gentoo auto-resync : 19:05:2024 - 00:01:59

9 files changed, 141 insertions, 63 deletions

diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz
index b6fb10d1da8a..2eeeb6158656 100644
--- a/sci-chemistry/Manifest.gz
+++ b/sci-chemistry/Manifest.gz
diff --git a/sci-chemistry/chemex/Manifest b/sci-chemistry/chemex/Manifest
index 910723bedde2..fd0cf00cefa4 100644
--- a/sci-chemistry/chemex/Manifest
+++ b/sci-chemistry/chemex/Manifest
@@ -1,5 +1,5 @@
-DIST chemex-2022.3.5.tar.gz 2845347 BLAKE2B 29b53ba8afcfd91e4f50119f212557de85d8576474b74d2ad925c8c2adb89397640e7b352b6785dc99a8c4e5007294609640219b2374cbb3144f94c5f9113d96 SHA512 3a92702d105e95e0a7b15e01b839d5982df55477afb98e58f7458a0e87230e94597c01d33c219ae469ed62e4ddaecdb787ae435453d428843d5a612159715d2b
 DIST chemex-2022.3.6.tar.gz 2843118 BLAKE2B e51b385dbf9e3c42f54f95f9929125e3263e12afa62beab8e5b8eb13e78a4fe9a0fb445f4f6c3cd4aa8e71748732ec58124682daa86be079eed036b78492ca71 SHA512 5c734e1b3ea39e9729bada93dfe5bc55f877b69ba6edd9612f95aab0d31949489582957a14f175646c7e6652644a5a55c26bcd74affc7fecc1e7b9cfdd4ceb63
-EBUILD chemex-2022.3.5.ebuild 1250 BLAKE2B d1f61563a971c3c6795b2d398d71073e1db4cc5cca62a6ffc7d9bd2b22b6517417faddc037369fa545fb7f6493d95f658d850c1319eea4adb8bb51c9109e9df7 SHA512 2b1a3a0ca2eeadc7256efadd15a70bdb6b866da1a26a6c209b42fe6e010e871b675f1f2448a2dfdb8fefcbd9c0e97f54ac757a13fb0d29c03bb93ede9c8be97a
+DIST chemex-2024.02.16.tar.gz 2756466 BLAKE2B 715499fc3c68079dd66b26a0c4c495029c506be6f009529196fd30a1ec8ff4c0ecbcc4580c9beafd4f3c7df82d6fee525d85c09b031a6dc31d511c1183d30f8d SHA512 7975157b86493c580ce00ef23549597743ff4aa03cebed7d0e0af1d644eed359b5dfa57c51e11f223acebe335d12cb43bd7694a46eeb2ccba70ac6147ba40eda
 EBUILD chemex-2022.3.6.ebuild 1240 BLAKE2B 46d4f9fd57f5dbc8ad5b527e8568337cd57d3c03f25581d275e15204e5e2ee2c2224c6e8ada71c8d91aed01128be697987cc808bdfd7d7e3abc5f655eb2abb44 SHA512 814348dc6b404698634ecb33ee3956479dd1c05f91f7ca82e4f8a15776a582dd911e30a2070bff727f2aeae678a609fe2d8b676f107741904886c83315dbeb78
+EBUILD chemex-2024.02.16.ebuild 1343 BLAKE2B 1cd03445f8cf230a728b0a0b40ed39ccc11e5ff90b53d6358620a19f9aca2f5d630445bd0a2c9ee1f1dc74e11e5a79740584ace23556bd7ede76959295860868 SHA512 b5a330a8ba2db2f057c7d1cd12de4021e2eb0375474aa8eb0692f8248f448e86354a47e61313b6e37d965447073ed1cb84f300d7ba4e026f8e51f8dd823281a7
 MISC metadata.xml 300 BLAKE2B a1ad769918094ddbda13ac92462ec69fa469dfcacde1202c653a4aa7443db661ffa5739cd039b6e38b13f0345a2680f276b4e071362106b162c95cd92007b5a8 SHA512 755c273f6bf67f79c388d06d970702a1d4a9f84338f8d889dd9146905c6994621917952225406ffba5bfe1e1b69f0bfd0f471374178b15343f4927af9de49aef
diff --git a/sci-chemistry/chemex/chemex-2022.3.5.ebuild b/sci-chemistry/chemex/chemex-2024.02.16.ebuild
index c27017ecebf0..403e48aa069d 100644
--- a/sci-chemistry/chemex/chemex-2022.3.5.ebuild
+++ b/sci-chemistry/chemex/chemex-2024.02.16.ebuild
@@ -1,11 +1,11 @@
-# Copyright 1999-2023 Gentoo Authors
+# Copyright 1999-2024 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
 
