gentoo auto-resync : 20:02:2025 - 00:15:26

14 files changed, 170 insertions, 25 deletions

diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz
index 898382ae07f2..ec4ae4f2eb0f 100644
--- a/sci-chemistry/Manifest.gz
+++ b/sci-chemistry/Manifest.gz
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index fda71e9bc451..977ae879b464 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -13,13 +13,13 @@ DIST regressiontests-2024.3.tar.gz 32776961 BLAKE2B 6a74977a396f8e82f7aba7a384cc
 DIST regressiontests-2024.4.tar.gz 32777006 BLAKE2B 41623de750b89410fa0a52037ea28d99a688b602b286cff732a6e8100b2b72072f579fc4f72bfe7c246ca086b6c6c1c10adb89874db6e1c9276494572e408a9f SHA512 dfbe8ee1b7c5b534842203f2295ea08875df6af3fb94798138b92ab8bc816719e3357db2935d2de4fd798d104ad7cb44860cd65887da7bb2438db422f35e6848
 DIST regressiontests-2024.5.tar.gz 32776573 BLAKE2B 5e397b6c601132ac96b826325bd0304d5939b87f0edaa89ba84d672a9df27351f26dbc9fde39fdb7a177be2743db93198316663a39145231741d08f3268d67cf SHA512 8594e8365f676f18f227b4d6b87fa6a1a8ceab8301302469a626380a7d29035a2cd8667b4d923b26491d3db9298d6660a9c9bde9274dfeba278dfabdb54ef424
 DIST regressiontests-2025-rc.tar.gz 32653300 BLAKE2B 6078855a0a2958732338f402fcce7e0cf0d117916930491977f894aa856ae40d968810f94e2f26f658201a8e00d2df782c27b942adab5d84063e4d2ed9dbfd07 SHA512 b9cfceef1495f43aaebc33d612c5c584c60418b2dab15d0ac78c8d5a52258221db7adce708f78bda70c3f9c48b6527777aceee32fafa603a4eca2d99ab166059
-EBUILD gromacs-2023.5.ebuild 9808 BLAKE2B 2550a71bbca68d787ce25a4e068dc203eb9642fd06c220f42cf50f86f8c4ee40494f28b23609d94a683e326792efc37f5e4c13035bb40315002d05006f4e17e0 SHA512 a41f7c8dcfdd5791b078a7a7fc67863f0b1a1e171bf7606508766b843e182404ce5dbe450fce17b55de292690c7f7afa3937ddc16c5f8b99e76aa29cc117b5c7
-EBUILD gromacs-2023.9999.ebuild 9810 BLAKE2B 2699ca418732f4d94f3bce156ed10fb1eed0d474bbd887563f07671c425022f219dfc279b5d822936f4b8f9382f2f987ed13fd6646aaa59820fe2832aa551f65 SHA512 482fa713381ac6710d4896948d97bb5d50e70b51f448a5f73f0c010cd567f9167f3bacbf7353eaf15c32d7d32859e5812caea63fbee0460141c2a61fbfe67506
-EBUILD gromacs-2024.3.ebuild 9861 BLAKE2B 91292003b82dd0a777dc4f20f2163c473d0f7bb59c8b2166146cb583611f4348cfcace6c72de7317c7b063d60460fe80b0b0d6f2dd656994e884884d9cebd540 SHA512 fc821eece5f1db1830bb52ca47f00eef6adde9d8db0e0410581cf43b9b07a98fa5896fb39d76d4806657faaa34618cacdd0c265d55a09489837efac2b63bc5c3
-EBUILD gromacs-2024.4.ebuild 9863 BLAKE2B e0426fcbdb1aa7479c672c310e83306e486a3a0b56ca9392af109c7c885b9ad21d7d5b6fd8c8291c871faa72bf775acd2bddd4886ac8a88f19f08723ad41b0f5 SHA512 b25a06c95486a102b661c52208a3439de0431eb37d0433198a43052575236a3fe78d7cf65f210ca4d0a96e0edbd6e95a0dba84c58b451c81a8260f2a73e3f087
