gentoo resync : 25.11.2020

author: V3n3RiX <venerix@redcorelinux.org> 2020-11-25 22:39:15 +0000
committer: V3n3RiX <venerix@redcorelinux.org> 2020-11-25 22:39:15 +0000
commit: d934827bf44b7cfcf6711964418148fa60877668 (patch)
tree: 0625f358789b5e015e49db139cc1dbc9be00428f /sci-chemistry
parent: 2e34d110f164bf74d55fced27fe0000201b3eec5 (diff)
28 files changed, 152 insertions, 777 deletions
diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz
index 1fecf4e508f9..164880108d31 100644
--- a/sci-chemistry/Manifest.gz
+++ b/sci-chemistry/Manifest.gz
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index 015a4eab9de9..aaf56d6ffa8d 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -2,24 +2,22 @@ AUX gromacs-2020_beta1-pytest.patch 630 BLAKE2B 1036e06589c24459006f0b579ee89c9d
 DIST gromacs-2018.8.tar.gz 29913703 BLAKE2B 8780032305928067fbfe1559efe9eedc4d47e27ab2f6ab54d6dba39edfcbeefbee4673d8910009048a850620b5a08ba8feb622db652c439cfa50a149ec5f0015 SHA512 6717895942f2ab7b54019511ed2aebadadde8e96d3c4b7414bb9168ffe418432d2dee330192e199f7b9d2f665c71f5d4f1ef0911aa7243d525a2ca182ef5b122
 DIST gromacs-2019.5.tar.gz 33445791 BLAKE2B 1e2e2764b0c8774c878abf4f32c2fa7ddd9b46f464cf1256deb48335433d92ef1b315f5534cdec9f766ae928a71361b5a4dd4a4def638269eb260ff98dbbe8bb SHA512 fdd177e4dfd29629b72bfbb4d61ff7bcdb37279f534883a9df8fd57569212fe1e9f8b8c9cec347fcc607539f31412d604d11ee3c0eb797251960435962b1bec6
 DIST gromacs-2019.6.tar.gz 33446147 BLAKE2B adc21fb6b841b06d499607f8c0166a673645ef5af0b40bd823d0fff5ea24397e6301c5e1e0070986ae1ce1deba8a42052b66da148b071c1e21f2fe3908fee275 SHA512 7c227a9539e5775d5d128ae9e872a24181d79cdcd2852b86453597987e8d7332ecec371da65d089f6e610c54aafbccc8824ce298743383dd6240719ebee692a8
-DIST gromacs-2020.1.tar.gz 29153989 BLAKE2B b1c0313da945c57c74040c2bcd50495b238b0e131cc4ebecd74ae0d01465b47d732ea456a52a2f9d998cd37e2bfdb93d52bd15177328c4b7a14e6b1d8bc00117 SHA512 130394ec70e5d75ea451e9fa77c4ea2dd4adb0c51cc7663ac8579972bab7a0b75d9143d0eebb21802fc93305deca8831393a8cb3f51b6d01f9477f3dadece037
-DIST gromacs-2020.2.tar.gz 29144614 BLAKE2B cd20b031dcec32d9a797d66f2679779077910c184702f12f12093d92e8417d42e07bfb17a8fe63e9d29a889d5f57461b5f86e11adfc26635f8d2b5a5df19473a SHA512 348c80fad93b34e6703906fec97c6c2294c0803c326d6145776b732e1c33cd58e0967ddb2ec4799e3583542c09e7a6a015e4d084d60cf97b81b3a92253cca76c
-DIST gromacs-2020.3.tar.gz 29143950 BLAKE2B ea88fcacc3958f1123c1fe4852f7160a04e4daff15dd2eb87c23197bff2e6379f396df0747b078dc86e7bb909ecbb4b6d98530a34234c989a636dbdb2327562d SHA512 8dbd13f8c6dd9ac337e0bea683aeff38010ee9b4ef438de230beb76e5a54884a5c1eda72f20294b7920758978e247900ac3db32b95c7452350fc1f5ef0a4bcc8
+DIST gromacs-2020.4.tar.gz 29149899 BLAKE2B a07c8efd96137d58c1edf4ac9b5aafeb16d9e65234b9459b71471827032654acacb58ed6ae87ec6e0e593a0acd799683cc4461b06cc883b089d740708619345e SHA512 0c56f058741af70660baf0177724ec940dd984c05ea141ede91ee51ce3744f76d00e31bdb5db907e46fa1639de5dca637b3ace26e89f908c2e74c69f0c21ed3a
+DIST gromacs-2021-beta2.tar.gz 30133767 BLAKE2B 01a8125b8d22c2642d7310e994b3333a44108fc35042b72180e8987a965af1b234ef1b009f822e1f5946f40e296c88ef0268e789698070805df0a71964a3341d SHA512 69f8638df183c0bd83b374cae5848ba356b9493d1fb853ce871270eb3d9c4310828ba9f901a8d95eea284d4929fd0d186bce4b2ebbd2ee4c198790935e0f6ec5
 DIST manual-2018.8.pdf 10025023 BLAKE2B afb0a6e6a72d78df743fcb57e7c1716848589e571dd35167b957a9b407ca27978ccfb6cb9e0df9c9439b888f352501a00ba32281ed1e0b4193bd606f1d77152e SHA512 b1972f7ce965bfc9377542993c5943ea4868a8ed23a969d4203264746d6bea3a7a65c6379196ece37fd6d68ec7ec80f827bde87d1049284af7082759a124f1d5
 DIST manual-2019.5.pdf 12702361 BLAKE2B cb80429a59019b190115bf2af689c0df23b0fec6e41a9ebc9eba20977d1b06eed79044c906c41228883767f673140e15d3a5ef947a0c1ec4fe84012089f4fa91 SHA512 baf27961b87e6120c49abc9dc58e25d12a15588b4ac787e1a086748d488692d4a1262229ac66e550d3cca3a6042545fb6ec472a2c98d6a8698b7a18b4397f605
 DIST manual-2019.6.pdf 12702376 BLAKE2B c350127bc06a9eb3dee73da39037c84daeb89500e23cb131bd19a150bf60602d4dde7611e0c6f0f344af4093e96a899303dac71b4df56fd0c44c3a48a56606b7 SHA512 dfdff67c2c1c9ce1f1c236b7686c5331b0fe86951da6c98eddd6a3e748815e0be0a9653ae4318469fcdd913c4e7c355d64a997cc80b9d9fbe6282ef6d98e61eb
 DIST regressiontests-2018.8.tar.gz 67855469 BLAKE2B 34c9b339f6229f483afbb5192ee6ba8b8f72d5c26907a853af9c53dfece0d88739e48f6b44b78d1c010f988f9385d077285300522164f533a5861e9dda879275 SHA512 3642389d27bd1942cd0f091c940ae97b197b94856a387fe581dc516b0d4169480f16551d4ba357f9282b3337d605c286d51dd38112ac87c826dda634904836bb
 DIST regressiontests-2019.5.tar.gz 67643634 BLAKE2B c4d9535d9a8a650869d67544ad5f367324f45e55325bb5074ece9b010f232f2f0dd97c9af97924d3f2368ed63015ca7330baff1cc681310e1439ec330b70ee8d SHA512 7c0917b76e7db35ab4e3271d523d268e0e2d858091e68ead863bfe6d1e56b381e30fdbf44f479f6e065c029e2eb27cfa0dbaa1b243f185144321aaf5084c55ce
 DIST regressiontests-2019.6.tar.gz 67643195 BLAKE2B 1e054e24b187946f7ea28090d4f20cf8e1d79a26253f57ba07d130e0773d8541b8a1552a38023d31a68ce8bc62d8e0af1d98609234bb3e7d3e6d567307ebb386 SHA512 eacf1c55b982515a305c29459fe80a7cd558a8481e5689962aa956148af542568b1d1ce59c6784ecb0afd4768c2b664afa21e12af2d89ae2b06b1ba61ad72036
-DIST regressiontests-2020.1.tar.gz 48541809 BLAKE2B 0fec2f0fb7fad0ad48bb790d7df6487e2c1931a0a2134795bf7da4a9087f0f2a3743288fc4ec057fa6b22412c2d8f312cfa3af38be8c5bea51d7a06afb5ac9f0 SHA512 664d29ce39629ed218de65179ce4a73e479d73d30bc96f5ae57624d7e4447298c6122dc09e7873b8cad458eaee0530866411fab20e009e46bf39b133e0de47e8
-DIST regressiontests-2020.2.tar.gz 48539492 BLAKE2B 08222ec18e70f551194fc0a060facda394c0d9999e162dace06029aa5f36e7237aeb2468a80d1198257a45fb076f8f633a7279a85976484900bf4154176aa070 SHA512 3066d92a59dafade78807612681d82a7b8a0bd9b74fa7e8784063a908418c55b4427482dc7feb261ff6981fabb2d64a800d3e90ed647ab45e201f4847347bac7
-DIST regressiontests-2020.3.tar.gz 48541439 BLAKE2B c8b3840b76b7974e5efd518d02da2be3c8e685a420462962cf4ffb7b234bd5ffec0fb83adc962e4ce4716098667e1431f7bc46911bf5400f369881c697c1d0cb SHA512 84848210b2c4c0387c3f347237d58a114bd28c2d248f359e40a4a5b3557fca7763c431d1e03f167dcf22296a48dd47413a644238d72edc1414e3f830dd732416
-EBUILD gromacs-2018.8.ebuild 6958 BLAKE2B 17452127d480265b57b435d84de5860729860e72a47f89ced75cfa18e9efc1b6dc478785545a86313e9fc6a93647d1ae9f4b78167654acc0a95288215df3d35a SHA512 a2c23b418af81162c22b06d4b5fe2114d09288f314dacb6ca7a5b0fecd50a3bf0069237ec036da8c420b133daaf1eef43d40d1b13c525df8f362f9a0a7b9ec51
-EBUILD gromacs-2019.5-r1.ebuild 7280 BLAKE2B 9d26c304b6e67d00a69d6919daf2bde5b542c9e1c5e1e2f44a2fb1350986a1175737bc9f7325c71cca8479a3e90fca63a0debb01eff5bb94113533a0be364839 SHA512 c991901aed3149fa7872f02647aaff424bd93508157c0f734cc0b14b9f81fe55ff996d8a5a7fb7ba1514cf737047cfbd389a54804d2b5659d728df6f004a847e
-EBUILD gromacs-2019.6.ebuild 7283 BLAKE2B 00055c4ba5cf660237d73232aa7a76857bc141eaa79fdbf81985d337c134123ad7fd92b69d017425ec3f11eb2f367a25e8c4168b948f1092b2a1e538cb991886 SHA512 c307ea57a5b7c468ddd454ee97743643363121757c50cda948398090fa9368dc7b52255e6c3a261565894edd77f91d62c221841c1aca3644691c7fb9a0a8d5ef
-EBUILD gromacs-2020.1-r1.ebuild 9844 BLAKE2B 9568558d0558311ed7a8b8d523ec287dea6682ff5eccb6b780e90739f876d262d20b9f938999bb3283a7c05677aa3a33e7c35071822be05fdd4cf4c74d9ec1d9 SHA512 86e3d58bedb8a87210a81bad1450c11dbfbc99623beac78a498c39dcef2628b2a9a6a7b85c036a79ead38e56ce40d3d15beba6072c4fa8cd62011181eacef97f
-EBUILD gromacs-2020.2.ebuild 9844 BLAKE2B 9568558d0558311ed7a8b8d523ec287dea6682ff5eccb6b780e90739f876d262d20b9f938999bb3283a7c05677aa3a33e7c35071822be05fdd4cf4c74d9ec1d9 SHA512 86e3d58bedb8a87210a81bad1450c11dbfbc99623beac78a498c39dcef2628b2a9a6a7b85c036a79ead38e56ce40d3d15beba6072c4fa8cd62011181eacef97f
-EBUILD gromacs-2020.3.ebuild 9844 BLAKE2B 9568558d0558311ed7a8b8d523ec287dea6682ff5eccb6b780e90739f876d262d20b9f938999bb3283a7c05677aa3a33e7c35071822be05fdd4cf4c74d9ec1d9 SHA512 86e3d58bedb8a87210a81bad1450c11dbfbc99623beac78a498c39dcef2628b2a9a6a7b85c036a79ead38e56ce40d3d15beba6072c4fa8cd62011181eacef97f
-EBUILD gromacs-2020.9999.ebuild 9759 BLAKE2B bf1d5b859c466f05b4909113c90faaed916512809ec9563c474461906d49261baeca9b8f7e5bdf85a3fffd32b1b84b4ec47d4523105bba3ed32ce73491d6e7d1 SHA512 cac942e6effce1c0c7ff99ac56c88d9422a89b1b275d3555c5a15a00640c253bd3a98301b9509daf14b3e4d3f1577a8fe6647aab10bf645645ccf35b57470208
-EBUILD gromacs-9999.ebuild 9755 BLAKE2B ee04718fea528c500f797f0ee1ebfb2307772ff5ab4cfc3293f3bf6f93a25ee6155c0b888a4d25371c6a9c4fb022d9e79da9a9df85d7fc82a97442755314ff28 SHA512 5338d8d45908e0b618c21908162e16fff4fba74d671a756229f1f05bce9fd578e923d6289609344cd4a28a78995e2609908de0598cc5d60d45a029ac97b7bba4
-MISC metadata.xml 1192 BLAKE2B 560c1c792102747fc16c22d475114480b9897263405da05946721dae5b781c599a02e1401adfa4d929bfb41b4d52791376438aa37d33de18beabc9edbeb779fa SHA512 136c49bfaca76e714e811077c7f7d214a5984c7b6c891c79ad4a754c304752e17450c9aee100dafce04d7bf3893a53224ef9b54504a278654d59fae9acdd0f77
+DIST regressiontests-2020.4.tar.gz 48542144 BLAKE2B 1dcde67525d40ababa74d9e8ba2dd3fdef1de7d1018491e102edd71d3a622925f213b5a0812e5448882b4cb5fb578317e8e5029bdc4bd53008aa8441a3d9dea1 SHA512 7c71f36a1cef22562f14dcd233e90ad2fe370ae1a7d3b5268727259b374e12d4754253735ac8745d3738bdbc1cc2067780fda5e393be2ff264f632fe4e0c1978
+DIST regressiontests-2021-beta2.tar.gz 48513581 BLAKE2B d9c98739f02b4ea06928197065bacd5785ea68a974f7affc2f08b5552d533bc7fee8398b67bb0d23d209394f2bffc877733f82d3725a287332509e3e73be6c0a SHA512 4db44e186d16e41f6186d0be50d90205f207c29ee7b28f24b49e32fd8c5de72857bf3dd38a996514ea88d5658652a11599934575842a1e46e6e11d00f64e6bfd
+EBUILD gromacs-2018.8.ebuild 6959 BLAKE2B 21224b7c0833bfde7324c22e18f1aab2463c6d2ddf0c7e4a38a6aa0e7280f84fe0809fd882d33cae14924c06104fb214d8925c238b7a3ae6c76f2b7bb96b6528 SHA512 dfe3e7265d4fd8cb9a16c324778d7b9b03e785674573706efda516a9257a341da107f36f8203e5ac1effed5d5783e42a19c203b72cf6f13bfd8f993545114b9c
+EBUILD gromacs-2019.5-r1.ebuild 7280 BLAKE2B e9e7e72bb57315aee7e3a99b5fe7a0c00cd88b19975040c328727053c69584a1c0c4dd31b47a9ca08ae801ba093c4390a56a08191f20476d0b9dc1d0f4999141 SHA512 51687a58b68e2c74ee5ce518e9b97188fb57d7927e9bcf8debc640f04cce0b708d40d2c16e60431bf5ba532c5d9d5fd89ca31900856486319ad268c39d90a03b
+EBUILD gromacs-2019.6.ebuild 7280 BLAKE2B e9e7e72bb57315aee7e3a99b5fe7a0c00cd88b19975040c328727053c69584a1c0c4dd31b47a9ca08ae801ba093c4390a56a08191f20476d0b9dc1d0f4999141 SHA512 51687a58b68e2c74ee5ce518e9b97188fb57d7927e9bcf8debc640f04cce0b708d40d2c16e60431bf5ba532c5d9d5fd89ca31900856486319ad268c39d90a03b
+EBUILD gromacs-2020.4.ebuild 9817 BLAKE2B 84edf30737044149b04e322d7e890fbc9c97b3b84df0c5d3ddc5616db464b4fc2d6a261d7b04c465cccb63637779a80029b0419c1355c75a46e2d9dd633317e0 SHA512 0e91d845c92a0aa256d4c05cc694cdf2c0c1b7c67bc83e60364b0b2e1bede91e75af459479e6653ab061f6a9159a75894febbbe11bda092ba6a2b0d2bb43e166
+EBUILD gromacs-2020.9999.ebuild 9820 BLAKE2B f06b0c8a379587cd873bce5b567a0e2f76f4d2300db3f18def76a56e611ed804ec3c6c6359e98e248252432fc815ce5d512df45e98bf7525a826ba6922495385 SHA512 80420cd8a6233af54f041b0bbdd5ba947b68729b029d3334cee4baa793ae3a48c475f2d93a417f700b8320b9d076bac5ebdbb1acc664789869df5aa68f72d775
+EBUILD gromacs-2021.9999.ebuild 9993 BLAKE2B bef54d362417bb28f5eabf492c451a1b6b8909e899a0c7dee36caf1a3fc0f4b5f4a66a18651c850905e493734df9ac3da2339b891b22f05f251e3d98dda79b46 SHA512 7d86c27e61e2b7eb10dbceeb224e7ccf6f5b52f3ed372ddff7af8a68c2b9ef8f6db31846113f7ea1dc277ca2d1e00fd58c02d6f843bbebb12c6306cc3d57e4ab
+EBUILD gromacs-2021_beta2.ebuild 9993 BLAKE2B bef54d362417bb28f5eabf492c451a1b6b8909e899a0c7dee36caf1a3fc0f4b5f4a66a18651c850905e493734df9ac3da2339b891b22f05f251e3d98dda79b46 SHA512 7d86c27e61e2b7eb10dbceeb224e7ccf6f5b52f3ed372ddff7af8a68c2b9ef8f6db31846113f7ea1dc277ca2d1e00fd58c02d6f843bbebb12c6306cc3d57e4ab
+EBUILD gromacs-9999.ebuild 9993 BLAKE2B bef54d362417bb28f5eabf492c451a1b6b8909e899a0c7dee36caf1a3fc0f4b5f4a66a18651c850905e493734df9ac3da2339b891b22f05f251e3d98dda79b46 SHA512 7d86c27e61e2b7eb10dbceeb224e7ccf6f5b52f3ed372ddff7af8a68c2b9ef8f6db31846113f7ea1dc277ca2d1e00fd58c02d6f843bbebb12c6306cc3d57e4ab
+MISC metadata.xml 1173 BLAKE2B 768befbbd08adbd39f92bb715798a7ff8d0559bb3dfc3bf58c282ae687d4946f06b32c5a75544dcc33b83e5a874538712021c8ecbee5a989a6f045d752ab359b SHA512 24363e3136b7c81288798ac01f779cf9c06c32482c0b5acd6d1c5f2a66733ddfdf35de661cedb6a23e1a5de08c012b79e6d2903172aee139a675897e5c72e7d3
diff --git a/sci-chemistry/gromacs/gromacs-2018.8.ebuild b/sci-chemistry/gromacs/gromacs-2018.8.ebuild
index f124a0eac166..7d248a91ad62 100644
--- a/sci-chemistry/gromacs/gromacs-2018.8.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2018.8.ebuild
@@ -7,9 +7,10 @@ CMAKE_MAKEFILE_GENERATOR="ninja"
 