 DISTUTILS_SINGLE_IMPL="yes"
-DISTUTILS_USE_PEP517=poetry
-PYTHON_COMPAT=( python3_{9..11} )
+DISTUTILS_USE_PEP517=pdm-backend
+PYTHON_COMPAT=( python3_{11..12} )
 
 inherit distutils-r1
 
@@ -14,8 +14,8 @@ HOMEPAGE="https://github.com/gbouvignies/chemex"
 SRC_URI="https://github.com/gbouvignies/ChemEx/archive/refs/tags/v${PV/_p/-dev}.tar.gz -> ${P}.tar.gz"
 S="${WORKDIR}/ChemEx-${PV/_p/-dev}"
 
-SLOT="0"
 LICENSE="BSD"
+SLOT="0"
 KEYWORDS="~amd64"
 IUSE="test"
 
@@ -25,18 +25,21 @@ RESTRICT="test"
 
 RDEPEND="
 	$(python_gen_cond_dep '
-		>=dev-python/asteval-0.9.25[${PYTHON_USEDEP}]
-		>=dev-python/cachetools-5.3.0[${PYTHON_USEDEP}]
-		>=dev-python/lmfit-1.2.0[${PYTHON_USEDEP}]
-		>=dev-python/matplotlib-3.7.1[${PYTHON_USEDEP}]
-		>=dev-python/numpy-1.24.3[${PYTHON_USEDEP}]
-		>=dev-python/pydantic-1.10.7[${PYTHON_USEDEP}]
-		>=dev-python/rapidfuzz-3.0.0[${PYTHON_USEDEP}]
-		>=dev-python/rich-13.3.4[${PYTHON_USEDEP}]
-		>=dev-python/scipy-1.10.1[${PYTHON_USEDEP}]
+		>=dev-python/annotated-types-0.6.0[${PYTHON_USEDEP}]
+		>=dev-python/cachetools-5.3.2[${PYTHON_USEDEP}]
+		>=dev-python/emcee-3.1.4[${PYTHON_USEDEP}]
+		>=dev-python/lmfit-1.2.2[${PYTHON_USEDEP}]
+		>=dev-python/matplotlib-3.8.0[${PYTHON_USEDEP}]
+		>=dev-python/numpy-1.26.1[${PYTHON_USEDEP}]
+		>=dev-python/pydantic-2.4.2[${PYTHON_USEDEP}]
+		>=dev-python/rapidfuzz-3.4.0[${PYTHON_USEDEP}]
+		>=dev-python/rich-13.6.0[${PYTHON_USEDEP}]
+		>=dev-python/scipy-1.11.3[${PYTHON_USEDEP}]
 		>=dev-python/tomli-2.0.1[${PYTHON_USEDEP}]
 	')
 "
 DEPEND="${RDEPEND}"
 
