12 files changed, 527 insertions, 208 deletions
diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz
index 245f3fb045b3..0b1ac4f3e282 100644
--- a/sci-chemistry/Manifest.gz
+++ b/sci-chemistry/Manifest.gz
diff --git a/sci-chemistry/avogadro2/Manifest b/sci-chemistry/avogadro2/Manifest
index 58a80f9492da..5bc683184cdd 100644
--- a/sci-chemistry/avogadro2/Manifest
+++ b/sci-chemistry/avogadro2/Manifest
@@ -1,5 +1,4 @@
-AUX avogadro2-1.95.1-qttest.patch 522 BLAKE2B f7a61dfc89e2066340a2e73deab81439d88b3d2e28853ec4df538a699e90189075d3c647e4d09b791771f3d24d108e6ebe8ebe25cf66b1104c78c2f110cd57a2 SHA512 c3507fcb4d9e57800a405683a05b84009c65b0bf488294b9fdf94ebc872c4019d296e59a9b3479da0696ac6e495754b517ed08274a5640737f96c79bd5f53c47
-DIST avogadro2-1.97.0-i18n.tar.gz 990218 BLAKE2B e76b2d69b74f2a2964383564018e61ff0248e53c62a4a2abb1033100bd7fadaefbc261e64bf9e809d6e12ef851bd1ca3661d78b70d07728476586f6564e44e63 SHA512 6a01a05d4a62f83a75ae13100229f2ac6f9e697412868a75f5a9fde6025fc4e886c7ac80704fe5b8390a2af437c7848b0dce19897a6f9da1c5cf4c83418523db
-DIST avogadro2-1.97.0.tar.gz 2931223 BLAKE2B b2f2146ebe94ef25f4f684b13f9b9c5fbba933978208524ee197c8971f96c733f687ec68e566d032381a5f45cf22defb2bf909bd738becdd70da0abccebc0755 SHA512 19a0bcf01a840da29c4bab6eed55c879c10d773ee5dcfab613e6666708916bfd8398e44237c18de4e5bb3247d3c4bed3844cac47cf7f3a94dc96d7df8eb13579
-EBUILD avogadro2-1.97.0.ebuild 1932 BLAKE2B 3b90d66a4c66c69d8f18d35ad37bce703c4c13026a05ceb0b3ab846b2d722ad834a51fa70e165e286f17295d08f133a0750b5af2d24f3c6eda0a91ac87f7e7a6 SHA512 0877b2a81a53e131add80a06742dbfa792b1b2a1fc4f92cbe6493bda63a8bc1e3bf4069d8d49eb3e60288dec666bae6e9f3e91e2ecd3c9e14b70f1d6dee5124a
-MISC metadata.xml 514 BLAKE2B 0a88a4b92fef923690f6e9767c572875d86c8522936aff89354f4b08ee74fe7c2f49e1eba143c850753d8f2cb5a7e7dc063e9864e433b70068ef7edcd0163683 SHA512 e7729ed111cfade53f238b9b49067c55c1a229489dbc1665d428ba8643c0f9ad0af402e8bf4c81399df1d1a786c7831a7a769bf9a5608157642546a1d0f45ee9
+DIST avogadro2-1.100.0-i18n.tar.gz 1225588 BLAKE2B a548952828764c3bbb2b487ecdfa649dd290473e3b241fcdb85c0fcf21e2b163e47e2007de2eb62845c2cfc368a2d8a115698c8988113d802504895a3ea5419d SHA512 261a1c3c165529731107346eca1b423fad6e64e790bf694dde64245e640cb3164735535574efac895d17f2b3ff1e236eb64535bf29de7d55ad4f008854e45164
+DIST avogadro2-1.100.0.tar.gz 3079141 BLAKE2B f9ddd73b9c85099db8594300976fcb64d9b74ac8349a611c536efacaf57aa7f10b7f5b2325b6a9cc8f64354768bbb4af9bc280784a9042c9226af68d06e519c7 SHA512 689999bad26d575c879bf3e64a32afb3a2b95ece26b7338b417a4f8a552ef97908c75cf4aa09880b657b74255ead18e9025b0faf46dfb6e3329e00647ce12c48
+EBUILD avogadro2-1.100.0.ebuild 1793 BLAKE2B 39b172b1dac9a0fb84b90c6d8745228f4a4623d6456b61425fef4d8b67eedaa03fdd37739205551f87a7940418ce4d83fd0172f3b5bcd898c9b2e6b94e0e3579 SHA512 d0f106dd20d375c981c9b64d5ede1f5e8cb51e66fe29a2dd1b07f34649fcba51cc1a656584e8805a29891d7b729e2506f89de5e2c475d1b9d9e6471f3ae111f7
+MISC metadata.xml 470 BLAKE2B 29e43b732928ca5aff525705f381fc859baa85c7c4b30f84d3938f7ead457648c4972be9741e404b399e5efea5210b66fa0ff0d0277029424f32285225dda9a7 SHA512 c77f9b3a0299095f7052569045dcd9c1ce0a35a522970918c1e3e6dca4afa2a5cce90c2c04a57113ddfb2616fe23e3e1c020c149a4e4a81fd6a89f2ced203c34
diff --git a/sci-chemistry/avogadro2/avogadro2-1.100.0.ebuild b/sci-chemistry/avogadro2/avogadro2-1.100.0.ebuild
new file mode 100644
index 000000000000..841b082db04d
--- /dev/null
+++ b/sci-chemistry/avogadro2/avogadro2-1.100.0.ebuild
@@ -0,0 +1,80 @@
+# Copyright 1999-2025 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+MY_PN=avogadroapp
+inherit cmake xdg
+
+DESCRIPTION="Advanced molecule editor and visualizer 2"
+HOMEPAGE="https://www.openchemistry.org/ https://two.avogadro.cc/"
+SRC_URI="
+	https://github.com/OpenChemistry/${MY_PN}/archive/${PV}.tar.gz -> ${P}.tar.gz
+	https://github.com/OpenChemistry/avogadro-i18n/archive/${PV}.tar.gz -> ${P}-i18n.tar.gz
+"
+S="${WORKDIR}/${MY_PN}-${PV}"
+
+LICENSE="BSD GPL-2+"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="doc vtk"
+
+RDEPEND="
+	dev-qt/qtbase:6[concurrent,gui,network,opengl,ssl,widgets]
+	>=sci-libs/avogadrolibs-${PV}[qt6,vtk?]
+	vtk? ( sci-libs/vtk:= )
+"
+DEPEND="${RDEPEND}
+	dev-cpp/eigen:3
+"
+BDEPEND="doc? ( app-text/doxygen )"
+
+src_unpack() {
+	default
+	mv "${WORKDIR}"/avogadro-i18n-${PV} "${WORKDIR}"/avogadro-i18n || die
+}
+
+src_prepare() {
+	if use doc; then
+		doxygen -u docs/doxyfile.in 2>/dev/null || die
+	fi
+
+	cmake_src_prepare
+}
+
+src_configure() {
+	local mycmakeargs=(
+		-DCMAKE_SKIP_RPATH=ON
+		-DBUILD_DOCUMENTATION=$(usex doc)
+		# rpc/molequeue is abandoned
+		# see https://github.com/OpenChemistry/avogadroapp/issues/561
+		-DAvogadro_ENABLE_RPC=OFF
+		# test requires qttesting/paraview
+		-DENABLE_TESTING=OFF
+		-DQT_VERSION=6
+		-DUSE_VTK=$(usex vtk)
+	)
+
+	# Need this to prevent overwriting the documentation OUTDIR
+	use doc && mycmakeargs+=(
+			-DChemData_SOURCE_DIR="${S}"
+			-DChemData_BINARY_DIR="${BUILD_DIR}"
+	)
+
+	cmake_src_configure
+}
+
+src_compile() {
+	cmake_src_compile
+
+	use doc && cmake_build documentation
+}
+
+src_install() {
+	use doc && local HTML_DOCS=( "${BUILD_DIR}"/docs/html/. )
+
+	cmake_src_install
+
+	# remove CONTRIBUTING, LICENSE and duplicate README
+	rm -r "${ED}"/usr/share/doc/${PF}/avogadro2 || die
+}
diff --git a/sci-chemistry/avogadro2/avogadro2-1.97.0.ebuild b/sci-chemistry/avogadro2/avogadro2-1.97.0.ebuild
deleted file mode 100644
index f4faa2f030e1..000000000000
--- a/sci-chemistry/avogadro2/avogadro2-1.97.0.ebuild
+++ /dev/null
@@ -1,82 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-MY_PN=avogadroapp
-
