gentoo resync : 28.04.2019

22 files changed, 328 insertions, 165 deletions

diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz
index 7eedd16905fe..244994443415 100644
--- a/sci-chemistry/Manifest.gz
+++ b/sci-chemistry/Manifest.gz
diff --git a/sci-chemistry/ParmEd/Manifest b/sci-chemistry/ParmEd/Manifest
index 63e7763ea1fa..810d6dc67374 100644
--- a/sci-chemistry/ParmEd/Manifest
+++ b/sci-chemistry/ParmEd/Manifest
@@ -1,5 +1,5 @@
 DIST ParmEd-2.7.3.tar.gz 34494858 BLAKE2B 8e3ac8776f30ac73b06fd2241e5d73ba54517805ffcef7cb2f71281248df4f8afdaa05c2186ff50ba0df45df313ebdecd69a4482c8339d41baf804c37069affe SHA512 a3444f915e188bcc924f28b6b4235246e2c063ae98881c48f6e13ebc685d085d6a1bcb61b29509a343cbe58369bc6233acc20ee620c6f1d42da2033772a12e07
 DIST ParmEd-3.0.3.tar.gz 35159355 BLAKE2B 76b4655905276fe498f38c6a3bd483e89e95d3a339fbcd9ceb90d16f68d417b62e0aacaf18143d0b57167ee7acdc726c44324c844462af4d2385872210daef2a SHA512 60b8ee100a301fbddec8323a3dba550c96ffa09624f41e457d4b3941a4e4a15e903c3da6de24a5183731406f19f9e6436a2111d654bc902c0f06ac8b643acf09
-EBUILD ParmEd-2.7.3.ebuild 834 BLAKE2B 6e4210b0f874f70b384373cfe13f56998850f9fad7eeafb4854054f847286e6b72da412328616245ba8df48cfb50d61c7c78c2f548e278ab3b1414859cd178c5 SHA512 af1046b0ea4ad34a6ec3871da13fb42b1290654d26278c77dc4a2d27bde941f4782acc0da7bf6c3b9fcb0599596938e1bce60572a7768bdef2cf516f888c6df3
-EBUILD ParmEd-3.0.3.ebuild 835 BLAKE2B 5ea026dffca8d6c7fca6514f8b0b0904d932125e980a9629b994cddcab47fb8d84886bebbef9748315c741bad2850db1e836d455343a8b643b50c5a98776cc0e SHA512 960747822dd07c0e24391f7bb3447e7518772af852ee7406f2fa80603a789293051ba2f0230504fdabf8c1a9afa3c88db262aa8749af92d05647d86b0832511a
+EBUILD ParmEd-2.7.3.ebuild 827 BLAKE2B 017b1b0fa51c1ce2758e780389fd3f87ed0eb0449a0101e0cdc09b5192bb85c1c14eb1002ef5b72d2e62671981021340b38aec51b1eadb2785af87fa04354f01 SHA512 1b7809f150e2e22c07e4c2c34c8c8f36ddc180ca6621dc4706b41c9e8780726e9efa7113159f05ca6349d5c0febaae1d9abed3b56de477fb225d667551d846fb
+EBUILD ParmEd-3.0.3.ebuild 828 BLAKE2B d44aa368223f04e91c50b68ed3525932ea14f79381ecc66dc7d0e3b16fc2f35b7536f98ca6402681bb9fdbb568ac6ec561d2feb40c91a166fd415f42c917b2db SHA512 a6a754e78715cedc5739c5c9d5cd06bb3676d9848a128f9796a09c33bc61a40c93f92617156ea7efd9f0b2a2466c23bbcde0977807adedfc7faa813d07dc9bb6
 MISC metadata.xml 468 BLAKE2B 2e3781c6ebea297fb8480c2d54be22da0e8d6906607513e3b78fe89a926cf691048fb90576cadde7321d964e8269950437f48bb54270c9a1bd487bfe3ce30b84 SHA512 47e3516aabe02112a52e851ac9294a0096001373d546462f9185754356c72dd37a0a8efa3b40311e43e27e2953ea5879c1141488649f3faef0aa43a692205499
diff --git a/sci-chemistry/ParmEd/ParmEd-2.7.3.ebuild b/sci-chemistry/ParmEd/ParmEd-2.7.3.ebuild
index 88e65d86e229..0e3074845a2f 100644
--- a/sci-chemistry/ParmEd/ParmEd-2.7.3.ebuild
+++ b/sci-chemistry/ParmEd/ParmEd-2.7.3.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
 
-PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} )
+PYTHON_COMPAT=( python{2_7,3_5,3_6} )
 
 if [[ $PV = *9999* ]]; then
 	scm_eclass=git-2
diff --git a/sci-chemistry/ParmEd/ParmEd-3.0.3.ebuild b/sci-chemistry/ParmEd/ParmEd-3.0.3.ebuild
index 6ea7bdee606e..002ac5a8c6f9 100644
--- a/sci-chemistry/ParmEd/ParmEd-3.0.3.ebuild
+++ b/sci-chemistry/ParmEd/ParmEd-3.0.3.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
 
-PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} )
+PYTHON_COMPAT=( python{2_7,3_5,3_6} )
 