 inherit bash-completion-r1 cmake cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils
 
-SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
-		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${PV/_/-}.pdf )
-		test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )"
+SRC_URI="
+	http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz
+	doc? ( http://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf )
+	test? ( https://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )"
 KEYWORDS="amd64 arm x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
 
 ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2"
diff --git a/sci-chemistry/gromacs/gromacs-2019.5-r1.ebuild b/sci-chemistry/gromacs/gromacs-2019.5-r1.ebuild
index 7ea93b91af9f..d534eb5dfcf3 100644
--- a/sci-chemistry/gromacs/gromacs-2019.5-r1.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2019.5-r1.ebuild
@@ -7,9 +7,10 @@ CMAKE_MAKEFILE_GENERATOR="ninja"
 
 inherit bash-completion-r1 cmake cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils
 
-SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
-		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${PV/_/-}.pdf )
-		test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )"
+SRC_URI="
+	http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz
+	doc? ( http://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf )
+	test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )"
 KEYWORDS="amd64 arm x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
 
 ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2"
diff --git a/sci-chemistry/gromacs/gromacs-2019.6.ebuild b/sci-chemistry/gromacs/gromacs-2019.6.ebuild
index 85004d2644a2..d534eb5dfcf3 100644
--- a/sci-chemistry/gromacs/gromacs-2019.6.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2019.6.ebuild
@@ -7,10 +7,11 @@ CMAKE_MAKEFILE_GENERATOR="ninja"
 
 inherit bash-completion-r1 cmake cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils
 
-SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
-		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${PV/_/-}.pdf )
-		test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )"
-KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+SRC_URI="
+	http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz
+	doc? ( http://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf )
+	test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )"
+KEYWORDS="amd64 arm x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
 
 ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2"
 
diff --git a/sci-chemistry/gromacs/gromacs-2020.1-r1.ebuild b/sci-chemistry/gromacs/gromacs-2020.4.ebuild
index ba456196edd8..acff64fd6d86 100644
--- a/sci-chemistry/gromacs/gromacs-2020.1-r1.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2020.4.ebuild
@@ -5,23 +5,24 @@ EAPI=7
 
 CMAKE_MAKEFILE_GENERATOR="ninja"
 
-PYTHON_COMPAT=( python3_{6,7,8} )
+PYTHON_COMPAT=( python3_{6,7,8,9} )
 
 DISTUTILS_SINGLE_IMPL=1
 
 inherit bash-completion-r1 cmake cuda distutils-r1 eutils flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils
 
 if [[ $PV = *9999* ]]; then
-	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
-		https://gerrit.gromacs.org/gromacs.git
+	EGIT_REPO_URI="
+		https://gitlab.com/gromacs/gromacs.git
 		https://github.com/gromacs/gromacs.git
-		https://repo.or.cz/r/gromacs.git"
+		git://git.gromacs.org/gromacs.git"
 	[[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}"
 	inherit git-r3
 else
-	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
-		test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )"
-	KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+	SRC_URI="
+		http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz
+		test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )"
+	KEYWORDS="amd64 arm x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
 fi
 
 ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2"
diff --git a/sci-chemistry/gromacs/gromacs-2020.9999.ebuild b/sci-chemistry/gromacs/gromacs-2020.9999.ebuild
index 92600477ee91..99d60e61ff70 100644
--- a/sci-chemistry/gromacs/gromacs-2020.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2020.9999.ebuild
@@ -5,22 +5,23 @@ EAPI=7
 
 CMAKE_MAKEFILE_GENERATOR="ninja"
 
-PYTHON_COMPAT=( python3_{6,7} )
+PYTHON_COMPAT=( python3_{6,7,8,9} )
 
 DISTUTILS_SINGLE_IMPL=1
 
-inherit bash-completion-r1 cmake cuda distutils-r1 eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils
+inherit bash-completion-r1 cmake cuda distutils-r1 eutils flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils
 
 if [[ $PV = *9999* ]]; then
-	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
-		https://gerrit.gromacs.org/gromacs.git
+	EGIT_REPO_URI="
+		https://gitlab.com/gromacs/gromacs.git
 		https://github.com/gromacs/gromacs.git
-		https://repo.or.cz/r/gromacs.git"
+		git://git.gromacs.org/gromacs.git"
 	[[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}"
 	inherit git-r3
 else
-	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
-		test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )"
+	SRC_URI="
+		http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz
+		test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )"
 	KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
 fi
 
@@ -34,7 +35,7 @@ HOMEPAGE="http://www.gromacs.org/"
 #        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
 LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
 SLOT="0/${PV}"
-IUSE="X blas cuda +doc -double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}"
+IUSE="X blas cuda +custom-cflags +doc -double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}"
 
 CDEPEND="
 	X? (
@@ -159,13 +160,17 @@ src_prepare() {
 src_configure() {
 	local mycmakeargs_pre=( ) extra fft_opts=( )
 
-	#go from slowest to fastest acceleration
-	local acce="None"
-	use cpu_flags_x86_sse2 && acce="SSE2"
-	use cpu_flags_x86_sse4_1 && acce="SSE4.1"
-	use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
-	use cpu_flags_x86_avx && acce="AVX_256"
-	use cpu_flags_x86_avx2 && acce="AVX2_256"
+	if use custom-cflags; then
+		#go from slowest to fastest acceleration
+		local acce="None"
+		use cpu_flags_x86_sse2 && acce="SSE2"
+		use cpu_flags_x86_sse4_1 && acce="SSE4.1"
+		use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
+		use cpu_flags_x86_avx && acce="AVX_256"
+		use cpu_flags_x86_avx2 && acce="AVX2_256"
+	else
+		strip-flags
+	fi
 