-EBUILD gromacs-2024.5.ebuild 9863 BLAKE2B 46da1edbae5d2f6b6243080f45be7479ac23a969879b52bdc696c1225b5b56ab25d724bd12cc3d7d4c839f0b549c731698abed52aba2f04ef56743497ad80d35 SHA512 f7369d4150224e6024125ecf2ac9fa487645a324cb63e26e7a9f272c46cf1531020977b39f1a7d1e2360299a99f96ce0f31293650246e131682b32d5840273a7
-EBUILD gromacs-2024.9999.ebuild 9817 BLAKE2B a7a7d5f1c6ad06465c8c1fdf2451eadeb7c954d3b55632a71df4e915867482b49956c0a1264ce067bd2b78ce7c84c3b15d4c8a23dd05a5f430e99ec6c7024e43 SHA512 a1d71b01c64605ab07dafe53f5d0d3f7ffe5fe698e9a5c5e7b1dfecaaa2cb95880e848714b566a7ebf58cd92243ded9642ebb4d5c5da15c0a9667795d31a421d
-EBUILD gromacs-2025.9999.ebuild 10389 BLAKE2B 61adfd034e8e3f7a87baca74d419c992ec6ed5a8c2800ccdd886c444a73a3cf9ca68ec9be6dfbeccd48ff6d5d5eb0654e69a16a9c7c6261a014ec44832cab3bf SHA512 e7dabee6598f22556d6445391338b242e452a4ccac1ca7febed7fcdcd2a6542927fa3dd73350fd0aa96d99af6c2fd8853b9b015ac61b3170011bf4340e043f13
-EBUILD gromacs-2025_rc.ebuild 10389 BLAKE2B f4de75ca58e7455e522b7eb04bd48b2091c0f05afdb41294be64d4fcb270e50df6abd8881aba45dc0a61a686dd65cd21a43139cd36ccde50e9244a80b733369a SHA512 b7f8d3c9ca2e1f7630b824e9a30c06a96cb7aa23e9c0c1e90ff2d5f4484b87e9d0c1314d283c39149a9e3f3c18cdc56770d28d78fc108f0a18be3d575c504765
-EBUILD gromacs-9999.ebuild 10428 BLAKE2B 00356f3a9d2a1d412db41ad76a0052dc5dded3172f02ff531dec289c00c67ff355d1c5a6e57434485caff0b1108a18787e24e20f1d6fe117d75dd54a30d473d9 SHA512 8ccd8693b292503008ed630af70769dae734fe57ef2bafd28453ef89fc92ece5ff688ba7c85e17e0107875be5410ea81e6409aba694ed73793784d1d7333559b
+EBUILD gromacs-2023.5.ebuild 9808 BLAKE2B bd101d7a3f09f383cec52c396e6e0edc4e6c29a01b691763cbadc967c51918b157643ebcd9f8760771b4ea5042f15882f2bd27a340aea73ada4dd9bcb75ef28f SHA512 2ba6d3829a0b8c1e198ef6e6062543a21c24790202020a4b63819a90708b18c655f73e447e79adc5bd5f2c635a4f3dd34b79388a5ef22d3bf8f04f505e874d9d
+EBUILD gromacs-2023.9999.ebuild 9810 BLAKE2B ddf7bb2a1a0789c2de9377c9e6ff8442725a310a0587b119683b6c07868e9aca82db184580b0a4f7e5a61dd5c6fc74d9c5186c7816850fcf66a065b91a755510 SHA512 a48956cf011570abdcdb0a31d5ed693027eb11da8ed3b8fbe545a0d1c21f52a7b3b0d9587a94af44cd6050025282c2da28f9d854d5a03fb97f7aee3fa04b67ea
+EBUILD gromacs-2024.3.ebuild 9861 BLAKE2B 631036fb1ce3f090d0c863a0c95db19e37464cbbd8dd0cee4e60dcfc9b13630313bcf63450aab6521927abd618f4fe315a8451110ef9e86a479ee95a913f19f7 SHA512 fcfa45fcd35f443582f74220bfb5d8556858ddeba9f2105d072ab8da95133a4445ac13d469147a44326377d1a9bd9bd843e907d1a42e7bd99f81752f4409083a