-DOCS_BUILDER="doxygen"
-DOCS_DEPEND="media-gfx/graphviz"
-DOCS_DIR="${WORKDIR}/${MY_PN}-${PV}_build/docs"
-# docs/CMakeLists.txt overwrites docs.eclass outdir if we do not set this
-DOCS_OUTDIR="${DOCS_DIR}/html"
-DOCS_CONFIG_NAME="doxyfile"
-inherit desktop docs cmake xdg
-
-I18N_COMMIT="13c4286102373658cea48a33b86536ab5793da66"
-
-DESCRIPTION="Advanced molecule editor and visualizer 2"
-HOMEPAGE="https://www.openchemistry.org/"
-SRC_URI="
-	https://github.com/OpenChemistry/${MY_PN}/archive/${PV}.tar.gz -> ${P}.tar.gz
-	https://github.com/OpenChemistry/avogadro-i18n/archive/${I18N_COMMIT}.tar.gz -> ${P}-i18n.tar.gz
-"
-S="${WORKDIR}/${MY_PN}-${PV}"
-
-SLOT="0"
-LICENSE="BSD GPL-2+"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="rpc test vtk"
-
-RDEPEND="
-	dev-qt/qtcore:5
-	dev-qt/qtgui:5
-	dev-qt/qtwidgets:5
-	>=sci-libs/avogadrolibs-${PV}[qt5,vtk?]
-	sci-libs/hdf5:=
-	rpc? ( sci-chemistry/molequeue )
-"
-DEPEND="${RDEPEND}
-	dev-cpp/eigen:3
-	test? ( dev-qt/qttest:5 )
-"
-
-RESTRICT="test"
-
-PATCHES=(
-	"${FILESDIR}/${PN}-1.95.1-qttest.patch"
-)
-
-src_unpack() {
-	default
-	mv "${WORKDIR}/avogadro-i18n-${I18N_COMMIT}" "${WORKDIR}/avogadro-i18n" || die
-}
-
-src_prepare() {
-	cmake_src_prepare
-	sed -e "/LICENSE/d" -i CMakeLists.txt || die
-}
-
-src_configure() {
-	local mycmakeargs=(
-		-DINSTALL_DOC_DIR="${EPREFIX}/usr/share/doc/${PF}"
-		-DBUILD_DOCUMENTATION=$(usex doc)
-		-DAvogadro_ENABLE_RPC=$(usex rpc)
-		-DENABLE_TESTING=$(usex test)
-		-DUSE_VTK=$(usex vtk)
-	)
-	# Need this to prevent overwriting the documentation OUTDIR
-	use doc && mycmakeargs+=( -DChemData_BINARY_DIR="${DOCS_OUTDIR}" )
-	cmake_src_configure
-}
-
-src_compile() {
-	cmake_src_compile
-	docs_compile
-}
-
-src_install() {
-	cmake_src_install
-	for size in 64 128 256 512; do
-		newicon -s "${size}" avogadro/icons/"${PN}"_"${size}".png "${PN}".png
-	done
-}
diff --git a/sci-chemistry/avogadro2/files/avogadro2-1.95.1-qttest.patch b/sci-chemistry/avogadro2/files/avogadro2-1.95.1-qttest.patch
deleted file mode 100644
index ed12da21e3f6..000000000000
--- a/sci-chemistry/avogadro2/files/avogadro2-1.95.1-qttest.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-diff --git a/avogadro/CMakeLists.txt b/avogadro/CMakeLists.txt
-index d2245ff..fe1857c 100644
---- a/avogadro/CMakeLists.txt
-+++ b/avogadro/CMakeLists.txt
-@@ -80,8 +80,8 @@ endif()
- 
- if(ENABLE_TESTING)
-   find_package(Qt5 COMPONENTS Test REQUIRED)
--  find_package(QtTesting REQUIRED NO_MODULE)
--  include_directories(${QtTesting_INCLUDE_DIRS})
-+  find_package(Qt5Test REQUIRED NO_MODULE)
-+  include_directories(${Qt5Test_INCLUDE_DIRS})
-   link_directories(${QtTesting_LIBRARY_DIR})
-   add_definitions(-DQTTESTING)
- endif()
diff --git a/sci-chemistry/avogadro2/metadata.xml b/sci-chemistry/avogadro2/metadata.xml
index b669d7480d2e..f14bff47877c 100644
--- a/sci-chemistry/avogadro2/metadata.xml
+++ b/sci-chemistry/avogadro2/metadata.xml
@@ -6,7 +6,6 @@
 		<name>Gentoo Chemistry Project</name>
 	</maintainer>
 	<use>
-		<flag name="rpc">Enable RPC server</flag>
 		<flag name="vtk">include vtk support</flag>
 	</use>
 	<upstream>
diff --git a/sci-chemistry/openbabel/Manifest b/sci-chemistry/openbabel/Manifest
index 12ada1118c65..b4905b6c44e0 100644
--- a/sci-chemistry/openbabel/Manifest
+++ b/sci-chemistry/openbabel/Manifest
@@ -1,8 +1,13 @@
 AUX openbabel-3.1.1-fix-time-check-cmake.patch 1030 BLAKE2B 4d6ecf7103cc96dbd96754b291700b58fc36bf84b67c24ccbb7e819b075992bec40808ae0bf9304b24e8943badf24d190e5ad80837a47ce15b15ab8df68ebb38 SHA512 dac73a275f64120d8697f24b75d08d4339dc62da301b8f53beae390ce254d7d656b6e8fb23b9f3829d677ed03f7a16f2dc2d5051854bfcb0bbebd17f1eaf2b6b
+AUX openbabel-3.1.1_p2024-fix_examples.patch 454 BLAKE2B 97a9385159388a0c9a6b6ab5cf924146a647a360c9988d2c6732f6c4cf40f2404af48f41e158222e797126633f46715432f0fb50f1bf0ea325f7158ff655798b SHA512 d99c07823527127ba69aca0cd2202f7538e107af1aa98a74d973dea00bc4ab9188db21a22ba6adfe1c241b2f507284e414c997ec9952719d28824a00babd3730
+AUX openbabel-3.1.1_p2024-fix_pybind.patch 1651 BLAKE2B 4245372c34662a90b235360eb53988ceb88d6c9e6acf7531217db0afd0e8c66cc5db166f2bf23f5a036dd85b80b24d5f8b189b39b5c1a6635c4917f9cedc3ede SHA512 de2b5c467b8e306ee789d3c691d015d8041bd7f7fa75f1429cd336ebf31094b95c25863fdd1970b8c5bfe4a076c9783689913196348527f8264dcfa7ca602c84
+AUX openbabel-python-r2.cmake 4480 BLAKE2B 61a09e433f946415a2820e840a77d6e6cbdfabb26f349f85d8efa6455a19395ac6f7134079661e18a82658dc3463ef4303f4da93ac22c3d7199224808902e44e SHA512 220ae20356e30e73ed3a47ac3ede77adb4b3db0672f142fc9b0cb562b3f381bcff92acecf9a666d58f5125a7094497282a2ca8ec753fb5fe76178e282a487e74
 AUX openbabel-python.cmake 4402 BLAKE2B 36c325a26f9b23c3957db22110628a0a922ad02b6a7415fc197713d3df8f1703475bf2f2c53b546b7915466ce30b6b3c72c505ea72443dd23a17a7f9131f4f6e SHA512 a7bcdf90588930b05d11312429e735d3cc6a94053e67117bef6c1614932651abee7c4e082916482a9012622c0f29c3ba62dd7788b72aca6c88293660c7f2a3db
 DIST openbabel-3.1.1_p20210225.tar.gz 36674527 BLAKE2B bb82fc96f704249d211bd86c73de0cf4e7cfe5e2ba5c745aa8b4f6f19583837e2181d85101377810095f6b71fc3b91bf2f6f5636726fc8271c6905f1f8c59e7b SHA512 9ff7cb4acbfad7a9c5c8d0dd8930ac0390d0d0f2758d1a6120009071f47ffe718f92ad620d37f26f196babb14649c52b5eb7bb161c342ef36aec655e0a172de4
+DIST openbabel-3.1.1_p20241221.tar.gz 36864825 BLAKE2B 55e6fbdd5c50a557c40fd5ffaca41753f73175b2b4eea22abe5c2b0031363e3c133acf9a8daf5b1cb362a3adb6398204497af036b9a7ba3630c1d8ccbce0f9d3 SHA512 44340c3d08b22783cf6a702c192480869b73fef21104641feaf5cbcd51f693fd17bb05ad31a3520f330aa57733d6f4be707b3c1243b3010d6ceccca8974e732f