 if [[ $PV = *9999* ]]; then
 	scm_eclass=git-r3
diff --git a/sci-chemistry/freeon/Manifest b/sci-chemistry/freeon/Manifest
index b9b666c60fee..d02f31d201c4 100644
--- a/sci-chemistry/freeon/Manifest
+++ b/sci-chemistry/freeon/Manifest
@@ -2,6 +2,6 @@ AUX freeon-1.0.10-stop.patch 970 BLAKE2B 6c1e5dfe5ad881fbbceb071c53cf3fcaa187ae1
 AUX freeon-1.0.8-blas.patch 5076 BLAKE2B 198f65079462b8c7af860b98894526bdc98172035c3d0b5ccd0cfd8bca14e36790c9e20771b7ec8ce5ca4d47f2d5dc7f768c7cf1a4b4868bb48285ef518851fd SHA512 89012c6f8583a8736344a7bfa74a64bbe1af793443b7255ccb1fd73366d44527ed40c6dc3124caff1af02f4e662227c66aeced8d8526dbd26bb7a50e294b5da3
 DIST freeon-1.0.10.tar.bz2 5872019 BLAKE2B c3fde00a9ed67550bb5820ac78ff32d9f6d011db9291c45c0b7e62cacb62b48e7506d7bf1aa86e176577d18e679e859435f0d3b63289bc08e502a35f86c036d3 SHA512 5bae89d6421600792bf986f6fb7504d321d5d51782587237ecba35191e54c1ec6c5ea1fdc50ed2d339551c527e4efcc5421048ccce0404c4b06875cbd0800862
 DIST freeon-1.0.8.tar.bz2 5957707 BLAKE2B b76ae0ca17cc8407b37fac243523d2f8db63382a6f39d24380d2f01356ac78fbe2fb905bb525d979c9832b820623bffa7a0930d312c36f29138defb0d8bce106 SHA512 1227f670a73b4ea39beb26e4136ad535e126ad17d66171c31b3bd403a3886eee150cda865806a2d9dad85646ccb086a6be4f645455eab24603cb064fb725efbd
-EBUILD freeon-1.0.10.ebuild 653 BLAKE2B 9e82178dbb316a870f8456ed3216628ce6200880975991539a089bcdf8c0859518db72d1c4c0cd9dcb880b6e4529832a639cf31c8de2f8308aaaf0723191e9d5 SHA512 2438b254eb1205f2403617154140db86e96e89d17ed5e620e37cf96c6ad98ce709a7b4efcba7370cc54547c0eb1973ae089c700e96bdc511f4bd7bd4b2d26b64
-EBUILD freeon-1.0.8-r1.ebuild 632 BLAKE2B 3d12642f554a6518e8dbebad08d1632a0a479cf799794994ee3c9fd56d460457dbbc3dd315a5b11e112ecad4ca4172045998c5b085cd366d755b8bd45c39f4f6 SHA512 5690b98cfb4d8e88c4b918104aa4d3a4007988a54ec8cbbfdae24e6b547bd4197cadd928767e31610d4ae48d5e178747562aa8f9bd1259dd9bc945e2bd8ab771
+EBUILD freeon-1.0.10.ebuild 649 BLAKE2B 11952531b3b20e712f6cbaaac37a6e0aa856c19b0150d11591f7bace60f45ec0266a8251b9efb017cce0eb79eac1f9641450391ccc594f553c9f4cc61a8e56dd SHA512 52bf70f409b594bc92cd611b05adc972cde0c02e69f38c022055e6de9f509045589a12ee86c36967e5fb9e8adf26e9bd378b7983dab0063099ad0518f5d5d210
+EBUILD freeon-1.0.8-r1.ebuild 626 BLAKE2B 5d5a53bd58c81ff88775f1370d0daf71e94d043b5c3fc825cb2e040cbdb4b3129c1b97b88b5eaaed1a21aaa592c0fa27fb4c7d403cacfdb5d2cfef724c8c72f9 SHA512 8474400965e790a50285e2d5687952535e5d2ee4797086dd64b7f62a990d993937f13d28f92f01057185378944f6baa939427b2a9253749cadb992afd9a72940
 MISC metadata.xml 528 BLAKE2B aa64697b42ac5f829fc893ae2c05f0bae6bb9bb16f067539ca9a11b9469a9a9f4b203eb2f0242f9fde744ea6905223da2249e50622a479975548ef552e7286dc SHA512 4eea3876d046b423706f565571cbe20dbe2ff724ecd8de7f92ba0103c83f78d9e1d28789d6c35e62a8f0527f13bdadf6303695c529b7b6622bc2e14cf57044da
diff --git a/sci-chemistry/freeon/freeon-1.0.10.ebuild b/sci-chemistry/freeon/freeon-1.0.10.ebuild
index f6ce62de1925..37eff15d2079 100644
--- a/sci-chemistry/freeon/freeon-1.0.10.ebuild
+++ b/sci-chemistry/freeon/freeon-1.0.10.ebuild
@@ -4,7 +4,7 @@
 EAPI=6
 
 FORTRAN_STANDARD=90
-PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} )
+PYTHON_COMPAT=( python{2_7,3_5,3_6} )
 
 inherit autotools fortran-2 python-any-r1
 
diff --git a/sci-chemistry/freeon/freeon-1.0.8-r1.ebuild b/sci-chemistry/freeon/freeon-1.0.8-r1.ebuild
index 41acb419c4f2..59b2b4ec6ffd 100644
--- a/sci-chemistry/freeon/freeon-1.0.8-r1.ebuild
+++ b/sci-chemistry/freeon/freeon-1.0.8-r1.ebuild
@@ -5,7 +5,7 @@ EAPI=5
 
 AUTOTOOLS_AUTORECONF=1
 FORTRAN_STANDARD=90
-PYTHON_COMPAT=( python{2_7,3_4} )
+PYTHON_COMPAT=( python2_7 )
 
 inherit autotools-utils fortran-2 python-any-r1
 
diff --git a/sci-chemistry/gmxapi/Manifest b/sci-chemistry/gmxapi/Manifest
index 2fbb4efa04bc..c099618e92b0 100644
--- a/sci-chemistry/gmxapi/Manifest
+++ b/sci-chemistry/gmxapi/Manifest
@@ -1,3 +1,3 @@
 DIST gmxapi-0.0.7.1.tar.gz 671400 BLAKE2B 5db024bceaed262fc1bd2ef35c0c24a31eff12abde7766ba0eea9d5aabe04c435cdf3c79c04d7932f2110de837a0d06e1f66239f22ba6f313410ed8c9d899788 SHA512 4103d67be3c869907613ec74fc46f14b15242ad93a973fc984dbb25e79bb0bb697d9d2ad9b67a8da2500e5a89b8f78ea1ef1632455af29830e11c2bf1f11bc44
-EBUILD gmxapi-0.0.7.1.ebuild 1239 BLAKE2B 3ee41035a390d32da209882d49e05ed017b697dc568e4a401b024208e34ea56235560d4b5b5605684eb5bb73a7ef88a90705cc62e446322600ab77cfa44e2c50 SHA512 9d09c4faa0997764e07cc33fb4521e248a9e3f74f9ee209457277611a0cc7e0fc19a4836dbeb44cfc98dae8d68b69163859c8f18ca680286b000c56ccc381cb7
+EBUILD gmxapi-0.0.7.1.ebuild 1237 BLAKE2B e516ec4e3d975635f9dfd13830b41694ab4d09ec2c14305617237587865086c4159ba860aa76228ee61d98ffe556e911555f887d8f83253012d502cf25da2410 SHA512 8e18895c146f44aa2daf125564667b654faacf7566d66b8b3bf41430232d1772fe5bca8008e76eefeac223fbe98e71c01b6545f6c34d76cfeaa5735929a196ab
 MISC metadata.xml 374 BLAKE2B d93e2ad2f09971909382ad65fc5f5033487979b0694f9dc656439573973f55ce1865e5a30584e55e1c48fdd93898601ac2b11e269fb2b1c5adc3ff8dde66f35d SHA512 1c61c58e1cfbbb42342f7a87625e0044e51523f7a2f7270ecfea537c622965e64195fc88eb8f70fac648a0154a19f4a852b88383de1dcd6e17ff0ac0dc6e22d8
diff --git a/sci-chemistry/gmxapi/gmxapi-0.0.7.1.ebuild b/sci-chemistry/gmxapi/gmxapi-0.0.7.1.ebuild
index babdf4029762..ab2e052e7dd5 100644
--- a/sci-chemistry/gmxapi/gmxapi-0.0.7.1.ebuild
+++ b/sci-chemistry/gmxapi/gmxapi-0.0.7.1.ebuild
@@ -5,7 +5,7 @@ EAPI=7
 