+EBUILD gromacs-2024.4.ebuild 9863 BLAKE2B 559852f8c287a1b9c536e701e166c7c2955f511f8819e9f8519cdd2dd806fb7cf0f6af0e91d47b2babcb133913476935022ac6fc53909148626e7dca2ce8861d SHA512 9d8dfd39afe26b4b020ca20632c4e7cc583cc4362a09ae082f582291f3f916fd3cf25f0cfc56ab918ddb0931d14d4b190d9ca2893e054c9fa1aae62418186a3b
+EBUILD gromacs-2024.5.ebuild 9863 BLAKE2B 559852f8c287a1b9c536e701e166c7c2955f511f8819e9f8519cdd2dd806fb7cf0f6af0e91d47b2babcb133913476935022ac6fc53909148626e7dca2ce8861d SHA512 9d8dfd39afe26b4b020ca20632c4e7cc583cc4362a09ae082f582291f3f916fd3cf25f0cfc56ab918ddb0931d14d4b190d9ca2893e054c9fa1aae62418186a3b
+EBUILD gromacs-2024.9999.ebuild 9817 BLAKE2B abce03519bf538e5fc7db11912b1beceafc49cfdcaba1dc9d4cc7ad6a69337789f875105b65da1cef86558f43fbdcdcae27d092825efba7b02a9b9d9644afc58 SHA512 890cc415cb0176772349650c5d90f1e3b93361bafbdb958661253bf84ee2794290566edf661ec0ea0e690872b414cd763be2f0468f82a7410d4090000c6d6221
+EBUILD gromacs-2025.9999.ebuild 10389 BLAKE2B e46f3fc0e6214863933cd98a675f4225a096c74876dfab052d0fd7fbbc4bc1a1d10122c43f78bfdda08a8ec076b4bdee3f0f1d6089e67d0c36452d0954ecadd4 SHA512 9b3fd0336dd22aae15a608f3217bca498fcb9771540a0f4350d507be1eba838584f85d58d1058e73e398d02d4f850d7bad48d0442039af1b87250f27168f0283
+EBUILD gromacs-2025_rc.ebuild 10389 BLAKE2B e46f3fc0e6214863933cd98a675f4225a096c74876dfab052d0fd7fbbc4bc1a1d10122c43f78bfdda08a8ec076b4bdee3f0f1d6089e67d0c36452d0954ecadd4 SHA512 9b3fd0336dd22aae15a608f3217bca498fcb9771540a0f4350d507be1eba838584f85d58d1058e73e398d02d4f850d7bad48d0442039af1b87250f27168f0283
+EBUILD gromacs-9999.ebuild 10428 BLAKE2B 8b2d94447cbfd0f67e40f8d906e74592165155d31aaadd0e6e24cb96f01306043b7fdca377eb3c3dd7d2b83ffc8f5a78cf08b1b2fe5f04a5017d9a17f1f53cce SHA512 0dfe5befff43283d8780f4ac29b4393c3e2ade46fc389b07042c1e7781af952953c37c2635913a62e16358c731d2a28728a240cbb162672e236f07f5e728305a
 MISC metadata.xml 1394 BLAKE2B d387fba17fee85119e42ff18968f18d26bcbf5997361b4b1e93eeea1a8df54a9173b614f7d315000ecd0e4fa247becfb1236697825c0579fa7dcaff51a8185e5 SHA512 f8d9ebc33ad1f391dde1b7e056ad9b7860a902b805363c988962743cd4f37af69a0b1acd3323a95b9740ded0abf20904895605d78fecebdf94a4562ccd3ab9e8
diff --git a/sci-chemistry/gromacs/gromacs-2023.5.ebuild b/sci-chemistry/gromacs/gromacs-2023.5.ebuild
index 83ceb0fceb65..4501472b953b 100644
--- a/sci-chemistry/gromacs/gromacs-2023.5.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2023.5.ebuild
@@ -1,11 +1,11 @@
-# Copyright 1999-2024 Gentoo Authors
+# Copyright 1999-2025 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
 