 	#to create man pages, build tree binaries are executed (bug #398437)
 	[[ ${CHOST} = *-darwin* ]] && \
@@ -320,7 +325,7 @@ src_install() {
 	for x in "${ED}"/usr/bin/gmx-completion-*.bash ; do
 		local n=${x##*/gmx-completion-}
 		n="${n%.bash}"
-		cat "${ED}"/usr/bin/gmx-completion-gmx.bash "$x" > "${T}/${n}" || die
+		cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die
 		newbashcomp "${T}"/"${n}" "${n}"
 	done
 	rm "${ED}"/usr/bin/gmx-completion*.bash || die
diff --git a/sci-chemistry/gromacs/gromacs-2020.2.ebuild b/sci-chemistry/gromacs/gromacs-2021.9999.ebuild
index ba456196edd8..c4951b414c97 100644
--- a/sci-chemistry/gromacs/gromacs-2020.2.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2021.9999.ebuild
@@ -5,26 +5,27 @@ EAPI=7
 
 CMAKE_MAKEFILE_GENERATOR="ninja"
 
-PYTHON_COMPAT=( python3_{6,7,8} )
+PYTHON_COMPAT=( python3_{6,7,8,9} )
 
 DISTUTILS_SINGLE_IMPL=1
 
 inherit bash-completion-r1 cmake cuda distutils-r1 eutils flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils
 
 if [[ $PV = *9999* ]]; then
-	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
-		https://gerrit.gromacs.org/gromacs.git
+	EGIT_REPO_URI="
+		https://gitlab.com/gromacs/gromacs.git
 		https://github.com/gromacs/gromacs.git
-		https://repo.or.cz/r/gromacs.git"
+		git://git.gromacs.org/gromacs.git"
 	[[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}"
 	inherit git-r3
 else
-	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
-		test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )"
+	SRC_URI="
+		http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz
+		test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )"
 	KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
 fi
 
-ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2"
+ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_avx512f cpu_flags_arm_neon"
 
 DESCRIPTION="The ultimate molecular dynamics simulation package"
 HOMEPAGE="http://www.gromacs.org/"
@@ -162,11 +163,18 @@ src_configure() {
 	if use custom-cflags; then
 		#go from slowest to fastest acceleration
 		local acce="None"
+		if (use amd64 || use x86); then
 		use cpu_flags_x86_sse2 && acce="SSE2"
 		use cpu_flags_x86_sse4_1 && acce="SSE4.1"
 		use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
 		use cpu_flags_x86_avx && acce="AVX_256"
 		use cpu_flags_x86_avx2 && acce="AVX2_256"
+		use cpu_flags_x86_avx512f && acce="AVX_512"
+		elif (use arm); then
+			use cpu_flags_arm_neon && acce="ARM_NEON"
+		elif (use arm64); then
+			use cpu_flags_arm_neon && acce="ARM_NEON_ASIMD"
+		fi
 	else
 		strip-flags
 	fi
@@ -226,24 +234,21 @@ src_configure() {
 			[[ ${x} = "double" ]] && suffix="_d"
 		local p
 		[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
-		local cuda=( "-DGMX_GPU=OFF" )
-		[[ ${x} = "float" ]] && use cuda && \
-			cuda=( "-DGMX_GPU=ON" )
-		local opencl=( "-DGMX_USE_OPENCL=OFF" )
-		use opencl && opencl=( "-DGMX_USE_OPENCL=ON" ) cuda=( "-DGMX_GPU=ON" )
+		local gpu=( "-DGMX_GPU=OFF" )
+		[[ ${x} = "float" ]] && use cuda && gpu=( "-DGMX_GPU=CUDA" )
+		use opencl && gpu=( "-DGMX_GPU=OPENCL" )
 		mycmakeargs=(
 			${mycmakeargs_pre[@]} ${p}
 			-DGMX_MPI=OFF
 			-DGMX_THREAD_MPI=$(usex threads)
 			-DGMXAPI=$(usex gmxapi)
 			-DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy)
-			"${opencl[@]}"
-			"${cuda[@]}"
+			"${gpu[@]}"
 			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
 			-DGMX_BINARY_SUFFIX="${suffix}"
 			-DGMX_LIBS_SUFFIX="${suffix}"
 			-DGMX_PYTHON_PACKAGE=$(usex python)
-			)
+		)
 		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure
 		[[ ${CHOST} != *-darwin* ]] || \
 		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
diff --git a/sci-chemistry/gromacs/gromacs-2020.3.ebuild b/sci-chemistry/gromacs/gromacs-2021_beta2.ebuild
index ba456196edd8..c4951b414c97 100644
--- a/sci-chemistry/gromacs/gromacs-2020.3.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2021_beta2.ebuild
@@ -5,26 +5,27 @@ EAPI=7
 
 CMAKE_MAKEFILE_GENERATOR="ninja"
 
-PYTHON_COMPAT=( python3_{6,7,8} )
+PYTHON_COMPAT=( python3_{6,7,8,9} )
 
 DISTUTILS_SINGLE_IMPL=1
 
 inherit bash-completion-r1 cmake cuda distutils-r1 eutils flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils
 
 if [[ $PV = *9999* ]]; then
-	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
-		https://gerrit.gromacs.org/gromacs.git
+	EGIT_REPO_URI="
+		https://gitlab.com/gromacs/gromacs.git
 		https://github.com/gromacs/gromacs.git
-		https://repo.or.cz/r/gromacs.git"
+		git://git.gromacs.org/gromacs.git"
 	[[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}"
 	inherit git-r3
 else
-	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
-		test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )"
+	SRC_URI="
+		http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz
+		test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )"
 	KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
 fi
 
-ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2"
+ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_avx512f cpu_flags_arm_neon"
 
 DESCRIPTION="The ultimate molecular dynamics simulation package"
 HOMEPAGE="http://www.gromacs.org/"
@@ -162,11 +163,18 @@ src_configure() {
 	if use custom-cflags; then
 		#go from slowest to fastest acceleration
 		local acce="None"
+		if (use amd64 || use x86); then
 		use cpu_flags_x86_sse2 && acce="SSE2"
 		use cpu_flags_x86_sse4_1 && acce="SSE4.1"
 		use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
 		use cpu_flags_x86_avx && acce="AVX_256"
 		use cpu_flags_x86_avx2 && acce="AVX2_256"
+		use cpu_flags_x86_avx512f && acce="AVX_512"
+		elif (use arm); then
+			use cpu_flags_arm_neon && acce="ARM_NEON"
+		elif (use arm64); then
+			use cpu_flags_arm_neon && acce="ARM_NEON_ASIMD"
+		fi
 	else
 		strip-flags
 	fi
@@ -226,24 +234,21 @@ src_configure() {
 			[[ ${x} = "double" ]] && suffix="_d"
 		local p
 		[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
-		local cuda=( "-DGMX_GPU=OFF" )
-		[[ ${x} = "float" ]] && use cuda && \
-			cuda=( "-DGMX_GPU=ON" )
-		local opencl=( "-DGMX_USE_OPENCL=OFF" )
-		use opencl && opencl=( "-DGMX_USE_OPENCL=ON" ) cuda=( "-DGMX_GPU=ON" )
+		local gpu=( "-DGMX_GPU=OFF" )
+		[[ ${x} = "float" ]] && use cuda && gpu=( "-DGMX_GPU=CUDA" )
+		use opencl && gpu=( "-DGMX_GPU=OPENCL" )
 		mycmakeargs=(
 			${mycmakeargs_pre[@]} ${p}
 			-DGMX_MPI=OFF
 			-DGMX_THREAD_MPI=$(usex threads)
 			-DGMXAPI=$(usex gmxapi)
 			-DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy)
-			"${opencl[@]}"
-			"${cuda[@]}"
+			"${gpu[@]}"
 			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
 			-DGMX_BINARY_SUFFIX="${suffix}"
 			-DGMX_LIBS_SUFFIX="${suffix}"
 			-DGMX_PYTHON_PACKAGE=$(usex python)
-			)
+		)
 		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure
 		[[ ${CHOST} != *-darwin* ]] || \
 		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index 203a0f716f57..c4951b414c97 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -5,26 +5,27 @@ EAPI=7
 
 CMAKE_MAKEFILE_GENERATOR="ninja"
 
-PYTHON_COMPAT=( python3_{6,7} )
+PYTHON_COMPAT=( python3_{6,7,8,9} )
 
 DISTUTILS_SINGLE_IMPL=1
 
-inherit bash-completion-r1 cmake cuda distutils-r1 eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils
+inherit bash-completion-r1 cmake cuda distutils-r1 eutils flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils
 
 if [[ $PV = *9999* ]]; then
-	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
-		https://gerrit.gromacs.org/gromacs.git
+	EGIT_REPO_URI="
+		https://gitlab.com/gromacs/gromacs.git
 		https://github.com/gromacs/gromacs.git
-		https://repo.or.cz/r/gromacs.git"
+		git://git.gromacs.org/gromacs.git"
 	[[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}"
 	inherit git-r3
 else
-	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
-		test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )"
+	SRC_URI="
+		http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz
+		test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )"
 	KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
 fi
 
-ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2"
+ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_avx512f cpu_flags_arm_neon"
 
 DESCRIPTION="The ultimate molecular dynamics simulation package"
 HOMEPAGE="http://www.gromacs.org/"
@@ -34,7 +35,7 @@ HOMEPAGE="http://www.gromacs.org/"
 #        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
 LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
 SLOT="0/${PV}"
-IUSE="X blas cuda +doc -double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}"
+IUSE="X blas cuda +custom-cflags +doc -double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}"
 
 CDEPEND="
 	X? (
@@ -159,13 +160,24 @@ src_prepare() {
 src_configure() {
 	local mycmakeargs_pre=( ) extra fft_opts=( )
 
-	#go from slowest to fastest acceleration
-	local acce="None"
-	use cpu_flags_x86_sse2 && acce="SSE2"
-	use cpu_flags_x86_sse4_1 && acce="SSE4.1"
-	use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
-	use cpu_flags_x86_avx && acce="AVX_256"
-	use cpu_flags_x86_avx2 && acce="AVX2_256"
+	if use custom-cflags; then
+		#go from slowest to fastest acceleration
+		local acce="None"
+		if (use amd64 || use x86); then
+		use cpu_flags_x86_sse2 && acce="SSE2"
+		use cpu_flags_x86_sse4_1 && acce="SSE4.1"
+		use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
+		use cpu_flags_x86_avx && acce="AVX_256"
+		use cpu_flags_x86_avx2 && acce="AVX2_256"
+		use cpu_flags_x86_avx512f && acce="AVX_512"
+		elif (use arm); then
+			use cpu_flags_arm_neon && acce="ARM_NEON"
+		elif (use arm64); then
+			use cpu_flags_arm_neon && acce="ARM_NEON_ASIMD"
+		fi
+	else
+		strip-flags
+	fi
 