 MAKE_MAKEFILE_GENERATOR="ninja"
 
-PYTHON_COMPAT=( python2_7 python3_{4,5,6} )
+PYTHON_COMPAT=( python2_7 python3_{5,6} )
 
 inherit cmake-utils python-r1
 
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index ead550313102..dd4745c9ae65 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -4,6 +4,7 @@ DIST gromacs-2018.4.tar.gz 29918276 BLAKE2B daf3f91e47bab61befee4ecd91e4885835fc
 DIST gromacs-2018.5.tar.gz 29911866 BLAKE2B 6f060d99ed6180ebc2c1b11d26548a8179312aaf9b356edcb8c6959a4aba5c081604a54e3d78d63dc0d8719a50a0bf5864b6b0186c280b38f59806d4e097857c SHA512 cb6c7624e6fa93c618ea0b412a3cac5f03ca07d2641231888b53501dc7de21e2b1a2d8630a9dbb065256c22a945e3d7b1c823a1b9f0fa01090e4e411eb34f4fb
 DIST gromacs-2018.6.tar.gz 29911431 BLAKE2B a85c20d60dcd550265fcf8591aafc804b2acb8af588e67c808cbd9d53d6dc996013d5f917a9da75960c2ca6a846447700c144b7e471f657d700df9c6fc328f55 SHA512 d62f17ef93d4265407860d4f5adee3e70dc13b94cbb0972d6cc2e17d137b4e49f582c2ff8eb2b97d7a8789841cd1cb9b86edd3f1738d87be81054c8f87587a8b
 DIST gromacs-2019.1.tar.gz 33435278 BLAKE2B c21c375e82c31686729bd3ea08592508f4e6ba64bb0d89781b5fde448e217f12b43c349e1d59c35b6d9697e32ab06ae304fb88632dd9fb9da71a85e4d65e8dc3 SHA512 22f6df47b2d6e569c7ea43e8a76d69afb18dd906c09a8c356b410c89204afcfe52c2f90a1f4e7fe0b6514e07a12f012763673d7f8c3276ef6bfa1fde34b1e327
+DIST gromacs-2019.2.tar.gz 33437869 BLAKE2B bebe4942688dace148856d4491b687b8e0fd2c86d7fbd9eecdb46824d316a0fc3854464ecafa79d8db92327ee8467be204b050c11f1e71132184efd812c3bf09 SHA512 da7ff24e8485774e22d1c2464fbe64675c3305ef0e21a3d17e363201031952e5d4a9b81f572d5284fb6f2596ed99daf62fe78d653387d9d714274f46bc750183
 DIST gromacs-2019.tar.gz 33428725 BLAKE2B 307838a5ee1a85554d6f2ef8cd9c9dd2f3d9cacd32c534545c23483b5f3a1c7d027bfbdf224b90661cd8cd3fb85c0c99c66cbd619698245a0cb45ebd512dec5d SHA512 54b11530e8ff671461e3ae9418d991fe242957943c944798cddf6efe740eee670a562cd5201dbba68b045f4bafd3afa2dc8de27e0643c7def4e05eaf0ccb5769
 DIST regressiontests-2016.5.tar.gz 67641413 BLAKE2B 4fcd30c198f3acbbabf1104c040d9a686de49536a97dbeb14732bfa0ed3cf37aa61b1b0f45393668985b993d1f1862a8985e416af819cf9793f5964f3e4f43cc SHA512 31764fd99cc4185d61de5d4443ee482c27b13533451a24aa0e4899997ce275a63685424eafacae38b1a3ffd4ce0d5ebe02a90348953b04c104f91376f0edfdff
 DIST regressiontests-2018.3.tar.gz 67857855 BLAKE2B acd7a05ae79d1b4eb47d0c68a3fec9ee19f028a5019f39c37a033f48cf6da2a468375180ad6ceca9ac4f685a8bead38550663a47d6427b51f84c32a5c810e5f0 SHA512 57980d49efe6dcc3b3d14b5913a30c68fc1de5b679ef986fec1a149c76f67139b0299c3ee2825451461294fab5f345c7ad4f42e90f8991b81aafe9c369f3ff0b
@@ -11,6 +12,7 @@ DIST regressiontests-2018.4.tar.gz 67860326 BLAKE2B 0160f701a8fa14ba4f175f4fca98
 DIST regressiontests-2018.5.tar.gz 67856231 BLAKE2B 3f9548a97088d552584e2115dbc25b7d54680b10bbfb732e96e064a3fc9eda1c21426875044cc664a1e2be37224209fe027310597aed45f4a033684d7552b5a0 SHA512 65134496efe04a978a4e9ce62873edcf98dc405d0fb93c82fafd0a0675465ccb662be4cb7e142c1a7a38e833e10a9ccdac5ea7ecd1bb61d3dfbdb92d78ac37b6
 DIST regressiontests-2018.6.tar.gz 67854737 BLAKE2B 1f501eacdb6d052a53e7ac08bfe3d7fd052c5129a28674dc3ec87ab67ee8a64cce5357c1fb4e940c931d4ac0687da77e2600c18c115390d764d620282a626000 SHA512 8b947382b8fc8831ec913a2e300e6e1abc487049fc60bb771695fed56fd33bc3fdf24c1d865029be0266e9deaad05a552651c1a59e25a5c32184cc2c21d749ca
 DIST regressiontests-2019.1.tar.gz 67603769 BLAKE2B f8937fc25b72bef52239e6197b4c5834723f2c5db755cd01117c2f26ca45b926efb338b2d7d1a9e340040800902d328f25a7cefb4afdf705c402347a0d54b5a7 SHA512 d16ccc01a6c368550b6b5e431368f6aaac9247def1543831253aed45c83b9caccca19ec9d21c18ee35ce0e12a06f2a08f99ec9d90e547c4b6c784252bdf727a1
+DIST regressiontests-2019.2.tar.gz 67643003 BLAKE2B 4178de5d62f194a81f97e442c10f123dc59c5e63f2078f7f07135709f3f6e530e0d237bf40264b285c084519d5ace75dfcbcddc16dc740c4f17233dc33542e45 SHA512 c1f25bc770d3f0a873c887d5563c1cd88179e81211b70ce6f5015696e6fa0b6931a8da7a449f2b223f3105b9e2e7eca67248e96fbfc2a7fd5fb360ba616f22ff
 DIST regressiontests-2019.tar.gz 67597618 BLAKE2B fb950d8518cf1e28db5ebb99bdda8d269c5e43dd49a117bdaae9f00857abc7c096766fb90ff1d2d95a12a875ba2e243b707bfc81a45d07fc8b340a154cf2ad0f SHA512 081e56d052c0a0d021a8a1566f802911e261e1f2b5b2141350fe2372bcad0844042f26121167ed31a31490bd4e042068690c4905fcbc80b539686a074621fc5e