 DIST openbabel.jpg 12159 BLAKE2B b701df2b8c29df607dc2bd3997a282aa9a726d56c789ff2db900d33234dc691f76b6af12a4c9ccda4f09984504b863c40c39e8bf91058939996714ede2dd37c7 SHA512 998ea526c8c92f87dd203527fdd9f4e001357e951409209f41ab68e0b730fe12d97f9079c12ca289be413854ea2abcf8bb691ae5af823a6f29d6a590e1a3e2b0
 DIST openbabel.png 29060 BLAKE2B 8d217d92125cc73462437411dd4e0cc05179cb0934f5ed15a307acc6b549b8ebab250a48a05ef7657f48c6df394f37da9b659de61efb1477b79b573a5b393ad3 SHA512 bbcaaa37663b526c9038ccb9edaf05ccc3ad1a861739a737f05f363098d8402a10b36e341fcc0aca636e809c6c32db99bf987b41719a0c756bf5e31444d3eb70
 EBUILD openbabel-3.1.1_p20210225-r1.ebuild 7465 BLAKE2B fedf37c6772c62b7d9d6a5c5cc2e89b396cfebe803d34abdd5a1a77248c9f4ce27fdcce42aa2aa625a79d29361d2fd9c31a104a8d4b886fbf63fe84af4e0066d SHA512 0089ac6f89ca13e1999fe440922f0bd864568d61f8cb8dac1519c2b1d2a9b73f278c325ffe177474f678991a4ebe1264baafdd4b419d5eacfebbaccebfd31195
-EBUILD openbabel-9999.ebuild 7465 BLAKE2B fedf37c6772c62b7d9d6a5c5cc2e89b396cfebe803d34abdd5a1a77248c9f4ce27fdcce42aa2aa625a79d29361d2fd9c31a104a8d4b886fbf63fe84af4e0066d SHA512 0089ac6f89ca13e1999fe440922f0bd864568d61f8cb8dac1519c2b1d2a9b73f278c325ffe177474f678991a4ebe1264baafdd4b419d5eacfebbaccebfd31195
+EBUILD openbabel-3.1.1_p20241221.ebuild 6136 BLAKE2B d49e6dc88d609287d285907387cbbcfd32d47969b0467c5094f6674268b8959c67e940930a7c6121ef3088a3a1a6cc1b77ddc3c7b9afac7a5fcd7580e0c9d5ef SHA512 7d1e3b293c137d0eca7afd5818686cee4ebb447c9481a25fd6e767aec33533fa7b56b9d7724c4a69524b6aa194414c59680c205db9001a9b6f7dec2a00548393
+EBUILD openbabel-9999.ebuild 6136 BLAKE2B d49e6dc88d609287d285907387cbbcfd32d47969b0467c5094f6674268b8959c67e940930a7c6121ef3088a3a1a6cc1b77ddc3c7b9afac7a5fcd7580e0c9d5ef SHA512 7d1e3b293c137d0eca7afd5818686cee4ebb447c9481a25fd6e767aec33533fa7b56b9d7724c4a69524b6aa194414c59680c205db9001a9b6f7dec2a00548393
 MISC metadata.xml 921 BLAKE2B c0797440e50f813777c4858cc1ce893546d7785e57243318ec7d2c601c6ec2ecb7ec5ab3dbacce960c8b71196eef51ddce07802257fff0d4cba0293f940a773f SHA512 8ee8a50230f374904a9ddaaf7337caf018788ab25a1839dbf5a48b0e5c49ac4e285a1fa759900fa6d993bc220d3586a923ae21158687be971fc51a6c302f12ad
diff --git a/sci-chemistry/openbabel/files/openbabel-3.1.1_p2024-fix_examples.patch b/sci-chemistry/openbabel/files/openbabel-3.1.1_p2024-fix_examples.patch
new file mode 100644
index 000000000000..b61d3bc29b98
--- /dev/null
+++ b/sci-chemistry/openbabel/files/openbabel-3.1.1_p2024-fix_examples.patch
@@ -0,0 +1,13 @@
+prevent installation of examples in /usr/bin
+all files from examples are 'RUNTIME', no lib
+--- a/doc/examples/CMakeLists.txt
++++ b/doc/examples/CMakeLists.txt
+@@ -7,7 +7,7 @@
+   add_executable(${example} ${example}.cpp)
+   target_link_libraries(${example} ${BABEL_LIBRARY})
+   install(TARGETS ${example}
+-    RUNTIME DESTINATION bin
++    RUNTIME DESTINATION ${CMAKE_INSTALL_DOCDIR}/examples
+     LIBRARY DESTINATION lib
+     ARCHIVE DESTINATION lib
+   )
diff --git a/sci-chemistry/openbabel/files/openbabel-3.1.1_p2024-fix_pybind.patch b/sci-chemistry/openbabel/files/openbabel-3.1.1_p2024-fix_pybind.patch
new file mode 100644
index 000000000000..ab1a24499306
--- /dev/null
+++ b/sci-chemistry/openbabel/files/openbabel-3.1.1_p2024-fix_pybind.patch
@@ -0,0 +1,25 @@
+--- a/scripts/CMakeLists.txt
++++ b/scripts/CMakeLists.txt
+@@ -69,13 +69,9 @@
+ 
+ if (DO_PYTHON_BINDINGS)
+ 
+-    include_directories(
+-        ${PYTHON_INCLUDE_PATH}
+-    )
+-
+     if(RUN_SWIG)
+       add_custom_command(OUTPUT ${openbabel_SOURCE_DIR}/scripts/python/openbabel/openbabel-python.cpp ${openbabel_SOURCE_DIR}/scripts/python/openbabel/openbabel.py
+-      COMMAND ${SWIG_EXECUTABLE} -python -c++ ${doxygen_switch} -small -O -templatereduce -naturalvar -I${openbabel_SOURCE_DIR}/include -I${openbabel_BINARY_DIR}/include -o ${openbabel_SOURCE_DIR}/scripts/python/openbabel/openbabel-python.cpp ${eigen_define} -outdir ${openbabel_SOURCE_DIR}/scripts/python/openbabel ${openbabel_SOURCE_DIR}/scripts/openbabel-python.i
++	      COMMAND ${SWIG_EXECUTABLE} -python -c++ ${doxygen_switch} -small -O -templatereduce -naturalvar -I${PYTHON_INCLUDE_PATH} -I${openbabel_SOURCE_DIR}/include -I${openbabel_BINARY_DIR}/include -o ${openbabel_SOURCE_DIR}/scripts/python/openbabel/openbabel-python.cpp ${eigen_define} -outdir ${openbabel_SOURCE_DIR}/scripts/python/openbabel ${openbabel_SOURCE_DIR}/scripts/openbabel-python.i
+               MAIN_DEPENDENCY openbabel-python.i
+               VERBATIM
+               )
+@@ -84,6 +80,7 @@
+     configure_file(${openbabel_SOURCE_DIR}/scripts/python/openbabel/__init__.py.in
+                    ${openbabel_SOURCE_DIR}/scripts/python/openbabel/__init__.py)
+     add_library(bindings_python MODULE ${openbabel_SOURCE_DIR}/scripts/python/openbabel/openbabel-python.cpp)
++    target_include_directories(bindings_python PRIVATE ${PYTHON_INCLUDE_PATH})
+ 
+     if(APPLE)
+       # Don't link against Python library on Mac
diff --git a/sci-chemistry/openbabel/files/openbabel-python-r2.cmake b/sci-chemistry/openbabel/files/openbabel-python-r2.cmake
new file mode 100644
index 000000000000..a16970deb0b1
--- /dev/null
+++ b/sci-chemistry/openbabel/files/openbabel-python-r2.cmake
@@ -0,0 +1,103 @@
+# The following is a cmake fragment taken from scripts/CMakeLists.txt and
+# edited for Gentoo python multibuild compatibility.
+
+if (DO_PYTHON_BINDINGS)
+	# Tags should be edited to reflect the active python implementation
+	set(EPYTHON @@EPYTHON@@)
+	set(PYTHON_INCLUDE_DIR @@PYTHON_INCLUDE_DIR@@)
+	set(PYTHON_LIBS @@PYTHON_LIBS@@)
+	set(PYTHON_SITEDIR @@PYTHON_SITEDIR@@)
+
+	add_custom_command(