 CMAKE_MAKEFILE_GENERATOR="ninja"
 
-PYTHON_COMPAT=( python3_{10..12} )
+PYTHON_COMPAT=( python3_{11..12} )
 
 DISTUTILS_OPTIONAL=1
 DISTUTILS_USE_PEP517=no
diff --git a/sci-chemistry/gromacs/gromacs-2023.9999.ebuild b/sci-chemistry/gromacs/gromacs-2023.9999.ebuild
index 5c6ffc9fc1a8..49be408cdcce 100644
--- a/sci-chemistry/gromacs/gromacs-2023.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2023.9999.ebuild
@@ -1,11 +1,11 @@
-# Copyright 1999-2024 Gentoo Authors
+# Copyright 1999-2025 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
 
 CMAKE_MAKEFILE_GENERATOR="ninja"
 
-PYTHON_COMPAT=( python3_{10..12} )
+PYTHON_COMPAT=( python3_{11..12} )
 
 DISTUTILS_OPTIONAL=1
 DISTUTILS_USE_PEP517=no
diff --git a/sci-chemistry/gromacs/gromacs-2024.3.ebuild b/sci-chemistry/gromacs/gromacs-2024.3.ebuild
index cc4c9393b140..d57a37462c1d 100644
--- a/sci-chemistry/gromacs/gromacs-2024.3.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2024.3.ebuild
@@ -1,11 +1,11 @@
-# Copyright 1999-2024 Gentoo Authors
+# Copyright 1999-2025 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
 
 CMAKE_MAKEFILE_GENERATOR="ninja"
 
-PYTHON_COMPAT=( python3_{10..12} )
+PYTHON_COMPAT=( python3_{11..12} )
 
 DISTUTILS_OPTIONAL=1
 DISTUTILS_USE_PEP517=no
diff --git a/sci-chemistry/gromacs/gromacs-2024.4.ebuild b/sci-chemistry/gromacs/gromacs-2024.4.ebuild
index 7f2e7152df0f..49ec16a5713f 100644
--- a/sci-chemistry/gromacs/gromacs-2024.4.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2024.4.ebuild
@@ -1,11 +1,11 @@
-# Copyright 1999-2024 Gentoo Authors
+# Copyright 1999-2025 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
 
 CMAKE_MAKEFILE_GENERATOR="ninja"
 
-PYTHON_COMPAT=( python3_{10..12} )
+PYTHON_COMPAT=( python3_{11..12} )
 
 DISTUTILS_OPTIONAL=1
 DISTUTILS_USE_PEP517=no
diff --git a/sci-chemistry/gromacs/gromacs-2024.5.ebuild b/sci-chemistry/gromacs/gromacs-2024.5.ebuild
index 385f80b9f758..49ec16a5713f 100644
--- a/sci-chemistry/gromacs/gromacs-2024.5.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2024.5.ebuild
@@ -5,7 +5,7 @@ EAPI=8
 
 CMAKE_MAKEFILE_GENERATOR="ninja"
 
-PYTHON_COMPAT=( python3_{10..12} )
+PYTHON_COMPAT=( python3_{11..12} )
 
 DISTUTILS_OPTIONAL=1
 DISTUTILS_USE_PEP517=no
diff --git a/sci-chemistry/gromacs/gromacs-2024.9999.ebuild b/sci-chemistry/gromacs/gromacs-2024.9999.ebuild
index b681516f603a..e30a7a974d56 100644
--- a/sci-chemistry/gromacs/gromacs-2024.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2024.9999.ebuild
@@ -1,11 +1,11 @@
-# Copyright 1999-2024 Gentoo Authors
+# Copyright 1999-2025 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
 
 CMAKE_MAKEFILE_GENERATOR="ninja"
 
-PYTHON_COMPAT=( python3_{10..12} )
+PYTHON_COMPAT=( python3_{11..12} )
 
 DISTUTILS_OPTIONAL=1
 DISTUTILS_USE_PEP517=no
diff --git a/sci-chemistry/gromacs/gromacs-2025.9999.ebuild b/sci-chemistry/gromacs/gromacs-2025.9999.ebuild
index bec110e3340c..e829adc6590f 100644
--- a/sci-chemistry/gromacs/gromacs-2025.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2025.9999.ebuild
@@ -1,11 +1,11 @@
-# Copyright 1999-2024 Gentoo Authors
+# Copyright 1999-2025 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
 