 	#to create man pages, build tree binaries are executed (bug #398437)
 	[[ ${CHOST} = *-darwin* ]] && \
@@ -222,24 +234,21 @@ src_configure() {
 			[[ ${x} = "double" ]] && suffix="_d"
 		local p
 		[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
-		local cuda=( "-DGMX_GPU=OFF" )
-		[[ ${x} = "float" ]] && use cuda && \
-			cuda=( "-DGMX_GPU=ON" )
-		local opencl=( "-DGMX_USE_OPENCL=OFF" )
-		use opencl && opencl=( "-DGMX_USE_OPENCL=ON" ) cuda=( "-DGMX_GPU=ON" )
+		local gpu=( "-DGMX_GPU=OFF" )
+		[[ ${x} = "float" ]] && use cuda && gpu=( "-DGMX_GPU=CUDA" )
+		use opencl && gpu=( "-DGMX_GPU=OPENCL" )
 		mycmakeargs=(
 			${mycmakeargs_pre[@]} ${p}
 			-DGMX_MPI=OFF
 			-DGMX_THREAD_MPI=$(usex threads)
 			-DGMXAPI=$(usex gmxapi)
 			-DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy)
-			"${opencl[@]}"
-			"${cuda[@]}"
+			"${gpu[@]}"
 			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
 			-DGMX_BINARY_SUFFIX="${suffix}"
 			-DGMX_LIBS_SUFFIX="${suffix}"
 			-DGMX_PYTHON_PACKAGE=$(usex python)
-			)
+		)
 		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure
 		[[ ${CHOST} != *-darwin* ]] || \
 		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml
index c31594084c8f..23a4ee60ef76 100644
--- a/sci-chemistry/gromacs/metadata.xml
+++ b/sci-chemistry/gromacs/metadata.xml
@@ -1,6 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
+	<stabilize-allarches/>
 	<maintainer type="person">
 		<email>alexxy@gentoo.org</email>
 		<name>Alexey Shvetsov</name>
@@ -19,7 +20,6 @@
 		<flag name="opencl">Enable opencl non-bonded kernels</flag>
 		<flag name="single-precision">Single precision version of gromacs (default)</flag>
 		<flag name="tng">Enable new trajectory format - tng</flag>
-		<!-- acceleration optimization flags -->
 		<flag name="mkl">Use <pkg>sci-libs/mkl</pkg> for fft, blas, lapack routines</flag>
 		<flag name="offensive">Enable gromacs partly offensive quotes</flag>
 	</use>
diff --git a/sci-chemistry/mdtraj/Manifest b/sci-chemistry/mdtraj/Manifest
index d42ea0a16668..8fb92e33df00 100644
--- a/sci-chemistry/mdtraj/Manifest
+++ b/sci-chemistry/mdtraj/Manifest
@@ -1,5 +1,5 @@
 DIST mdtraj-1.9.1.tar.gz 1985711 BLAKE2B 625b7c1da998bd46732604dcc93c76f970f3c79f10e81aa9f4b3051ee45101efea8afd803d539ba1831dac3e7ed208d7c3773f74189a3887063cbff2b4d79df6 SHA512 015d9d1e258a7a207ac3b7e7a81b87c308e8684ee0a173ae9b722a90910e95e7f2ee18158c163212fae39d093b0cf397293d6e713538acb1fd20a7b70f2adc76
 DIST mdtraj-1.9.4.tar.gz 2133297 BLAKE2B c1507246bf0c8d7f6753f3d505f940e6f2f001361e42f10c9775647a7e6b58edf2d3953a8e48932f6bf9ad90b27e1baf30df6a7c1a590e49a860175822a25360 SHA512 55f67546db20ce63da3af2231df459e9983e15a65da960784613f746dcce820fe6b0deffbb21b528e93fc6cf674dc7a25ee11110894d2a89e5504e20d200ca38
 EBUILD mdtraj-1.9.1.ebuild 904 BLAKE2B f9d83a07faa64fd2d2cfc842683f77bcd9763cbe74e8b0a3981ede65be15bcc61e0d32bd950fec69c6fa39b06919d9c572d24679e84ea6d7f0c0ecadd4069c9a SHA512 9b67d016fa023bdd12b224559a86456b969b033b8f2c9ada250494e6b30e123fd91ae1f448b8891d77be0bb37652f8b450f9e48452a3abf0fa8b0ecbd0aff530
-EBUILD mdtraj-1.9.4.ebuild 1071 BLAKE2B 85fc5d891ac4e6b05c43102928a241d40391656b1a805e282e57034a2bd8b1fc0da5a4225bdfd2d37155d2023dae7e1b1d59a6a236de7cc5657f317cfa7df686 SHA512 66bb3f8324063a7fe6190970b00350effc18d77d551e6c5bd2a977c709540c5cf3c59583f6c96d62f5706e249e015b63899a42ba396f5beca85ef8eb9fe2ca3c
+EBUILD mdtraj-1.9.4.ebuild 1075 BLAKE2B cc3523394f3b289f3be8f2df7a72d82c81962f9338a31d0c97c49323cdf070da76bc0ff3d8efe6ed0a56924f1a0bf893cd67357808f885dbc44350507d288066 SHA512 e50dc8a4e3615b78255f6b0a950943a8152a948eef8796c2a144e18b6f91e99e4a9de847df9cdc9cee6aadffd17bb4d465f49374883eea166a77702e0f2635fc
 MISC metadata.xml 259 BLAKE2B dfc879984b6adce945d0e0a50f6ede2bca87147b9db99491359cdeccc2e74a20d56e14ae8903dbb80c94854f89bee539f14a4e3ce864204e277accf3f124a748 SHA512 19fb78cf4029c154954a40df40e28fc8d98a8b7e6b42f97259f664d44c29b284feffb9d073cadc7f90b5654a64b2466e186cb677d3a11830206f173eb9057706
diff --git a/sci-chemistry/mdtraj/mdtraj-1.9.4.ebuild b/sci-chemistry/mdtraj/mdtraj-1.9.4.ebuild
index fba1fb10eed2..b2c7bf93d80d 100644
--- a/sci-chemistry/mdtraj/mdtraj-1.9.4.ebuild
+++ b/sci-chemistry/mdtraj/mdtraj-1.9.4.ebuild
@@ -2,7 +2,7 @@
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
-PYTHON_COMPAT=( python3_{6,7} )
+PYTHON_COMPAT=( python3_{6,7,8,9} )
 DISTUTILS_USE_SETUPTOOLS=rdepend
 
 inherit distutils-r1
diff --git a/sci-chemistry/mopac7/Manifest b/sci-chemistry/mopac7/Manifest
index 978cbe206d0a..274811a00582 100644
--- a/sci-chemistry/mopac7/Manifest
+++ b/sci-chemistry/mopac7/Manifest
@@ -1,6 +1,6 @@
-AUX Makefile 458 BLAKE2B dab61e16f1382f173c1f46b8bf1331cd27c5f26ad0d4a6ad9b13f29ae777d169a735cf577862dbf2be4921fc6643b7ce4a7e863a9688bd25f83807247aff08d2 SHA512 e127a839ea7363e0ad68e522311e953900d262c6712bd7fcb58d971ff0a80d0d587c8f9d43f698f2295b2ec218a31aad47259c4a42925064110b4ff46a6d62b5
+AUX Makefile 387 BLAKE2B b0c4b3a009c8bf8c779953edf3e233434656033a661cb307079eebc980a827215fcd0dc04cf1df245ec20a6f95c151e4f9a9816c56cf8d6c1da6f77214fb41a5 SHA512 5bde85940d1d850ae65d23802aefb57660fda512d452660fdc37a19ae1f50c7f1240bfeffdd81a52cbd0a3140dad76272ca60333b60d40d1d79fdfe7297857dd
 DIST dcart.f 11044 BLAKE2B 7414804ecfab9a7cbddee664b85e6e2e8c1d8fe1e1f73d480dd1a387c5e349d26ec4ae1a37f27e38b7c051fcce2c1bdf77de12ec628298fd3edf79040a8a0c5a SHA512 788a184fd8419ff742e49c1a652d5ea093f9114dbe4f272665b8fb9eeac2afb7f7042628c288f2b81d0f54d8a7ef2f400490cd3aff39dda59a6d70a0deab5b80
 DIST gmxmop.f 38956 BLAKE2B e411feca5104e91ae8fd2008de61d18cc214beb3b2a7aa09a80269fb935e27ba1b1cb89fa30eedbfc4f6c4734c22d932e57d5905c175ae9f56c4affee7b0ca04 SHA512 38bb2e5749c4d3c8c24f15682f72e40cb4edb6517c7916cecee1d21675b1870c0fe331ba2ec40312408dec473141e7742d1e155d4b64f1c2a25bfa4e11885194
 DIST mopac7-1.15.tar.gz 764547 BLAKE2B 6e037862007221955d0ad65f3c002a3d2e461950a2bc0efac9d195cf1d9d856842d02bc380ce236c3d48f863a144875950f5c86f8f3ac936b8b098472f7f7a0d SHA512 e0ccd643caa6dbd7e156867530d79e50e10243f5e3b5f8bc57781e68e1daf26f2a0e6987fff00afe07eb0fcb98cbd9f01e4cfa5d20acc0d8ab3cca632968636e
-EBUILD mopac7-1.15-r1.ebuild 1816 BLAKE2B 6fe72656e446e1ef3e6a4c543c6a8703e8965ba751e1934c6c4673806283dc7a4bf41d121cc6e7a756fb4e599006ea368f75e753b8a5ec97cda8680e76a5d3bc SHA512 5e75215a6e8d2f18b01bab66d28b754cb0a9406051b089ac4415bed12a2425d1a15a9387668e680e51f33d29b782619f48acd50bf440a83b8e4ea57d458a4cf7
+EBUILD mopac7-1.15-r1.ebuild 1814 BLAKE2B 6ceef187223119bdcc1d772981573756c6b591bd9ab4886fea99ac3bccd08f755a1687b15e524d0db4030955b0a0e85b2793478788e910c65963019f85b396b4 SHA512 44211bb723a2e39e4059309ceef512e49b4010d18b66fa8509f5538cac0c59d4d29eaba887eb1101710bf59d70863a15c1605fe32b5ce9734019099d3c6d64f0
 MISC metadata.xml 434 BLAKE2B 011dd4486a917b69a58d398027b3af606bae6a6ea2b470b2f3f3d15f64b6db46a8a77ae4a52d78249ac8917d1a25bcbbcb5af62bea6677c5d4b433e47e9a8356 SHA512 77b3e0b69436a4f199c5ae3d9382c9b6cf2049ffd98144a2dc291495de9e8daa9deb6141d77b917f6e29902ad862c9044e7661ca7f0ae5e4fc68983857b3f6f2
diff --git a/sci-chemistry/mopac7/files/Makefile b/sci-chemistry/mopac7/files/Makefile
index 50370b3c2784..bcada8b0a889 100644
--- a/sci-chemistry/mopac7/files/Makefile
+++ b/sci-chemistry/mopac7/files/Makefile
@@ -16,8 +16,3 @@ clean:
 libgmxmopac7: $(objects)
 	$(FC) -shared $(LDFLAGS) -Wl,-soname,libgmxmopac7.so.$(MAJOR) -o $@.so.$(VERSION) $^ $(LIBS)
 	ln -sf $@.so.$(VERSION) libgmxmopac7.so
-
-static: $(objects)
-	ar rcv libgmxmopac7.a *.o
-	ranlib libgmxmopac7.a
-
diff --git a/sci-chemistry/mopac7/mopac7-1.15-r1.ebuild b/sci-chemistry/mopac7/mopac7-1.15-r1.ebuild
index 98848fcad10d..3cb18cba78fe 100644
--- a/sci-chemistry/mopac7/mopac7-1.15-r1.ebuild
+++ b/sci-chemistry/mopac7/mopac7-1.15-r1.ebuild
@@ -15,7 +15,7 @@ SRC_URI="
 LICENSE="public-domain"
 SLOT="0"
 KEYWORDS="amd64 ppc x86 ~amd64-linux"
-IUSE="gmxmopac7 static-libs"
+IUSE="gmxmopac7"
 
 DEPEND="dev-libs/libf2c"
 RDEPEND="${DEPEND}"
@@ -36,6 +36,10 @@ src_prepare() {
 	append-fflags -std=legacy -fno-automatic
 }
 
+src_configure() {
+	econf --disable-static
+}
+
 src_compile() {
 	emake
 	if use gmxmopac7; then
@@ -46,7 +50,6 @@ src_compile() {
 		cp -f "${DISTDIR}"/gmxmop.f "${DISTDIR}"/dcart.f . || die
 		sed "s:GENTOOVERSION:${PV}:g" -i Makefile
 		emake FC=$(tc-getFC)
-		use static-libs && emake static
 	fi
 }
 