 distutils_enable_tests pytest
+
+export PDM_BUILD_SCM_VERSION=${PV}
diff --git a/sci-chemistry/dssp/Manifest b/sci-chemistry/dssp/Manifest
index 6eee7db05314..fd6cdbe6dd2c 100644
--- a/sci-chemistry/dssp/Manifest
+++ b/sci-chemistry/dssp/Manifest
@@ -3,12 +3,10 @@ AUX dssp-2.1.0-gentoo.patch 1513 BLAKE2B aabdcfff1083d7552392c35897eb8a84b07323c
 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-4.3.1.tar.gz 226842 BLAKE2B 86318f05b8381d94fa9c65a956f5fb607ef8072b0395d912e20697ba36836c449ddff31a4a64d0005bbfe34899f71853c0f15a911042389fc894934c08fc34c8 SHA512 4dc1a3f5c7ba258ebf548674c7b33c36b0e3a7d14911394eb8d2955c235f3cb1d6c50cb03f411db55a8a9d7aa93e4d03354c47f9f0126b0bdcbf40dc9391d403
-DIST dssp-4.4.1.tar.gz 161797 BLAKE2B d6bfb40a730f39e9d5a0988ce22a9dd377ec08a09e29f77e5afaac26d512cf87f6e289c1e4e3e63cfef7354b10fb57bf410bcc169604b1b6a6078380e4f08d26 SHA512 1bcf9e16efc5d3a7de11e24ed63e47d3263123af4670b8f3daa97cdf7cc33202fb4d564acac3024ed4edcce1ef8278f71f5312f27a234d2957afa6f563c88ed6
 DIST dssp-4.4.4.1.tar.gz 162809 BLAKE2B 6c3f588a48778cf5f20b40b93736e150a4d366bf44d214b4064362c2a3bce69db415f5d12568a8523d99e2e5a47749d450ff0251dc3035628dbef9343d37e99a SHA512 291810391d74da7ab65bcf4aab61fa4ae1a5518a361fa02d5c15ed0e5c94139fde65e7612a978f5326bd7d93f2ac6ea01b2b65514d6b64f4d062adf112c48deb
+DIST dssp-4.4.7.tar.gz 163831 BLAKE2B 195c8fb183df00105098967850b01c0d6acf776f7cfa409fc536c8291e7a467da2adfb5f34d8191e33dbb29bfd254cd414c1b7b76ed3f3b854928c4dc8a5fcdd SHA512 2fe2d8a494b570934c0d28804fe69b6569089ded58ec92bf3d83b25ce60a3b9486490909e187b511328f13498ca9027869e922d95a355cf0e21c2564c2db1b5a
 EBUILD dssp-2.2.1-r3.ebuild 870 BLAKE2B 9b7542d9ec45b60f5671830e5068e1d1cbcca4b82cf22cc0e2d9804c221f9977cfade439cc6e41a67375b438faca3ffa64fdec23db2b417b58615513fd60ad44 SHA512 964bfd70d98a80e6afd7f28fc6bf7359bbde105e77903211cec04c5adcdce273f1d7142a6d206d644300a1185cba1352bf584499d864809dadad69b2023e50d0
 EBUILD dssp-3.0.11.ebuild 875 BLAKE2B 6344416239b93804755b1829dcfcb9e8e461606c217938945bb2fc75e9680f2849b39bdbf0ed361592e703fea493a2dacabca498b26e696c969735a585e5d183 SHA512 353f4f5d7b1b195753c738ecc9fb17b429cdeada757806f5cf9a3da65c6318e3885d2c92fa904d5b3a546756eb87ec90787d158e8a9450b4730dd97b45af970d
-EBUILD dssp-4.3.1.ebuild 900 BLAKE2B d99a9024e58e5b2c53cbbfebb662a3fc546dd2a7b16a31394b312a2320bde8df9b62ecdef82295d924141e8427aee56a1e7277132e7767f481041dde6fd7c292 SHA512 1ac6d76fc9c37d5af8eecede2225d86517d27cd96a65ea4a6c9f1ce45eaf2e48fe0772838154639eebdbbccde3dd92bc6f5c9f8b2c37e3c9ca158534e5f8b8fc