+		OUTPUT ${CMAKE_SOURCE_DIR}/scripts/${EPYTHON}/openbabel-python.cpp ${CMAKE_SOURCE_DIR}/scripts/${EPYTHON}/openbabel.py
+		COMMAND ${SWIG_EXECUTABLE} -python -c++ -small -O -templatereduce -naturalvar -I${PYTHON_INCLUDE_DIR} -I${CMAKE_SOURCE_DIR}/include -I${CMAKE_BINARY_DIR}/include -o ${CMAKE_SOURCE_DIR}/scripts/${EPYTHON}/openbabel-python.cpp ${eigen_define} -outdir ${CMAKE_SOURCE_DIR}/scripts/${EPYTHON} ${CMAKE_SOURCE_DIR}/scripts/openbabel-python.i
+		MAIN_DEPENDENCY openbabel-python.i
+		VERBATIM
+	)
+
+	configure_file(${CMAKE_SOURCE_DIR}/scripts/python/openbabel/__init__.py.in
+		${CMAKE_BINARY_DIR}/scripts/${EPYTHON}/openbabel/__init__.py)
+
+	add_library(bindings_python_${EPYTHON} MODULE ${CMAKE_SOURCE_DIR}/scripts/${EPYTHON}/openbabel-python.cpp)
+    	target_include_directories(bindings_python_${EPYTHON} PRIVATE ${PYTHON_INCLUDE_DIR})
+	target_link_libraries(bindings_python_${EPYTHON} ${PYTHON_LIBS} ${BABEL_LIBRARY})
+
+	set_target_properties(bindings_python_${EPYTHON}
+		PROPERTIES
+		OUTPUT_NAME _openbabel
+		LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/scripts/${EPYTHON}/openbabel
+		PREFIX ""
+		SUFFIX .so )
+
+	add_dependencies(bindings_python_${EPYTHON} openbabel)
+
+	install(TARGETS bindings_python_${EPYTHON}
+		LIBRARY DESTINATION ${PYTHON_SITEDIR}/openbabel
+		COMPONENT bindings_python)
+	install(FILES ${CMAKE_BINARY_DIR}/scripts/${EPYTHON}/openbabel/__init__.py
+		DESTINATION ${PYTHON_SITEDIR}/openbabel
+		COMPONENT bindings_python)
+	install(FILES ${CMAKE_SOURCE_DIR}/scripts/${EPYTHON}/openbabel.py
+		DESTINATION ${PYTHON_SITEDIR}/openbabel
+		COMPONENT bindings_python)
+	install(FILES ${CMAKE_SOURCE_DIR}/scripts/python/openbabel/pybel.py
+		DESTINATION ${PYTHON_SITEDIR}/openbabel
+		COMPONENT bindings_python)
+
+	if (ENABLE_TESTS)
+		# Make sure all module files are together in the same directory for testing
+		add_custom_command(TARGET bindings_python_${EPYTHON} POST_BUILD
+			COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_SOURCE_DIR}/scripts/${EPYTHON}/openbabel.py ${CMAKE_BINARY_DIR}/scripts/${EPYTHON}/openbabel/
+			COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_SOURCE_DIR}/scripts/python/openbabel/pybel.py ${CMAKE_BINARY_DIR}/scripts/${EPYTHON}/openbabel/)
+		set(TEST_SOURCE_DIR ${CMAKE_SOURCE_DIR}/test)
+		# define TESTDATADIR for tests that need input files
+		add_definitions(-DTESTDATADIR="${TEST_SOURCE_DIR}/files/")
+		# define FORMATDIR for location of format plugin binaries
+		set(FORMATDIR "${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}/")
+		add_definitions(-DFORMATDIR="${FORMATDIR}/")
+		include_directories(${TEST_SOURCE_DIR})
+
+		# The macro is modified from cmake/modules/UsePythonTest.cmake
+		MACRO(ADD_PYTHON_TEST TESTNAME FILENAME)
+			GET_SOURCE_FILE_PROPERTY(loc ${FILENAME} LOCATION)
+			STRING(REGEX REPLACE ";" " " wo_semicolumn "${ARGN}")
+			FILE(WRITE ${CMAKE_BINARY_DIR}/test/${TESTNAME}.cmake
+"
+	MESSAGE(\"${PYTHONPATH}\")
+	EXECUTE_PROCESS(
+		COMMAND ${EPYTHON} ${loc} ${wo_semicolumn}
+		RESULT_VARIABLE import_res
+		OUTPUT_VARIABLE import_output
+		ERROR_VARIABLE  import_output
+	)
+
+	# Pass the output back to ctest
+	IF(import_output)
+		MESSAGE(\${import_output})
+	ENDIF(import_output)
+	IF(import_res)
+		MESSAGE(SEND_ERROR \${import_res})
+	ENDIF(import_res)
+"
+			)
+			ADD_TEST(${TESTNAME} ${CMAKE_COMMAND} -P ${CMAKE_BINARY_DIR}/test/${TESTNAME}.cmake)
+		ENDMACRO(ADD_PYTHON_TEST)
+
+		set(pybindtests
+			bindings
+			_pybel
+			example 
+			obconv_writers
+			cdjsonformat
+			pcjsonformat
+			roundtrip
+			)
+		foreach(pybindtest ${pybindtests})
+			ADD_PYTHON_TEST(pybindtest_${pybindtest}_${EPYTHON} ${TEST_SOURCE_DIR}/test${pybindtest}.py)
+			set_tests_properties(pybindtest_${pybindtest}_${EPYTHON} PROPERTIES
+				ENVIRONMENT "PYTHONPATH=${CMAKE_BINARY_DIR}/scripts/${EPYTHON}:${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX};LD_LIBRARY_PATH=${CMAKE_BINARY_DIR}/scripts/${EPYTHON}:${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}:\$ENV{LD_LIBRARY_PATH};BABEL_LIBDIR=${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}/;BABEL_DATADIR=${CMAKE_SOURCE_DIR}/data"
+				FAIL_REGULAR_EXPRESSION "ERROR;FAIL;Test failed"
+			)
+		endforeach(pybindtest ${pybindtests})
+	endif (ENABLE_TESTS)
+endif(DO_PYTHON_BINDINGS)
diff --git a/sci-chemistry/openbabel/openbabel-3.1.1_p20241221.ebuild b/sci-chemistry/openbabel/openbabel-3.1.1_p20241221.ebuild
new file mode 100644
index 000000000000..84485db4537d
--- /dev/null
+++ b/sci-chemistry/openbabel/openbabel-3.1.1_p20241221.ebuild
@@ -0,0 +1,236 @@
+# Copyright 1999-2025 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..13} )
+WX_GTK_VER=3.2-gtk3
+
+inherit cmake desktop flag-o-matic perl-functions python-r1 toolchain-funcs wxwidgets xdg
+
+DESCRIPTION="Interconverts file formats used in molecular modeling"
+HOMEPAGE="https://openbabel.org/ https://github.com/openbabel/openbabel/"
+
+if [[ "${PV}" == *9999* ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/openbabel/${PN}.git"
+else
+	if [[ "${PV}" == *_p* ]]; then	# eg., openbabel-3.1.1_p20210325
+		# Set to commit hash
+		OPENBABEL_COMMIT="889c350feb179b43aa43985799910149d4eaa2bc"
+		SRC_URI="https://github.com/${PN}/${PN}/archive/${OPENBABEL_COMMIT}.tar.gz -> ${P}.tar.gz"
+		S="${WORKDIR}/${PN}-${OPENBABEL_COMMIT}"
+	else
+		MY_P="${PN}-$(ver_rs 1- -)"
+		SRC_URI="https://github.com/${PN}/${PN}/archive/${MY_P}.tar.gz -> ${P}.tar.gz"
+		S="${WORKDIR}/${PN}-${MY_P}"
+	fi
+	KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
+fi
+
+LICENSE="GPL-2"
+# See src/CMakeLists.txt for LIBRARY_VERSION
+SLOT="0/7.0.0"