@@ -60,6 +63,7 @@ src_install() {
 	if use gmxmopac7; then
 		cd "${S}"/fortran/libgmxmopac7
 		dolib.so libgmxmopac7.so*
-		use static-libs && dolib.a libgmxmopac7.a
 	fi
+
+	find "${ED}" -name '*.la' -delete || die
 }
diff --git a/sci-chemistry/ortep3/Manifest b/sci-chemistry/ortep3/Manifest
deleted file mode 100644
index f5dfb2628e17..000000000000
--- a/sci-chemistry/ortep3/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST ortep.f 177237 BLAKE2B ab081b3fb14823522a5418cc64d90f763a9dc7be5743836c1c432235e84edf22c76c7abb8d06bc7622360cc4108d44e5e71a898fa32890c28e4288c57368f46a SHA512 83e78fde2a798d7ee6b902133790f04787f54ceb62a1296ce8262cb8085bebf26e1c3b8f9c9c51ee0823f827bae40a75cede758c6cbe2c1b98a48bc49be6dd0b
-EBUILD ortep3-1.0.3-r1.ebuild 716 BLAKE2B d9064fae5d8e707eeb01a1e766877e273bcb9471e95fafb656f00494e7f2be86ffeac438bb3ff5bb9f6282e4584f342add3e8969e09457b31f167d6bc7e6f2b5 SHA512 a7bc01b102c140b1cfaf12135f3527af86def2ac9f3894b1f8efd8ddbbf5ddac35097c1ae06e5a59b826746311834fc383670e6c20bead46d820db451821605c
-MISC metadata.xml 265 BLAKE2B d5a98b9309829a0486c4b8a4336c2d24a0fe34e926d52afd0cc87e16fcc887ca4c18851e58afb33866823121fa8f221a90e0d726dbd85552a4caf66cf03b7b4a SHA512 470f6c178e88c4e83afa46d5e901a45fc2427a779ae832df7fa2d6e25e9e8b4ce77cd3a8fe191e6242d6df3b673f0de6b4f90f1e147aa8b8dd566f18163cc73a
diff --git a/sci-chemistry/ortep3/metadata.xml b/sci-chemistry/ortep3/metadata.xml
deleted file mode 100644
index da36ecbfcd6a..000000000000
--- a/sci-chemistry/ortep3/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?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>
-</pkgmetadata>
diff --git a/sci-chemistry/ortep3/ortep3-1.0.3-r1.ebuild b/sci-chemistry/ortep3/ortep3-1.0.3-r1.ebuild
deleted file mode 100644
index 6998ade89559..000000000000
--- a/sci-chemistry/ortep3/ortep3-1.0.3-r1.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=4
-
-inherit fortran-2 toolchain-funcs
-
-DESCRIPTION="Thermal ellipsoid plot program for crystal structure illustrations"
-HOMEPAGE="http://www.ornl.gov/sci/ortep/"
-SRC_URI="ftp://ftp.ornl.gov/pub/ortep/src/ortep.f"
-
-SLOT="0"
-LICENSE="public-domain"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="
-	sci-libs/pgplot
-	x11-libs/libX11"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}"
-
-src_unpack() {
-	cp "${DISTDIR}"/${A} "${S}" || die
-}
-
-src_compile() {
-	COMMAND="$(tc-getFC) ${FFLAGS:- -O2} ${LDFLAGS} -o ${PN} ortep.f -lpgplot -lX11"
-	echo ${COMMAND}
-	${COMMAND} || die "Compilation failed"
-}
-
-src_install() {
-	dobin ${PN}
-}
diff --git a/sci-chemistry/procheck/Manifest b/sci-chemistry/procheck/Manifest
index 70593b6047cf..b75562cce9bf 100644
--- a/sci-chemistry/procheck/Manifest
+++ b/sci-chemistry/procheck/Manifest
@@ -3,5 +3,5 @@ AUX procheck-3.5.4-ldflags.patch 1649 BLAKE2B 64506db2dbe1eba43dfc07bca233d57364
 DIST procheck-3.5.4-README 6585 BLAKE2B c61606848f30728b67d2ab51e0beadec1c30aaa0ca65a68834bff3ed3e3f466e34a0e4b64323e80cce9cee83854650ebe0805abf0509c0a9154bf08e3e0a2d6b SHA512 c6eff94cef9b67fd61884e88fa77ec381553d4dba53f477023738e1e44a6191c4241b14543ee7ecb93b049f16f262db2a09cf5d1a63248057633aab290f1f82a
 DIST procheck-3.5.4-manual.tar.gz 517840 BLAKE2B 33c5da5888bcd263e900cf2839f9287373e032fdde234e0375af061ec1c588d1ea5d2718da2a050da8060ba4003748a8fef3ff35b22f424c1cf6a1892aec0fe6 SHA512 0fa9c7d50b7ca43c626d5261c524166938d3a92be1d02221721bc7ce7e91ac4919e7200b946ce563f9bb696d7dab9588c1d1b31a4d551cafa2f2bce4931a212c
 DIST procheck-3.5.4.tar.gz 522013 BLAKE2B be6764bc741ec3f868aee349fc7e23608c612758029d0b745c421f40b47c896dd48de84ee7df6d09a64a20695bd5a1ed0a96464e6dcaf44de03da1ae231787f8 SHA512 1dd78b53070484fbcdca51001fd147ab13fd5e51b3d1da54fd529531917c31012393751ee514f0c79d579b17a1701dde04f81b1c9ac27b2b835a43fa96785ecc
-EBUILD procheck-3.5.4-r3.ebuild 1717 BLAKE2B ec8ef86ca7e9deade0d2c31f5d213ef447e55aa3eb825f7297746be00f6a4df66856af7e670ca24d9809d4ec90c6e81b110dc7a15333dad24a16fd3b720c7e3e SHA512 ff2774d4d1f6545988f67526fdcc97654a1ae38f3ec4863234e7ab52517fc22f90a931a449e2a95bf60ad814dab797311c96de0d85e92642acad8bb2160f59ea
+EBUILD procheck-3.5.4-r3.ebuild 1712 BLAKE2B bedc72cd6d9d6ea15e488ace793c20ef87cabdcb2ed4e0379c46e97a582e218ccf2ed35e735e431bd824f2ba06e007c587bec41ae409f5b77cc9bd0cf8263a2c SHA512 037c6c6e86a471de8e6388c3934fad98d21e4b4615b9933aaf4051605be54268cbac45f932a4c19d802fda836cd4c921c0eb8d5ee0e6274c5a16bb3178e5756f
 MISC metadata.xml 271 BLAKE2B a446884cbe7a6789e0bcd82759f57bf1ab7b29c5ab714057ffa821c90f799d1fa9f9310c187ee4c3a8ae2476f6ea9d15f368045779f1581e68d02802c61c884c SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92
diff --git a/sci-chemistry/procheck/procheck-3.5.4-r3.ebuild b/sci-chemistry/procheck/procheck-3.5.4-r3.ebuild
index cc536d671b84..1a700ee4110f 100644
--- a/sci-chemistry/procheck/procheck-3.5.4-r3.ebuild
+++ b/sci-chemistry/procheck/procheck-3.5.4-r3.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -6,7 +6,7 @@ EAPI=6
 inherit fortran-2 multilib toolchain-funcs versionator
 
 DESCRIPTION="Checks the stereochemical quality of a protein structure"
-HOMEPAGE="http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html"
+HOMEPAGE="https://www.ebi.ac.uk/thornton-srv/software/PROCHECK"
 SRC_URI="
 	${P}.tar.gz ${P}-README
 	doc? ( ${P}-manual.tar.gz )"
@@ -24,7 +24,7 @@ RESTRICT="fetch"
 S="${WORKDIR}/${PN}"
 
 pkg_nofetch() {
-	elog "Please visit http://www.ebi.ac.uk/thornton-srv/software/PROCHECK/download.html"
+	elog "Please visit https://www.ebi.ac.uk/thornton-srv/software/PROCHECK/download.html"
 	elog "and follow the instruction for downloading."
 	elog "Files should be renamed in the following way before being copied to your"
 	elog "DISTDIR directory:"
diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
index 80203d4cea2a..54467b7a712d 100644
--- a/sci-chemistry/pymol/Manifest
+++ b/sci-chemistry/pymol/Manifest
@@ -1,4 +1,4 @@
 DIST pymol-1.8.4.0.png.xz 19528 BLAKE2B f3d23d4cedca3d8bb96b20646a548da4be570697e3346a11b01c5c3599b536ba4697be08472dfa8a4f6533167defc1a37a1de332931a73857319cb28fd42cd2b SHA512 40bb0d3f226476f6e047b5361956aad955232a97641474765eaa5204f0539aee3810e0266213618a45364f9f31f6eb18380b17e0c79f64065f7b62a9016caa7c
 DIST pymol-2.3.0.tar.gz 10448674 BLAKE2B 0d508587d880ce7f2e8a0481bf664e6bfe6eb1d68b0f48b9266cde756824bd8c0144d7243e958bbc5e571d60fca9dafff125d81a8a3d32107e78ad2ff8dffc05 SHA512 e1dcea1c97bcd9045d3543e92902f240e6affbf61a38e8d2a0be04309e3dbabfe1a869847d1423b3151008978d4c305bbf3ce994fc9d453c0063ce020100c133
-EBUILD pymol-2.3.0-r3.ebuild 3016 BLAKE2B c048aadae470e41d56109d82d61bc9250667a6b40641ac60d8ca0d672087a7e998ef9c9089a76dc1da5ad6864da5bd0114e348c4f6cb45bf2b195977222116ad SHA512 9bd12710a79f331f1da261e7233650f262942de73d574cbec85f1d91bcd1931dc46f18e04b5b0a0fbea645484de0ab46862f4510c63d40fd9bd0e02e6a00225e
+EBUILD pymol-2.3.0-r3.ebuild 3018 BLAKE2B 86e626d7a8c0f1dbfd92d73f07895c61cbabcaf2a468a0f58635139fe0fd772f9a5418b5b16267831341f3c36e109be46d018518dca56ba10b6b224da4dd64b2 SHA512 f6f8feca5c943800b8df207b4c71ca1dbc92fc4e4a1df5a8a29205c349d915fe367d145bb29ec4044c1824b4a2a820377f8da37f4c430e2e2805f24508b6e8ed
 MISC metadata.xml 439 BLAKE2B 68df7dfc8ca3d4d4b18b419532bade69491f2e9362f10ae2397c804132b7fc9cd08dcf9703c0a89c44588c570e0c0c1bb9bffb7394d51faf1283142dbc5f70b3 SHA512 f5a3eded9b12fa715ba2e6e10b41c75d9bd823ca0dd40acbffc3f5bfc4b36c687f720b1a4e119b4540a31faf849985778cbd72b0b2cd35af8c52ca0f808d71e4
diff --git a/sci-chemistry/pymol/pymol-2.3.0-r3.ebuild b/sci-chemistry/pymol/pymol-2.3.0-r3.ebuild
index e469b6431e82..0a2e041f0dad 100644
--- a/sci-chemistry/pymol/pymol-2.3.0-r3.ebuild
+++ b/sci-chemistry/pymol/pymol-2.3.0-r3.ebuild
@@ -3,7 +3,7 @@
 
 EAPI=7
 
-PYTHON_COMPAT=( python3_{6,7,8} )
+PYTHON_COMPAT=( python3_{6,7,8,9} )
 