 EBUILD gromacs-2016.5.ebuild 7971 BLAKE2B 889ded117d36d17c224bdf65ddc8a2e5fcbdb5cdbf58b5774e308fc45e42a7b3734aae1f87d1d95fb3751c18342025a86317e2bf05a82ffa7f9dfaeb47533e5b SHA512 a2ad66f58d79b03e0832ae0daf9b6cbcdceae2873d25318ee7fb9235a41acc1403708206682848c35d2c347ad2ccb72f75c38df38e8899ba07033040b296eb81
 EBUILD gromacs-2016.9999.ebuild 7974 BLAKE2B 5568ed9513fd44da7382370e418ffe456db73076c0000101c96bba4e704e6eece7ef6131379ddbe95c42e9fa4b082346db2ee4f6bb15a25d8c6afd9209db2e5c SHA512 911a5f71d9dde20d11a13cff416db12d6722cf9fb9609895a3d3bd2381c36a875f80f1617f6960deae2ceaa951f60a14738dfe5065f41560cfeecf7ad26b7c70
@@ -21,6 +23,7 @@ EBUILD gromacs-2018.5.ebuild 7825 BLAKE2B c15f1b890f9948e30cf81c880eaffb37af5045
 EBUILD gromacs-2018.6.ebuild 7825 BLAKE2B c15f1b890f9948e30cf81c880eaffb37af50453b04522cb651c862f84240883ca56fad9de6a40c0b5206031d753b5ccec195f2868bf9a8b8f2c69fcbbf9f88ad SHA512 d9893acb9a7913a5539e6dbe4620507038f506964bb8436c9f3dabcad70665f3a0db5ac2fda2d32313bf2f3a0c12b24d3b7a41ea4071886babfd8bac0e031e8e
 EBUILD gromacs-2018.9999.ebuild 7825 BLAKE2B 359b7f832c98d897e9ccaa1ecbe39f7b8e7077bbdc2f32b1b722c2a221ebf4c187ed691a14dcb5c044a3d243d319963e50297bcb347c6433e4ddeafb0ba1c1fd SHA512 730eef3897293939c0b00a236b3f8d0964354fba7cf89170e2b028510f7c0aee8a0925f4c0b7d765d5631bedd90e8a3010e190f08dd8ed71505710b79d9061d5
 EBUILD gromacs-2019.1.ebuild 9112 BLAKE2B 636084295bc6c0c4188bf7a1785f4da01139571f32fbea28546c9eb11d0f0c9c00a27965d8f77da39818f1464da9474041a33a1d3b0fb925d86f5b72e85c761b SHA512 fd73f858613c3c3a13f9983f21de504959e0190cdc1a0bc08e2c9f576dbdd03a316b4f5ce30763265411accf364615f3b1867314eb79f31510526786690f4e55
+EBUILD gromacs-2019.2.ebuild 9112 BLAKE2B 636084295bc6c0c4188bf7a1785f4da01139571f32fbea28546c9eb11d0f0c9c00a27965d8f77da39818f1464da9474041a33a1d3b0fb925d86f5b72e85c761b SHA512 fd73f858613c3c3a13f9983f21de504959e0190cdc1a0bc08e2c9f576dbdd03a316b4f5ce30763265411accf364615f3b1867314eb79f31510526786690f4e55
 EBUILD gromacs-2019.9999.ebuild 9112 BLAKE2B 0b972db0fe7e4c4730e9b480ea981b01a9930d128cef5fd589ad06b3f245d845721f74d0ac7b9e08dbed8f85985d3a0a84f361b02221318daf809ef37df9413f SHA512 363db0dfce3fa8459e6f8a07f6c5e5061d143deebc78fdb852557b101cee3fc342cc3c342a878153ced8edb8d8c567b9ab91bb275d3190034dcef6255003c9d7
 EBUILD gromacs-2019.ebuild 9112 BLAKE2B 0b972db0fe7e4c4730e9b480ea981b01a9930d128cef5fd589ad06b3f245d845721f74d0ac7b9e08dbed8f85985d3a0a84f361b02221318daf809ef37df9413f SHA512 363db0dfce3fa8459e6f8a07f6c5e5061d143deebc78fdb852557b101cee3fc342cc3c342a878153ced8edb8d8c567b9ab91bb275d3190034dcef6255003c9d7
 EBUILD gromacs-9999.ebuild 8092 BLAKE2B 42eef753c8cc34bfef79a710311a0eab2b445cfc2a88a552a729692a89d3c73348c9fbe210feaa299adc232be2f2b7548a262c3a16f43df31a0797e7007ac40a SHA512 d51775e52a42f01b95d829b6efc083de3a919778384fbf986b47c56459cd25a9b620fc8ae3a6237330989a763d8f0b7f9a7c4cc9878a725bb9a08d5c2fcaa234
diff --git a/sci-chemistry/gromacs/gromacs-2019.2.ebuild b/sci-chemistry/gromacs/gromacs-2019.2.ebuild
new file mode 100644
index 000000000000..18717cf66cc4
--- /dev/null
+++ b/sci-chemistry/gromacs/gromacs-2019.2.ebuild
@@ -0,0 +1,307 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+CMAKE_MAKEFILE_GENERATOR="ninja"
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit bash-completion-r1 cmake-utils cuda eutils multilib python-single-r1 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
+		https://github.com/gromacs/gromacs.git
+		http://repo.or.cz/r/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"
+fi
+
+ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2"
+
+DESCRIPTION="The ultimate molecular dynamics simulation package"
+HOMEPAGE="http://www.gromacs.org/"
+
+# see COPYING for details
+# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
+#        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 +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +single-precision test +threads +tng ${ACCE_IUSE}"
+
+CDEPEND="
+	X? (
+		x11-libs/libX11
+		x11-libs/libSM
+		x11-libs/libICE
+		)
+	blas? ( virtual/blas )
+	cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14 )
+	opencl? ( virtual/opencl )
+	fftw? ( sci-libs/fftw:3.0 )
+	hwloc? ( sys-apps/hwloc )
+	lapack? ( virtual/lapack )
+	lmfit? ( sci-libs/lmfit )
+	mkl? ( sci-libs/mkl )
+	mpi? ( virtual/mpi )
+	"
+DEPEND="${CDEPEND}
+	virtual/pkgconfig
+	doc? (
+		app-doc/doxygen
+		dev-python/sphinx[${PYTHON_USEDEP}]
