 1 files changed, 4 insertions(+), 4 deletions(-)
-
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 940ebf4..7eb3db4 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -426,8 +426,8 @@ SET(CMAKE_RUNTIME_OUTPUT_DIRECTORY "${PROJECT_BINARY_DIR}/bin")
- ## These variables are used in all install-targets
- IF (NOT ${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
- 	SET(BALL_RUNTIME_INSTALL_DIRECTORY "bin")
--	SET(BALL_LIBRARY_INSTALL_DIRECTORY "lib")
--	SET(BALL_ARCHIVE_INSTALL_DIRECTORY "lib")
-+	SET(BALL_LIBRARY_INSTALL_DIRECTORY ${CMAKE_INSTALL_LIBDIR})
-+	SET(BALL_ARCHIVE_INSTALL_DIRECTORY ${CMAKE_INSTALL_LIBDIR})
- 	SET(BALL_HEADER_INSTALL_DIRECTORY   ".")
- 	SET(BALL_DATA_INSTALL_DIRECTORY    "share/BALL")
- 	SET(BALL_DOCUMENTATION_INSTALL_DIRECTORY    "share/BALL/doc")
-@@ -435,8 +435,8 @@ IF (NOT ${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
- 		SET(BALL_PYTHON_INSTALL_DIRECTORY  "bin")
- 		SET(BALL_PLUGIN_INSTALL_DIRECTORY  "bin")
- 	ELSE()
--		SET(BALL_PYTHON_INSTALL_DIRECTORY  "lib")
--		SET(BALL_PLUGIN_INSTALL_DIRECTORY  "lib")
-+		SET(BALL_PYTHON_INSTALL_DIRECTORY  ${CMAKE_INSTALL_LIBDIR})
-+		SET(BALL_PLUGIN_INSTALL_DIRECTORY  ${CMAKE_INSTALL_LIBDIR})
- 	ENDIF()
- ELSE()
- 	SET(BALL_BUNDLE_INSTALL_DIRECTORY  					"Applications")
--- 
-1.7.8.5
-
diff --git a/sci-chemistry/ball/files/ball-1.4.2-Fix-compilation-of-sipModularWidget.patch b/sci-chemistry/ball/files/ball-1.4.2-Fix-compilation-of-sipModularWidget.patch
deleted file mode 100644
index 3ec2f6e983a8..000000000000
--- a/sci-chemistry/ball/files/ball-1.4.2-Fix-compilation-of-sipModularWidget.patch
+++ /dev/null
@@ -1,40 +0,0 @@
-From da49802f8620562f91ac2c947520dccd223ee26b Mon Sep 17 00:00:00 2001
-From: Andreas Hildebrandt <andreas.hildebrandt@uni-mainz.de>
-Date: Wed, 15 Jan 2014 17:42:01 +0100
-Subject: [PATCH] Fix compilation of sipModularWidget
-
----
- source/PYTHON/EXTENSIONS/VIEW/modularWidget.sip | 10 +++++-----
- 1 file changed, 5 insertions(+), 5 deletions(-)
-
-diff --git a/source/PYTHON/EXTENSIONS/VIEW/modularWidget.sip b/source/PYTHON/EXTENSIONS/VIEW/modularWidget.sip
-index 522b0ed..7b8ba3e 100644
---- a/source/PYTHON/EXTENSIONS/VIEW/modularWidget.sip
-+++ b/source/PYTHON/EXTENSIONS/VIEW/modularWidget.sip
-@@ -22,18 +22,18 @@ class ModularWidget
- 	static Size countInstances();
- 	static ModularWidget* getInstance(Position);
- 
--  ModularWidget(const char* = "<ModularWidget>")	throw();
--	ModularWidget(const ModularWidget&) throw();
-+  ModularWidget(const char* = "<ModularWidget>");
-+	ModularWidget(const ModularWidget&);
-  	~ModularWidget() throw();
- 				
--	virtual void destroy() throw();
--	virtual void clear() throw();
-+//	virtual void destroy();
-+	virtual void clear();
- 
- 	static void registerWidget(ModularWidget*) throw(NullPointer);
- //	virtual void initializeWidget(MainControl&);
- // 	virtual void finalizeWidget(MainControl&);
- 	virtual void checkMenu(MainControl&) throw();
--//	virtual void initializePreferencesTab(Preferences&)	throw();
-+//	virtual void initializePreferencesTab(Preferences&);
- //	virtual void finalizePreferencesTab(Preferences&)	throw();
- 	virtual void applyPreferences() throw();
-   virtual void fetchPreferences(INIFile&) throw();
--- 
-1.9.1
-
diff --git a/sci-chemistry/ball/files/ball-1.4.2-PDBFile-Fix-compilation-with-gcc-4.8.patch b/sci-chemistry/ball/files/ball-1.4.2-PDBFile-Fix-compilation-with-gcc-4.8.patch
deleted file mode 100644
index f6b8ff45fa7f..000000000000
--- a/sci-chemistry/ball/files/ball-1.4.2-PDBFile-Fix-compilation-with-gcc-4.8.patch
+++ /dev/null
@@ -1,28 +0,0 @@
-From e7cc50705bed20e160bd4b637b23f57270f580a8 Mon Sep 17 00:00:00 2001
-From: Daniel Stoeckel <dstoeckel@bioinf.uni-sb.de>
-Date: Sat, 6 Apr 2013 01:06:55 +0200
-Subject: [PATCH] PDBFile:Fix compilation with gcc 4.8
-
-Apparently the automatic conversion from boost::shared_ptr<CrystalInfo>
-to boost::shared_ptr<PersistentObject> is no longer supported.
