diff options
58 files changed, 595 insertions, 404 deletions
diff --git a/sci-chemistry/GromacsWrapper/Manifest b/sci-chemistry/GromacsWrapper/Manifest index 871587ba1e22..e7ce748fe3cb 100644 --- a/sci-chemistry/GromacsWrapper/Manifest +++ b/sci-chemistry/GromacsWrapper/Manifest @@ -1,5 +1,5 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA256 +Hash: SHA512 AUX 0001-Drop-chmod-hack.patch 863 SHA256 1a54e89fd14ab57db0a928dc7ac3e9cd505bb4659e7c6ec849e213aca9e089a2 SHA512 d37a73ca6ecd54c149699177cd10af9782a7ee48c77911a027705728f76a1631f71b37d0263285373877c2e5db8b00dcaafd3e1d6a8dd7d62b1253a905fc5d58 WHIRLPOOL e387b678ed67b3fdba2f1dbe0b9160db3909c331f09faec3824e69147da567acad6719fc3d2dcad616071be83be7f865a7bc524839244a0c4153049d072315d5 DIST GromacsWrapper-0.3.1.tar.gz 1575486 SHA256 ddd2668060668528878370961a9a33257cf3643fd0d9e9191b1d26d4f78e803b SHA512 655dae431bf575963af58a5f75abe6703fe1ecdddba5839b671d9237ddee0e33ab19b528e89bcba4db9063fe30622d44e8f47c7b6452b4d1eed8c7400873a012 WHIRLPOOL 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a/sci-chemistry/apbs/Manifest b/sci-chemistry/apbs/Manifest index 77056013f174..55e433dbfe4d 100644 --- a/sci-chemistry/apbs/Manifest +++ b/sci-chemistry/apbs/Manifest @@ -1,5 +1,5 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA256 +Hash: SHA512 AUX apbs-1.2.0-contrib.patch 382 SHA256 0b2a1c518c66de6010954f101c1622cfd570bbfcc4774d98607174e57e67f1b3 SHA512 42f29854c122ea48c9a8eb0c92f0e7bb3f1c4ee353437fee9e7dffe302d85b4cd44b8b0a0e6cf6da7697c6f86a8f019e4c05491f8271e4e9d1fe27a34c9b5260 WHIRLPOOL 3a4e1b1f2b7055727337bf27fb8118441b2d7f18ddde31c738f70d3e3a604a840ca18ab3b7bb366b029c9285f31ad2073a38f6dcc1e9bcdbd4f06a450ace8505 AUX apbs-1.2.0-link.patch 1716 SHA256 37faa758d6439f22853aa9d4524e3e8770437d3986e00649a193b0a97f369bba SHA512 79cae71f2d09cbed168cdb5630b1278167d9442cedbb789f42ff3dc3cb6dc0e07b7d6acfa0251085ee8034ffecf4a0d3641bc0cdbf9b70da5b4efee89d7b160e WHIRLPOOL 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Continuum electrostatics plays an important role in several areas of biomolecular simulation </longdescription> + <upstream> + <remote-id type="github">Electrostatics/apbs-pdb2pqr</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-chemistry/avogadro/Manifest b/sci-chemistry/avogadro/Manifest index b3b9f1a08941..82228200303b 100644 --- a/sci-chemistry/avogadro/Manifest +++ b/sci-chemistry/avogadro/Manifest @@ -9,23 +9,23 @@ DIST avogadro-1.1.0.tar.bz2 10741835 SHA256 6b4eaf57ae52bf43df9b103c77e6abae71e0 EBUILD avogadro-1.0.3-r2.ebuild 1362 SHA256 10a32cca7dcbe31345dbfcc0a2ccd211caf100ad9b4eca0b54aa6862ec07df17 SHA512 753c8d3d9c3e16359d97e1c931f29eb312c7f8366fa14986678d984567cae8ef79731e58fc71f9fcbd51d1a66a2c31ac45afe9b90f8a464587e1ea84049f0dfa WHIRLPOOL 359e52cf203ab2195e4c186a3f3a7c3d46467a36990331907f03ea5c63315867a2e409d5f340863c5c16b3de9fb48e5c17a7e1b19ad06efd988a2fd460ace7e9 EBUILD avogadro-1.1.0.ebuild 1486 SHA256 