diff options
Diffstat (limited to 'sci-chemistry')
27 files changed, 648 insertions, 23 deletions
diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz Binary files differindex 3ffbf99dca28..515f77421774 100644 --- a/sci-chemistry/Manifest.gz +++ b/sci-chemistry/Manifest.gz diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest index f98e1e7a611a..f8cd6987508d 100644 --- a/sci-chemistry/gromacs/Manifest +++ b/sci-chemistry/gromacs/Manifest @@ -1,8 +1,10 @@ +AUX gromacs-2018-fix-build.patch 2797 BLAKE2B 410cf7dd4fe6f47dcdc0ce828884accc8c9f6e973ea130f20a9bf74b153e1ce118ac9c808e7305aad01cce947dd7e1546617becc61e0626278f67c6dce6fa454 SHA512 229dfb531d0bc240fca8e4548b5a3afd8280e7ebbe8006f6da9f59108469808b25ba90b7145ceb8f50e99adc93385daafc97f594ebd86ab11bf683f7e8af44c7 DIST gromacs-2016.1.tar.gz 27336258 SHA256 9e7d2892a903777b982bc9ab4306de969d92cb45b51a562f523ec5fe58db41e3 SHA512 d30a4ad5faa6e12c95b8e94acaabc387d9aab3780490f5442c48ccac2f86bef6dca60df5bb6097dbc68ab28e6f1a15e234e1244606afdf12a841b88ece65c97b WHIRLPOOL 4be9c84d99286889dda23d9f1e2dd7b2d87a70740fb686bd58e59155771e897471d0920b02c5ec529a01a4b01428ebb2ca5b27e4d8df9034d2d3b33c5ab1a1ca DIST gromacs-2016.2.tar.gz 27339623 SHA256 b6ac3632b848ab0c19f8f319dd5b58fcd09b8e2005ee7509478606613e5409a5 SHA512 f5e74bb8c126823c90d205ac0f0835e61fdd13a4550bc15aa9c972ee9b187f6451cdc90877c17276d2f889d61abb5eaa5ea1b54f7cbf3da67074146c749c1aa6 WHIRLPOOL 698c4d4e67266483be4f1047eb947b243b5c8caa3c5e30bdab6b5f0dd302bb51ac5aa6e3a3357beab567cf71c1b8ecc1f9684a89754d18f963dd6f5fc90a33f4 DIST gromacs-2016.3.tar.gz 27342692 SHA256 7bf00e74a9d38b7cef9356141d20e4ba9387289cbbfd4d11be479ef932d77d27 SHA512 16593df0a52620766fb86cfeb16328793503f860cb07cdbbd503ba7f41e6430efb4848389b7179ca3907b57311162666d05224b454e1afb1b74b220f38498d86 WHIRLPOOL dfe31f212545ae2baf7373fde31f715a8df203d098d3ace915d4269b7bf16d06a1f91ead33ccbf8a17e9e0091b593818d0ce2eff151ce532238a8c27f5e20cda DIST gromacs-2016.4.tar.gz 27368706 SHA256 4be9d3bfda0bdf3b5c53041e0b8344f7d22b75128759d9bfa9442fe65c289264 SHA512 69661d2a7a8a5259be277de35e2baa4b688d1f7bef225fc7d733a9b00c6ee135dcbad517c7c9f751121647c2fbd085f2c9cdf22dbd941c7ebc5d3b09e7e08f1f WHIRLPOOL c1586377d2a27f0b529370efb63e09ecca64cdb3d418fe9bc4f3ea1ff82ff5293d159834f4ed5d0136d801095d6f4085722e0d91bce873776fa4549853497ff7 DIST gromacs-2016.tar.gz 27321561 SHA256 aa0a27cd13050a4b70aacfbd169ddce2fe507c7e668f460ecf6cf32afcac5771 SHA512 756771baaa85a1d16e7d5b8e4c96bbd1c04c7acdc536a253886cff186316330f06d60d206a0159efb15f47f161c779d3757dc5dbceab8c097241c1382d376201 WHIRLPOOL 1cc3d3797e1aaf93e1e0cb2e71173896e33fee2bb03f4e97e06be3ab85842e6da3feaf8701425358f1d701e00159ff6ce3b24fa1488d5e8ef70a1acbb914361c +DIST gromacs-2018-beta1.tar.gz 29857800 BLAKE2B 221ed414c1dc73b59df27dfb6dd22ef094152bba7a8346cd0d0164e9a0aa5463a7d836dfb13e98ac8cdbef2ae4a0503763a5c445a5e1c73815b3592d8b8f97fe SHA512 6e827b7b33589ccc7ef1d237c4e8ce06749a2c47f59956d383fdb59439a34874a9e0e3a3cca1d209425353a7dcf0f963de035dd0281d4c8aad0c921e6bbc7b93 DIST gromacs-5.0.4.tar.gz 26342095 SHA256 78068eeccc0b950018ddb45c41280e53c8bedae4639dca48e17c940f8896b23b SHA512 bc62b623bf71dcaa948aaf7563a3d3afa973da0702062848a20323db202e862dcee413197dacd1472866ccb40fce7709e283177b1c6c49514064f23e6c46b5ee WHIRLPOOL d8458d3d563e015e830622ae0c924e896765a6329ffe4cb1a31c7aef3c804f392d29e3f1db5617051e85058403422f7d69a160a6c7cc810564696d88f9d50bd4 DIST gromacs-5.1.3.tar.gz 27095702 SHA256 c962d9446939a9ba9905e7ca440c9306fd310f08600da3b744806bfd0eacccde SHA512 9ab26e1b2268f8d567b89b2d99d0b75b937b28edceaec56d17ca3243c76faa31255ffc0c45d762c7c693fe500b00e36ad43b80572d1d7f92dc87f9d2d98c0ba6 WHIRLPOOL bdd9c63ceb5e61963c4edd0af815cc34a3f237d8dee410c834b9b55bb82374de65b437828390a668282e50428b9907b887cd5265caf2a2007fc7673e7ab23733 DIST regressiontests-2016.1.tar.gz 67094518 SHA256 10c9f50ff3cb32cf629aa35e35d957965dcfce4af84a6569e6d65a16c4e09eb7 SHA512 fc01c802d81400373a147171881f3b7b9309402e8ffb08287ba393aefbb701ba93bbe0b9549ff6fa264a8befbba445c2d2c7450633063a724f78ec8ca81ae8c9 WHIRLPOOL e8c54164558fcbaa1e65e9280e438882c96bbbaa6c9389a2ee5aed37d70b83b6b36e95dd5141b4e64b303e3799411ee01cf04aa919f25014d172011e49714126 @@ -10,6 +12,7 @@ DIST regressiontests-2016.2.tar.gz 67095329 SHA256 53fa9ad062cc3e269fc6186db1ccb DIST regressiontests-2016.3.tar.gz 67093968 SHA256 a3d1b09acfc61820dddd765a381f706190b4657606488f1e676becb859ea7ecc SHA512 ee87df9f339954da0e1f1b4c8b8d4deb574f3b73d174010a295a7a0e8bc462ead7691090ea7cf8ac3d984a6cd70f1cd22c3592fa161b2967061ae5ba2796286b WHIRLPOOL 2e986136f7faf6db108bc79e6fb6db9fe81d05f5af8bc27037b80cd25869f7cd4162d5cabc03994b36c71945910be79a217ff27f61463d1548cbdff6acd99f56 DIST regressiontests-2016.4.tar.gz 67643648 SHA256 d58d1a2a53c22c06e2dc03bd98ae1eea0a0d51696a1f20f635dfc394fa3da957 SHA512 367438b897a05e1cc0dcd1d3872fb6a0e9ff6b1146e9448d941d6517dce789f0c478d20cf0a4f3565070f132dc88872441aadb8b499f59efa0e1e4a6dd6a7135 WHIRLPOOL 695a3b7f81915247a90e95c0a83823c0297fba6ae6266195e86c61ec540ca58afd8d01ba236c5ddb3f44b41fb9301ba6a836b15cad1875bae42ba6276670daff DIST regressiontests-2016.tar.gz 66908712 SHA256 30a72362f011fd9e3a8d33004018126f938536c13fcb70f590afc74beaec5406 SHA512 59902c1973c33ea8f003f21a737dc7cc64da3258112322eedc9834b53628134a6817d5ee5b3950c9bfd97a3a0580aef88ddef0609ef2c58693c96c7575651e01 WHIRLPOOL 9d210aed00ddfa57df47733169997ef04dec84c524eb5a9c5c6dd9b05ad9ec2d7f3c8a5a43f2ade9be166d80f35a260c04b1a48ac092f5969a213475bb63ae20 +DIST regressiontests-2018-beta1.tar.gz 67870909 BLAKE2B e9aff43331394c4a50cbc626d0327498f1571cf457e6b924f0cfe8eb688a9cd8d2b66c13c900da8737b124861fb567f9129aff840a294e92233b9a2214ff20d7 SHA512 