+		media-gfx/mscgen
+		dev-texlive/texlive-latex
+		dev-texlive/texlive-latexextra
+		media-gfx/imagemagick
+	)"
+RDEPEND="${CDEPEND}"
+
+REQUIRED_USE="
+	|| ( single-precision double-precision )
+	cuda? ( single-precision )
+	cuda? ( !opencl )
+	mkl? ( !blas !fftw !lapack )"
+
+DOCS=( AUTHORS README )
+
+if [[ ${PV} != *9999 ]]; then
+	S="${WORKDIR}/${PN}-${PV/_/-}"
+fi
+
+pkg_pretend() {
+	[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
+	use openmp && ! tc-has-openmp && \
+		die "Please switch to an openmp compatible compiler"
+}
+
+src_unpack() {
+	if [[ ${PV} != *9999 ]]; then
+		default
+	else
+		git-r3_src_unpack
+		if use test; then
+			EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
+			EGIT_BRANCH="${EGIT_BRANCH}" \
+			EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
+				git-r3_src_unpack
+		fi
+	fi
+}
+
+src_prepare() {
+	#notes/todos
+	# -on apple: there is framework support
+
+	xdg_environment_reset #591952
+
+	cmake-utils_src_prepare
+
+	use cuda && cuda_src_prepare
+
+	GMX_DIRS=""
+	use single-precision && GMX_DIRS+=" float"
+	use double-precision && GMX_DIRS+=" double"
+
+	if use test; then
+		for x in ${GMX_DIRS}; do
+			mkdir -p "${WORKDIR}/${P}_${x}" || die
+			cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die
+		done
+	fi
+
+	DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
+
+	# try to create policy for imagemagik
+	mkdir -p ${HOME}/.config/ImageMagick
+	cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF
+	<?xml version="1.0" encoding="UTF-8"?>
+	<!DOCTYPE policymap [
+	<!ELEMENT policymap (policy)+>
+	!ATTLIST policymap xmlns CDATA #FIXED ''>
+	<!ELEMENT policy EMPTY>
+	<!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED
+			name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED
+			stealth NMTOKEN #IMPLIED value CDATA #IMPLIED>
+	]>
+	<policymap>
+		<policy domain="coder" rights="read | write" pattern="PS" />
+		<policy domain="coder" rights="read | write" pattern="PS2" />
+		<policy domain="coder" rights="read | write" pattern="PS3" />
+		<policy domain="coder" rights="read | write" pattern="EPS" />
+		<policy domain="coder" rights="read | write" pattern="PDF" />
+		<policy domain="coder" rights="read | write" pattern="XPS" />
+	</policymap>
+	EOF
+}
+
+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"
+
+	#to create man pages, build tree binaries are executed (bug #398437)
+	[[ ${CHOST} = *-darwin* ]] && \
+		extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
+
+	if use fftw; then
+		fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
+	elif use mkl && has_version "=sci-libs/mkl-10*"; then
+		fft_opts=( -DGMX_FFT_LIBRARY=mkl
+			-DMKL_INCLUDE_DIR="${MKLROOT}/include"
+			-DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)"
+		)
+	elif use mkl; then
+		local bits=$(get_libdir)
+		fft_opts=( -DGMX_FFT_LIBRARY=mkl
+			-DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)"
+			-DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)"
+		)
+	else
+		fft_opts=( -DGMX_FFT_LIBRARY=fftpack )
+	fi
+
+	if use lmfit; then
+		local lmfit_opts=( -DGMX_USE_LMFIT=EXTERNAL )
+	else
+		local lmfit_opts=( -DGMX_USE_LMFIT=INTERNAL )
+	fi
+
+	mycmakeargs_pre+=(
+		"${fft_opts[@]}"
+		"${lmfit_opts[@]}"
+		-DGMX_X11=$(usex X)
+		-DGMX_EXTERNAL_BLAS=$(usex blas)
+		-DGMX_EXTERNAL_LAPACK=$(usex lapack)
+		-DGMX_OPENMP=$(usex openmp)
+		-DGMX_COOL_QUOTES=$(usex offensive)
+		-DGMX_USE_TNG=$(usex tng)
+		-DGMX_BUILD_MANUAL=$(usex doc)
+		-DGMX_HWLOC=$(usex hwloc)
+		-DGMX_DEFAULT_SUFFIX=off
+		-DGMX_SIMD="$acce"
+		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
+		-DBUILD_TESTING=$(usex test)
+		-DGMX_BUILD_UNITTESTS=$(usex test)
+		-DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}"
+		${extra}
+	)
+
+	for x in ${GMX_DIRS}; do
+		einfo "Configuring for ${x} precision"
+		local suffix=""
+		#if we build single and double - double is suffixed
+		use double-precision && use single-precision && \
+			[[ ${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" )
+		mycmakeargs=(
+			${mycmakeargs_pre[@]} ${p}
+			-DGMX_MPI=OFF
+			-DGMX_THREAD_MPI=$(usex threads)
+			-DGMXAPI=$(usex gmxapi)
+			"${opencl[@]}"
+			"${cuda[@]}"
+			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
+			-DGMX_BINARY_SUFFIX="${suffix}"
+			-DGMX_LIBS_SUFFIX="${suffix}"