 inherit distutils-r1 desktop optfeature flag-o-matic xdg-utils
 
diff --git a/sci-chemistry/vmd/Manifest b/sci-chemistry/vmd/Manifest
index 5584e3b1e4cc..227f020fbc77 100644
--- a/sci-chemistry/vmd/Manifest
+++ b/sci-chemistry/vmd/Manifest
@@ -1,7 +1,7 @@
 AUX vmd-1.9.4-gentoo-paths.patch 11523 BLAKE2B 3e02c73b49a3686ce00deb44f4bca0809c527a53d7fb13315c5799c5e9fe1d8ada9664452e41f49ad084abed96d2e5a6d01b000e49393e97eeb5fb2378af888f SHA512 da8e723d12ca7728d67dffcd0bf2e9c856764917d3f3ef07756febbc981bae20b061e0ead3fa617de18b94918d855c09f68c24a979c6f9f0cdea12b343a22756
-AUX vmd-1.9.4-gentoo-plugins.patch 24618 BLAKE2B 6fbcf2e3bb59765e0980a5ed46f02e29d7b72a313865849c15891f2398d2aaf9afe6069f993a61257572d031556ce523c622858e29611ca6795be6030f4bb186 SHA512 9b8675811992d6392e9ec49cdcbcfd0da99dce1e164be4f8bf9bd07e0582b6b1e1d25f3e90fbc91cad7f94984bd091e644713c136628d0e4cc60e782a855fb63
 AUX vmd-1.9.4-tmpdir.patch 398 BLAKE2B cf61240688f111d4763f458f0e10319a8154c5427172ba99d4bcfc7a9d8fd559fe7777c1ff703f81b68b2f10ec2a8c4af5cf61fd91d147aec2f4fafcf6753c82 SHA512 c5f96b3ef880ccdcf86d3927308c85aeaf3260ed0e54d60cbf186a0d63f6a88da16e49b14d6815d97bfd1ff4500bf9ce99d183d26ee78b67fed388e2217a7f10
 DIST vmd-1.9.3-gentoo-patches.tar.xz 14804 BLAKE2B 64e5df40ed88c23c924d32636495f0383590f91dbb714e64c73551072bb50d72b4e5f188fb2da58d32e84b4bc96ff0297d7ff1bf02b0481198901c4e12e4ee59 SHA512 5d506d4df5ca4a3edb33d77aeeb440fcb4750a250c77103b99f385f356eb9d71d954173b981d3a50f7a714cfc872587e5040868904e50fa1f6fd69d7e4d9f1b1
+DIST vmd-1.9.4-gentoo-plugins.patch 24618 BLAKE2B 6fbcf2e3bb59765e0980a5ed46f02e29d7b72a313865849c15891f2398d2aaf9afe6069f993a61257572d031556ce523c622858e29611ca6795be6030f4bb186 SHA512 9b8675811992d6392e9ec49cdcbcfd0da99dce1e164be4f8bf9bd07e0582b6b1e1d25f3e90fbc91cad7f94984bd091e644713c136628d0e4cc60e782a855fb63
 DIST vmd-1.9.4a43.src.tar 123955200 BLAKE2B a99ee2bce1024613ad951fc97f4cd4b6f6ad114aea67a0a6644f687c69eae488eb862fd5ea5bff31e12f01a95f6f60be04dad2a82879603b9b457443267bb18f SHA512 3e3d5d7b0d220f070d4978940ff5ab8af531e507a224cdd15e4871e263de64b4ba24e9d964cb680b31f376afbdc08f46cb4070e3cd4a474b9bfe0732c7b3cff0
-EBUILD vmd-1.9.4_alpha43.ebuild 7910 BLAKE2B 79a150dca7841f97bbc47c75f30f99a9c88dca284655ecf54ad328516ae6207b4bc800d6de3584c4e14b30b7789562c14a9c46c49d99b15567e14612ccbfbe3f SHA512 63393f786285588f970f2e817145b77f93c0d62c3e87e2b83e7edd52a168f2556fcec14c8ce06c67e521e8b92d04470bbdfd143f505acc8a6b64f457ca24107a
+EBUILD vmd-1.9.4_alpha43.ebuild 7987 BLAKE2B cc83436e0391fb105ae56fc6db820020318d7c62606f7818d24c8d43001a66a881c75cac9d3a588c36e433e2be61d738b85ad8922bb40f355024e7cb49a613ad SHA512 dd35f7d545edb864c237feb10be0e59a53b6c7367257c6b3404f44af46b1513de5f8e0fbd2078b184be33342f3ddb70d9f349ef7a20563925f0cb1e2de6588d4
 MISC metadata.xml 778 BLAKE2B 6c4202950f57a4d7a3004e966c761325a0a31ab19fe06a6bd69882bd685e41424953104ff653c03d6cbbcb60bb9aba45fbcec43cd228c4bb57fcb1c63a2bd881 SHA512 b967b71fb9f1b47a9d3b69e6958dfb0314a9f071dade7ed1876e91dfa73188748faf11ef832d240a71745b36a30422bde79de2e9ff8e5ec6b6da4b11b40d19c9
diff --git a/sci-chemistry/vmd/files/vmd-1.9.4-gentoo-plugins.patch b/sci-chemistry/vmd/files/vmd-1.9.4-gentoo-plugins.patch
deleted file mode 100644
index c6ea769932f3..000000000000
--- a/sci-chemistry/vmd/files/vmd-1.9.4-gentoo-plugins.patch
+++ /dev/null
@@ -1,604 +0,0 @@
-From c33a68684cd06424ec78c6983f93336109d91cb5 Mon Sep 17 00:00:00 2001
-From: Stefan Kuczera <stefan.ku@yahoo.com>
-Date: Sat, 21 Jan 2017 13:20:45 +0100
-Subject: [PATCH] Squashed patches
-
----
- plugins/Make-arch               |   3 +-
- plugins/Makefile                |  20 +++---
- plugins/autopsf/Makefile        |   4 +-
- plugins/catdcd/Makefile         |   4 +-
- plugins/cionize/Makefile        |   6 +-
- plugins/clustalw/Makefile       |   2 +-
- plugins/cluster/Makefile        |   2 +-
- plugins/hesstrans/Makefile      |   2 +-
- plugins/libbiokit/Makefile      |  14 ++--
- plugins/molfile_plugin/Makefile | 144 ++++++++++++++++++++--------------------
- plugins/phylotree/Makefile      |   2 +-
- plugins/rnaview/Makefile        |   2 +-
- plugins/stamp/Makefile          |   2 +-
- 13 files changed, 105 insertions(+), 102 deletions(-)
-
-diff --git a/plugins/Make-arch b/plugins/Make-arch
-index 19d2b6c..937ad9e 100755
---- a/plugins/Make-arch
-+++ b/plugins/Make-arch
-@@ -313,7 +313,8 @@ LINUX:
- 	"AR = ar" \
- 	"NM = nm -p" \
- 	"RANLIB = touch" \
--	"SHLD = gcc -shared"
-+	"SHLD = gcc -shared" \
-+	"SHXXLD = g++ -shared"
- 	
- LINUXALPHA:
- 	$(MAKE) dynlibs staticlibs bins \
-diff --git a/plugins/Makefile b/plugins/Makefile
-index 0fee349..6b07606 100755
---- a/plugins/Makefile
-+++ b/plugins/Makefile
-@@ -150,25 +150,27 @@ distrib:
- 
- include Make-arch
- 
--molfilelibs:
--	cd molfile_plugin; $(MAKE) dynlibs && cd .. || exit 1
--	cd molfile_plugin; $(MAKE) staticlibs && cd .. || exit 1
-+molfilelibs_static:
-+	$(MAKE) -C molfile_plugin staticlibs
-+
-+molfilelibs_dyn:
-+	$(MAKE) -C molfile_plugin dynlibs
- 
- win32molfilelibs:
- 	cd molfile_plugin; $(MAKE) dynlibs && cd .. || exit 1
- 	cd molfile_plugin; $(MAKE) win32staticlibs && cd .. || exit 1
- 
--dynlibs: molfilelibs
--	for dir in $(BUILDDIRS); do cd $$dir && $(MAKE) dynlibs && cd .. || exit 1 ; done
-+dynlibs: molfilelibs_dyn
-+	for dir in $(BUILDDIRS); do $(MAKE) -C $$dir dynlibs; done
- 
--staticlibs: molfilelibs
--	for dir in $(BUILDDIRS); do cd $$dir && $(MAKE) staticlibs && cd .. || exit 1 ; done
-+staticlibs: molfilelibs_static
-+	for dir in $(BUILDDIRS); do $(MAKE) -C $$dir staticlibs; done
- 
- win32staticlibs: win32molfilelibs
- 	for dir in $(BUILDDIRS); do cd $$dir && $(MAKE) win32staticlibs && cd .. || exit 1 ; done
- 
--bins:
--	for dir in molfile_plugin $(BUILDDIRS); do cd $$dir && $(MAKE) bins && cd .. || exit 1 ; done
-+bins: molfilelibs_dyn
-+	for dir in $(BUILDDIRS); do $(MAKE) -C $$dir bins; done
- 
- win32bins:
- 	for dir in molfile_plugin $(BUILDDIRS); do cd $$dir && $(MAKE) win32bins && cd .. || exit 1 ; done
-diff --git a/plugins/autopsf/Makefile b/plugins/autopsf/Makefile
-index 3b35d10..8e1527e 100644
---- a/plugins/autopsf/Makefile
-+++ b/plugins/autopsf/Makefile
-@@ -49,8 +49,8 @@ AUTOPSFOBJS=${ARCHDIR}/psfatom.o  \
- 
- ${ARCHDIR}/psfcheck.so : ${AUTOPSFOBJS}
- 	if [ -n "${TCLSHLD}" ]; \
--	then ${TCLSHLD} $(LOPTO)$@ ${AUTOPSFOBJS} ${TCLLIB} ${TCLLDFLAGS} ${LDFLAGS}; \
--	else ${SHLD} $(LOPTO)$@ ${AUTOPSFOBJS} ${TCLLIB} ${TCLLDFLAGS} ${LDFLAGS}; \
-+	then ${TCLSHLD} ${LDFLAGS} $(LOPTO)$@ ${AUTOPSFOBJS} ${TCLLIB} ${TCLLDFLAGS}; \
-+	else ${SHXXLD} ${LDFLAGS} $(LOPTO)$@ ${AUTOPSFOBJS} ${TCLLIB} ${TCLLDFLAGS}; \
- 	fi
- 
- ${ARCHDIR}/psfatom.o : psfatom.h psfatom.C
-diff --git a/plugins/catdcd/Makefile b/plugins/catdcd/Makefile
-index d6c58c5..1637a3c 100644
---- a/plugins/catdcd/Makefile
-+++ b/plugins/catdcd/Makefile
-@@ -45,8 +45,8 @@ ${ARCHDIR}/catdcd.exe : ${CATDCDOBJS} ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfi
- 	LINK ${CATDCDOBJS} /OUT:${ARCHDIR}/catdcd.exe /LIBPATH:${COMPILEDIR}/lib_${ARCH}/molfile libmolfile_plugin.lib ${TCLLIB} ${TCLLDFLAGS} ${NETCDFLIB} ${NETCDFLDFLAGS} ${EXPATLIB} ${EXPATLDFLAGS} ${SQLITELIB} ${SQLITELDFLAGS}
- 
- # all other platforms
--${ARCHDIR}/catdcd : ${CATDCDOBJS} ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfile_plugin.a
--	${CXX} ${CXXFLAGS} ${CATDCDOBJS} -o ${ARCHDIR}/catdcd -L${COMPILEDIR}/lib_${ARCH}/molfile -lmolfile_plugin ${TCLLIB} ${TCLLDFLAGS} ${NETCDFLIB} ${NETCDFLDFLAGS} ${EXPATLIB} ${EXPATLDFLAGS} ${SQLITELIB} ${SQLITELDFLAGS} -lm
-+${ARCHDIR}/catdcd : ${CATDCDOBJS} ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfile_plugin.a ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfile_plugin.h
-+	${CXX} ${LDFLAGS} ${CXXFLAGS} ${CATDCDOBJS} -o ${ARCHDIR}/catdcd -L${COMPILEDIR}/lib_${ARCH}/molfile -lmolfile_plugin ${TCLLIB} ${TCLLDFLAGS} ${NETCDFLIB} ${NETCDFLDFLAGS} ${EXPATLIB} ${EXPATLDFLAGS} ${SQLITELIB} ${SQLITELDFLAGS} -lm
- 
- ${ARCHDIR}/hash.o: hash.h hash.c
- 	${CXX} ${CXXFLAGS} ${INCDIR} -c ${SRCDIR}/hash.c $(COPTO)${ARCHDIR}/hash.o
-diff --git a/plugins/cionize/Makefile b/plugins/cionize/Makefile
-index bcb2510..e02241b 100644
---- a/plugins/cionize/Makefile
-+++ b/plugins/cionize/Makefile
-@@ -52,8 +52,8 @@ ${ARCHDIR}/cionize.exe : ${IONIZEOBJS} ${MGPOTOBJS} ${ARCHDIR}/cionize.o ${COMPI
- 	LINK ${IONIZEOBJS} ${MGPOTOBJS} /OUT:${ARCHDIR}/cionize.exe /LIBPATH:${COMPILEDIR}/lib_${ARCH}/molfile libmolfile_plugin.lib ${TCLLIB} ${TCLLDFLAGS} ${NETCDFLIB} ${NETCDFLDFLAGS} ${EXPATLIB} ${EXPATLDFLAGS} ${SQLITELIB} ${SQLITELDFLAGS}
- 
- # all other platforms
--${ARCHDIR}/cionize: ${IONIZEOBJS} ${MGPOTOBJS} ${ARCHDIR}/cionize.o ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfile_plugin.a
--	${CXX} ${CXXFLAGS} ${ARCHDIR}/cionize.o ${IONIZEOBJS} ${MGPOTOBJS} -o ${ARCHDIR}/cionize -L${COMPILEDIR}/lib_${ARCH}/molfile -lmolfile_plugin ${TCLLIB} ${TCLLDFLAGS} ${NETCDFLIB} ${NETCDFLDFLAGS} ${EXPATLIB} ${EXPATLDFLAGS} ${SQLITELIB} ${SQLITELDFLAGS} -lm
-+${ARCHDIR}/cionize: ${IONIZEOBJS} ${MGPOTOBJS} ${ARCHDIR}/cionize.o ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfile_plugin.a  ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfile_plugin.h
-+	${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/cionize.o ${IONIZEOBJS} ${MGPOTOBJS} -o ${ARCHDIR}/cionize -L${COMPILEDIR}/lib_${ARCH}/molfile -lmolfile_plugin ${TCLLIB} ${TCLLDFLAGS} ${NETCDFLIB} ${NETCDFLDFLAGS} ${EXPATLIB} ${EXPATLDFLAGS} ${SQLITELIB} ${SQLITELDFLAGS} -lm
- 
- ${ARCHDIR}/hash.o: hash.h hash.c
- 	${CC}  ${CCFLAGS} ${INCDIR} -c ${SRCDIR}/hash.c $(COPTO)${ARCHDIR}/hash.o
-@@ -66,7 +66,7 @@ ${ARCHDIR}/util.o: util.h util.c
- 
- ${ARCHDIR}/getplugins.o: getplugins.h getplugins.c
- 	${CC}  ${CCFLAGS} ${INCDIR} -c ${SRCDIR}/getplugins.c $(COPTO)${ARCHDIR}/getplugins.o
--	
-+
- ${ARCHDIR}/energythr.o: energythr.h energythr.c ${ARCHDIR}/util.o ${ARCHDIR}/threads.o
- 	${CC}  ${CCFLAGS} ${INCDIR} -c ${SRCDIR}/energythr.c $(COPTO)${ARCHDIR}/energythr.o
- 
-diff --git a/plugins/clustalw/Makefile b/plugins/clustalw/Makefile
-index 6329f64..3443720 100644
---- a/plugins/clustalw/Makefile
-+++ b/plugins/clustalw/Makefile
-@@ -66,7 +66,7 @@ OBJS = ${ARCHDIR}/alnscore.o \
- ${ARCHDIR}/clustalw.exe: ${OBJS}
- 	LINK ${OBJS} /OUT:${ARCHDIR}/clustalw.exe
- ${ARCHDIR}/clustalw: ${OBJS}
--	${CC} ${CCFLAGS} ${OBJS} -o ${ARCHDIR}/clustalw -lm
-+	${CC} ${LDFLAGS} ${CCFLAGS} ${OBJS} -o ${ARCHDIR}/clustalw -lm
-     
-     
- # Objects.
-diff --git a/plugins/cluster/Makefile b/plugins/cluster/Makefile
-index 99d347e..c2d30ae 100644
---- a/plugins/cluster/Makefile
-+++ b/plugins/cluster/Makefile
-@@ -48,7 +48,7 @@ ${ARCHDIR}/cluster.exe : ${OBJS}
- 
- # all other platforms
- ${ARCHDIR}/cluster : ${OBJS}
--	${CXX} ${CXXFLAGS} ${OBJS} -o ${ARCHDIR}/cluster -lm
-+	${CXX} ${LDFLAGS} ${CXXFLAGS} ${OBJS} -o ${ARCHDIR}/cluster -lm
- 
- ${ARCHDIR}/cluster.o: ${SRCDIR}/cluster.c
- 	${CXX} ${CXXFLAGS} ${INCDIR} -c ${SRCDIR}/cluster.c $(COPTO)${ARCHDIR}/cluster.o
-diff --git a/plugins/hesstrans/Makefile b/plugins/hesstrans/Makefile
-index 76ee306..db46b82 100644
---- a/plugins/hesstrans/Makefile
-+++ b/plugins/hesstrans/Makefile
-@@ -85,7 +85,7 @@ HESSTRANSOBJS=${ARCHDIR}/newmat1.o \
- ${ARCHDIR}/hesstrans.so : ${HESSTRANSOBJS}
- 	if [ -n "${TCLSHLD}" ]; \
- 	then ${TCLSHLD} $(LOPTO)$@ ${HESSTRANSOBJS} ${TCLLIB} ${TCLLDFLAGS} ${LDFLAGS}; \
--	else ${SHLD} $(LOPTO)$@ ${HESSTRANSOBJS} ${TCLLIB} ${TCLLDFLAGS} ${LDFLAGS}; \
-+	else ${SHXXLD} $(LOPTO)$@ ${HESSTRANSOBJS} ${TCLLIB} ${TCLLDFLAGS} ${LDFLAGS}; \
- 	fi
- 
- 
-diff --git a/plugins/libbiokit/Makefile b/plugins/libbiokit/Makefile
-index 7a66d08..da764dd 100644
---- a/plugins/libbiokit/Makefile
-+++ b/plugins/libbiokit/Makefile
-@@ -98,7 +98,7 @@ OBJS = ${DYNLIBOBJS} \
- ${ARCHDIR}/tcl_libbiokit.so : ${ARCHDIR}/tcl_libbiokit_wrap.o ${ARCHDIR}/tcl_libbiokit.o ${DYNLIBOBJS}
- 	if [ -n "${TCLSHLD}" ]; \
- 	then ${TCLSHLD} $(LOPTO)$@ ${ARCHDIR}/tcl_libbiokit_wrap.o ${ARCHDIR}/tcl_libbiokit.o ${DYNLIBOBJS} ${TCLLIB} ${TCLLDFLAGS} ${LDFLAGS}; \
--	else ${SHLD} $(LOPTO)$@ ${ARCHDIR}/tcl_libbiokit_wrap.o ${ARCHDIR}/tcl_libbiokit.o ${DYNLIBOBJS} ${TCLLIB} ${TCLLDFLAGS} ${LDFLAGS}; \
-+	else ${SHXXLD} $(LOPTO)$@ ${ARCHDIR}/tcl_libbiokit_wrap.o ${ARCHDIR}/tcl_libbiokit.o ${DYNLIBOBJS} ${TCLLIB} ${TCLLDFLAGS} ${LDFLAGS}; \
- 	fi
- ${ARCHDIR}/tcl_libbiokit_wrap.o : ${INTERFACESRCDIR}/tcl_libbiokit_wrap.cpp
- 	${CXX} ${CXXFLAGS} ${TCLINC} ${INCDIR} -c ${INTERFACESRCDIR}/tcl_libbiokit_wrap.cpp $(COPTO)${ARCHDIR}/tcl_libbiokit_wrap.o
-@@ -111,7 +111,7 @@ ${INTERFACESRCDIR}/tcl_libbiokit_wrap.cpp : ${INTERFACESRCDIR}/tcl_libbiokit.i
- ${ARCHDIR}/percid.exe: ${ARCHDIR}/percid.o ${OBJS}
- 	LINK ${ARCHDIR}/percid.o ${OBJS} /OUT:${ARCHDIR}/percid.exe
- ${ARCHDIR}/percid: ${ARCHDIR}/percid.o ${OBJS}
--	${CXX} ${CXXFLAGS} ${ARCHDIR}/percid.o ${OBJS} -o ${ARCHDIR}/percid -lm
-+	${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/percid.o ${OBJS} -o ${ARCHDIR}/percid -lm
- ${ARCHDIR}/percid.o: ${UTILSRCDIR}/percid.cpp
- 	${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/percid.cpp $(COPTO)${ARCHDIR}/percid.o