509175cbbb8528d9bb1394c726c6e89291c2077880a3c4bf99a330ff457ca233ae74e771b8a753b0c94bba8de02840b1e5460b7c226e177742b1dee289833c0f DIST regressiontests-5.0.4.tar.gz 65193251 SHA256 89ad9bc067035ac8f340319b538c446983d937b910067e871911d7afe2ecb3f0 SHA512 747725fa28c1c9525596bdeeb8809e45268e19036c11dac67d043aa1c51748688ca37eb6014eb7e819eb927a8b9ca2631d0ace4cdff8ed491b08c316c530ab65 WHIRLPOOL e15ccab0a0beefac41aeff11e2e596e971167f1590eed159ff82c4a8e3aec1d234287be597026951904ecfe6099f30ef3bcd48f2098b9f5201bde62e15fbc4f9 DIST regressiontests-5.1.3.tar.gz 66994083 SHA256 fd5797dcfd29f7ae70857a438dcd4200a8006fce222f297892c8e90123993ebc SHA512 486e86eb3b75bae822abe82dac4e1098aa13723bd04214021f835a2f0b847303f015a9ececc33aa5ae63d31a2eeae07e512f22464b6c0e26d1286b0781578022 WHIRLPOOL 6ddb76859ee8fa3aba4d995e397970e6fd270acbdd6cc07ab77de0aebb0bfdbd2bd1107ae39d4410e750641047ae4b75c703eafad95a57ff42deb3bf1c742d08 EBUILD gromacs-2016.1.ebuild 7987 BLAKE2B 45d8b50b3ee54c8c701eb8c6533c1dc7d680eb0f5c40cdf1a75e81b59bd2d603b4235f6e4942e40211b748b7cf8239c90f8d613b20bdc44fca48d23f9c45ae14 SHA512 ce2b0d2730e87831a517468033cada7097ba431d8a60dcef77a04c9e05bf4cfacb6eb500a5196e378f4c69e5020f8e9f871eac6e61dd2776834aee006ecb167f @@ -18,10 +21,12 @@ EBUILD gromacs-2016.3.ebuild 7974 BLAKE2B ec37b1dbbbbe9c3aab0d7819f48c15e7c29d28 EBUILD gromacs-2016.4.ebuild 7987 BLAKE2B 45d8b50b3ee54c8c701eb8c6533c1dc7d680eb0f5c40cdf1a75e81b59bd2d603b4235f6e4942e40211b748b7cf8239c90f8d613b20bdc44fca48d23f9c45ae14 SHA512 ce2b0d2730e87831a517468033cada7097ba431d8a60dcef77a04c9e05bf4cfacb6eb500a5196e378f4c69e5020f8e9f871eac6e61dd2776834aee006ecb167f EBUILD gromacs-2016.9999.ebuild 7987 BLAKE2B 45d8b50b3ee54c8c701eb8c6533c1dc7d680eb0f5c40cdf1a75e81b59bd2d603b4235f6e4942e40211b748b7cf8239c90f8d613b20bdc44fca48d23f9c45ae14 SHA512 ce2b0d2730e87831a517468033cada7097ba431d8a60dcef77a04c9e05bf4cfacb6eb500a5196e378f4c69e5020f8e9f871eac6e61dd2776834aee006ecb167f EBUILD gromacs-2016.ebuild 7968 BLAKE2B c0ba44661dce5ccda3c2378fad57e88ca90d15cb1914d6214ee4559e8ebd6c6c700624b32abf168a4a653cc5794fac9fab71024a9b7bc5464d404d768ac74ef1 SHA512 3ca5d4ae9b01a106b279bc828e42366a017b9517a450b773b944c6d12dce64199e3a80d280e4c475c637c70009a1a0fd1ca74f99b03f08067a10d9e9ad450d8f +EBUILD gromacs-2018.9999.ebuild 7899 BLAKE2B 8053de4c12e2201d37e8d0a077d33fc0b103b79d73379488c46bc638ba763b55ebf69ae53180ffd850e4b860fc03a1c3ec57049f1b257e04e0322ed482afcd51 SHA512 734710474160c6a55206b332e5370bd9e2d0092aed19c4c1ccab7f5d9567eac2a47d163a50aa607f8c7e8e2ccc6eadeb9b394e9f638ac85eafe5f74ced68fd02 +EBUILD gromacs-2018_beta1.ebuild 7955 BLAKE2B c26e1b835fa94c9e7531a292a6aa79a3a0659fea032085a02b1aff77ce71388017760a4be5bd72bc5a41cf688489ba78e5d6ab134b4c086300e2c0c2f9b36f01 SHA512 5c14d982e7db5ec1727df4d4a8578c5b28cbc0d8f192d20fd18cc88efdf2bf3f26ead61c08136227d8f043f726967a84bc5f252a2da830852cf8c396a3bd1d98 EBUILD gromacs-4.6.9999.ebuild 8110 BLAKE2B dd8ac9cbc4abfcc75a3a188c59cdbe5111f363404ff5a787f64b05d4bd411deebb50f172f09963800ed87997788b2e678617805e65a523bed19aa6ef18fe2b96 SHA512 2206e257f0b29b6f3a90c5d7739079b9add3e04f2a3acbd58c814811b389b5d51b3594815a94529d1de43deb380504029c302d18fc16d63a81c92727254e863e EBUILD gromacs-5.0.4.ebuild 8429 BLAKE2B c06c423365fa79befd5a4f0b6314e77b96d983c84df776ce84fddc79d35ce735d856d1184e5913af0c8cd3a0c4e9087110af9bd4402e2bce1f014e64a8a585a7 SHA512 d1e91cc25c5f90bd0fbad15060cae9c8bf1235ca45a2b72521b3a4f5f091bdd7d32ec2e6ff2bb22cd3fe165092f11a24ea148ae8000b8517f0b8671f6c2af6f2 EBUILD gromacs-5.0.9999.ebuild 8439 BLAKE2B 33d51254e62593a58c636bd902f43edc553ad11af306d1d022278b223eda15b0772097f26565df74a1118bd5b144e5b93aac09cdb995123ccbae2856889c31b2 SHA512 6756116cdeae9c21b094f74ea1b1d9f41617467dc736878cdcff27fed9f53b338830a608e23e87238d0756884799fbc5d62f02685774ea86c239ecc3e8804814 EBUILD gromacs-5.1.3.ebuild 7783 BLAKE2B d8154b902324d1f47d4b0d4d316bb0e1154379e3c9e3732e195f269386fe9666ba546ab624df95b201c1dbf63c0d7c24cab0e5be92ac70180c53a362e37e71c9 SHA512 8cf9573ec5dfa09e283b1d50513863214ca216007ad76cce15bc54caa2f1e55de8c992db8bd4b2e4fa95bc3f5d50eef32fce78ca61bc09cae2fe37e35a4cee68 EBUILD gromacs-5.1.9999.ebuild 7783 BLAKE2B d8154b902324d1f47d4b0d4d316bb0e1154379e3c9e3732e195f269386fe9666ba546ab624df95b201c1dbf63c0d7c24cab0e5be92ac70180c53a362e37e71c9 SHA512 8cf9573ec5dfa09e283b1d50513863214ca216007ad76cce15bc54caa2f1e55de8c992db8bd4b2e4fa95bc3f5d50eef32fce78ca61bc09cae2fe37e35a4cee68 EBUILD gromacs-9999.ebuild 7710 BLAKE2B efd556f55dc198d8526df775fed3c2aa55fa88794ea9618a222d67886ee46371c19c7ac0b58d37c11b5e0605e08caaeb42de9883db2bdab86c8baacbc372b639 SHA512 a3cb96cf8ada5f278b4b932fafac93659ca2c65ab530337567bf87be53ddea7123e2e03c0c3fefd2faca8bc3ce9494ebf960f1fdf9cff000b548790b5e0c9d81 -MISC metadata.xml 1189 BLAKE2B a2a0750d0d6ee1de3b820d0d6864508a7eb92eddb553d8a699c281f505b9e3641b94c018664d5c4fc4300aeeab94325dbdb38b7ee3c1a2599695274357f9a272 SHA512 0152b721a378b736fdcfcf61971047e7e9b09c1a8b70e858f86ae29947a83bc3aded34fc8151758151a56785d3ee4fac469b244266a57392f49db5b673e5171d +MISC metadata.xml 1251 BLAKE2B 324e432ebfca2fea64aa5ec331c51263422f22ef6f326f7034fd0d3e97ff0a408b8bf06e09d488fea89176b2996ec9a7f02597ef5dd65ee718c16c38298d0acb SHA512 b84b070eb8d6e264e036945c9903020cb1b9b8407c9c136ccbac0387f659c2943eb1c3f5c74c2627873bab7eb68d637152da759830f18a996aaa09e63d546e37 diff --git a/sci-chemistry/gromacs/files/gromacs-2018-fix-build.patch b/sci-chemistry/gromacs/files/gromacs-2018-fix-build.patch new file mode 100644 index 000000000000..2ed6a19f31b0 --- /dev/null +++ b/sci-chemistry/gromacs/files/gromacs-2018-fix-build.patch @@ -0,0 +1,71 @@ +From 81e68584512b21ec572d2561c25a1b19982aa0be Mon Sep 17 