+			)
+		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
+		[[ ${CHOST} != *-darwin* ]] || \
+		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
+		use mpi || continue
+		einfo "Configuring for ${x} precision with mpi"
+		mycmakeargs=(
+			${mycmakeargs_pre[@]} ${p}
+			-DGMX_THREAD_MPI=OFF
+			-DGMX_MPI=ON ${cuda}
+			-DGMX_OPENMM=OFF
+			-DGMXAPI=OFF
+			-DGMX_BUILD_MDRUN_ONLY=ON
+			-DBUILD_SHARED_LIBS=OFF
+			-DGMX_BUILD_MANUAL=OFF
+			-DGMX_BINARY_SUFFIX="_mpi${suffix}"
+			-DGMX_LIBS_SUFFIX="_mpi${suffix}"
+			)
+		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
+		[[ ${CHOST} != *-darwin* ]] || \
+		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die
+	done
+}
+
+src_compile() {
+	for x in ${GMX_DIRS}; do
+		einfo "Compiling for ${x} precision"
+		BUILD_DIR="${WORKDIR}/${P}_${x}"\
+			cmake-utils_src_compile
+		# not 100% necessary for rel ebuilds as available from website
+		if use doc; then
+			BUILD_DIR="${WORKDIR}/${P}_${x}"\
+				cmake-utils_src_compile manual
+		fi
+		use mpi || continue
+		einfo "Compiling for ${x} precision with mpi"
+		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
+			cmake-utils_src_compile
+	done
+}
+
+src_test() {
+	for x in ${GMX_DIRS}; do
+		BUILD_DIR="${WORKDIR}/${P}_${x}"\
+			cmake-utils_src_make check
+	done
+}
+
+src_install() {
+	for x in ${GMX_DIRS}; do
+		BUILD_DIR="${WORKDIR}/${P}_${x}" \
+			cmake-utils_src_install
+		if use doc; then
+			newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
+		fi
+		use mpi || continue
+		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
+			cmake-utils_src_install
+	done
+
+	if use tng; then
+		insinto /usr/include/tng
+		doins src/external/tng_io/include/tng/*h
+	fi
+	# drop unneeded stuff
+	rm "${ED}"usr/bin/GMXRC* || die
+	for x in "${ED}"usr/bin/gmx-completion-*.bash ; do
+		local n=${x##*/gmx-completion-}
+		n="${n%.bash}"
+		cat "${ED}"usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die
+		newbashcomp "${T}"/"${n}" "${n}"
+	done
+	rm "${ED}"usr/bin/gmx-completion*.bash || die
+	readme.gentoo_create_doc
+}
+
+pkg_postinst() {
+	einfo
+	einfo  "Please read and cite:"
+	einfo  "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
+	einfo  "https://dx.doi.org/10.1021/ct700301q"
+	einfo
+	readme.gentoo_print_elog
+}
diff --git a/sci-chemistry/nmrglue/Manifest b/sci-chemistry/nmrglue/Manifest
index b96f65e75c6e..c9c16933c73c 100644
--- a/sci-chemistry/nmrglue/Manifest
+++ b/sci-chemistry/nmrglue/Manifest
@@ -1,4 +1,4 @@
 AUX nmrglue-0.5-nohyper.patch 1408 BLAKE2B 8e91e270183ce8f4c361fd3577dc4942b2afab81ee8f59df5c8dd9056dbf639653d2e84f9dc04026636dda98e28a244586ba5bc2cd4ed5c43c8a31d0c0cab4d1 SHA512 f68ea345f2692123e24fc41335001a0a8418b84003d864e9d673935d4a517aa82353e08f4f554b33ddc18cea96c9442827715cdabad6303dc60f5dd18cd103dd
 DIST nmrglue-0.5.tar.gz 142604 BLAKE2B 9a018a73bea46176fc06042013cb23b3eeb962df8a595388da536d17f1d2d4d550065c5492df28de860ea1290314d2fa1110af349be0c2a8b1b31677b3e4afbc SHA512 2a4b94eb6bae966000bfdee4dd16f4e312568915fb5f19f59f84c6deff690703f54f76366d3f9299f7ec187192ff64f2bf62836617a424d4c5c895c67d819af2
-EBUILD nmrglue-0.5-r1.ebuild 731 BLAKE2B 8d13063ea428f7f3f6134c7be79f1ba3951f105560f1280f3fa7484c06a6e29d5d1babaab066995c444552acc9d56725a3f8fec524caed788034e2da3276d190 SHA512 22d3bae493423dc2e3fa3a3c5a5e9a110f68ada07b0a9d30176c350f4705d0e5a96697c3a4864241ee8b9c428313b8f47fee70850fcfabfac3a971c0346ca51f
+EBUILD nmrglue-0.5-r1.ebuild 726 BLAKE2B f67232037b0cc6e96837387790d96a530aac385decb8f53317f4ea28221e798c6f1e61cce20e4665df92826291f3e730d8aac1c819fba562c77c6b6b13e6d7b4 SHA512 a896e0d38e5772ec35ec9da9ef198cde44b1b88adfb58d3df1229b3e04bff8e066a330549d852e0abbcd05163dd8f61c42953550ccd6368d72cc30b59b98f976
 MISC metadata.xml 1338 BLAKE2B 480651ef6112e93e3c70e734f4ca7d7b24653109f503fab6a340c9dc246b881b5ab103b90f8ffbc92a6d5352b399c15a33072292e549b4ffcc2689f049996cfd SHA512 7defa016b2c5f51327f282ef8dbb5f99767e554112baf10d72a6c86462d86bf7bd3129226340bbdb00f9e95b2349fc3594b6d0d8cd0175457bbb5f034e31aa7c
diff --git a/sci-chemistry/nmrglue/nmrglue-0.5-r1.ebuild b/sci-chemistry/nmrglue/nmrglue-0.5-r1.ebuild
index 9f1cae764afb..939e9307cc50 100644
--- a/sci-chemistry/nmrglue/nmrglue-0.5-r1.ebuild
+++ b/sci-chemistry/nmrglue/nmrglue-0.5-r1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
 