-Just change the type of the pointer and work around this issue.
----
- source/FORMAT/PDBFileDetails.C | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/source/FORMAT/PDBFileDetails.C b/source/FORMAT/PDBFileDetails.C
-index 97c2572..aedc5db 100644
---- a/source/FORMAT/PDBFileDetails.C
-+++ b/source/FORMAT/PDBFileDetails.C
-@@ -901,7 +901,7 @@ namespace BALL
- 	{
- 		if (!(current_protein_->hasProperty("CRYSTALINFO")))
- 		{
--			boost::shared_ptr<CrystalInfo> temp_ptr(new CrystalInfo());
-+			boost::shared_ptr<PersistentObject> temp_ptr(new CrystalInfo());
- 			current_protein_->setProperty(NamedProperty("CRYSTALINFO", temp_ptr));
- 		}
- 
--- 
-1.9.1
-
diff --git a/sci-chemistry/ball/files/ball-1.4.2-QT4_EXTRACT_OPTIONS-CMake-macro-changed-in-CMake-2.8.patch b/sci-chemistry/ball/files/ball-1.4.2-QT4_EXTRACT_OPTIONS-CMake-macro-changed-in-CMake-2.8.patch
deleted file mode 100644
index 615a92290805..000000000000
--- a/sci-chemistry/ball/files/ball-1.4.2-QT4_EXTRACT_OPTIONS-CMake-macro-changed-in-CMake-2.8.patch
+++ /dev/null
@@ -1,44 +0,0 @@
-From 1e76c9cb1920e9176b725269985c7eb43126d188 Mon Sep 17 00:00:00 2001
-From: Luis de la Garza <delagarza@informatik.uni-tuebingen.de>
-Date: Fri, 22 Nov 2013 15:18:55 +0100
-Subject: [PATCH] QT4_EXTRACT_OPTIONS CMake macro changed in CMake 2.8.12;
- fixed BALLMacros.cmake
-
----
- cmake/BALLMacros.cmake | 14 ++++++++++----
- 1 file changed, 10 insertions(+), 4 deletions(-)
-
-diff --git a/cmake/BALLMacros.cmake b/cmake/BALLMacros.cmake
-index f81ab89..0ac1b87 100644
---- a/cmake/BALLMacros.cmake
-+++ b/cmake/BALLMacros.cmake
-@@ -6,16 +6,22 @@
- ### minor modifications (marked with ## BALL ###)
- ###
- MACRO(QT4_WRAP_UI_BALL outfiles )
--  QT4_EXTRACT_OPTIONS(ui_files ui_options ${ARGN})
--
--	### BALL ###
-+  # since 2.8.12 qt4_extract_options has an additional argument
-+  # copied fix from OpenMS
-+  IF(${CMAKE_VERSION} VERSION_LESS "2.8.12")
-+      QT4_EXTRACT_OPTIONS(ui_files ui_options ${ARGN})
-+  ELSE()
-+      QT4_EXTRACT_OPTIONS(ui_files ui_options ui_target ${ARGN})
-+  ENDIF()
-+
-+  ### BALL ###
-   # create output directory (will not exist for out-of-source builds)
-   FILE(MAKE_DIRECTORY ${PROJECT_BINARY_DIR}/include/BALL/VIEW/UIC/)
- 
-   FOREACH (it ${ui_files})
-     GET_FILENAME_COMPONENT(outfile ${it} NAME_WE)
-     GET_FILENAME_COMPONENT(infile ${it} ABSOLUTE)
--		### BALL ###
-+    ### BALL ###
-     SET(outfile ${PROJECT_BINARY_DIR}/include/BALL/VIEW/UIC/ui_${outfile}.h)
-     ADD_CUSTOM_COMMAND(OUTPUT ${outfile}
-       COMMAND ${QT_UIC_EXECUTABLE}
--- 
-1.9.1
-
diff --git a/sci-chemistry/ball/files/ball-1.4.2-fix-python-bindings.patch b/sci-chemistry/ball/files/ball-1.4.2-fix-python-bindings.patch
deleted file mode 100644
index a13ea2f36ec0..000000000000
--- a/sci-chemistry/ball/files/ball-1.4.2-fix-python-bindings.patch
+++ /dev/null
@@ -1,22 +0,0 @@
-From 38a955ad9588817073a330c79d4b4476afcf69d5 Mon Sep 17 00:00:00 2001
-From: Daniel Stoeckel <dstoeckel@bioinf.uni-sb.de>
-Date: Thu, 14 Apr 2016 19:30:04 +0200
-Subject: [PATCH] Fix Python bindings for Box
-
----
- source/PYTHON/EXTENSIONS/VIEW/box.sip | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/source/PYTHON/EXTENSIONS/VIEW/box.sip b/source/PYTHON/EXTENSIONS/VIEW/box.sip
-index 341b1a4..592765e 100644
---- a/source/PYTHON/EXTENSIONS/VIEW/box.sip
-+++ b/source/PYTHON/EXTENSIONS/VIEW/box.sip
-@@ -6,7 +6,7 @@
- 
- class Box