00:00:00 2001 +From: Alexey Shvetsov <alexxy@omrb.pnpi.spb.ru> +Date: Fri, 1 Dec 2017 17:12:36 +0300 +Subject: [PATCH] Fix build with cmake 3.10 on Linux + +Without this fix cmake will fail with + +-- Detecting CXX compiler ABI info - done +-- Detecting CXX compile features +-- Detecting CXX compile features - done +CMake Error at cmake/gmxCTestUtilities.cmake:56 (file): + file STRINGS file + "/var/tmp/portage/sci-chemistry/gromacs-2018_beta1/work/gromacs-2018_beta1_float/DartConfiguration.tcl" + cannot be read. +Call Stack (most recent call first): + CMakeLists.txt:89 (gmx_ctest_init) + +-- Performing Test CXXFLAG_STD_CXX0X +-- Performing Test CXXFLAG_STD_CXX0X - Success +-- Performing Test CXX11_SUPPORTED +-- Performing Test CXX11_SUPPORTED - Success +.... +.... +.... +-- Looking for inttypes.h +-- Looking for inttypes.h - found +-- <<< Gentoo configuration >>> +Build type Gentoo +Install path /usr +Compiler flags: +C -march=core-avx2 -O2 -pipe -march=native -mtune=native -mfpmath=sse -mavx2 +C++ -march=core-avx2 -O2 -pipe -march=native -mtune=native -mfpmath=sse -mavx2 -std=c++11 +Linker flags: +Executable -Wl,-O1 -Wl,--as-needed +Module -Wl,-O1 -Wl,--as-needed +Shared -Wl,-O1 -Wl,--as-needed + +-- Configuring incomplete, errors occurred! +See also "/var/tmp/portage/sci-chemistry/gromacs-2018_beta1/work/gromacs-2018_beta1_float/CMakeFiles/CMakeOutput.log". +See also "/var/tmp/portage/sci-chemistry/gromacs-2018_beta1/work/gromacs-2018_beta1_float/CMakeFiles/CMakeError.log". + +Change-Id: Ie04c2e5f5884f05c3648fed7289157e73fd8d81f +Signed-off-by: Alexey Shvetsov <alexxy@omrb.pnpi.spb.ru> +--- + cmake/gmxCTestUtilities.cmake | 10 ++++++---- + 1 file changed, 6 insertions(+), 4 deletions(-) + +diff --git a/cmake/gmxCTestUtilities.cmake b/cmake/gmxCTestUtilities.cmake +index 89715f910..3685df648 100644 +--- a/cmake/gmxCTestUtilities.cmake ++++ b/cmake/gmxCTestUtilities.cmake +@@ -50,10 +50,12 @@ macro (gmx_ctest_init) + set(MEMORYCHECK_TYPE "AddressSanitizer") + endif() + include(CTest) +- # At least with CMake 3.4.1 on OS X, AddressSanitizer support in CTest +- # does not work without this... +- set(_ctest_config_file "${PROJECT_BINARY_DIR}/DartConfiguration.tcl") +- file(STRINGS ${_ctest_config_file} _existing REGEX "^CMakeCommand: ") ++ if(APPLE) ++ # At least with CMake 3.4.1 on OS X, AddressSanitizer support in CTest ++ # does not work without this... ++ set(_ctest_config_file "${PROJECT_BINARY_DIR}/DartConfiguration.tcl") ++ file(STRINGS ${_ctest_config_file} _existing REGEX "^CMakeCommand: ") ++ endif() + if (NOT _existing) + file(APPEND ${_ctest_config_file} "\nCMakeCommand: ${CMAKE_COMMAND}\n") + endif() +-- +2.15.0 + diff --git a/sci-chemistry/gromacs/gromacs-2018.9999.ebuild b/sci-chemistry/gromacs/gromacs-2018.9999.ebuild new file mode 100644 index 000000000000..315835fdc606 --- /dev/null +++ b/sci-chemistry/gromacs/gromacs-2018.9999.ebuild @@ -0,0 +1,272 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +inherit bash-completion-r1 cmake-utils cuda eutils 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 + 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 + KEYWORDS="" +else + SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz + test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )" + KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~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 +hwloc lapack mkl mpi +offensive opencl openmp +single-precision test +threads +tng ${ACCE_IUSE}" + +CDEPEND=" + X? ( + x11-libs/libX11 + x11-libs/libSM + x11-libs/libICE + ) + blas? ( virtual/blas ) + cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) + opencl? ( virtual/opencl ) + fftw? ( sci-libs/fftw:3.0 ) + hwloc? ( sys-apps/hwloc ) + lapack? ( virtual/lapack ) + mkl? ( sci-libs/mkl ) + mpi? ( virtual/mpi ) + " +DEPEND="${CDEPEND} + virtual/pkgconfig + doc? ( + app-doc/doxygen + 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" +} + +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 + + mycmakeargs_pre+=( + "${fft_opts[@]}" + -DGMX_X11=$(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_LIB_INSTALL_DIR="$(get_libdir)" + -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" + -DBUILD_TESTING=$(usex test) + -DGMX_BUILD_UNITTESTS=$(usex test) + ${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) + "${opencl[@]}" + "${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 ${cuda} + -DGMX_OPENMM=OFF + -DGMX_BUILD_MDRUN_ONLY=ON + -DBUILD_SHARED_LIBS=OFF + -DGMX_BUILD_MANUAL=OFF + -DGMX_BINARY_SUFFIX="_mpi${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/gromacs/gromacs-2018_beta1.ebuild b/sci-chemistry/gromacs/gromacs-2018_beta1.ebuild new file mode 100644 index 000000000000..3e0dd9b80bc9 --- /dev/null +++ b/sci-chemistry/gromacs/gromacs-2018_beta1.ebuild @@ -0,0 +1,276 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +inherit bash-completion-r1 cmake-utils cuda eutils 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 + 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 + KEYWORDS="" +else + SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz + test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )" + KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~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 +hwloc lapack mkl mpi +offensive opencl openmp +single-precision test +threads +tng ${ACCE_IUSE}" + +CDEPEND=" + X? ( + x11-libs/libX11 + x11-libs/libSM + x11-libs/libICE + ) + blas? ( virtual/blas ) + cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) + opencl? ( virtual/opencl ) + fftw? ( sci-libs/fftw:3.0 ) + hwloc? ( sys-apps/hwloc ) + lapack? ( virtual/lapack ) + mkl? ( sci-libs/mkl ) + mpi? ( virtual/mpi ) + " +DEPEND="${CDEPEND} + virtual/pkgconfig + doc? ( + app-doc/doxygen + dev-texlive/texlive-latex + dev-texlive/texlive-latexextra + media-gfx/imagemagick + )" +RDEPEND="${CDEPEND}" + +REQUIRED_USE=" + || ( single-precision double-precision ) + cuda? ( single-precision ) + cuda? ( !opencl ) + mkl? ( !blas !fftw !lapack )" + +DOCS=( AUTHORS README ) + +PATCHES=( + "${FILESDIR}/${PN}-2018-fix-build.patch" + ) + +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" +} + +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 + + mycmakeargs_pre+=( + "${fft_opts[@]}" + -DGMX_X11=$(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_LIB_INSTALL_DIR="$(get_libdir)" + -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" + -DBUILD_TESTING=$(usex test) + -DGMX_BUILD_UNITTESTS=$(usex test) + ${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) + "${opencl[@]}" + "${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 ${cuda} + -DGMX_OPENMM=OFF + -DGMX_BUILD_MDRUN_ONLY=ON + -DBUILD_SHARED_LIBS=OFF + -DGMX_BUILD_MANUAL=OFF + -DGMX_BINARY_SUFFIX="_mpi${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/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml index c9beb4a5a326..844b34dd014b 100644 --- a/sci-chemistry/gromacs/metadata.xml +++ b/sci-chemistry/gromacs/metadata.xml @@ -15,6 +15,7 @@ </maintainer> <use> <flag name="cuda">Enable cuda non-bonded kernels</flag> + <flag name="opencl">Enable opencl non-bonded kernels</flag> <flag name="double-precision">More precise calculations at the expense of speed</flag> <flag name="single-precision">Single precision version of gromacs (default)</flag> <flag name="boost">Enable external boost library</flag> diff --git a/sci-chemistry/gsim/Manifest b/sci-chemistry/gsim/Manifest index d21ff0525f0d..68e13788c777 100644 --- a/sci-chemistry/gsim/Manifest +++ b/sci-chemistry/gsim/Manifest @@ -1,5 +1,5 @@ AUX gsim-21.3-build.conf.patch 1897 BLAKE2B 3f9d538cbe10d2abb1c366866f5f57ebd5d772025e3b3955006de553a455da45a60eb28903a64b4d6c18915ec83e43d680d38e6e755cf4180eec810cc64d9b64 SHA512 d1bd0fb6ce8279edfa5aff48ce9d7174825c17531b6d71b5fa872b744160d9c836f80c751e184b34308b05e1f7a817c4fd6b9071bab7e874ca2d59280adc8312 DIST gsim-21.3.tar.gz 4100589 SHA256 d3dd161078862fa990b40ff5df988bb82c8469e17dda8e81eda5f1419742de47 SHA512 0a65ec416a11893fe9f249126ed8e7b9f7991dc8f02d6b62b01962de6dfabda805acdc3d7fc6939b609ff018f16cefff616f37ee906776712209460374bb225d WHIRLPOOL d8dde220a52608b5dc48e494fb1b0bad49f13f770e132641b9671cd544c951cdd03a4578bf983492dfb0b74567e51ef716ecbb828ba40b2a3385d26788b83bea EBUILD gsim-21.3-r1.ebuild 1794 BLAKE2B 3191cc861c77cfde8140a8ee90add2388c44a254c8d0989541fd1af40a7a65bd2ab3d3980c7aa4d1eafbe1fe65eb44757415fa63960151df8463984870c2042c SHA512 7222acbf7145886e3f4e1b6758ffba1d656edbf536e6f3caa25989812df67dbfd9794e77578394fb0a51879db8512d7be5ed119f08327ca465ad37cf5c0f786f -EBUILD gsim-21.3.ebuild 1584 BLAKE2B 0b9b4916b59326be8c04eec345db73424d2c83d298d5a28f8a0076e5412192f23dd1899a3f98c509a4c666c85232e27cb063ebcf65b1eab7b077f8ba914d34ae SHA512 44b321797c196099c93ccf07747aed4c1d023da78edf44e3deb87a17905cf11adc15b4c20eba649337734634e80bb170bc89142e592f16e1d9d5cf4a5c78c57a +EBUILD gsim-21.3.ebuild 1571 BLAKE2B 27d68a9642f7ed3998e967be374a1363e6ce3bfc076d2f2c3390437e9e0791499ab4f2f11fc3a4380a6a77010bec9e2a9d5003326242363680ad5213db107917 SHA512 5bd8d17eb573c3813c1ab71bf0f0b2935f3b48a818086eb09c64252ee8b67b1ca15f00cf9666f62cdbbc2f3ed82e6859ecd8725937818bb028e64d56d2756739 MISC metadata.xml 418 BLAKE2B e3c99faf5bfb099a10a4e7629cd01b44dc0cb3237627ea73480681aa64ce425894a9f07726e626ebaf7c805c6ec6998bbae4b58f622cf5aca19c5ab50b3ce3fb SHA512 d7ff66672b3e97b217dae26956f7cb56deeded4893eee1f27ad35c203917c2ab2e820b5eed5748fc63378cc7987cb45d699e05aab9fd80c4baa5a17a472f3ff8 diff --git a/sci-chemistry/gsim/gsim-21.3.ebuild b/sci-chemistry/gsim/gsim-21.3.ebuild index 332b51b655e0..4aa1830ac648 100644 --- a/sci-chemistry/gsim/gsim-21.3.ebuild +++ b/sci-chemistry/gsim/gsim-21.3.ebuild @@ -5,7 +5,7 @@ EAPI=5 inherit eutils qt4-r2 toolchain-funcs -DESCRIPTION="Programm for visualisation and processing of experimental and simulated NMR spectra" +DESCRIPTION="Visualisation and processing of experimental and simulated NMR spectra" HOMEPAGE="https://sourceforge.net/projects/gsim/" SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" diff --git a/sci-chemistry/molscript/Manifest b/sci-chemistry/molscript/Manifest index 727c8989ec6e..465b6b6b732e 100644 --- a/sci-chemistry/molscript/Manifest +++ b/sci-chemistry/molscript/Manifest @@ -4,5 +4,5 @@ AUX 2.1.2-prll.patch 409 BLAKE2B 83eefcd062c9904a06a69ccafa9da14578f102af96ad1b3 AUX fix-makefile-shared.patch 2051 BLAKE2B 145edf9dc11ee0f59325fcc3e2f981de03aeaa582bea06ca80406cc88ce38971590b687aa9dd40b37fb8edd07c9b30a0f81aa20ab38dcdb02378a407ba068878 SHA512 0c12bd5aea0a6175b7647ed61ae139113329058c42cfb56105ee35af35bdab9f61adfe635a1c3322dbff00ddfcee06383bbd6bd048cc7ded1961f3997a527358 AUX glutbitmap.h 845 BLAKE2B e5c5a6fed84021a35e132301c06efa9b877fc475a1230a58c93e9e24fb0b220cea1bcb68d411ed17897877dd3b9c4e3d6a1646906b0f09819449e6321e8f108a SHA512 a11e8c23472ed8950c8b56fdfd57ddd9c6539f427437ab26a2d3561ad388ca24a36029dee9ff6b8af759eeadf89fbd45dd10279d8089e6978eec07858624c7da DIST molscript-2.1.2.tar.gz 412497 SHA256 01252931f5a3542d5659ddaa4ebceaed2e75becb8ed150dfa14b59da9a63ca01 SHA512 0f82936da3123770c0fdb703094dbb5289cc39e9f9ffd034d8dba563f8d615788f67040d38158ac2f203b480c5838a7d8e71ca07bc5098181c1e3cfea26703a4 WHIRLPOOL 1588f4dd47117f8da797a8bf62a2eba071106b1faca4f79b06e3093fe76092cae54476f1a0be995e3637173561ae6003fded264dd6d3a424d235488f95085a75 -EBUILD molscript-2.1.2-r2.ebuild 1407 BLAKE2B 946053dd6b4ea7ba849255fca58af98679254b0e805e1d386beb5a2952918cd9f95dd0ce2d38c2311a173bc6f700114f5f2669b2625677bfccf666f4ef3db493 SHA512 37358b677743c89b94c7960b3c5eaa458f8bd77494d412deb6cd4f583d59848bf8eadc10bb0d6bf7e3afdac24e2abb166b07d4d2143558147b29b847e1a746cc +EBUILD molscript-2.1.2-r2.ebuild 1389 BLAKE2B cccb057490775272bc67e4195628b95f59fbdba89645bbd461e86e681a5c834b1d6503ee9bb2e187ef324e17bff6c74fc4f1930f3779249ba9608cc50e37c87d SHA512 588e960f0ab9c4678ba16a196803293b0ef7e59c5d2f20972caa64af438e3c502a03abcf8b860fa2357dd87344762375a07a212b9492fc304f2b095194b22849 MISC metadata.xml 271 BLAKE2B a446884cbe7a6789e0bcd82759f57bf1ab7b29c5ab714057ffa821c90f799d1fa9f9310c187ee4c3a8ae2476f6ea9d15f368045779f1581e68d02802c61c884c SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 diff --git a/sci-chemistry/molscript/molscript-2.1.2-r2.ebuild b/sci-chemistry/molscript/molscript-2.1.2-r2.ebuild index 054edd99f7ff..87c16c05a6d7 100644 --- a/sci-chemistry/molscript/molscript-2.1.2-r2.ebuild +++ b/sci-chemistry/molscript/molscript-2.1.2-r2.ebuild @@ -5,7 +5,7 @@ EAPI=5 inherit eutils toolchain-funcs -DESCRIPTION="Display molecular 3D structures, such as proteins, in both schematic and detailed representations" +DESCRIPTION="Display 3D molecules (e.g., proteins) in schematic and detailed representations" HOMEPAGE="http://www.avatar.se/molscript/" SRC_URI="${P}.tar.gz" diff --git a/sci-chemistry/msms-bin/Manifest b/sci-chemistry/msms-bin/Manifest index cb7ff4654217..229c8762e1dd 100644 --- a/sci-chemistry/msms-bin/Manifest +++ b/sci-chemistry/msms-bin/Manifest @@ -1,4 +1,4 @@ DIST msms_i86Linux2_2.6.1.tar.gz 112762 SHA256 ab4f9e60df6fe18a5ac05550bf074b287792638a818a047697ead049d8737caf SHA512 814a5b5fa760b57c773f6900d42cacc5b68a2bf16d8792aa63cfa779aeabdab4e05064b86de6fb2551194543db925d83e07cf4ef74be8c08935ef5ecc8dcfe73 WHIRLPOOL dab6bfd4e8dca59939cd9d0fd6638a3304314dec023b684a09a34eb9bf90fcdc348091af4ea0676a4bf246e30b685a97e1750e0ccfbfccc8e9a90c1cf8445994 DIST msms_i86_64Linux2_2.6.1.tar.gz 593147 SHA256 5f0ca50360b5938e74c538e0399d582abc4a40ef4cf410e66f31a1f91e6e3e1f SHA512 630da1ae57b2d8d072247b650636a71e5ef6f07a245c8c4d07b26e20618d9c5dbaffcff563d0504b9b899ca263ba5f3458447f0e649bbfb895aea34305c1c8f8 WHIRLPOOL dff76b55ff1cd53770a4b0fc91d9c7c4f2ae7422008f1081a630965858718bd5cbb2b8e5167809f5957123fb55909e0042c9ca469596eecea7c44cb1c587f085 -EBUILD msms-bin-2.6.1-r1.ebuild 1063 BLAKE2B ea74e8704401b6ba2e984c0821a1068d96081dc4a76d22e520017d901819ae50e5a2a0654928126a46e9e4e0ac2708840f682f65435f949f6ce78e351614ee36 SHA512 e0041ed3ffab683b8be0456cfa216124d04447c9a5640e3637bfb1443bf8cebaea196c95b97bb01bd32ec22dd2c9e951564149a25fc74aa45e079a59e86abbce +EBUILD msms-bin-2.6.1-r1.ebuild 1054 BLAKE2B 6dc62885906e5b91e824878e13b81bc43f0279d83ba0e452d16cc476249005176d12011cfaf3f77c3d69d7024f76ef7fa6449c432095137f4b73169058f23022 SHA512 855c9613f269e8b76a353bf7a5ac0ce479e1cd2302671f9d17d3e3090f01ade5dcb5ffd18fbfb3cb23ca840abd151d8ae77be822833dd61f8ababca9ad918f7e MISC metadata.xml 342 BLAKE2B e5edc8e8d81d013be77e02718bb4fe50564226ec1c028daad92c3c5b882b2eb840be28ce78dfc83ab3a58e1a428b55caed99971b9b84a8bec23349952496eea1 SHA512 2dbd8b2bdf37d4a2d4127cb373db2c6ff8fc4de6bf294e4518f1d424115860c0b083d538935a8b1a54543b396b968985e46a7ca293367ee1a0b462d11639b7ab diff --git a/sci-chemistry/msms-bin/msms-bin-2.6.1-r1.ebuild b/sci-chemistry/msms-bin/msms-bin-2.6.1-r1.ebuild index 75e928623167..aaca48a6b1a8 100644 --- a/sci-chemistry/msms-bin/msms-bin-2.6.1-r1.ebuild +++ b/sci-chemistry/msms-bin/msms-bin-2.6.1-r1.ebuild @@ -3,7 +3,7 @@ EAPI=4 -DESCRIPTION="MSMS allows to compute very efficiently triangulations of Solvent Excluded Surfaces" +DESCRIPTION="MSMS very efficiently computes triangulations of Solvent Excluded Surfaces" HOMEPAGE="http://mgl.scripps.edu/people/sanner/html/msms_home.html" SRC_URI=" amd64? ( msms_i86_64Linux2_2.6.1.tar.gz ) diff --git a/sci-chemistry/pdb-tools/Manifest b/sci-chemistry/pdb-tools/Manifest index 90e39ce6bd4c..71e7512de354 100644 --- a/sci-chemistry/pdb-tools/Manifest +++ b/sci-chemistry/pdb-tools/Manifest @@ -1,4 +1,4 @@ DIST pdbTools_0.2.1.tar.gz 103835 SHA256 317a5246e806a2b3d0425d080d679646fc77388e3e855412527603f945fa37ae SHA512 9c43c10e8739f8a34dbb1a3bba710cc727f7d8392ff979681371bd4460c67203253fb01852438eb93b214c4a009789608d200ca551f30399652fb76d702cf724 WHIRLPOOL 36d8cf71ba9f9b28e3ad59828539f4e94bbb8bc4514f050ddcbec63857b154ecdc7c32c2945c0d15f4d718c4fe5ab3adcb2e62a4368bfd819b80e9641a9dfd88 -EBUILD pdb-tools-0.2.1-r1.ebuild 1675 BLAKE2B 9267443f3b6454299828bc846a476046081d1bf4e2942cd68dd3dce44f80fe64c2a5d672acaffb088132fe80cd7e9675827eb3ffd7fef50d3af535bcd15714c4 SHA512 f356c319d545920d550bdee48fd84ceebc7ad022d3dc58c28c79060da2aeb953c87328b3faeb08b6b8c4973ee9dd2b97a42a857ef51b1b4949b91a5333f9d147 -EBUILD pdb-tools-0.2.1-r2.ebuild 1740 BLAKE2B 6106258c22dc7df8fb9a4508bc16063ec8ce665000c3faf3193b90e5b8bbe7ccedb488665b9aee3b5f7c1a681cb638087e33427519a2fa786c78346d203f8389 SHA512 06ce18d1f7aaa9b2e4e1f8c29fa7e187737af741ee53570a65b41b28c9bdb3ba23e8cda4b37d70fb169eed84829ebf425c22193bef587dbc87dbbdfec2a8f30b +EBUILD pdb-tools-0.2.1-r1.ebuild 1669 BLAKE2B 6fb471e4908d4aed5efb4b5129ca4a54f2f45d6b8d0c1cc716bba8a8ce20cb9ecc64cd91223cf5b2a39714e3c2e2d0a8d7d5baafb8c1fb8ac1be485f651ae457 SHA512 806c9517f124a674bf4772d6f3e6379da075760a4b6cd60d00676410d3419306d73d367fbf95462fa9515589cdef94f1b4fae6e69249955d1dfe2bf0a89123ac +EBUILD pdb-tools-0.2.1-r2.ebuild 1734 BLAKE2B f1b28c6b9c60c5573c9bf6ab092c32f3e4aa6df7bc484dca74aeda8c12f78dafcd94db9f1976932264be4be24c01f29a38750cfe1081058fe0e964345bfe9565 