+IUSE="cpu_flags_arm_neon cpu_flags_x86_sse2 cpu_flags_x86_sse4_2 doc examples +inchi json minimal openmp perl png python test wxwidgets"
+RESTRICT="!test? ( test )"
+REQUIRED_USE="
+	python? ( ${PYTHON_REQUIRED_USE} )
+	test? ( inchi !minimal python? ( json png ) ${PYTHON_REQUIRED_USE} )
+"
+
+RDEPEND="
+	dev-cpp/eigen:3
+	sys-libs/zlib:=
+	inchi? ( sci-libs/inchi )
+	json? ( >=dev-libs/rapidjson-1.1.0 )
+	!minimal? (
+		dev-libs/libxml2:2
+		png? ( x11-libs/cairo )
+	)
+	perl? ( dev-lang/perl:= )
+	python? ( ${PYTHON_DEPS} )
+	wxwidgets? ( x11-libs/wxGTK:${WX_GTK_VER}[X] )
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+	dev-lang/perl
+	doc? (
+		app-text/doxygen
+		dev-texlive/texlive-latex
+	)
+	perl? ( dev-lang/swig )
+	python? ( dev-lang/swig )
+	test? ( dev-lang/python )
+"
+
+PATCHES=(
+	# Set include dir only for global implementation
+	"${FILESDIR}"/${PN}-3.1.1_p2024-fix_pybind.patch
+	# prevent installation of examples in /usr/bin
+	"${FILESDIR}"/${PN}-3.1.1_p2024-fix_examples.patch
+)
+
+pkg_pretend() {
+	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
+}
+
+pkg_setup() {
+	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
+}
+
+gen_python_bindings() {
+	mkdir -p scripts/${EPYTHON} || die
+	# Appends to scripts/CMakeLists.txt, substituting the correct tags, for
+	# each valid python implementation,
+	cat "${FILESDIR}"/${PN}-python-r2.cmake | \
+		sed -e "s|@@EPYTHON@@|${EPYTHON}|" \
+			-e "s|@@PYTHON_INCLUDE_DIR@@|$(python_get_includedir)|" \
+			-e "s|@@PYTHON_LIBS@@|$(python_get_LIBS)|" \
+			-e "s|@@PYTHON_SITEDIR@@|$(python_get_sitedir)|" >> \
+				scripts/CMakeLists.txt || die
+}
+
+src_prepare() {
+	cmake_src_prepare
+
+	# Prevent bundled inchi as fallback
+	rm -r include/inchi || die
+
+	use python && python_foreach_impl gen_python_bindings
+}
+
+src_configure() {
+	if use json; then
+		# -DOPTIMIZE_NATIVE=ON also forces -march=native so use
+		# cpu_flags to set defines instead
+		use cpu_flags_x86_sse2 && append-cppflags -DRAPIDJSON_SSE2
+		use cpu_flags_x86_sse4_2 && append-cppflags -DRAPIDJSON_SSE42
+		use cpu_flags_arm_neon && append-cppflags -DRAPIDJSON_NEON
+	fi
+
+	use wxwidgets && setup-wxwidgets
+
+	use_bindings() {
+		(use perl || use python) && (echo 'yes' || die) || (echo 'no' || die)
+	}
+
+	local mycmakeargs=(
+		$(cmake_use_find_package png Cairo)
+		$(cmake_use_find_package wxwidgets wxWidgets)
+		-DCMAKE_SKIP_RPATH=ON
+		-DBUILD_DOCS=$(usex doc)
+		-DBUILD_EXAMPLES=$(usex examples)
+		-DBUILD_GUI=$(usex wxwidgets)
+		-DENABLE_OPENMP=$(usex openmp)
+		-DENABLE_TESTS=$(usex test)
+		-DMINIMAL_BUILD=$(usex minimal)
+		# All three required to comply w/ useflag and prevent bundled lib
+		-DOPENBABEL_USE_SYSTEM_INCHI=$(usex inchi)
+		-DADD_INCHI_FORMAT=$(usex inchi)
+		-DWITH_INCHI=$(usex inchi)
+		-DOPTIMIZE_NATIVE=OFF
+		-DPERL_BINDINGS=$(usex perl)
+		-DPYTHON_BINDINGS=$(usex python)
+		-DRUN_SWIG=$(use_bindings)
+		-DWITH_COORDGEN=false
+		-DWITH_JSON=$(usex json)
+		# MEAPARSER
+		-DCMAKE_DISABLE_FIND_PACKAGE_Boost=ON
+		-DWITH_MAEPARSER=false
+	)
+
+	if use perl; then
+		perl_set_version
+		mycmakeargs+=(
+			-DPERL_INSTDIR="${VENDOR_ARCH}"
+		)
+	fi
+
+	if use test; then
+		# Help cmake find the python interpreter when dev-lang/python-exec is built
+		# without native-symlinks support.
+		python_setup
+		mycmakeargs+=(
+			-DPYTHON_EXECUTABLE="${PYTHON}"
+		)
+	fi
+
+	cmake_src_configure
+}
+
+src_test() {
+	local CMAKE_SKIP_TESTS=(
+		# https://github.com/openbabel/openbabel/issues/2766
+		test_align_{4,5}
+	)
+	! use wxwidgets && CMAKE_SKIP_TESTS+=(
+		test_tautomer_{22,27}
+	)
+
+	# Weird deadlock causes system_load to keep rising
+	cmake_src_test -j1
+}
+
+openbabel-optimize() {
+	python_optimize "${D}/$(python_get_sitedir)"/openbabel || die
+}
+
+src_install() {
+	cmake_src_install
+
+	docinto html
+	for x in doc/*.html; do
+		[[ ${x} != doc/api*.html ]] && dodoc ${x}
+	done
+
+	if use doc; then
+		cmake_src_install docs
+		docinto html/API
+		dodoc -r doc/API/html/.
+	fi
+
+	if use examples; then
+		# no compression since we want ready-to-run scripts
+		docompress -x /usr/share/doc/${PF}/examples
+
+		# ${PV} doesn't correspond to the internal BABEL_VERSION for
+		# live or patch release builds so we grep it
+		local babel_ver=$(
+			grep '^#define BABEL_VERSION' < \
+				"${BUILD_DIR}"/include/openbabel/babelconfig.h | \
+				cut -d \" -f 2 || die
+		)
+		docinto examples/povray
+		dodoc doc/dioxin.* doc/README*.pov*
+		# Needed by the povray example
+		dosym ../../../../${PN}/${babel_ver}/babel_povray3.inc \
+			/usr/share/doc/${PF}/examples/povray/babel31.inc
+	fi
+
+	if use perl; then
+		docinto /
+		newdoc scripts/perl/Changes Changes.perl
+		newdoc scripts/perl/README README.perl
+		if use examples; then
+			docinto examples/perl
+			dodoc -r scripts/perl/examples/.
+		fi
+	fi
+
+	if use python; then
+		python_foreach_impl openbabel-optimize
+		docinto /
+		newdoc scripts/python/README.rst README.python.rst
+		docinto html
+		dodoc scripts/python/*.html
+		if use examples; then
+			docinto examples/python
+			dodoc -r scripts/python/examples/.
+		fi
+	fi
+
+	if use wxwidgets; then
+		make_desktop_entry obgui "Open Babel" ${PN}
+		newicon "${S}"/src/GUI/babel.xpm ${PN}.xpm
+	fi
+}
diff --git a/sci-chemistry/openbabel/openbabel-9999.ebuild b/sci-chemistry/openbabel/openbabel-9999.ebuild
index fc4d6cab575e..84485db4537d 100644
--- a/sci-chemistry/openbabel/openbabel-9999.ebuild
+++ b/sci-chemistry/openbabel/openbabel-9999.ebuild
@@ -1,12 +1,12 @@
-# Copyright 1999-2024 Gentoo Authors
+# Copyright 1999-2025 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
 