- 	: GeometricObject,
--		Vertex2
-+	  Box3
- {
- %TypeHeaderCode
- 	#include <BALL/VIEW/PRIMITIVES/box.h>
diff --git a/sci-chemistry/ball/files/ball-1.4.2-std-namespace-isnan.patch b/sci-chemistry/ball/files/ball-1.4.2-std-namespace-isnan.patch
deleted file mode 100644
index cea6377b6a20..000000000000
--- a/sci-chemistry/ball/files/ball-1.4.2-std-namespace-isnan.patch
+++ /dev/null
@@ -1,16 +0,0 @@
-Fix C++11 changes to isnan():
-* /var/tmp/portage/sci-chemistry/ball-1.4.2/work/BALL-1.4.2/source/MOLMEC/MINIMIZATION/shiftedLVMM.C:769:46:   required from here
-* /var/tmp/portage/sci-chemistry/ball-1.4.2/work/BALL-1.4.2/include/BALL/MATHS/common.h:175:18: error: ‘isnan’ was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive]
-*      return (isnan(t) != 0);
-
---- BALL-1.4.2/include/BALL/MATHS/common.h
-+++ BALL-1.4.2/include/BALL/MATHS/common.h
-@@ -172,7 +172,7 @@
- 			#elif  defined(BALL_OS_DARWIN)
- 				return ( __inline_isnand(t) != 0);
- 			#else
--				return (isnan(t) != 0);
-+				return (std::isnan(t) != 0);
- 			#endif
- 		}
- 
diff --git a/sci-chemistry/ball/files/ball-1.4.2-struct-swap-attribute.patch b/sci-chemistry/ball/files/ball-1.4.2-struct-swap-attribute.patch
deleted file mode 100644
index da334915f410..000000000000
--- a/sci-chemistry/ball/files/ball-1.4.2-struct-swap-attribute.patch
+++ /dev/null
@@ -1,80 +0,0 @@
-Silence warning pollution due to misplaced attributes:
-* /var/tmp/portage/sci-chemistry/ball-1.4.2/work/BALL-1.4.2/include/BALL/COMMON/logStream.h:165:22: note: attribute for ‘struct BALL::LogStreamBuf::StreamStruct’ must follow the ‘struct’ keyword
-
---- BALL-1.4.2/include/BALL/COMMON/logStream.h
-+++ BALL-1.4.2/include/BALL/COMMON/logStream.h
-@@ -162,7 +162,7 @@
- 		virtual int overflow(int c = -1);
- 		//@}
- 
--		BALL_EXPORT struct StreamStruct
-+		struct BALL_EXPORT StreamStruct
- 		{
- 			std::ostream*				stream;
- 			string							prefix;
---- BALL-1.4.2/include/BALL/FORMAT/MOL2File.h
-+++ BALL-1.4.2/include/BALL/FORMAT/MOL2File.h
-@@ -33,7 +33,7 @@
- 		public:
- 
- 		/// A class used for storing TRIPOS sets
--		BALL_EXPORT struct SetStruct
-+		struct BALL_EXPORT SetStruct
- 		{
- 			String			name;
- 			bool				is_static;
-@@ -136,7 +136,7 @@
- 
- 		bool containsAtomChilds_(AtomContainerConstIterator& frag_it);
- 
--		BALL_EXPORT struct AtomStruct
-+		struct BALL_EXPORT AtomStruct
- 		{
- 			String		name;
- 			Vector3		position;
-@@ -146,14 +146,14 @@
- 			float			charge;
- 		};
- 
--		BALL_EXPORT struct BondStruct
-+		struct BALL_EXPORT BondStruct
- 		{
- 			Position	atom1;
- 			Position	atom2;
- 			String		type;
- 		};
- 
--		BALL_EXPORT struct MoleculeStruct
-+		struct BALL_EXPORT MoleculeStruct
- 		{
- 			String			name;
- 			Size				number_of_atoms;
-@@ -166,7 +166,7 @@
- 			String			comment;
- 		};
- 
--		BALL_EXPORT struct SubstructureStruct
-+		struct BALL_EXPORT SubstructureStruct
- 		{
- 			String			name;
- 			Size				root_atom;
-@@ -178,7 +178,7 @@
- 			String			comment;
- 		};
- 
--		BALL_EXPORT struct CommentStruct
-+		struct BALL_EXPORT CommentStruct
- 		{
- 			String name;
- 			String value;
---- BALL-1.4.2/include/BALL/FORMAT/MOLFile.h
-+++ BALL-1.4.2/include/BALL/FORMAT/MOLFile.h
-@@ -41,7 +41,7 @@
- 				@see PropertyManager::setProperty
- 				@see PropertyManager::getProperty
- 		*/
--		BALL_EXPORT struct Property
-+		struct BALL_EXPORT Property
- 		{
- 			///
- 			static const String ATOM_MASS_DIFFERENCE;