- 
-@@ -119,7 +119,7 @@ ${ARCHDIR}/percid.o: ${UTILSRCDIR}/percid.cpp
- ${ARCHDIR}/qpair.exe: ${ARCHDIR}/qPair.o ${OBJS}
- 	LINK ${ARCHDIR}/qPair.o ${OBJS} /OUT:${ARCHDIR}/qpair.exe
- ${ARCHDIR}/qpair: ${ARCHDIR}/qPair.o ${OBJS}
--	${CXX} ${CXXFLAGS} ${ARCHDIR}/qPair.o ${OBJS} -o ${ARCHDIR}/qpair -lm
-+	${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/qPair.o ${OBJS} -o ${ARCHDIR}/qpair -lm
- ${ARCHDIR}/qPair.o: ${UTILSRCDIR}/qPair.cpp
- 	${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/qPair.cpp $(COPTO)${ARCHDIR}/qPair.o
- 
-@@ -127,7 +127,7 @@ ${ARCHDIR}/qPair.o: ${UTILSRCDIR}/qPair.cpp
- ${ARCHDIR}/rmsd.exe: ${ARCHDIR}/rmsd.o ${OBJS}
- 	LINK ${ARCHDIR}/rmsd.o ${OBJS} /OUT:${ARCHDIR}/rmsd.exe
- ${ARCHDIR}/rmsd: ${ARCHDIR}/rmsd.o ${OBJS}
--	${CXX} ${CXXFLAGS} ${ARCHDIR}/rmsd.o ${OBJS} -o ${ARCHDIR}/rmsd -lm
-+	${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/rmsd.o ${OBJS} -o ${ARCHDIR}/rmsd -lm
- ${ARCHDIR}/rmsd.o: ${UTILSRCDIR}/rmsd.cpp
- 	${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/rmsd.cpp $(COPTO)${ARCHDIR}/rmsd.o
- 
-@@ -135,7 +135,7 @@ ${ARCHDIR}/rmsd.o: ${UTILSRCDIR}/rmsd.cpp
- ${ARCHDIR}/q.exe: ${ARCHDIR}/Q.o ${OBJS}
- 	LINK ${ARCHDIR}/Q.o ${OBJS} /OUT:${ARCHDIR}/q.exe
- ${ARCHDIR}/q: ${ARCHDIR}/Q.o ${OBJS}
--	${CXX} ${CXXFLAGS} ${ARCHDIR}/Q.o ${OBJS} -o ${ARCHDIR}/q -lm
-+	${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/Q.o ${OBJS} -o ${ARCHDIR}/q -lm
- ${ARCHDIR}/Q.o: ${UTILSRCDIR}/Q.cpp
- 	${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/Q.cpp $(COPTO)${ARCHDIR}/Q.o
- 
-@@ -143,7 +143,7 @@ ${ARCHDIR}/Q.o: ${UTILSRCDIR}/Q.cpp
- ${ARCHDIR}/seqqr.exe: ${ARCHDIR}/seqqr.o ${OBJS}
- 	LINK ${ARCHDIR}/seqqr.o ${OBJS} /OUT:${ARCHDIR}/seqqr.exe
- ${ARCHDIR}/seqqr: ${ARCHDIR}/seqqr.o ${OBJS}
--	${CXX} ${CXXFLAGS} ${ARCHDIR}/seqqr.o ${OBJS} -o ${ARCHDIR}/seqqr -lm
-+	${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/seqqr.o ${OBJS} -o ${ARCHDIR}/seqqr -lm
- ${ARCHDIR}/seqqr.o: ${UTILSRCDIR}/seqqr.cpp
- 	${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/seqqr.cpp $(COPTO)${ARCHDIR}/seqqr.o
- 
-@@ -151,7 +151,7 @@ ${ARCHDIR}/seqqr.o: ${UTILSRCDIR}/seqqr.cpp
- ${ARCHDIR}/structqr.exe : ${ARCHDIR}/structqr.o ${OBJS}
- 	LINK ${ARCHDIR}/structqr.o ${OBJS} /OUT:${ARCHDIR}/structqr.exe
- ${ARCHDIR}/structqr: ${ARCHDIR}/structqr.o ${OBJS}
--	${CXX} ${CXXFLAGS} ${ARCHDIR}/structqr.o ${OBJS} -o ${ARCHDIR}/structqr -lm
-+	${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/structqr.o ${OBJS} -o ${ARCHDIR}/structqr -lm
- ${ARCHDIR}/structqr.o: ${UTILSRCDIR}/structqr.cpp
- 	${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/structqr.cpp $(COPTO)${ARCHDIR}/structqr.o
-     
-diff --git a/plugins/molfile_plugin/Makefile b/plugins/molfile_plugin/Makefile
-index 4c47615..1c77ddf 100644
---- a/plugins/molfile_plugin/Makefile
-+++ b/plugins/molfile_plugin/Makefile
-@@ -15,7 +15,7 @@
- VPATH = src ../include ${ARCHDIR}
- 
- SCCFLAGS = $(CCFLAGS) $(DEF)"STATIC_PLUGIN"
--SCXXFLAGS = $(CCFLAGS) $(DEF)"STATIC_PLUGIN"
-+SCXXFLAGS = $(CXXFLAGS) $(DEF)"STATIC_PLUGIN"
- 
- #
- # Rules
-@@ -206,209 +206,209 @@
- #
- 
- abinitplugin.so: ${ARCHDIR}/abinitplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- amiraplugin.so: ${ARCHDIR}/amiraplugin.o 
- 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- avsplugin.so: ${ARCHDIR}/avsplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- babelplugin.so: ${ARCHDIR}/babelplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- basissetplugin.so: ${ARCHDIR}/basissetplugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- bgfplugin.so: ${ARCHDIR}/bgfplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- binposplugin.so: ${ARCHDIR}/binposplugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- biomoccaplugin.so: ${ARCHDIR}/biomoccaplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- brixplugin.so: ${ARCHDIR}/brixplugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- carplugin.so: ${ARCHDIR}/carplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- ccp4plugin.so: ${ARCHDIR}/ccp4plugin.o
- 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- corplugin.so: ${ARCHDIR}/corplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- cpmdplugin.so: ${ARCHDIR}/cpmdplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- crdplugin.so: ${ARCHDIR}/crdplugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- cubeplugin.so: ${ARCHDIR}/cubeplugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- dcdplugin.so: ${ARCHDIR}/dcdplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- dlpolyplugin.so: ${ARCHDIR}/dlpolyplugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- dsn6plugin.so: ${ARCHDIR}/dsn6plugin.o
- 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- dxplugin.so: ${ARCHDIR}/dxplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- edmplugin.so: ${ARCHDIR}/edmplugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- fs4plugin.so: ${ARCHDIR}/fs4plugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- gamessplugin.so: ${ARCHDIR}/gamessplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- graspplugin.so: ${ARCHDIR}/graspplugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- grdplugin.so: ${ARCHDIR}/grdplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- gridplugin.so: ${ARCHDIR}/gridplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- gromacsplugin.so: ${ARCHDIR}/gromacsplugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- jsplugin.so: ${ARCHDIR}/jsplugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- lammpsplugin.so: ${ARCHDIR}/lammpsplugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- mapplugin.so: ${ARCHDIR}/mapplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- mdfplugin.so: ${ARCHDIR}/mdfplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- mol2plugin.so: ${ARCHDIR}/mol2plugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- moldenplugin.so: ${ARCHDIR}/moldenplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- molemeshplugin.so: ${ARCHDIR}/molemeshplugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- msmsplugin.so: ${ARCHDIR}/msmsplugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- namdbinplugin.so: ${ARCHDIR}/namdbinplugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- offplugin.so: ${ARCHDIR}/offplugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- orcaplugin.so: ${ARCHDIR}/orcaplugin.o
- 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- parm7plugin.so: ${ARCHDIR}/parm7plugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- parmplugin.so: ${ARCHDIR}/parmplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- pbeqplugin.so: ${ARCHDIR}/pbeqplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- pdbplugin.so: ${ARCHDIR}/pdbplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- pdbxplugin.so: ${ARCHDIR}/pdbxplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- phiplugin.so: ${ARCHDIR}/phiplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- pltplugin.so: ${ARCHDIR}/pltplugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- plyplugin.so: ${ARCHDIR}/plyplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- pqrplugin.so: ${ARCHDIR}/pqrplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- psfplugin.so: ${ARCHDIR}/psfplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- raster3dplugin.so: ${ARCHDIR}/raster3dplugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- rst7plugin.so: ${ARCHDIR}/rst7plugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- situsplugin.so: ${ARCHDIR}/situsplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- spiderplugin.so: ${ARCHDIR}/spiderplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- stlplugin.so: ${ARCHDIR}/stlplugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- tinkerplugin.so: ${ARCHDIR}/tinkerplugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- uhbdplugin.so: ${ARCHDIR}/uhbdplugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- vaspchgcarplugin.so: ${ARCHDIR}/vaspchgcarplugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- vaspoutcarplugin.so: ${ARCHDIR}/vaspoutcarplugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- vaspparchgplugin.so: ${ARCHDIR}/vaspparchgplugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- vaspposcarplugin.so: ${ARCHDIR}/vaspposcarplugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- vasp5xdatcarplugin.so: ${ARCHDIR}/vasp5xdatcarplugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- vaspxdatcarplugin.so: ${ARCHDIR}/vaspxdatcarplugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- vaspxmlplugin.so: ${ARCHDIR}/vaspxmlplugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- vtkplugin.so: ${ARCHDIR}/vtkplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- xbgfplugin.so: ${ARCHDIR}/xbgfplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- xsfplugin.so: ${ARCHDIR}/xsfplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- xyzplugin.so: ${ARCHDIR}/xyzplugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- 
- ##
- ## In-development plugins that aren't part of the build quite yet...
- ##
- cpmdlogplugin.so: ${ARCHDIR}/cpmdlogplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- gaussianplugin.so: ${ARCHDIR}/gaussianplugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- 
- ##
-@@ -416,31 +416,31 @@
- ## dependencies of some kind
- ##
- dmsplugin.so: ${ARCHDIR}/dmsplugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(SQLITELIB) $(SQLITELDFLAGS) $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(SQLITELIB) $(SQLITELDFLAGS) $(LDFLAGS)
- 
- dtrplugin.so: ${ARCHDIR}/dtrplugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- hoomdplugin.so: ${ARCHDIR}/hoomdplugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(EXPATLIB) $(EXPATLDFLAGS) $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(EXPATLIB) $(EXPATLDFLAGS) $(LDFLAGS)
- 
- lmplugin.so: ${ARCHDIR}/lmplugin.o
- 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(HDFLIB) $(HDFLDFLAGS) $(LDFLAGS)
- 
- maeffplugin.so: ${ARCHDIR}/maeffplugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- netcdfplugin.so: ${ARCHDIR}/netcdfplugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(NETCDFLIB) $(NETCDFLDFLAGS) $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(NETCDFLIB) $(NETCDFLDFLAGS) $(LDFLAGS)
- 
- tngplugin.so: ${ARCHDIR}/tngplugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(TNGLIB) $(TNGLDFLAGS) $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(TNGLIB) $(TNGLDFLAGS) $(LDFLAGS)
- 
- vtfplugin.so: ${ARCHDIR}/vtfplugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(TCLLIB) $(TCLLDFLAGS) $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(TCLLIB) $(TCLLDFLAGS) $(LDFLAGS)
- 
- webpdbplugin.so: ${ARCHDIR}/webpdbplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(TCLLIB) $(TCLLDFLAGS) $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(TCLLIB) $(TCLLDFLAGS) $(LDFLAGS)
- 
- 
- #
-diff --git a/plugins/phylotree/Makefile b/plugins/phylotree/Makefile
-index 6442747..0aceb4d 100644
---- a/plugins/phylotree/Makefile
-+++ b/plugins/phylotree/Makefile
-@@ -54,7 +54,7 @@ ${ARCHDIR}/upgmaclu.exe : ${OBJS}
- 
- # all other platforms
- ${ARCHDIR}/upgmaclu : ${OBJS}
--	${CXX} ${CXXFLAGS} ${OBJS} -o ${ARCHDIR}/upgmaclu -lm
-+	${CXX} ${LDFLAGS} ${CXXFLAGS} ${OBJS} -o ${ARCHDIR}/upgmaclu -lm
- 
- ${ARCHDIR}/upgmaclu.o: ${SRCDIR}/upgmaclu.c
- 	${CXX} ${CXXFLAGS} ${INCDIR} -c ${SRCDIR}/upgmaclu.c $(COPTO)${ARCHDIR}/upgmaclu.o
-diff --git a/plugins/rnaview/Makefile b/plugins/rnaview/Makefile
-index 16f070a..da71248 100644
---- a/plugins/rnaview/Makefile
-+++ b/plugins/rnaview/Makefile
-@@ -67,7 +67,7 @@ OBJS = ${ARCHDIR}/analyze.o \
- ${ARCHDIR}/rnaview.exe: ${OBJS}
- 	LINK ${OBJS} /OUT:${ARCHDIR}/rnaview.exe
- ${ARCHDIR}/rnaview: ${OBJS}
--	${CC} ${CCFLAGS} ${OBJS} -o ${ARCHDIR}/rnaview -lm
-+	${CC} ${LDFLAGS} ${CCFLAGS} ${OBJS} -o ${ARCHDIR}/rnaview -lm
- 
- ${ARCHDIR}/analyze.o: ${SRCDIR}/analyze.c
- 	${CC} ${CCFLAGS} ${INCDIR} -c ${SRCDIR}/analyze.c $(COPTO)${ARCHDIR}/analyze.o
-diff --git a/plugins/stamp/Makefile b/plugins/stamp/Makefile
-index f0fb515..aa8f6b6 100644
---- a/plugins/stamp/Makefile
-+++ b/plugins/stamp/Makefile
-@@ -101,7 +101,7 @@ OBJS = ${ARCHDIR}/a3to1.o \
- ${ARCHDIR}/stamp.exe: ${OBJS}
- 	LINK ${OBJS} /OUT:${ARCHDIR}/stamp.exe
- ${ARCHDIR}/stamp: ${OBJS}
--	${CC} ${CCFLAGS} ${OBJS} -o ${ARCHDIR}/stamp -lm
-+	${CC} ${LDFLAGS} ${CCFLAGS} ${OBJS} -o ${ARCHDIR}/stamp -lm
-     
-     
- # Objects.
--- 
-2.5.5
-
diff --git a/sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild b/sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild
index db9e4f49e522..d449af190b42 100644
--- a/sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild
+++ b/sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild
@@ -14,6 +14,7 @@ MY_P="${PN}-${MY_PV}"
 SRC_URI="
 	${MY_P}.src.tar
 	https://dev.gentoo.org/~jlec/distfiles/${PN}-1.9.3-gentoo-patches.tar.xz
+	https://dev.gentoo.org/~juippis/distfiles/tmp/vmd-1.9.4-gentoo-plugins.patch
 "
 