-PYTHON_COMPAT=( python3_{10..12} )
+PYTHON_COMPAT=( python3_{10..13} )
 WX_GTK_VER=3.2-gtk3
 
-inherit cmake desktop flag-o-matic perl-functions python-r1 toolchain-funcs wxwidgets xdg-utils
+inherit cmake desktop flag-o-matic perl-functions python-r1 toolchain-funcs wxwidgets xdg
 
 DESCRIPTION="Interconverts file formats used in molecular modeling"
 HOMEPAGE="https://openbabel.org/ https://github.com/openbabel/openbabel/"
@@ -17,7 +17,7 @@ if [[ "${PV}" == *9999* ]]; then
 else
 	if [[ "${PV}" == *_p* ]]; then	# eg., openbabel-3.1.1_p20210325
 		# Set to commit hash
-		OPENBABEL_COMMIT=08e23f39b0cc39b4eebd937a5a2ffc1a7bac3e1b
+		OPENBABEL_COMMIT="889c350feb179b43aa43985799910149d4eaa2bc"
 		SRC_URI="https://github.com/${PN}/${PN}/archive/${OPENBABEL_COMMIT}.tar.gz -> ${P}.tar.gz"
 		S="${WORKDIR}/${PN}-${OPENBABEL_COMMIT}"
 	else
@@ -25,63 +25,49 @@ else
 		SRC_URI="https://github.com/${PN}/${PN}/archive/${MY_P}.tar.gz -> ${P}.tar.gz"
 		S="${WORKDIR}/${PN}-${MY_P}"
 	fi
-	KEYWORDS="amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
+	KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
 fi
 