 CMAKE_MAKEFILE_GENERATOR="ninja"
 
-PYTHON_COMPAT=( python3_{10..12} )
+PYTHON_COMPAT=( python3_{11..12} )
 
 DISTUTILS_OPTIONAL=1
 DISTUTILS_USE_PEP517=no
diff --git a/sci-chemistry/gromacs/gromacs-2025_rc.ebuild b/sci-chemistry/gromacs/gromacs-2025_rc.ebuild
index d0af77e59df9..e829adc6590f 100644
--- a/sci-chemistry/gromacs/gromacs-2025_rc.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2025_rc.ebuild
@@ -5,7 +5,7 @@ EAPI=8
 
 CMAKE_MAKEFILE_GENERATOR="ninja"
 
-PYTHON_COMPAT=( python3_{10..12} )
+PYTHON_COMPAT=( python3_{11..12} )
 
 DISTUTILS_OPTIONAL=1
 DISTUTILS_USE_PEP517=no
diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index 1cc913c0aeed..eb3dd80c5f84 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -1,11 +1,11 @@
-# Copyright 1999-2024 Gentoo Authors
+# Copyright 1999-2025 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
 
 CMAKE_MAKEFILE_GENERATOR="ninja"
 
-PYTHON_COMPAT=( python3_{10..12} )
+PYTHON_COMPAT=( python3_{11..12} )
 