-PYTHON_COMPAT=( python2_7 python3_{4,5,6} )
+PYTHON_COMPAT=( python2_7 python3_{5,6} )
 
 inherit distutils-r1
 
diff --git a/sci-chemistry/openbabel-python/Manifest b/sci-chemistry/openbabel-python/Manifest
index fb43c0117165..decaeb88f1c3 100644
--- a/sci-chemistry/openbabel-python/Manifest
+++ b/sci-chemistry/openbabel-python/Manifest
@@ -1,4 +1,4 @@
 AUX openbabel-python-2.3.2-gcc-6_and_7-backport.patch 635 BLAKE2B 4e98dedd149b14d5bb02fb6d2fa03e07242d100c7b41f36f749ff3d587080eeca44aa26ca095d31e0309e45f3780b67deaa97f1177ed35a9b7407bd7c33f78ff SHA512 e1b4402f34d01ced5b4caaa184b4e5544cf47893cfe7958054052b05a57dc34b4d44239a212c7d909f29b9366b83b6df74993f844a20f23748c01272ec093081
 DIST openbabel-2.4.1.tar.gz 11618304 BLAKE2B 8fc051e83add9be6456e281a109bd6bbec282a64ffc83309819f0decbf167b4914fbb7f1966e95e103f268754045b804317f51c79a952ace707c6af2bd320125 SHA512 427e678f0a911bd27b9a8a05e60b6e09f113be4e5dd180daaf80c28d06368e52b57501261755ab3817a8d31f2754db24471fd0ceee706d029386d6f70800e9c6
-EBUILD openbabel-python-2.4.1-r1.ebuild 2175 BLAKE2B a940a18ee6b73bd62143546a9a1bee6f8d06637af8f366cbfdde1a6827ea8e2ac707df4c354cf6a782282bf008befb92e903f40b8289ec19f5c131d0071bf711 SHA512 a4174ac5fabedd91719a7adba9bfac803ca231e223243a32eff6bfd98a95d6d21e0ab7c9ac0457f43b064866bb5876fb684449f6389764afa2365a83aa749ae2
+EBUILD openbabel-python-2.4.1-r1.ebuild 2170 BLAKE2B ff6345bd83a8bb97071710f9215e83516aab062ab5e40f30adfddf7e5883b702503f94ab6d2c177589958b127a3fc2422893e5c4f4e9ca4cbc700f3c36ef53bc SHA512 a993e4c10c36e51af247d6065c0f823f593f47f37cae1b9aafdf95cd9ee99264a71fe440497217bde42ec6a0945e2282ae40a3dee1b4658ff97c05cb15ec6b55
 MISC metadata.xml 737 BLAKE2B 9a5fe97df44ce22c6ee27133bbc6144132ee3775db77440adcd6c3e9c44b87cefbace4ebe17906af87f841e07deef5183e451a8c193232d2a6ca7da05c7a0ed7 SHA512 7ff97ef3f6752a8fed578676aa2cb9706b7d68e31ee22d26e90d4bbb01c10ff410b66da20a91b078293add3bcb3a3711ad180d5174368e0d588ea718ad297d7e
diff --git a/sci-chemistry/openbabel-python/openbabel-python-2.4.1-r1.ebuild b/sci-chemistry/openbabel-python/openbabel-python-2.4.1-r1.ebuild
index 84f9aa89e74b..92382447cd1a 100644
--- a/sci-chemistry/openbabel-python/openbabel-python-2.4.1-r1.ebuild
+++ b/sci-chemistry/openbabel-python/openbabel-python-2.4.1-r1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
 
-PYTHON_COMPAT=( python2_7 python3_{4,5,6} )
+PYTHON_COMPAT=( python2_7 python3_{5,6} )
 