SHA512 dd9a534af4c275a3fba95ce88e4a9e22e5f182c63210717fb66ab62afd67e179541e58d6d1a3af03a550f5718166f9d0974f7d2f47b401adf670b27376f73cf8 MISC metadata.xml 413 BLAKE2B f3fc199d95acf174f2d5cf9e0ea9c645e3b49e7241122bde730db90a095a0ef0f763dd3dcbcd5f14c1da520630c58bf9e7fe40828d267cb5a2ad5c796b72993e SHA512 74abf290517514aa17fadf8271d2af124fef766b473199502959a662d3bf7a8fed59746b43b3084b83bc14f8d5b9048b419f59d901dec100cbdd81975864cce2 diff --git a/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r1.ebuild b/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r1.ebuild index 88c1f246e8a2..8dc55d31e546 100644 --- a/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r1.ebuild +++ b/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r1.ebuild @@ -9,7 +9,7 @@ inherit fortran-2 python-single-r1 toolchain-funcs MY_PN="pdbTools" -DESCRIPTION="Tools for manipulating and doing calculations on wwPDB macromolecule structure files" +DESCRIPTION="Tools for manipulating and calculations on wwPDB macromolecule structure files" HOMEPAGE="https://github.com/harmslab/pdbtools" SRC_URI="https://${PN}.googlecode.com/files/${MY_PN}_${PV}.tar.gz" diff --git a/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r2.ebuild b/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r2.ebuild index 35910807746f..a476a801611a 100644 --- a/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r2.ebuild +++ b/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r2.ebuild @@ -9,7 +9,7 @@ inherit fortran-2 python-single-r1 toolchain-funcs MY_PN="pdbTools" -DESCRIPTION="Tools for manipulating and doing calculations on wwPDB macromolecule structure files" +DESCRIPTION="Tools for manipulating and calculations on wwPDB macromolecule structure files" HOMEPAGE="https://github.com/harmslab/pdbtools" SRC_URI="https://${PN}.googlecode.com/files/${MY_PN}_${PV}.tar.gz" diff --git a/sci-chemistry/pdb2pqr/Manifest b/sci-chemistry/pdb2pqr/Manifest index f54e2d263607..f2c9db478630 100644 --- a/sci-chemistry/pdb2pqr/Manifest +++ b/sci-chemistry/pdb2pqr/Manifest @@ -3,5 +3,5 @@ AUX pdb2pqr 263 BLAKE2B 3cbd33cf9fb9fd6469c71d8d167ed0fb85ad7b87b6caf27dabb2490b AUX pdb2pqr-1.9.0-flags.patch 1392 BLAKE2B b6b6ac64f98944d85fc93c076d7258c8f980a0391d2cf086edc46bca3f4ef15a5cb720ef8ae2dc38007962a462fb88e92eb4f439c4f3267a5d1d83de5a848dd6 SHA512 deed0aef88dc43515745204f2b4209bd6b42702d9004d48797d642b8f497229424bd0bb92017982cec54c448ea35de563bd42017cd5dc042840acae8495d135b AUX pdb2pqr-1.9.0-install-py.patch 578 BLAKE2B 91ad4b40ce3d13b574ad6d9ea84e55b08803fa018490a7327dae5621a371adfeda509188c049144301cbc023f4407f6c0daf7b57e7d3c10d95d78ab570a6f540 SHA512 902ad717e32790e9c691851dc4b92412f07ac79caf74b2b5794a10fa75cca7fa19e8814df4d8ba71bd2ecc98a3d777d0b79e6e43009171a32e8c99756d81d4d2 DIST pdb2pqr-src-1.9.0.tar.gz 9051969 SHA256 d9d91bf27a023732be33d1d780ef283ae28d3b0e256c53e86c37ac001dd7ef53 SHA512 7f3f191cca9879a0e166e82700c706f8c99bb66558a218e54845f10c3324b6c45d413da80b0782d96a8d56df1463262609db075aba3768db3942cb928ee7b98f WHIRLPOOL 4a4b883200dad3e7467392e508c2372ad6876e78005da14e5747f3b7b12d0e3d5695e3cc590812b835ae67703819b201620809dff05af0a7c363c23d22046bae -EBUILD pdb2pqr-1.9.0-r1.ebuild 2911 BLAKE2B c1e6f8d18c1d47dee8abd1b5c3ecbdb780fbf20f5c8d4f52a2d42ba510017a8b5d46e1e8b1eaf9c95de7b45bdd09ddf3526b73e5e9bd08230632721cbf11fdee SHA512 88d06dee9fcb6423a2cae4fbb8e1e175ef6b8b45bb371b556b2fd15314d2d11c5ec9ffec294f8fb814f03f2f1dfb37d92574361b9a8aa89c9c42c483a5dd79d8 +EBUILD pdb2pqr-1.9.0-r1.ebuild 2908 BLAKE2B 6d605543d94ae2ad9a0b8184854c01bc007908dcb5af30da444d6ee5ec14ffeb9a0a73c0e832ac6d7b93cd1c0f3ad797ef8a09521df9eede8f010446a3483f2b SHA512 61df8503529a0032d72c068c1abdbb54bb2ce504bcd8e02dbac080901a30dc0aff9d7a848c21f0c7e6b1108e1574fa03d9aa3a73d68f4def6a790e355ec5611e MISC metadata.xml 511 BLAKE2B 70a1bf9ff6db44bdbae39b1f58ac5b80769738b2ce8fbb19b3bcb9fbf7cec2a9eab215a7a922025b9110673cb834255240adf10613fd78a8fea47fa7be4fbba9 SHA512 11a010eea3bbbaaf4150a23dadcd10c45737745d51a3341cd7e69cc8537215f313d1ab57059eff265e73e34aeaef435585bb652f5497508dd12b99f67b8580c0 diff --git a/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild b/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild index 8b58ae48c5c7..46766b7715e6 100644 --- a/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild +++ b/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild @@ -7,7 +7,7 @@ PYTHON_COMPAT=( python2_7 ) inherit scons-utils fortran-2 flag-o-matic python-r1 toolchain-funcs -DESCRIPTION="An automated pipeline for performing Poisson-Boltzmann electrostatics calculations" +DESCRIPTION="Automated pipeline for performing Poisson-Boltzmann electrostatics calculations" HOMEPAGE="http://www.poissonboltzmann.org/" SRC_URI="https://github.com/Electrostatics/apbs-${PN}/releases/download/${P}/${PN}-src-${PV}.tar.gz" diff --git a/sci-chemistry/pdbcns/Manifest b/sci-chemistry/pdbcns/Manifest index 6c49d0676b83..e06fda82a493 100644 --- a/sci-chemistry/pdbcns/Manifest +++ b/sci-chemistry/pdbcns/Manifest @@ -1,3 +1,3 @@ DIST pdbcns.2.0.010504.perl.tgz 6806 SHA256 a2c66e44e036b6a1ff2eff90b59c4adf20edb70d3f704bd7bc7f356040d8f98a SHA512 5174cb51dbe3ead405fa1005d81a7ee063bf4be4268b0e728f1ca0aa3e6cbc005fb0bac3e21e06f872c6f4d42c23f50b6e6130391e3b825260c890070e6f766b WHIRLPOOL b3749fadfe274bcdfca5e18a4f9044ebb8804f2a26e3ebaa22d813c37433c6eefc614a5740744296b1c3b549e3cc39dd8c73772da1a84b010556f8a36a465c39 -EBUILD pdbcns-2.0.010504.ebuild 683 BLAKE2B d82432d6133c174129b0a78c78247979b7b9acb7112a4d50dd4f911541a24bb0c19a21868216f9677dac1d57d21f3f2421881d095a62907f9e59e136d098a5d0 SHA512 