-EBUILD dssp-4.4.1.ebuild 1327 BLAKE2B 1e84f9fb6e0fa6bf81a3381cd433b7ddcb0e298b5c34f6a8d3007b0a34583e4ea3037b3b1881dab20cb4b0c7c2c9b5e2addca4dd47fa39dba9b992f4c3e140ab SHA512 3bd89956458a91c5f1b56cff97a95b5010904ef1cd1cca591a93be2f5adaf8ad1a6bb5c570dd107a3ff7d78eca9019133b383b2fae1b96a0e70bad5c9f50c97d
 EBUILD dssp-4.4.4.1.ebuild 1321 BLAKE2B ba06063adc7c9ac9a20c078eeb98c95f0003c5ae58c0db0b5bbb888b194de86e22de9c1549d1911e25e4d5b7a3f99089c0083c281441eeed3dde3ea5e3b8cd14 SHA512 77683bc3bc0aebeb867ffaf94d5f7ce1090f78a73fc739da01c73d3bdab142fc409bce66f85349b627e54376e1279b45a9096a71cac080be10ab0ba4f84d33cb
+EBUILD dssp-4.4.7.ebuild 1311 BLAKE2B 6744df1780355e0ac3931c7d87426fc33132db57dbfe6dd237f7df94bb57c3de128f0fa5009391f0b166ce92f0b4e47e8a7f8c1bb2ea492459aeb8f22fdd015a SHA512 dc5ea7e546cb50b2737f0d185cd2f562865319b6bf5d9d1d6ffbdffaa72a4ba2ff9a5d59a37b68798a09b992640b0f57840c896e90641b0f6c02a4bb301cf6a9
 MISC metadata.xml 295 BLAKE2B 4355bbe00822cc702acdf70031ab9cd1f2a8f6e076d71016c1783f2a6c052c2da0a1a4a1860062562bb837161787f2481fa6f49c4319c546482a263ebe149bb0 SHA512 ace35ca21c614a7c0cbdea2496be3190a907295053566707c1875836a306cc9e9c96816cca6ce2b514935f6fcd494d2e813f4d94ba88552cd7b86831f30501f4
diff --git a/sci-chemistry/dssp/dssp-4.3.1.ebuild b/sci-chemistry/dssp/dssp-4.3.1.ebuild
deleted file mode 100644
index daf7c4f9314d..000000000000
--- a/sci-chemistry/dssp/dssp-4.3.1.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-inherit cmake
-
-DESCRIPTION="The protein secondary structure standard"
-HOMEPAGE="https://swift.cmbi.umcn.nl/gv/dssp/ https://github.com/PDB-REDO/dssp"
-SRC_URI="https://github.com/PDB-REDO/${PN}/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-BDEPEND="
-	dev-libs/boost:=[zlib]
-	>=dev-libs/libmcfp-1.2.2
-	>=sci-libs/libcifpp-5.1.0
-"
-DEPEND=""
-RDEPEND="${BDEPEND}"
-
-src_configure() {
-	# gxrio not packaged
-	local mycmakeargs=(
-		-DBUILD_WEBSERVER=OFF
-	)
-	cmake_src_configure
-}
-
-pkg_postinst() {
-	if has_version "<=sci-chemistry/gromacs-2022"; 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/dssp-4.4.1.ebuild b/sci-chemistry/dssp/dssp-4.4.7.ebuild
index d79883c4e211..cebac1ce3a1a 100644
--- a/sci-chemistry/dssp/dssp-4.4.1.ebuild
+++ b/sci-chemistry/dssp/dssp-4.4.7.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2023 Gentoo Authors
+# Copyright 1999-2024 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
@@ -18,14 +18,13 @@ KEYWORDS="~amd64 ~x86"
 CDEPEND="
 	dev-libs/boost:=[zlib]
 	>=dev-libs/libmcfp-1.2.2
-	>=sci-libs/libcifpp-5.1.0
+	>=sci-libs/libcifpp-7.0.3
 "
 BDEPEND="${CDEPEND}"
 #	doc? (
 #		|| ( app-text/pandoc-bin[pandoc-symlink] app-text/pandoc )
 #		dev-python/weasyprint
 #	)
-DEPEND=""
 RDEPEND="${CDEPEND}"
 