 inherit cmake-utils python-r1
 
diff --git a/sci-chemistry/prody/Manifest b/sci-chemistry/prody/Manifest
deleted file mode 100644
index 50ffba89d172..000000000000
--- a/sci-chemistry/prody/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST prody-1.6.tar.gz 5333629 BLAKE2B 73d268d0e717ff1e53be73da31e313aca8d4ccb2633f5bc8a43124b68f4945685c3edafc885998f58d7114363485e0b7a1e4882d35be134babc081cd4e1e1f86 SHA512 d913ad45b034f1b0e7e36428a6f8f199b365b94bd85bee5ade8eb9eb2b04a18c93d894a2abd18b3a1342597725ffbf96f8ce8a49191fc27e5608f3d2c9a3c49a
-EBUILD prody-1.6.ebuild 989 BLAKE2B 8778e06b09ff46ef13fee1dd8531c02138e98454a8b6f0c00704d9b3df33c6cafccaf791c194dae1f71cae159f4ae91aa18fe3d53ab07447111fa59a136ce5fe SHA512 c7d56510fcdf606616fde3b0e7199237c3114e053d3ccb03851db34b56cfbac7077e6c714b5a758942be5a29f6e2e92a0fc2945e29382234f439e8225b559cc1
-MISC metadata.xml 351 BLAKE2B 317181e52b8fe5644e8ec783cbb67ecc8ec469b5036092ce39b146c92132d542085a785c9221145d8916ebeb68a2ff3ad1d4fa992503b7fde919c5b795e9e883 SHA512 7e6be0c59b593d2de0f9e0237a039624a136b791c28afddad157c878a3d7efdf02637bb0e6b862957a057f3ab7aaf3db113eed6208e1491e4950795547ea4b2c
diff --git a/sci-chemistry/prody/metadata.xml b/sci-chemistry/prody/metadata.xml
deleted file mode 100644
index d798ea1d6cdf..000000000000
--- a/sci-chemistry/prody/metadata.xml
+++ /dev/null
@@ -1,11 +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>
-  <upstream>
-    <remote-id type="github">prody/ProDy</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-chemistry/prody/prody-1.6.ebuild b/sci-chemistry/prody/prody-1.6.ebuild
deleted file mode 100644
index abab32d7927e..000000000000
--- a/sci-chemistry/prody/prody-1.6.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="Protein Dynamics Analysis"
-HOMEPAGE="http://prody.csb.pitt.edu/ https://github.com/prody/ProDy"
-SRC_URI="https://github.com/prody/ProDy/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-SLOT="0"
-LICENSE="MIT"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="test"
-
-RDEPEND="
-	dev-python/ipython[${PYTHON_USEDEP}]
-	dev-python/matplotlib[${PYTHON_USEDEP}]
-	>=dev-python/numpy-1.7[${PYTHON_USEDEP}]
-	dev-python/pyparsing[${PYTHON_USEDEP}]
-	sci-biology/biopython[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]
-"
-DEPEND="${RDEPEND}
-	test? ( dev-python/nose[${PYTHON_USEDEP}] )"
-
-S="${WORKDIR}"/ProDy-${PV}
-
-DISTUTILS_IN_SOURCE_BUILD=true
-
-python_prepare_all() {
-	emake remove
-	distutils-r1_python_prepare_all
-}
-
-python_test() {
-	cd "${BUILD_DIR}" || die
-	PATH="${S}"/scripts:${PATH} \
-		nosetests --verbose || die
-}
diff --git a/sci-chemistry/pymol-plugins-dynamics/Manifest b/sci-chemistry/pymol-plugins-dynamics/Manifest
deleted file mode 100644
index 5f6eac7b4632..000000000000
--- a/sci-chemistry/pymol-plugins-dynamics/Manifest
+++ /dev/null
@@ -1,5 +0,0 @@
-DIST pymol-plugins-dynamics-2.0.7.tar.gz 822680 BLAKE2B 3c8b3418dff65d9cad4f632b5062f13626bdf267190a9b11a96d63fec345532eed4d54014f5caf2c62a7d6e86705fb667f42bba378aa8ba0dab19c6bcd212984 SHA512 0d57e3e90a86a59cb96b11371ff1227b2b3e8f5b82cce713f4a855d6e7f5a10524508d4cb4dad7d9f77562fc1753b1af3c9240d4333e0189dabeef07c40d78a1
-DIST pymol-plugins-dynamics-2.1.1.tar.gz 816623 BLAKE2B bd065b176f3f779962c4f48e715a74afefbac2ee6dd31bb9f52208fae171f16847ff70692a7df3739dbaa23be215f73e4fe265328b05c4fb3dd598def48c9ff1 SHA512 e872c131e7d4ae37bd0e33e56d5d51e83ad732a125a46802ad9fa08648906d49de166bf75fbeca1431726aa9df781671c29578a799f580a94dc1fd89fb398b3c
-EBUILD pymol-plugins-dynamics-2.0.7.ebuild 762 BLAKE2B 84d0defcfd41568c51fca2c73b98ddbed5c48577c7d15cd2766c5b08ea2db3b5cc1a8c083e75f231d30ad2d186534bcf6c487576394752f90e261c56e4335504 SHA512 7d56fad6af90be0e978ce97867effc548ec1a0d268e6ba7e4e7bd4c1755ca7c7509d92b70c3a75724526aecf686aebe21cae3473515b5a1ebe928201783b06c5
-EBUILD pymol-plugins-dynamics-2.1.1.ebuild 762 BLAKE2B 84d0defcfd41568c51fca2c73b98ddbed5c48577c7d15cd2766c5b08ea2db3b5cc1a8c083e75f231d30ad2d186534bcf6c487576394752f90e261c56e4335504 SHA512 7d56fad6af90be0e978ce97867effc548ec1a0d268e6ba7e4e7bd4c1755ca7c7509d92b70c3a75724526aecf686aebe21cae3473515b5a1ebe928201783b06c5
-MISC metadata.xml 365 BLAKE2B c10b106dc69e286e5d35b0f38c988dc75f025f1e62230c7d4859012605169bfca737e68cf9aa23c44259b5707466ac625a49a4daf60a82f752f620969810d20c SHA512 470165dfdb7117d8a87f1a7fbb21d806c5ff5eca77d450aa2a3ca32bb32347a4014bfb205d139e9597d8d6da0eba97bb3acb662c63b2d5ce42fdc63e5366d82f
diff --git a/sci-chemistry/pymol-plugins-dynamics/metadata.xml b/sci-chemistry/pymol-plugins-dynamics/metadata.xml
deleted file mode 100644
index d0be20ea989c..000000000000
--- a/sci-chemistry/pymol-plugins-dynamics/metadata.xml
+++ /dev/null
@@ -1,11 +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>
-  <upstream>
-    <remote-id type="github">tomaszmakarewicz/Dynamics</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-chemistry/pymol-plugins-dynamics/pymol-plugins-dynamics-2.0.7.ebuild b/sci-chemistry/pymol-plugins-dynamics/pymol-plugins-dynamics-2.0.7.ebuild
deleted file mode 100644
index a860012cf6ff..000000000000
--- a/sci-chemistry/pymol-plugins-dynamics/pymol-plugins-dynamics-2.0.7.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit python-r1
-
-MY_PN="Dynamics"
-MY_P="${MY_PN}-${PV}"
-
-DESCRIPTION="Molecular dynamics in Pymol"
-HOMEPAGE="https://github.com/tomaszmakarewicz/Dynamics"
-SRC_URI="https://github.com/tomaszmakarewicz/Dynamics/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-SLOT="0"
-LICENSE="GPL-3"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-DEPEND="
-	${PYTHON_DEPS}
-	sci-chemistry/prody[${PYTHON_USEDEP}]
-	"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/${MY_P}
-
-DOCS=( manual.odt )
-
-src_install() {
-	python_moduleinto pmg_tk/startup
-	python_foreach_impl python_domodule pymol_plugin_dynamics.py
-}
diff --git a/sci-chemistry/pymol-plugins-dynamics/pymol-plugins-dynamics-2.1.1.ebuild b/sci-chemistry/pymol-plugins-dynamics/pymol-plugins-dynamics-2.1.1.ebuild
deleted file mode 100644
index a860012cf6ff..000000000000
--- a/sci-chemistry/pymol-plugins-dynamics/pymol-plugins-dynamics-2.1.1.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit python-r1
-
-MY_PN="Dynamics"
-MY_P="${MY_PN}-${PV}"
-
-DESCRIPTION="Molecular dynamics in Pymol"
-HOMEPAGE="https://github.com/tomaszmakarewicz/Dynamics"
-SRC_URI="https://github.com/tomaszmakarewicz/Dynamics/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-SLOT="0"
-LICENSE="GPL-3"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-DEPEND="
-	${PYTHON_DEPS}
-	sci-chemistry/prody[${PYTHON_USEDEP}]
-	"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/${MY_P}
-
-DOCS=( manual.odt )
-
-src_install() {
-	python_moduleinto pmg_tk/startup
-	python_foreach_impl python_domodule pymol_plugin_dynamics.py
-}