 SLOT="0"
@@ -85,7 +86,7 @@ src_prepare() {
 
 	# https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/32121.html
 	# https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/32116.html
-	eapply "${FILESDIR}"/${PN}-1.9.4-gentoo-plugins.patch
+	eapply "${DISTDIR}"/${PN}-1.9.4-gentoo-plugins.patch
 
 	use cuda && cuda_sanitize
 
diff --git a/sci-chemistry/votca-csg/Manifest b/sci-chemistry/votca-csg/Manifest
index df8a29f5511f..5256db400e98 100644
--- a/sci-chemistry/votca-csg/Manifest
+++ b/sci-chemistry/votca-csg/Manifest
@@ -30,5 +30,5 @@ EBUILD votca-csg-1.6.1.ebuild 2369 BLAKE2B a6d8e7e9049f55f2e916614586bb6ec68e122
 EBUILD votca-csg-1.6.2.ebuild 2340 BLAKE2B 97934fdd4b56cfbc58d5c2f47179ed3f747600ae870fe86fc7829fcdecb8e72e67ec129b49cc25e0a04b1dccb878ae79f7e693f59184da4e447eacbceb794b12 SHA512 30e0ef70ef8cf7c791a8579b01440fb7013ed4344a2132e955e17d1b8a5edac7982dae46d796122f8066584583f4b9356a478b512334ec4f0dae647ed4fa8f6e
 EBUILD votca-csg-1.6.ebuild 2365 BLAKE2B 585240513e8b06c9c35aab0dfb75962c59e2d42853837eaa67d86c728c5cd3d8485061a4974c71898caba41d6d44a1cf93ba27c16824427b767f965e8f9a07ab SHA512 38b6ff068367ac79717f9a364b2b6a83824cec0c804af934f15d3f19ca1cf50eddd8b94cc64c0b035724a6abca2f32a40ec598396c646f5a31c0ea0748bff976
 EBUILD votca-csg-1.6_rc1.ebuild 2358 BLAKE2B 5124239dade6f735c1f1da0071e30bf245728431a46f4361271d1eea9962249ff1bcc621db193f69ae04b61343aaafa01c64cfb4a131c6ce83b9135c5a7f39c5 SHA512 a8f2298c212299689a96d4a15e73b851725f45c6ad9fc20610a155625c5d58d1d462ba7c01fdd206fba8b43fe032b65f992ee58107e1245565cb482f8507d6ac
-EBUILD votca-csg-9999.ebuild 2340 BLAKE2B 97934fdd4b56cfbc58d5c2f47179ed3f747600ae870fe86fc7829fcdecb8e72e67ec129b49cc25e0a04b1dccb878ae79f7e693f59184da4e447eacbceb794b12 SHA512 30e0ef70ef8cf7c791a8579b01440fb7013ed4344a2132e955e17d1b8a5edac7982dae46d796122f8066584583f4b9356a478b512334ec4f0dae647ed4fa8f6e
+EBUILD votca-csg-9999.ebuild 2346 BLAKE2B 4d668ea57aae259c3eb414bb199748526ba525b1fb7b8d5a04d85ba4798d89d0b75ea514d3cfb2c45227f545b12a566183a11eb654f96ab06aad270250f36266 SHA512 8365c0e1b29d830dcba136eae22ec834c89dcb07c0c987680b843a9f666411998262cd52ae19fc19efae3339629a4f942603af938029d33ab21dd09201df8047
 MISC metadata.xml 676 BLAKE2B b3f2e43f5cb505876216b0a329410c9cef1b44a9bbd7e1c61faa4acd00dbe87ea0cebb00ed78dc00b9e1d2b08b95e3c40d25fecc0738c992a3f933e430f94e2b SHA512 14ecd498eeeed1576923d8da9bc5dc98e47c1d162173b7f2419ad367fa84e227555bd0365709be8a456dc5388ea6fa6734fa7df3c82fd4efcd1cf3460c7e12a1
diff --git a/sci-chemistry/votca-csg/votca-csg-9999.ebuild b/sci-chemistry/votca-csg/votca-csg-9999.ebuild
index c77bb3e40fa8..426d1572404d 100644
--- a/sci-chemistry/votca-csg/votca-csg-9999.ebuild
+++ b/sci-chemistry/votca-csg/votca-csg-9999.ebuild
@@ -40,7 +40,7 @@ DEPEND="${RDEPEND}
 	>=app-text/txt2tags-2.5
 	virtual/pkgconfig"
 
-DOCS=( README.md NOTICE CHANGELOG.md )
+DOCS=( README.rst NOTICE.rst CHANGELOG.rst )
 
 src_unpack() {
 	if [[ ${PV} != *9999 ]]; then
author	V3n3RiX <venerix@redcorelinux.org>	2020-11-25 22:39:15 +0000
committer	V3n3RiX <venerix@redcorelinux.org>	2020-11-25 22:39:15 +0000
commit	d934827bf44b7cfcf6711964418148fa60877668 (patch)
tree	0625f358789b5e015e49db139cc1dbc9be00428f /sci-chemistry
parent	2e34d110f164bf74d55fced27fe0000201b3eec5 (diff)