e0db8eaa8405403e4b41e1501706a8ccbea5a3b28f6a421ff8daa6e4dadbfc6fc8c86f4646b322a31e4865f1d49f31bd1d387a8c812de51d977fe9a1bf20ef7c +EBUILD pdbcns-2.0.010504.ebuild 668 BLAKE2B e85485f753dc383e8f477eda221069436dc4049807e25c05d4ceb55405ecacad828296906a0bdb8abc56e89e6f4ec8889194c6d2cd1270dd1c6f1f99320f9b46 SHA512 6426d86b45e7af51fe2a0baad95d378d3ceb16a729ed6469a3b00ecd44aed368b942498fd1c53f0b62060f2170ce6191a9dca04fd23f3de2d58911614cd552c0 MISC metadata.xml 265 BLAKE2B d5a98b9309829a0486c4b8a4336c2d24a0fe34e926d52afd0cc87e16fcc887ca4c18851e58afb33866823121fa8f221a90e0d726dbd85552a4caf66cf03b7b4a SHA512 470f6c178e88c4e83afa46d5e901a45fc2427a779ae832df7fa2d6e25e9e8b4ce77cd3a8fe191e6242d6df3b673f0de6b4f90f1e147aa8b8dd566f18163cc73a diff --git a/sci-chemistry/pdbcns/pdbcns-2.0.010504.ebuild b/sci-chemistry/pdbcns/pdbcns-2.0.010504.ebuild index 90903a11b2de..b0b57ed0d51f 100644 --- a/sci-chemistry/pdbcns/pdbcns-2.0.010504.ebuild +++ b/sci-chemistry/pdbcns/pdbcns-2.0.010504.ebuild @@ -3,7 +3,7 @@ EAPI=4 -DESCRIPTION="Convert atom names for common amino acids and nucleic acid bases from PDB format to CNS or back" +DESCRIPTION="Convert atom names for amino acids/nucleic acid bases between PDB and CNS format" HOMEPAGE="http://www.mybiosoftware.com/3d-molecular-model/314/" #SRC_URI="http://kinemage.biochem.duke.edu/php/downlode.php?filename=/downloads/software/scripts/${PN}.${PV}.perl.tgz" SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${PN}.${PV}.perl.tgz" diff --git a/sci-chemistry/prekin/Manifest b/sci-chemistry/prekin/Manifest index 2972ea93c06d..c07f81b89285 100644 --- a/sci-chemistry/prekin/Manifest +++ b/sci-chemistry/prekin/Manifest @@ -1,5 +1,5 @@ AUX 6.51.081122-Makefile.patch 1456 BLAKE2B 769c5237659ddc6abcbeea88d620993b7c52f77ee4b12a8bb200e452b0e5dd8fe41ba2c18056439998ba7d2dea90351e2fc7997cc71e5ec447e128e3c1535b62 SHA512 96b8cda8fc71b2e72c0e8e0a70560a7928456fe81aaa40810a8bcbe77835a7242e8e0d39fac3258e5848a4e4ac14bf9d7dfd4dff8385eb983f359a9f85af9838 AUX 6.51.081122-overflow.patch 1156 BLAKE2B 86c70ec89564972a451d23a41863969e31b2d0b866c0282728625fe200928aaf87bec7751e8df3fefbce6c2d4f0a21aba13b1d117247ab6b2b14c7d1db2e45b8 SHA512 fe0ff6e3432177653d29ef51ef3a767dc3872fc0a5350c786b3623b6b4d63866fbfbaf4369676feb545766cac5620b209bd87e92c0ecf2280bb39470e7dd5f7b DIST prekin.6.51.081122.src.tgz 350756 SHA256 74a771cd8be000df13ac908f23a2e945e8bd3590884c6bc6ccff75804cc0fb7a SHA512 9a41f30a9de955c78ee5685807482b2b073705643cceb53bf57eaf7c0c4753dc88fa8dc19f09d4c8a07124c3c3c73716f29126860ae37ff4dd6fb6178b829d1f WHIRLPOOL 29e5b3a0f060bd46c8e00322a31365526be8e3eec0c4c95b630d3e5d6a22bd3e2538c649774a88c7a3c10841ae34f1b23163ab4b625237b46aabaadec35b0c79 -EBUILD prekin-6.51.081122-r1.ebuild 1082 BLAKE2B 75d8d7ad80ee7610c35db7d475989cf3cc4ff39e6136fb37e24f171e34bcc808b2d9bee0233ec838f87dcdd7d1f0abbc1a61e48572e4638cf9467240d8152643 SHA512 582752645be5f5b5c672b1f69cf3e42415dc0c7bfeefc8f5f7304457b59530cc3ca2eb936416113db203dbf12ec0651db8d96af1acaabd8125d3fa959461f41b +EBUILD prekin-6.51.081122-r1.ebuild 1052 BLAKE2B 8738d2f9cf0f55938eacc0c9871431913ef36ad819835cee717f9f021d5600bae001e28abf87ebad60f7205817efa561e0f9f7fcba8ba01056f922ff9cf85939 SHA512 5149cbb41bc53b92c2c6c467d30adb271c32cd7233480ed0d6c2bf01f61d7b1f159c44cb656aafe1c6cfffb918aba2d448723a0700725a70e8369fb90691d776 MISC metadata.xml 261 BLAKE2B 509ce9958149f9cd522a2c68dd0d23ed851d19d02494611456592897093378d180a6006cddf1575fd60106119e72726255c49db2e10fde1b370bdf2f3cf8c94a SHA512 72682d17ec2b918131b551bd1ff41004965d3cf0c00d24222b34741d2eabf601cf36d4266be70ba7fb7bd0ab55d9dcb5b8e4ca41125bc31f176516797459c8c7 diff --git a/sci-chemistry/prekin/prekin-6.51.081122-r1.ebuild b/sci-chemistry/prekin/prekin-6.51.081122-r1.ebuild index 7f90ace13b9b..8bea9cc52301 100644 --- a/sci-chemistry/prekin/prekin-6.51.081122-r1.ebuild +++ b/sci-chemistry/prekin/prekin-6.51.081122-r1.ebuild @@ -7,7 +7,7 @@ inherit toolchain-funcs eutils multilib MY_P=${PN}.${PV} -DESCRIPTION="Prepares molecular kinemages (input files for Mage & KiNG) from PDB-format coordinate files" +DESCRIPTION="Prepares molecular kinemages from PDB-format coordinate files" HOMEPAGE="http://kinemage.biochem.duke.edu/software/prekin.php" SRC_URI="http://kinemage.biochem.duke.edu/downloads/software/${PN}/${MY_P}.src.tgz" diff --git a/sci-chemistry/propka/Manifest b/sci-chemistry/propka/Manifest index 2e7d8e028a47..bacb3440467a 100644 --- a/sci-chemistry/propka/Manifest +++ b/sci-chemistry/propka/Manifest @@ -1,3 +1,3 @@ DIST propka-3.1_p140511.tar.xz 151284 SHA256 42b4f6b98bbbefa11fba5e603aa33f1747362746c1170c9958ad408dc34e39af SHA512 c2938af41ed386e267cd045b14e34779889b3c206016d747b68c400f2c8b37bd50cc3b74d055d931476065ac6817a2dd2cb87d68de9911adfff1c8e34a667fc3 WHIRLPOOL 0553ef5f519d41af508885f1900a68627fcf3fb2f901c5d1cef54fe6a5774ef08caf42bf5e80f08cba4c76c9e330be89502e648cf5604aca411c168d4ecda6fa -EBUILD propka-3.1_p140511.ebuild 818 BLAKE2B 293d92f717efce535e7f224f3a637d6a3efc67b45a59518ca4ced1630f0a245d296b3fc731f1782ce540fcf547bc42f8b253d8169dd47c9db0d29e68de00ec0d SHA512 11067e38fe55d39e0379f739db6385d28e6bdb45545d61607c3e2f4d5780235eb0959c40d5c2f4ef0e2a7965c169c720cb27be9ef445f272953d308479a2f430 +EBUILD propka-3.1_p140511.ebuild 809 BLAKE2B a16f0aecb2e419afff73e4162c82ad0ece517e767cc26d40ef9c2466be00e29bf2a62f0405c6a3f632415e2436c615fb7a625d9a7cf3b245655c640d0a892f35 SHA512 594f0b00d9ef1782e881e522b6ffdaf5941adde282901a616d9ce548a322812079914fe9b830a5eb498c74f878a4917bc0b1c8af9eccd77087f3ac3d62e72640 MISC metadata.xml 271 BLAKE2B a446884cbe7a6789e0bcd82759f57bf1ab7b29c5ab714057ffa821c90f799d1fa9f9310c187ee4c3a8ae2476f6ea9d15f368045779f1581e68d02802c61c884c SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 diff --git a/sci-chemistry/propka/propka-3.1_p140511.ebuild b/sci-chemistry/propka/propka-3.1_p140511.ebuild index 2d34b8da5d5f..4b90e9aeab97 100644 --- a/sci-chemistry/propka/propka-3.1_p140511.ebuild +++ b/sci-chemistry/propka/propka-3.1_p140511.ebuild @@ -7,7 +7,7 @@ PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 -DESCRIPTION="Prediction of the pKa values of ionizable groups in proteins and protein-ligand complexes" +DESCRIPTION="pKa-value prediction of ionizable groups in protein and protein-ligand complexes" HOMEPAGE="http://propka.ki.ku.dk/" SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz" diff --git a/sci-chemistry/shelx/Manifest b/sci-chemistry/shelx/Manifest index 7ce41329f3fe..6c981e7abb5f 100644 --- a/sci-chemistry/shelx/Manifest +++ b/sci-chemistry/shelx/Manifest @@ -16,5 +16,5 @@ DIST shelxt_amd64.bz2 8862210 SHA256 519c695b8f6c0425f2635dc021be8138ef029761a43 DIST shelxt_x86.bz2 4441488 SHA256 ca64d86718d306d8d5269f0d7ca92fc2921f1a199afa1bc181b5f6cc339a012c SHA512 83027d24d58863030a284e5e573df27db760ce61f7c8d7da5741471bd814256ae5ade1316aa3e262a54c4c4fb6ad231dacfcef043c3279d381d2969e0b73dd14 WHIRLPOOL ec91f0e6d192507854cbcc2baa751c17185df70f2220eab8f487a1db082bc055aefe2b5f437e144fbbf60c01f1d735057c07ff2f71ab77c88c13a1a19ffe7a65 DIST shredcif_amd64.bz2 1371002 SHA256 eddf6237b70114bab99845c228d5ba6240a2a9e019bf59678f2222e2ddc52cfe SHA512 5846f7a14936ae4c710ead752a83dd8d73bbcd6037c38f2c566156f87678a84c1db3fd5d0a6e3c6dfb04a2ed7c96c8497c36faaf2bf2ca99ace74f98152ba3be WHIRLPOOL 11b82847cd4f3529c7708de7d0ae7da4e741a58da58ac01954e7136ca2f02c599a81485c70ff36916cdce97e86ab67efe61ec544231db9d7ad903edfd68e232b DIST shredcif_x86.bz2 461442 SHA256 aa06e0b3f2b7face7f486029d4c83e9fd591c46b2a41db6ce8e3014f6a713d78 SHA512 8097b6285d3e9269989663e52a4d903b279f9cdd0a5650c91d605dd324c62361de619c0873968a3178d3c125f59a9b448465a09542e2582779fbb8cca1f9ebf7 WHIRLPOOL 37f9410d1fcf2881b3e83b752d5170859ebab2063da8124715d5f627a83b9ef2ba4694a2a77a213e8c1b92d474304a7aea83b1f03111fd2abbb3fcd13d054052 -EBUILD shelx-20141228.ebuild 1106 BLAKE2B b29975eadbce80fd40a9d5d4f35108885951a41f328f016f830472ba93fb48a5d54c39eac8af9ce8332a85e93f614b550e42bf0d77f3b15b85cb01f4196cef1d SHA512 b50a1b7db705633d9eb6654fd8485164c4f16dbe4f632ce834018b9dee9e605fb63c8fa04b4bb8f6a8689b73ab2481df8b0a9ba8ed858b69094f39c653775419 +EBUILD shelx-20141228.ebuild 1093 BLAKE2B fef0b656bffa33a4be13e34d101b1e55f4eec5d6ae790971a6919e0a753f3c28783e0b6480641d9815204fd84d1b4d2495dd0538746a021189dec6d4503918e3 SHA512 4e35de5c607eebb0484e8144cb34e03040efe733e7fbeace80d99efca1aecca1a13a1bfe1a01c6ad20d7f7c0e14a318603dc839ef5172752920c759325119919 MISC metadata.xml 271 BLAKE2B a446884cbe7a6789e0bcd82759f57bf1ab7b29c5ab714057ffa821c90f799d1fa9f9310c187ee4c3a8ae2476f6ea9d15f368045779f1581e68d02802c61c884c SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 diff --git a/sci-chemistry/shelx/shelx-20141228.ebuild b/sci-chemistry/shelx/shelx-20141228.ebuild index 541cbfb83802..d2b279bf8d1e 100644 --- a/sci-chemistry/shelx/shelx-20141228.ebuild +++ b/sci-chemistry/shelx/shelx-20141228.ebuild @@ -3,7 +3,7 @@ EAPI=5 -DESCRIPTION="Programs for crystal structure determination from single-crystal diffraction data" +DESCRIPTION="Crystal structure determination from single-crystal diffraction data" HOMEPAGE="http://shelx.uni-ac.gwdg.de/SHELX/" SRC_URI=" amd64? ( diff --git a/sci-chemistry/suitename/Manifest b/sci-chemistry/suitename/Manifest index dd7a37c2b5c0..6c9b760d088d 100644 --- a/sci-chemistry/suitename/Manifest +++ b/sci-chemistry/suitename/Manifest @@ -1,3 +1,3 @@ DIST suitename.0.3.070628.src.tgz 29914 SHA256 5c2a709aa2d815b259475344aa2b982c157868eb9a7e5d6407b8f525f7e28c4c SHA512 27811e2511da760c3c35d0a44aa798a35610a0e80a72d8aa58b78cb780156508f96e1890f558b1aa43bc3469d433352b29e53dca79f3a876ae2b7073f8e73088 WHIRLPOOL f4d84180df12062ebfe402231276808bd28280c44c83559330071225aaa8f29c70cd7edf24c7657bdc53d6359df6dc61b7a601f01cb5e164eca3b017d386c6ec -EBUILD suitename-0.3.070628.ebuild 760 BLAKE2B 85fe6f6f8b784c55dce02232e1036a4c3cce551fbb1ad2aefebf39513e2e76b960d99a821d9b5cb448dac3ad5c360e24b020b21ef34ff3cf29f07f70e58f1f5a SHA512 59764e2a91931807a5a0f3f18de7b21064f6bb31311350d921a59d2d602b5433fc849ff16117504ababefc70ca007b302a67fb68f80ea38d01cd695fdf48cd4c +EBUILD suitename-0.3.070628.ebuild 726 BLAKE2B ab5cc3123c164466949a49ae93935e9909329edc592eec3ee824dea0cd1089f86662574cbe303f19ee685a4db5737c57f88b8f354d84b6dda26a630d98289097 SHA512 508b64119cf3c2ae72e5e321d7364401c33939490595bb2febae866df6ce2a00d506d78425d4de644fbe49191dc9163283e60835dd1ccb3bc428c9b9d1f4f079 MISC metadata.xml 1118 BLAKE2B f10c14e983382b489ea47eec41a17e39df81660cc56ea001ddfc9b6c67f8e96f65f52cb5e8c24d5d5211dfbf5fa17293f3dac1d2924a77e3b517d1b3796f7892 SHA512 7b2b6baa9bbc3e4ff3e2b2c0ba15dce0af04b06133c96872bbbb3626566a025d1b7d5472fc159e879e7be0cf50b5c27ebbcbd8def5cb182fc3654b893d88f2f2 diff --git a/sci-chemistry/suitename/suitename-0.3.070628.ebuild b/sci-chemistry/suitename/suitename-0.3.070628.ebuild index e0306fac8f29..8441770df5ca 100644 --- a/sci-chemistry/suitename/suitename-0.3.070628.ebuild +++ b/sci-chemistry/suitename/suitename-0.3.070628.ebuild @@ -7,7 +7,7 @@ inherit toolchain-funcs MY_P="${PN}.${PV}" -DESCRIPTION="The ROC RNA Ontology Consortium consensus RNA backbone nomenclature and conformer-list development" +DESCRIPTION="The ROC RNA Ontology nomenclature and conformer-list development" HOMEPAGE="http://kinemage.biochem.duke.edu/software/suitename.php" SRC_URI="http://kinemage.biochem.duke.edu/downloads/software/${PN}/${MY_P}.src.tgz" |