 #src_prepare() {
@@ -38,8 +37,8 @@ RDEPEND="${CDEPEND}"
 
 src_configure() {
 	local mycmakeargs=(
-		#-DGENERATE_DOCUMENTATION=$(usex doc)
-		-DGENERATE_DOCUMENTATION=NO
+		#-DBUILD_DOCUMENTATION=$(usex doc)
+		-DBUILD_DOCUMENTATION=NO
 	)
 	cmake_src_configure
 }
diff --git a/sci-chemistry/molmol/Manifest b/sci-chemistry/molmol/Manifest
index c89726c20774..5fdb76ae39ea 100644
--- a/sci-chemistry/molmol/Manifest
+++ b/sci-chemistry/molmol/Manifest
@@ -1,6 +1,8 @@
+AUX molmol-2k_p2-gcc14-fix.patch 357 BLAKE2B e7c1692e7a45ed2b83c38fa8b7ffe1a563f752660f3e2dc2098eb1de4491cd8919190d04cdc9d31f036b42a8fda6d6200fa347dfc7aed0fa46d75e1e3103e6cb SHA512 6138806de3222b073ce0f77c2c6d7060cbc9e3ba729553f61b93e44c671008da0e1ce64bc6fc0d9293dba203d71ae76cff1bea698e03a42d3e5a5901e6e8ccc0
 DIST molmol-2k.2.0-doc.tar.gz 1062297 BLAKE2B 082d4eea5544bab52ffc1ff6364c50304348f76759dd3125cd74d02e629383d4a566f28ac77ab89ecf5e17a82617b8f61525e6f454689840b27899827399d866 SHA512 131f747a5762859398ebe9b676a07df56c82c8864ecc035ec914f1dea74dafcd67f87993421dfe5899c640470c7e1e1ef03ae262b04a9b360ae329eb19a331fe
 DIST molmol-2k.2.0-src.tar.gz 1088805 BLAKE2B cd649604f6ee491d3a4485391ecdaa48dc1bc4bcd82865cd4a01ca460a6653f8cbba636050bfab9027b9b95dbefa28a8deeff7065b9b461f518001242af4a849 SHA512 6ab01a6fd3d19752634a2cf22919a20e43d195768bd4bdacd5f0bbe016c3058c94915bad4c7fa64dcd86576be39cad0ae112cb62f5e69ffb10041518101e7a9b
 DIST molmol-patches.tbz2 17528 BLAKE2B b91270a980f290edc169be00639e86b3272281c9fe237750f5778eab1605ed482c09bdaf90660a5edf74bd04b3e31adc755e77e39aea6c75d88b6db9bf47a6d6 SHA512 bd94baf0a378f40f854f396963edd9b9e4afc5c56462ee6f8b68889290afdb4c5d9b10878aa5619d0a70153453fe6ee8e7540064522c6db0291ae9162bba9287
 DIST molmol_256.png 22668 BLAKE2B c7d75b8e0d738b48790bea25e21ec60d57a8181253518c70d6f18d93c64eef3c9acf90213fdbdf2dde272e85a04a6442e4e4a9c375829f369380d88c9c0ca57c SHA512 5e7975f54a7462161dc630ee973e9a8126b9c120e0d8d6b62007384c970ce39792e52300edc25dc7a85209845801d749d9ecba02899f3e18b18f5a5fdbc28a97
 EBUILD molmol-2k_p2-r8.ebuild 2284 BLAKE2B fa9954fca3dd8b52450beb1c0901abc71743672d7a76e2daa2bb05f52280ecf7dec5c401da24ce3e72f429cb69b27738117e33d41b49a96836b1b407efef67f0 SHA512 d813743572479b5eb0ed4181d42743402c4bd0a5a8e012f32bad03c4be68f38329722b749abc91845ba9c25642b19f5e2c4b5578ed9d3f7d03beaabbaa3345f5
+EBUILD molmol-2k_p2-r9.ebuild 2314 BLAKE2B f54b8793c88c3e5d14a128e922d9d22dcc5ad861c76a205b84a0a4d8f36ccdf8e6259955e71257689424ac48819fcd3350105e4472202681e8a9bc80c43d9d21 SHA512 56e0839d1f3d971d549c2bcde64115b17e3b7adccaf63b75e7221247684c7b7ee40df89d30c2b0d0acd28aa4e147523644f34ce496cf6a9e51ff540616123bda
 MISC metadata.xml 272 BLAKE2B 531e98b72776bbe9126811b70943add0f6f43141b01cb75b17ac2c8d1cfb6a9b349022fd411894d2b8eeb0612a73db10aed4ba71f9624bd6dbd172a05fca2c76 SHA512 04f5575703aaaa95e575460ae3de428d3da173b3b741ab52b4aad31e381fef78b325f49f99622ec26a65024437759ea013fc525bd63ee553003c71afcc40d10c
diff --git a/sci-chemistry/molmol/files/molmol-2k_p2-gcc14-fix.patch b/sci-chemistry/molmol/files/molmol-2k_p2-gcc14-fix.patch
new file mode 100644