 DISTUTILS_OPTIONAL=1
 DISTUTILS_USE_PEP517=no
diff --git a/sci-chemistry/molmol/Manifest b/sci-chemistry/molmol/Manifest
index e540122ad8fe..dcfce0f7a0c7 100644
--- a/sci-chemistry/molmol/Manifest
+++ b/sci-chemistry/molmol/Manifest
@@ -1,7 +1,9 @@
 AUX molmol-2k_p2-gcc14-fix.patch 357 BLAKE2B e7c1692e7a45ed2b83c38fa8b7ffe1a563f752660f3e2dc2098eb1de4491cd8919190d04cdc9d31f036b42a8fda6d6200fa347dfc7aed0fa46d75e1e3103e6cb SHA512 6138806de3222b073ce0f77c2c6d7060cbc9e3ba729553f61b93e44c671008da0e1ce64bc6fc0d9293dba203d71ae76cff1bea698e03a42d3e5a5901e6e8ccc0
+AUX molmol-2k_p2-transform-makefiles.patch 966 BLAKE2B 0bb3b8a5801b29f21d961e48a3bbe1221c2ddb0961c685466ba802e22ff52632d81cd4f88c083923b1fd3ed51f8c3947ec4e55eefd11e06b10e67d38d9995d3b SHA512 b255e8f858d4960aebef88452297dce1ebf993fc7343f54e713bf219d41ec7d5661b16d63a1f363bba9d6e1c0282ba894864e489210ce6294e49f72c3d56209f
 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-r10.ebuild 2442 BLAKE2B 35313fce20508bcd7c09e7e748d8f00675acb6ece1139b8b3ea68f988bc749a6c47b8a00725514c81198de44f17e94295420ed05142247f8a44c9cfcebb475c3 SHA512 3fb8451bad09df6e6c895884b614e1e2773a39942b734eeefcc74531ae513d4a90e276f88adf0d71409539104e3164a7bda67e3652ac1ae9e0fccbf3cecabd45
 EBUILD molmol-2k_p2-r9.ebuild 2562 BLAKE2B b197c856d551f1b634efe0d978a297362c9d1260029cc7ecc2644fc3a3ce6bde20a7000f3aa2f4056b34454b17f357103f74535315d2f530483ae72a051ae96e SHA512 7668a27c2962fdaa40e96f55e48bcd3307cf6d146bfeba6f27bc0ae8e924e0dcc7853bee3a6a57b861de2868fa220a7ba071e1944e44364519b2f60b4ff46b4a
 MISC metadata.xml 272 BLAKE2B 531e98b72776bbe9126811b70943add0f6f43141b01cb75b17ac2c8d1cfb6a9b349022fd411894d2b8eeb0612a73db10aed4ba71f9624bd6dbd172a05fca2c76 SHA512 04f5575703aaaa95e575460ae3de428d3da173b3b741ab52b4aad31e381fef78b325f49f99622ec26a65024437759ea013fc525bd63ee553003c71afcc40d10c
diff --git a/sci-chemistry/molmol/files/molmol-2k_p2-transform-makefiles.patch b/sci-chemistry/molmol/files/molmol-2k_p2-transform-makefiles.patch
new file mode 100644
index 000000000000..6129ed03b3ab
--- /dev/null
+++ b/sci-chemistry/molmol/files/molmol-2k_p2-transform-makefiles.patch
@@ -0,0 +1,40 @@
+Transformed multiple seds to this patch. `MOLMOLHOME` is the runtime variable
+that depends on knowledge of paths that I didn't think of how to correctly
+pass beyond editing it with sed. For everything else, it is here and changed
+to work correctly with build system.
+Rolled up sed transformations were to made build system non-parallel,
+fix environmental variables, remove sleep and add use right shell and
+build dependencies in startup script.
+--- a/makedef.lnx
++++ b/makedef.lnx
+@@ -11,12 +11,12 @@
+ 
+ XINCL   = -I/usr/X11R6/include
+ 
+-CC=gcc
++CC ?= gcc
+ MCPPFLAGS =
+-MCFLAGS =-pipe -O3 -ffast-math -march=i686 -mcpu=i686
++MCFLAGS := $(CFLAGS)
+ 
+ RANLIB   = /bin/true
+-WAIT     = sleep 2
++WAIT     = sleep 0
+ SHELL    = /bin/sh
+ CPP      = /lib/cpp
+ 
+--- a/molmol
++++ b/molmol
+@@ -1,9 +1,10 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # startup script for MOLMOL
+ #
+ 
+-MOLMOLHOME=/opt/group/MOLMOL
++MOLMOLHOME=/;
++MOLMOLDEV="Motif/OpenGL"
+ export MOLMOLHOME
+ export MOLMOLDEV
+ 
diff --git a/sci-chemistry/molmol/molmol-2k_p2-r10.ebuild b/sci-chemistry/molmol/molmol-2k_p2-r10.ebuild
new file mode 100644
index 000000000000..f9425f749a99
--- /dev/null
+++ b/sci-chemistry/molmol/molmol-2k_p2-r10.ebuild
@@ -0,0 +1,103 @@
+# Copyright 1999-2025 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+inherit desktop toolchain-funcs flag-o-matic
+
+MY_PV="${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
+	media-fonts/font-adobe-100dpi
+"
+DEPEND="${RDEPEND}"
+
+PATCHES=(
+	"${FILESDIR}"/${P}-gcc14-fix.patch
+	# Patch from http://pjf.net/science/molmol.html, where src.rpm is provided
+	"${WORKDIR}"/patches/pjf_RH9_molmol2k2.diff
+	"${WORKDIR}"/patches/ldflags.patch
+	"${WORKDIR}"/patches/opengl.patch
+	"${WORKDIR}"/patches/cast.patch
+	# patch from fink
+	# fixes numerous bad bracings and hopefully the OGL bug 429974
+	"${WORKDIR}"/patches/${P}-fink.patch
+	"${WORKDIR}"/patches/wild.patch
+
+	"${FILESDIR}"/${P}-transform-makefiles.patch
+)
+
+pkg_setup() {
+	MMDIR="/usr/$(get_libdir)/molmol"
+}
+
+src_prepare() {
+	default
+	eapply -p0 "${WORKDIR}"/patches/libpng15.patch
+	rm -rf tiff*
+
+	sed \
+		-e "s|^MOLMOLHOME.*|MOLMOLHOME=${EPREFIX}/${MMDIR}|" \
+		-i "${S}"/molmol || die
+
+	ln -s makedef.lnx "${S}"/makedef || die
+
+	# Parallel build fails (#880621) and cannot be disabled by MAKEOPTS
+	# (#880621, #941488).
+	find . -name Makefile -exec sed -i -e "1i .NOTPARALLEL:" {} + || die
+
+	# https://bugs.gentoo.org/944200
+	# uses C polymorphism. Can't be trivially patched
+	append-cflags -std=gnu17
+	tc-export AR CC
+}
+
+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
+}