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It can draw ornaments easily, and exports to EPS with LaTeX fonts among other things. </longdescription> + <upstream> + <remote-id type="sourceforge">easychem</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-chemistry/elem/Manifest b/sci-chemistry/elem/Manifest index 67d8418708da..22c0268f4eb4 100644 --- a/sci-chemistry/elem/Manifest +++ b/sci-chemistry/elem/Manifest @@ -1,15 +1,27 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA256 +Hash: SHA512 DIST elem-src-1.0.3-Linux.tgz 58364 SHA256 a570736165b939841a9dbf273110a6c01ddfd77559e5b020574aad8e3f5af296 EBUILD elem-1.0.3-r1.ebuild 786 SHA256 8205a82bb24a3cc6c9b0797a937066d0bf7729813d5677a36f99adf9b9ff7b17 SHA512 7960a8289cd426365d18849c722eb5a349c59577f6c6575c69afa0ddf65bab492c266e0bb6b6032fc0a3f9bbd8f38e2b8e1ff08aedc1c6b06d33459891e030df WHIRLPOOL d41933e34e8947faeaa531c1124103a3ea6923fa7343389fef1446926d37790834d38e71ac080b368868716366c3f7b60bfe3be457bfad3e24ec166ad03b70bb EBUILD elem-1.0.3-r2.ebuild 919 SHA256 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<pkgmetadata> -<herd>sci-chemistry</herd> -<maintainer> -<email>je_fro@gentoo.org</email> -<name>Jeff Gardner</name> -</maintainer> -<longdescription lang="en"> + <herd>sci-chemistry</herd> + <maintainer> + <email>je_fro@gentoo.org</email> + <name>Jeff Gardner</name> + </maintainer> + <longdescription lang="en"> GTK-Gamess is a frontend to GAMESS that allows users to queue up GAMESS calculations and run them sequentially. </longdescription> + <upstream> + <remote-id type="sourceforge">gtk-gamess</remote-id> + </upstream> </pkgmetadata> - diff --git a/sci-chemistry/jmol/Manifest b/sci-chemistry/jmol/Manifest index 5bd539158474..1f73f446a30d 100644 --- a/sci-chemistry/jmol/Manifest +++ b/sci-chemistry/jmol/Manifest @@ -1,5 +1,5 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA256 +Hash: SHA512 AUX 12.0.45/jmol-manifest.patch 3726 SHA256 74cdf274352161ffdf155b34b8d9110dad9c4a15720467f73d301104005566bd SHA512 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-10,4 +10,7 @@ molecules quick and easily. Of course you're creation can be exported afterwards in high quality in a number of vector and bitmap formats. </longdescription> + <upstream> + <remote-id type="sourceforge">molsketch</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-chemistry/mongochem/Manifest b/sci-chemistry/mongochem/Manifest index 1a16bdfb3dd8..0361bb490513 100644 --- a/sci-chemistry/mongochem/Manifest +++ b/sci-chemistry/mongochem/Manifest @@ -4,21 +4,23 @@ Hash: SHA512 DIST mongochem-0.7.0.tar.gz 448002 SHA256 a93f53e8d945f2e3b97efac8187cfaeae0a7e491265cd65d66d25e34577cf883 SHA512 076f79c9dbed372cc760c972d5529fc3a10ea23ba2a58bf1034b736c5394a9283223562c0d6d14a135cdf87786a222991ca613765484d5a36c31f65c2ccccb05 WHIRLPOOL 4b044e00e44b1333e3faec04e15eaf46e7b17eecd4c155099fc5f06dc9c62bde70adc8bb8a9793df9b305efc89f5e44bdea77eeaac1da3554c002cba117fe8c1 EBUILD