diff --git a/sci-chemistry/ball/files/ball-1.4.2-underlinking.patch b/sci-chemistry/ball/files/ball-1.4.2-underlinking.patch
deleted file mode 100644
index 825f41978c13..000000000000
--- a/sci-chemistry/ball/files/ball-1.4.2-underlinking.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- source/APPLICATIONS/BALLVIEW/CMakeLists.txt | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/source/APPLICATIONS/BALLVIEW/CMakeLists.txt b/source/APPLICATIONS/BALLVIEW/CMakeLists.txt
-index 6d16212..f94ce76 100644
---- a/source/APPLICATIONS/BALLVIEW/CMakeLists.txt
-+++ b/source/APPLICATIONS/BALLVIEW/CMakeLists.txt
-@@ -85,7 +85,7 @@ IF (UNIX)
- 	LIST(APPEND BALLVIEW_SUPPORT_LIBRARIES "pthread")
- ENDIF ()
- 
--TARGET_LINK_LIBRARIES(BALLView BALL VIEW ${BALLVIEW_SUPPORT_LIBRARIES})
-+TARGET_LINK_LIBRARIES(BALLView BALL VIEW ${BALLVIEW_SUPPORT_LIBRARIES} X11)
- 
- #Setup the translations
- INCLUDE(${CMAKE_SOURCE_DIR}/cmake/BALLViewTranslations.cmake)
diff --git a/sci-chemistry/ball/files/ball-1.5.0-gnuinstalldirs.patch b/sci-chemistry/ball/files/ball-1.5.0-gnuinstalldirs.patch
new file mode 100644
index 000000000000..f9fedc58bb6f
--- /dev/null
+++ b/sci-chemistry/ball/files/ball-1.5.0-gnuinstalldirs.patch
@@ -0,0 +1,355 @@
+From a8cade5ed7090c704aed53871fb664a0fe07af54 Mon Sep 17 00:00:00 2001
+From: Andreas Sturmlechner <andreas.sturmlechner@gmail.com>
+Date: Sat, 21 Apr 2018 20:07:09 +0200
+Subject: [PATCH 1/3] Use GNUInstallDirs
+
+---
+ CMakeLists.txt | 30 ++++++++++++++++--------------
+ 1 file changed, 16 insertions(+), 14 deletions(-)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index be57fe90c..1a54446fb 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -65,6 +65,8 @@ INCLUDE(BALLCompilerSpecific)
+ # Determine BALL configuration
+ INCLUDE(BALLConfiguration)
+ 
++INCLUDE(GNUInstallDirs)
++
+ # We do not have a Component-based installer in MacOS
+ IF(NOT APPLE)
+ 	INCLUDE(BALLComponents)
+@@ -473,20 +475,20 @@ SET(CMAKE_RUNTIME_OUTPUT_DIRECTORY "${PROJECT_BINARY_DIR}/bin")
+ 
+ ## These variables are used in all install-targets
+ IF (NOT APPLE)
+-	SET(BALL_RUNTIME_INSTALL_DIRECTORY "bin")
+-	SET(BALL_LIBRARY_INSTALL_DIRECTORY "lib")
+-	SET(BALL_ARCHIVE_INSTALL_DIRECTORY "lib")
+-	SET(BALL_HEADER_INSTALL_DIRECTORY   ".")
+-	SET(BALL_DATA_INSTALL_DIRECTORY    "share/BALL")
+-	SET(BALL_DOCUMENTATION_INSTALL_DIRECTORY    "share/BALL/doc")
+-	SET(BALL_TOOLS_INSTALL_DIRECTORY   "bin/BALLTools")
++	SET(BALL_RUNTIME_INSTALL_DIRECTORY ${CMAKE_INSTALL_BINDIR})
++	SET(BALL_LIBRARY_INSTALL_DIRECTORY ${CMAKE_INSTALL_LIBDIR})
++	SET(BALL_ARCHIVE_INSTALL_DIRECTORY ${CMAKE_INSTALL_LIBDIR})
++	SET(BALL_HEADER_INSTALL_DIRECTORY  ${CMAKE_INSTALL_INCLUDEDIR})
++	SET(BALL_DATA_INSTALL_DIRECTORY    ${CMAKE_INSTALL_DATAROOTDIR}/BALL)
++	SET(BALL_DOCUMENTATION_INSTALL_DIRECTORY    ${CMAKE_INSTALL_DOCDIR})
++	SET(BALL_TOOLS_INSTALL_DIRECTORY   ${CMAKE_INSTALL_BINDIR}/BALLTools)
+ 
+ 	IF(WIN32)
+ 		SET(BALL_PYTHON_INSTALL_DIRECTORY  "bin")
+ 		SET(BALL_PLUGIN_INSTALL_DIRECTORY  "bin")
+ 	ELSE()
+-		SET(BALL_PYTHON_INSTALL_DIRECTORY  "lib")
+-		SET(BALL_PLUGIN_INSTALL_DIRECTORY  "lib")
++		SET(BALL_PYTHON_INSTALL_DIRECTORY  ${CMAKE_INSTALL_LIBDIR})
++		SET(BALL_PLUGIN_INSTALL_DIRECTORY  ${CMAKE_INSTALL_LIBDIR})
+ 	ENDIF()
+ ENDIF()
+ 
+@@ -710,21 +712,21 @@ IF(NOT APPLE)
+ 	## care of data files and headers
+ 	IF (NOT "${CMAKE_INSTALL_PREFIX}" STREQUAL ".")