-SRC_URI="${SRC_URI}
-	https://openbabel.org/docs/dev/_static/babel130.png -> ${PN}.png
-	https://openbabel.org/OBTitle.jpg ->  ${PN}.jpg"
-
+LICENSE="GPL-2"
 # See src/CMakeLists.txt for LIBRARY_VERSION
 SLOT="0/7.0.0"
-LICENSE="GPL-2"
 IUSE="cpu_flags_arm_neon cpu_flags_x86_sse2 cpu_flags_x86_sse4_2 doc examples +inchi json minimal openmp perl png python test wxwidgets"
-
 RESTRICT="!test? ( test )"
-
-# Inaccurate dependency logic upstream
 REQUIRED_USE="
 	python? ( ${PYTHON_REQUIRED_USE} )
-	test? ( inchi json !minimal wxwidgets )
-"
-
-BDEPEND="
-	dev-lang/perl
-	doc? (
-		app-text/doxygen
-		dev-texlive/texlive-latex
-	)
-	perl? ( >=dev-lang/swig-2 )
-	python? ( >=dev-lang/swig-2 )
-	test? ( dev-lang/python )
+	test? ( inchi !minimal python? ( json png ) ${PYTHON_REQUIRED_USE} )
 "
 
-COMMON_DEPEND="
+RDEPEND="
 	dev-cpp/eigen:3
-	dev-libs/libxml2:2
 	sys-libs/zlib:=
 	inchi? ( sci-libs/inchi )
 	json? ( >=dev-libs/rapidjson-1.1.0 )
-	png? ( x11-libs/cairo )
+	!minimal? (
+		dev-libs/libxml2:2
+		png? ( x11-libs/cairo )
+	)
+	perl? ( dev-lang/perl:= )
 	python? ( ${PYTHON_DEPS} )
 	wxwidgets? ( x11-libs/wxGTK:${WX_GTK_VER}[X] )
 "
-
-DEPEND="
-	${COMMON_DEPEND}
-	perl? ( dev-lang/perl )
-"
-
-RDEPEND="
-	${COMMON_DEPEND}
-	perl? (
-		dev-lang/perl:=
-		!sci-chemistry/openbabel-perl
+DEPEND="${RDEPEND}"
+BDEPEND="
+	dev-lang/perl
+	doc? (
+		app-text/doxygen
+		dev-texlive/texlive-latex
 	)
+	perl? ( dev-lang/swig )
+	python? ( dev-lang/swig )
+	test? ( dev-lang/python )
 "
 