index 000000000000..7041ced28efe
--- /dev/null
+++ b/sci-chemistry/molmol/files/molmol-2k_p2-gcc14-fix.patch
@@ -0,0 +1,12 @@
+Bug: https://bugs.gentoo.org/923325
+--- a/src/motogl/MotOGLDump.c
++++ b/src/motogl/MotOGLDump.c
+@@ -245,7 +245,7 @@ jpegErrHand(j_common_ptr jpegInfoP)
+ 
+ #ifdef PNG_SUPPORT
+ static void
+-pngErrHand(png_structp pngStrucP, char *errMsg)
++pngErrHand(png_structp pngStrucP, const char *errMsg)
+ {
+   IORaiseError(errMsg);
+   longjmp(png_jmpbuf(pngStrucP), 1);
diff --git a/sci-chemistry/molmol/molmol-2k_p2-r9.ebuild b/sci-chemistry/molmol/molmol-2k_p2-r9.ebuild
new file mode 100644
index 000000000000..29769cede153
--- /dev/null
+++ b/sci-chemistry/molmol/molmol-2k_p2-r9.ebuild
@@ -0,0 +1,103 @@
+# Copyright 1999-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+inherit desktop toolchain-funcs
+
+MY_PV="${PV/_p/.}.0"
+MY_P="${PN}-${MY_PV}"
+
+DESCRIPTION="Publication-quality molecular visualization package"
+
+# Original page dead
+#HOMEPAGE="http://hugin.ethz.ch/wuthrich/software/molmol/index.html"
+HOMEPAGE="
+	http://www.csb.yale.edu/userguides/graphics/molmol/molmol_descrip.html
+	http://pjf.net/science/molmol.html
+"
+SRC_URI="
+	ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-src.tar.gz
+	ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-doc.tar.gz
+	https://dev.gentoo.org/~soap/distfiles/${PN}-patches.tbz2
+	https://dev.gentoo.org/~pacho/${PN}/${PN}_256.png
+"
+S="${WORKDIR}"
+
+LICENSE="molmol"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+
+RDEPEND="
+	|| (
+		(
+			media-libs/mesa[X(+)]
+			x11-libs/libGLw
+		)
+		media-libs/mesa[motif(-),X(+)]
+	)
+	media-libs/libjpeg-turbo:=
+	media-libs/libpng:=
+	media-libs/tiff:=
+	sys-libs/zlib
+	virtual/glu
+	x11-libs/libXpm
+	x11-libs/motif:0
+	x11-apps/xdpyinfo
+"
+DEPEND="${RDEPEND}"
+
+PATCHES=(
+	"${FILESDIR}"/${P}-gcc14-fix.patch
+)
+
+pkg_setup() {
+	MMDIR="/usr/$(get_libdir)/molmol"
+	MAKEOPTS="${MAKEOPTS} -j1" #880621
+}
+
+src_prepare() {
+	default
+
+	rm -rf tiff*
+	# Patch from http://pjf.net/science/molmol.html, where src.rpm is provided
+	eapply "${WORKDIR}"/patches/pjf_RH9_molmol2k2.diff
+
+	eapply "${WORKDIR}"/patches/ldflags.patch
+	eapply "${WORKDIR}"/patches/opengl.patch
+
+	ln -s makedef.lnx "${S}"/makedef || die
+
+	sed \
+		-e "s|ksh|sh|" \
+		-e "s|^MOLMOLHOME.*|MOLMOLHOME=${EPREFIX}/${MMDIR};MOLMOLDEV=\"Motif/OpenGL\"|" \
+		-i "${S}"/molmol || die
+	sed \
+		-e "s|^MCFLAGS.*|MCFLAGS = ${CFLAGS}|" \
+		-e "s|^CC.*|CC = $(tc-getCC)|" \
+		-i "${S}"/makedef || die
+
+	eapply "${WORKDIR}"/patches/cast.patch
+	eapply -p0 "${WORKDIR}"/patches/libpng15.patch
+
+	# patch from fink
+	# fixes numerous bad bracings and hopefully the OGL bug 429974
+	eapply "${WORKDIR}"/patches/${P}-fink.patch
+
+	eapply "${WORKDIR}"/patches/wild.patch
+	tc-export AR
+}
+
+src_install() {
+	dobin molmol
+
+	exeinto ${MMDIR}
+	doexe src/main/molmol
+	insinto ${MMDIR}
+	doins -r auxil help macros man setup tips
+
+	make_desktop_entry "${PN}" MOLMOL
+	newicon "${DISTDIR}/${PN}_256.png" "${PN}.png"
+
+	einstalldocs
+	dodoc HISTORY
+}