+ 		### Install the data directories
+-		INSTALL(DIRECTORY data DESTINATION "${BALL_DATA_INSTALL_DIRECTORY}" COMPONENT ${COMPONENT_LIBBALL})
++		INSTALL(DIRECTORY data/ DESTINATION "${BALL_DATA_INSTALL_DIRECTORY}" COMPONENT ${COMPONENT_LIBBALL})
+ 
+ 		### Install the includes
+-		INSTALL(DIRECTORY include DESTINATION "${BALL_HEADER_INSTALL_DIRECTORY}" COMPONENT ${COMPONENT_LIBBALL_DEV})
++		INSTALL(DIRECTORY include/ DESTINATION "${BALL_HEADER_INSTALL_DIRECTORY}" COMPONENT ${COMPONENT_LIBBALL_DEV})
+ 	ENDIF()
+ 
+ 	## The configured files have to be copied in any case
+ 	INSTALL(FILES ${PROJECT_BINARY_DIR}/include/BALL/CONFIG/config.h
+-		DESTINATION "${BALL_HEADER_INSTALL_DIRECTORY}/include/BALL/CONFIG"
++		DESTINATION "${BALL_HEADER_INSTALL_DIRECTORY}/BALL/CONFIG"
+ 		COMPONENT ${COMPONENT_LIBBALL_DEV}
+ 	)
+ 
+ 	INSTALL(FILES
+ 		${PROJECT_BINARY_DIR}/include/BALL/PYTHON/BALLPythonConfig.h
+-		DESTINATION "${BALL_HEADER_INSTALL_DIRECTORY}/include/BALL/PYTHON"
++		DESTINATION "${BALL_HEADER_INSTALL_DIRECTORY}/BALL/PYTHON"
+ 		COMPONENT ${COMPONENT_LIBBALL_DEV}
+ 	)
+ 
+@@ -866,7 +868,7 @@ EXPORT(PACKAGE BALL)
+ # Generate CMake package configuration for BALL installation
+ IF(NOT APPLE)
+ 	# Installation path for BALL CMake package configuration files
+-	SET(BALL_CMAKE_EXPORT_PATH "lib/cmake/BALL" CACHE PATH "Path to the cmake package configuration files")
++	SET(BALL_CMAKE_EXPORT_PATH ${CMAKE_INSTALL_LIBDIR}/cmake/BALL CACHE PATH "Path to the cmake package configuration files")
+ 
+ 	LIST(REMOVE_ITEM BALL_INCLUDE_DIRS "${PROJECT_BINARY_DIR}/include")
+ 	LIST(REMOVE_ITEM BALL_INCLUDE_DIRS "${PROJECT_SOURCE_DIR}/include")
+-- 
+2.17.0
+
+
+From 17cbef40ad91cf051ca83b1ccf53dd2ccb22fc8d Mon Sep 17 00:00:00 2001
+From: Andreas Sturmlechner <andreas.sturmlechner@gmail.com>
+Date: Sat, 21 Apr 2018 21:20:01 +0200
+Subject: [PATCH 2/3] Drop superfluous cmake variables
+
+---
+ CMakeLists.txt                                | 34 +++++++------------
+ cmake/BALLDoc.cmake                           |  6 ++--
+ source/APPLICATIONS/BALLVIEW/CMakeLists.txt   |  4 +--
+ source/EXTENSIONS/BALLAXY/CMakeLists.txt      |  2 +-
+ source/EXTENSIONS/JUPYTER/CMakeLists.txt      |  2 +-
+ source/EXTENSIONS/PRESENTABALL/CMakeLists.txt |  2 +-
+ source/PYTHON/EXTENSIONS/CMakeLists.txt       | 12 +++----
+ 7 files changed, 27 insertions(+), 35 deletions(-)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 1a54446fb..9b9f3513b 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -475,14 +475,6 @@ SET(CMAKE_RUNTIME_OUTPUT_DIRECTORY "${PROJECT_BINARY_DIR}/bin")
+ 
+ ## These variables are used in all install-targets
+ IF (NOT APPLE)
+-	SET(BALL_RUNTIME_INSTALL_DIRECTORY ${CMAKE_INSTALL_BINDIR})
+-	SET(BALL_LIBRARY_INSTALL_DIRECTORY ${CMAKE_INSTALL_LIBDIR})
+-	SET(BALL_ARCHIVE_INSTALL_DIRECTORY ${CMAKE_INSTALL_LIBDIR})
+-	SET(BALL_HEADER_INSTALL_DIRECTORY  ${CMAKE_INSTALL_INCLUDEDIR})
+-	SET(BALL_DATA_INSTALL_DIRECTORY    ${CMAKE_INSTALL_DATAROOTDIR}/BALL)
+-	SET(BALL_DOCUMENTATION_INSTALL_DIRECTORY    ${CMAKE_INSTALL_DOCDIR})
+-	SET(BALL_TOOLS_INSTALL_DIRECTORY   ${CMAKE_INSTALL_BINDIR}/BALLTools)
+-
+ 	IF(WIN32)
+ 		SET(BALL_PYTHON_INSTALL_DIRECTORY  "bin")
+ 		SET(BALL_PLUGIN_INSTALL_DIRECTORY  "bin")
+@@ -693,18 +685,18 @@ IF(NOT APPLE)
+ 	INSTALL(TARGETS BALL
+ 		EXPORT BALLExportGroup
+ 		COMPONENT "${COMPONENT_LIBBALL}"
+-		RUNTIME DESTINATION "${BALL_RUNTIME_INSTALL_DIRECTORY}"
+-		LIBRARY DESTINATION "${BALL_LIBRARY_INSTALL_DIRECTORY}"
+-		ARCHIVE DESTINATION "${BALL_ARCHIVE_INSTALL_DIRECTORY}"
++		RUNTIME DESTINATION "${CMAKE_INSTALL_BINDIR}"
++		LIBRARY DESTINATION "${CMAKE_INSTALL_LIBDIR}"
++		ARCHIVE DESTINATION "${CMAKE_INSTALL_LIBDIR}"
+ 	)
+ 
+ 	IF(BALL_HAS_VIEW)
+ 		INSTALL(TARGETS VIEW
+ 			EXPORT BALLExportGroup
+ 			COMPONENT "${COMPONENT_LIBVIEW}"
+-			RUNTIME DESTINATION "${BALL_RUNTIME_INSTALL_DIRECTORY}"
+-			LIBRARY DESTINATION "${BALL_LIBRARY_INSTALL_DIRECTORY}"
+-			ARCHIVE DESTINATION "${BALL_ARCHIVE_INSTALL_DIRECTORY}"
++			RUNTIME DESTINATION "${CMAKE_INSTALL_BINDIR}"
++			LIBRARY DESTINATION "${CMAKE_INSTALL_LIBDIR}"
++			ARCHIVE DESTINATION "${CMAKE_INSTALL_LIBDIR}"
+ 		)
+ 	ENDIF()
+ 
+@@ -712,21 +704,21 @@ IF(NOT APPLE)
+ 	## care of data files and headers
+ 	IF (NOT "${CMAKE_INSTALL_PREFIX}" STREQUAL ".")