 PATCHES=(
-	"${FILESDIR}"/openbabel-3.1.1-fix-time-check-cmake.patch
+	# Set include dir only for global implementation
+	"${FILESDIR}"/${PN}-3.1.1_p2024-fix_pybind.patch
+	# prevent installation of examples in /usr/bin
+	"${FILESDIR}"/${PN}-3.1.1_p2024-fix_examples.patch
 )
 
 pkg_pretend() {
@@ -92,13 +78,13 @@ pkg_setup() {
 	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
 }
 
-prepare_python_bindings() {
+gen_python_bindings() {
 	mkdir -p scripts/${EPYTHON} || die
 	# Appends to scripts/CMakeLists.txt, substituting the correct tags, for
 	# each valid python implementation,
-	cat "${FILESDIR}"/${PN}-python.cmake | \
+	cat "${FILESDIR}"/${PN}-python-r2.cmake | \
 		sed -e "s|@@EPYTHON@@|${EPYTHON}|" \
-			-e "s|@@PYTHON_INCUDE_DIR@@|$(python_get_includedir)|" \
+			-e "s|@@PYTHON_INCLUDE_DIR@@|$(python_get_includedir)|" \
 			-e "s|@@PYTHON_LIBS@@|$(python_get_LIBS)|" \
 			-e "s|@@PYTHON_SITEDIR@@|$(python_get_sitedir)|" >> \
 				scripts/CMakeLists.txt || die
@@ -107,51 +93,10 @@ prepare_python_bindings() {
 src_prepare() {
 	cmake_src_prepare
 
-	if use perl; then
-		perl_set_version
-
-		sed -e "/\${LIB_INSTALL_DIR}\/auto/s|\${LIB_INSTALL_DIR}|${VENDOR_ARCH}|" \
-			-e "/\${LIB_INSTALL_DIR}\/Chemistry/s|\${LIB_INSTALL_DIR}|${VENDOR_ARCH}|" \
-			-i scripts/CMakeLists.txt || die
-	fi
-
-	if use python; then
-		# Skip the python bindings sections as we'll append our own
-		sed -e '/^if (PYTHON_BINDINGS)$/s|PYTHON_BINDINGS|false|' \
-			-i {scripts,test}/CMakeLists.txt || die
-		if use test; then
-			# Problems with testbindings built with -O2
-			local test_skip="@unittest.skip('Similar to Issue #2138')"
-			sed -e "/def testTemplates/s|^|    ${test_skip}\\n|" \
-				-i test/testbindings.py || die
-			test_skip="@unittest.skip('Similar to Issue #2246')"
-			sed -e "/^def test_write_string/s|^|${test_skip}\\n|" \
-				-i test/testobconv_writers.py || die
-			fi
-		python_foreach_impl prepare_python_bindings
-	fi
-
-	# Remove dependency automagic
-	if ! use png; then
-		sed -e '/^find_package(Cairo/d' -i CMakeLists.txt || die
-	fi
-	if ! use wxwidgets; then
-		sed -e '/^find_package(wxWidgets/d' -i CMakeLists.txt || die
-	fi
-	if ! use inchi; then
-		sed -e '/^else()$/s|else\(\)|elseif\(false\)|' \
-			-i cmake/modules/FindInchi.cmake || die
-	fi
-
-	# Don't install example bins to /usr/bin
-	if use examples; then
-		sed -e "/RUNTIME DESTINATION/s|bin|share/doc/${PF}/examples|" \
-			-i doc/examples/CMakeLists.txt || die
-	fi
+	# Prevent bundled inchi as fallback
+	rm -r include/inchi || die
 
-	# boost is only used if building with gcc-3.x, which isn't supported in
-	# Gentoo. Still, it shouldn't look for, and include, its headers
-	sed -e '/find_package(Boost/d' -i {{tools,src}/,}CMakeLists.txt || die
+	use python && python_foreach_impl gen_python_bindings
 }
 
 src_configure() {
@@ -170,36 +115,59 @@ src_configure() {
 	}
 
 	local mycmakeargs=(
+		$(cmake_use_find_package png Cairo)
+		$(cmake_use_find_package wxwidgets wxWidgets)
+		-DCMAKE_SKIP_RPATH=ON
 		-DBUILD_DOCS=$(usex doc)
 		-DBUILD_EXAMPLES=$(usex examples)
 		-DBUILD_GUI=$(usex wxwidgets)
 		-DENABLE_OPENMP=$(usex openmp)
 		-DENABLE_TESTS=$(usex test)
 		-DMINIMAL_BUILD=$(usex minimal)
-		# Set this, otherwise it defaults to true and forces WITH_INCHI=true
+		# All three required to comply w/ useflag and prevent bundled lib
 		-DOPENBABEL_USE_SYSTEM_INCHI=$(usex inchi)
+		-DADD_INCHI_FORMAT=$(usex inchi)
+		-DWITH_INCHI=$(usex inchi)
 		-DOPTIMIZE_NATIVE=OFF
 		-DPERL_BINDINGS=$(usex perl)
 		-DPYTHON_BINDINGS=$(usex python)
 		-DRUN_SWIG=$(use_bindings)
 		-DWITH_COORDGEN=false
-		-DWITH_INCHI=$(usex inchi)
 		-DWITH_JSON=$(usex json)
+		# MEAPARSER
+		-DCMAKE_DISABLE_FIND_PACKAGE_Boost=ON
 		-DWITH_MAEPARSER=false
 	)
 
+	if use perl; then
+		perl_set_version
+		mycmakeargs+=(
+			-DPERL_INSTDIR="${VENDOR_ARCH}"
+		)
+	fi
+
 	if use test; then
 		# Help cmake find the python interpreter when dev-lang/python-exec is built
 		# without native-symlinks support.
 		python_setup
-		mycmakeargs+=( -DPYTHON_EXECUTABLE="${PYTHON}" )
+		mycmakeargs+=(
+			-DPYTHON_EXECUTABLE="${PYTHON}"
+		)
 	fi
 
 	cmake_src_configure
 }
 
 src_test() {
-	# Wierd deadlock causes system_load to keep rising
+	local CMAKE_SKIP_TESTS=(
+		# https://github.com/openbabel/openbabel/issues/2766
+		test_align_{4,5}
+	)
+	! use wxwidgets && CMAKE_SKIP_TESTS+=(
+		test_tautomer_{22,27}
+	)
+
+	# Weird deadlock causes system_load to keep rising
 	cmake_src_test -j1
 }
 
@@ -214,9 +182,6 @@ src_install() {
 	for x in doc/*.html; do
 		[[ ${x} != doc/api*.html ]] && dodoc ${x}
 	done
-	# Rendered in some html pages
-	newdoc "${DISTDIR}"/${PN}.png babel130.png
-	newdoc "${DISTDIR}"/${PN}.jpg OBTitle.jpg
 
 	if use doc; then
 		cmake_src_install docs
@@ -240,7 +205,6 @@ src_install() {
 		# Needed by the povray example
 		dosym ../../../../${PN}/${babel_ver}/babel_povray3.inc \
 			/usr/share/doc/${PF}/examples/povray/babel31.inc
-
 	fi
 
 	if use perl; then
@@ -267,14 +231,6 @@ src_install() {
 
 	if use wxwidgets; then
 		make_desktop_entry obgui "Open Babel" ${PN}
-		doicon "${DISTDIR}"/${PN}.png
+		newicon "${S}"/src/GUI/babel.xpm ${PN}.xpm
 	fi
 }
-
-pkg_postinst() {
-	use wxwidgets && xdg_desktop_database_update
-}
-
-pkg_postrm() {
-	use wxwidgets && xdg_desktop_database_update
-}