+ 		### Install the data directories
+-		INSTALL(DIRECTORY data/ DESTINATION "${BALL_DATA_INSTALL_DIRECTORY}" COMPONENT ${COMPONENT_LIBBALL})
++		INSTALL(DIRECTORY data/ DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/BALL COMPONENT ${COMPONENT_LIBBALL})
+ 
+ 		### Install the includes
+-		INSTALL(DIRECTORY include/ DESTINATION "${BALL_HEADER_INSTALL_DIRECTORY}" COMPONENT ${COMPONENT_LIBBALL_DEV})
++		INSTALL(DIRECTORY include/ DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}" COMPONENT ${COMPONENT_LIBBALL_DEV})
+ 	ENDIF()
+ 
+ 	## The configured files have to be copied in any case
+ 	INSTALL(FILES ${PROJECT_BINARY_DIR}/include/BALL/CONFIG/config.h
+-		DESTINATION "${BALL_HEADER_INSTALL_DIRECTORY}/BALL/CONFIG"
++		DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}/BALL/CONFIG"
+ 		COMPONENT ${COMPONENT_LIBBALL_DEV}
+ 	)
+ 
+ 	INSTALL(FILES
+ 		${PROJECT_BINARY_DIR}/include/BALL/PYTHON/BALLPythonConfig.h
+-		DESTINATION "${BALL_HEADER_INSTALL_DIRECTORY}/BALL/PYTHON"
++		DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}/BALL/PYTHON"
+ 		COMPONENT ${COMPONENT_LIBBALL_DEV}
+ 	)
+ 
+@@ -744,14 +736,14 @@ IF(NOT APPLE)
+ 		FOREACH(LIB ${BALL_DEP_OPT_DLLS})
+ 			STRING(TOLOWER "${LIB}" LOWER_LIB)
+ 			INSTALL(FILES "${LIB}"
+-				DESTINATION "${BALL_RUNTIME_INSTALL_DIRECTORY}"
++				DESTINATION "${CMAKE_INSTALL_BINDIR}"
+ 				COMPONENT ${COMPONENT_LIBBALL})
+ 		ENDFOREACH()
+ 
+ 		IF(QT_DEPLOY_EXECUTABLE)
+ 			INSTALL(CODE
+-				"EXECUTE_PROCESS(COMMAND ${QT_DEPLOY_EXECUTABLE} \$\{CMAKE_INSTALL_PREFIX\}/${BALL_RUNTIME_INSTALL_DIRECTORY}/BALL.dll)
+-				EXECUTE_PROCESS(COMMAND ${QT_DEPLOY_EXECUTABLE} \$\{CMAKE_INSTALL_PREFIX\}/${BALL_RUNTIME_INSTALL_DIRECTORY}/VIEW.dll)"
++				"EXECUTE_PROCESS(COMMAND ${QT_DEPLOY_EXECUTABLE} \$\{CMAKE_INSTALL_PREFIX\}/${CMAKE_INSTALL_BINDIR}/BALL.dll)
++				EXECUTE_PROCESS(COMMAND ${QT_DEPLOY_EXECUTABLE} \$\{CMAKE_INSTALL_PREFIX\}/${CMAKE_INSTALL_BINDIR}/VIEW.dll)"
+ 				COMPONENT "${COMPONENT_LIBBALL}")
+ 		ENDIF()
+ 	ENDIF()
+diff --git a/cmake/BALLDoc.cmake b/cmake/BALLDoc.cmake
+index 061b9c95f..2d7c17466 100644
+--- a/cmake/BALLDoc.cmake
++++ b/cmake/BALLDoc.cmake
+@@ -20,7 +20,7 @@ ENDIF()
+ 
+ IF(NOT APPLE)
+ 	INSTALL(DIRECTORY   "${PROJECT_SOURCE_DIR}/doc/examples/"
+-		DESTINATION "${BALL_DOCUMENTATION_INSTALL_DIRECTORY}/EXAMPLES"
++		DESTINATION "${CMAKE_INSTALL_DOCDIR}/EXAMPLES"
+ 		COMPONENT   "${COMPONENT_DOCUMENTATION_EXAMPLES}")
+ ENDIF()
+ 
+@@ -53,7 +53,7 @@ IF (DOXYGEN_FOUND)
+ 
+ 	IF(NOT APPLE)
+ 		INSTALL(DIRECTORY   "${PROJECT_BINARY_DIR}/doc/html/"
+-			DESTINATION "${BALL_DOCUMENTATION_INSTALL_DIRECTORY}/BALL"
++			DESTINATION "${CMAKE_INSTALL_DOCDIR}/BALL"
+ 			COMPONENT   "${COMPONENT_DOCUMENTATION_HTML}"
+ 		)
+ 	ENDIF()
+@@ -107,7 +107,7 @@ IF (LATEX_COMPILER AND DVIPS_CONVERTER)
+ 
+ 	IF(NOT APPLE)
+ 		INSTALL(FILES   ${PROJECT_BINARY_DIR}/doc/tutorial.pdf
+-			DESTINATION "${BALL_DOCUMENTATION_INSTALL_DIRECTORY}/TUTORIAL"
++			DESTINATION "${CMAKE_INSTALL_DOCDIR}/TUTORIAL"
+ 			COMPONENT   "${COMPONENT_DOCUMENTATION_PDF}"
+ 			OPTIONAL
+ 		)
+diff --git a/source/APPLICATIONS/BALLVIEW/CMakeLists.txt b/source/APPLICATIONS/BALLVIEW/CMakeLists.txt
+index b4b96c31c..5fd21ee68 100644
+--- a/source/APPLICATIONS/BALLVIEW/CMakeLists.txt
++++ b/source/APPLICATIONS/BALLVIEW/CMakeLists.txt
+@@ -59,13 +59,13 @@ IF(APPLE)
+ ELSE()
+ 	INSTALL(TARGETS BALLView
+ 		COMPONENT "${COMPONENT_BALLVIEW}"
+-		RUNTIME DESTINATION "${BALL_RUNTIME_INSTALL_DIRECTORY}"
++		RUNTIME DESTINATION "${CMAKE_INSTALL_BINDIR}"
+ 		BUNDLE DESTINATION "${BALL_BUNDLE_INSTALL_DIRECTORY}"
+ 	)
+ 
+ 	IF(WIN32)
+ 		IF(QT_DEPLOY_EXECUTABLE)
+-			INSTALL(CODE "EXECUTE_PROCESS(COMMAND ${QT_DEPLOY_EXECUTABLE} \$\{CMAKE_INSTALL_PREFIX\}/${BALL_RUNTIME_INSTALL_DIRECTORY}/BALLView.exe)"
++			INSTALL(CODE "EXECUTE_PROCESS(COMMAND ${QT_DEPLOY_EXECUTABLE} \$\{CMAKE_INSTALL_PREFIX\}/${CMAKE_INSTALL_BINDIR}/BALLView.exe)"
+ 				COMPONENT "${COMPONENT_BALLVIEW}")
+ 		ENDIF()
+ 	ENDIF()
+diff --git a/source/EXTENSIONS/BALLAXY/CMakeLists.txt b/source/EXTENSIONS/BALLAXY/CMakeLists.txt
+index 2fdfcbeed..1eed12c37 100644
+--- a/source/EXTENSIONS/BALLAXY/CMakeLists.txt
++++ b/source/EXTENSIONS/BALLAXY/CMakeLists.txt
+@@ -66,7 +66,7 @@ IF(NOT APPLE)
+ 
+ 	IF(WIN32)
+ 		IF(QT_DEPLOY_EXECUTABLE)
+-			INSTALL(CODE "EXECUTE_PROCESS(COMMAND ${QT_DEPLOY_EXECUTABLE} \$\{CMAKE_INSTALL_PREFIX\}/${BALL_RUNTIME_INSTALL_DIRECTORY}/pluginBALLaxy.dll)"
++			INSTALL(CODE "EXECUTE_PROCESS(COMMAND ${QT_DEPLOY_EXECUTABLE} \$\{CMAKE_INSTALL_PREFIX\}/${CMAKE_INSTALL_BINDIR}/pluginBALLaxy.dll)"
+ 				COMPONENT "Unspecified")
+ 		ENDIF()
+ 	ENDIF()
+diff --git a/source/EXTENSIONS/JUPYTER/CMakeLists.txt b/source/EXTENSIONS/JUPYTER/CMakeLists.txt
+index bb7e91921..24a459fbf 100644
+--- a/source/EXTENSIONS/JUPYTER/CMakeLists.txt
++++ b/source/EXTENSIONS/JUPYTER/CMakeLists.txt
+@@ -78,7 +78,7 @@ IF(NOT APPLE)
+ 
+ 	IF(WIN32)
+ 		IF(QT_DEPLOY_EXECUTABLE)
+-			INSTALL(CODE "EXECUTE_PROCESS(COMMAND ${QT_DEPLOY_EXECUTABLE} \$\{CMAKE_INSTALL_PREFIX\}/${BALL_RUNTIME_INSTALL_DIRECTORY}/pluginJupyter.dll)"
++			INSTALL(CODE "EXECUTE_PROCESS(COMMAND ${QT_DEPLOY_EXECUTABLE} \$\{CMAKE_INSTALL_PREFIX\}/${CMAKE_INSTALL_BINDIR}/pluginJupyter.dll)"
+ 				COMPONENT "Unspecified")
+ 		ENDIF()
+ 	ENDIF()
+diff --git a/source/EXTENSIONS/PRESENTABALL/CMakeLists.txt b/source/EXTENSIONS/PRESENTABALL/CMakeLists.txt
+index 8606f2f26..ad027fd03 100644
+--- a/source/EXTENSIONS/PRESENTABALL/CMakeLists.txt
++++ b/source/EXTENSIONS/PRESENTABALL/CMakeLists.txt
+@@ -66,7 +66,7 @@ IF(NOT APPLE)
+ 
+ 	IF(WIN32)
+ 		IF(QT_DEPLOY_EXECUTABLE)
+-			INSTALL(CODE "EXECUTE_PROCESS(COMMAND ${QT_DEPLOY_EXECUTABLE} \$\{CMAKE_INSTALL_PREFIX\}/${BALL_RUNTIME_INSTALL_DIRECTORY}/pluginPresentaBALL.dll)"
++			INSTALL(CODE "EXECUTE_PROCESS(COMMAND ${QT_DEPLOY_EXECUTABLE} \$\{CMAKE_INSTALL_PREFIX\}/${CMAKE_INSTALL_BINDIR}/pluginPresentaBALL.dll)"
+ 				COMPONENT "Unspecified")
+ 		ENDIF()
+ 	ENDIF()
+diff --git a/source/PYTHON/EXTENSIONS/CMakeLists.txt b/source/PYTHON/EXTENSIONS/CMakeLists.txt
+index 590e1de3a..374732519 100644
+--- a/source/PYTHON/EXTENSIONS/CMakeLists.txt
++++ b/source/PYTHON/EXTENSIONS/CMakeLists.txt
+@@ -49,15 +49,15 @@ IF(BALL_PYTHON_SUPPORT)
+ 	IF(NOT APPLE)
+ 		INSTALL(TARGETS BALLCoremodule
+ 			COMPONENT "${COMPONENT_PYTHON_BINDINGS_BALL}"
+-			RUNTIME DESTINATION ${BALL_RUNTIME_INSTALL_DIRECTORY}
+-			LIBRARY DESTINATION ${BALL_LIBRARY_INSTALL_DIRECTORY}
++			RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
++			LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
+ 		)
+ 
+ 		IF(BALL_HAS_VIEW)
+ 			INSTALL(TARGETS VIEWmodule
+ 				COMPONENT "${COMPONENT_PYTHON_BINDINGS_VIEW}"
+-				RUNTIME DESTINATION ${BALL_RUNTIME_INSTALL_DIRECTORY}
+-				LIBRARY DESTINATION ${BALL_LIBRARY_INSTALL_DIRECTORY}
++				RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
++				LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
+ 			)
+ 		ENDIF()
+ 
+@@ -69,7 +69,7 @@ IF(BALL_PYTHON_SUPPORT)
+ 		IF (WIN32)
+ 			#		INSTALL(FILES ${PYTHON_EXECUTABLE}
+ 			#	COMPONENT "${COMPONENT_PYTHON_BINDINGS_BALL}"
+-			#	DESTINATION "${BALL_RUNTIME_INSTALL_DIRECTORY}"
++			#	DESTINATION "${CMAKE_INSTALL_BINDIR}"
+ 			#)
+ 
+ 
+@@ -78,7 +78,7 @@ IF(BALL_PYTHON_SUPPORT)
+ 
+ 			INSTALL(DIRECTORY "${PYTHON_SITE_PACKAGES_DIR}"
+ 				COMPONENT "${COMPONENT_PYTHON_BINDINGS_BALL}"
+-				DESTINATION "${BALL_RUNTIME_INSTALL_DIRECTORY}"
++				DESTINATION "${CMAKE_INSTALL_BINDIR}"
+ 			)
+ 		ENDIF ()
+ 	ENDIF()
+-- 
+2.17.0
+
+
+From 666ca19b00b14752e69c05600725724fb4f6d488 Mon Sep 17 00:00:00 2001
+From: Andreas Sturmlechner <andreas.sturmlechner@gmail.com>
+Date: Sat, 21 Apr 2018 22:02:14 +0200
+Subject: [PATCH 3/3] Install html doc into "html" dir
+
+---
+ cmake/BALLDoc.cmake | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/cmake/BALLDoc.cmake b/cmake/BALLDoc.cmake
+index 2d7c17466..a070613c8 100644
+--- a/cmake/BALLDoc.cmake
++++ b/cmake/BALLDoc.cmake
+@@ -53,7 +53,7 @@ IF (DOXYGEN_FOUND)
+ 
+ 	IF(NOT APPLE)
+ 		INSTALL(DIRECTORY   "${PROJECT_BINARY_DIR}/doc/html/"
+-			DESTINATION "${CMAKE_INSTALL_DOCDIR}/BALL"
++			DESTINATION "${CMAKE_INSTALL_DOCDIR}/html"
+ 			COMPONENT   "${COMPONENT_DOCUMENTATION_HTML}"
+ 		)
+ 	ENDIF()
+-- 
+2.17.0
+
diff --git a/sci-chemistry/ball/metadata.xml b/sci-chemistry/ball/metadata.xml
index 72d683b18460..6f18011f2e04 100644
--- a/sci-chemistry/ball/metadata.xml
+++ b/sci-chemistry/ball/metadata.xml
@@ -1,11 +1,11 @@
 <?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>
+	<maintainer type="project">
+		<email>sci-chemistry@gentoo.org</email>
+		<name>Gentoo Chemistry Project</name>
+	</maintainer>
+	<longdescription>
 Rapid Software Prototyping can significantly reduce development times in the 
 field of Computational Molecular Biology and Molecular Modeling. 
 BALL (Biochemical Algorithms Library) is an application framework in C++ that 
@@ -23,9 +23,14 @@ structures and algorithms.
 Based on BALL we have developed a stand-alone tool for molecular visualization,
 BALLView . BALLView makes the broad functionality available through an 
 integrated user-friendly GUI.
-</longdescription>
-  <use>
-    <flag name="sql">Include SQL database support</flag>
-    <flag name="cuda">Include cuda support</flag>
-  </use>
+	</longdescription>
+	<use>
+		<flag name="cuda">Include cuda support</flag>
+		<flag name="fftw">Build with <pkg>sci-libs/fftw</pkg> (switching BALL to GPL3)</flag>
+		<flag name="gui">Build VIEW library required for visualization and graphical user interfaces</flag>
+		<flag name="lpsolve">Enable support for the Mixed Integer Linear Programming solver</flag>
+		<flag name="openbabel">Enable support for <pkg>sci-chemistry/openbabel</pkg> (switching BALL to GPL3)</flag>
+		<flag name="svm">Enable support for the Support Vector Machine module</flag>
+		<flag name="webengine">Enable QtWebEngine support with Qt5 (requires gui)</flag>
+	</use>
 </pkgmetadata>