mongochem-0.7.0.ebuild 868 SHA256 52b7483217751a607c5fae25acb60d81e4f74103bb8f3a68cf87ef70a4e17e40 SHA512 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This package enables to access OpenBabel library from Perl programs. </longdescription> + <upstream> + <remote-id type="sourceforge">openbabel</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-chemistry/openbabel-python/Manifest b/sci-chemistry/openbabel-python/Manifest index 84433b83983d..5e839ec36eaf 100644 --- a/sci-chemistry/openbabel-python/Manifest +++ b/sci-chemistry/openbabel-python/Manifest @@ -7,23 +7,23 @@ AUX openbabel-python-2.3.2-testpybel.patch 1105 SHA256 d39e2530c31f074aa2860f0de DIST openbabel-2.3.2.tar.gz 20509105 SHA256 4eaca26679aa6cc85ebf96af19191472ac63ca442c36b0427b369c3a25705188 SHA512 d0e1f8b758ffdd65ec6c31d988bffe3279355e286ce69fad12c5905b3b832e2b73ee95b1061b1576aba1ee9fe4da5e31ec30350c473be17493c657dc80caf919 WHIRLPOOL 74eff18b73d24c8f702e5573a58ba6afba8402e9ce8782de95dc0568575a7d2d632dbc8e8a98b3cd25efdfa7379494f7dcd449342c81ddf73f42a387bce77aaa EBUILD openbabel-python-2.3.2.ebuild 2355 SHA256 8da52644ff0721f8e5848f6eaa3f5b9e5fe99c2e7e7421aa286960c4ec19f650 SHA512 0e4314ff787187dcca67f55923d023658342d1044035f07de7de8b9c10b779414c48ef665edcd182663dfb2cdafc6e033a2d75f72e2ddd01a77aaadc3f3aead3 WHIRLPOOL af799f8eacef73be6974274edad2771355148210e02b5ddb3b79d4d112a3e4c979956c98c7393fcd0bb1f40a406d211b9e3197c5dce0e1c079e4582f115c47f2 MISC ChangeLog 4102 SHA256 c30f6456ce0ecfd6fb53bb298b7914b8fcc854fdd61e6ae42d8783879455f73d SHA512 37d5868f760fa81e706899ab2edae697e801c2782a0516351c25cbd13475d0394d6ad00b749f6cc6cb29d1539fe0c1340c8e800ba543c240c8f987ce5726717c WHIRLPOOL 87719dbd543810a3815b60f98c2e35486a6ed725a91842992ee305bf30ed89a4f1bc453a4c4d89f28f46a0ce101912068108913e5f374a3886c2f19fdff17e80 -MISC metadata.xml 551 SHA256 1bb4d6cf369cf20c39c52bdcdd18984e00538f51ae747ae08d81d5162a426bcc SHA512 f3ccfd4c6b6b32d130c959e8bc7ff82b6307f8e997c5ca8ca9eb20ef4ef9bf4c52854579431d91fde6701f2b4ad096578e752be4367f3c7b61f9a721938ec6a6 WHIRLPOOL 3c5f7bc1a3500a6fa96a8bfb211fe07e9880ba2cc44d132f235b2458e9bf5d5c986a51cb384668733254a59aa63802dca738b39694632eb1127838100b0f0710 +MISC metadata.xml 634 SHA256 e8a96e98c6c36d4c116a02ae8271e2c69ddc015c9613a103b1e9a326dd0ccf69 SHA512 c5203dd678a88b9c5afb1d7ddc3c6c133b8d393d5522d88deaf278768ba747b4625a0afeb9be460f7314e57c9c6a49f1681bfb22368ebc93fb942fa76e8796f3 WHIRLPOOL 1ef2a6c201b77f41b05a00bcac1226d22fc29f04e75eb33977b8fb9e7c074fad58b3c461ce04097d239540d283cb9f2235091e18d555fd78ef72f57c0d78f8f3 -----BEGIN PGP SIGNATURE----- -Version: GnuPG v2.1 +Version: GnuPG v2.0 -iQJ8BAEBCgBmBQJVSJBPXxSAAAAAAC4AKGlzc3Vlci1mcHJAbm90YXRpb25zLm9w -ZW5wZ3AuZmlmdGhob3JzZW1hbi5uZXQyQ0JDQjFGMzBDQ0UxMjFGNENDNDgxMDdC -OUQ0RjIzMUJEMTU1OEFCAAoJELnU8jG9FVirLvYP+wW3z0ZedjcWTEHHJtbFVZjW -Uhd3NImLzUBS68YHRBIWPvnkKMj4719oz1otUBO3jYAeQ81UXfYkIhwJ8tAKfy7b -sa26shiZ0MuN5X78U3nEIzh7+O2oHWSD/6vOWX7ghaqS/eTzfOJtNkgs1EFOQkmq -7Q8wwUhRyrHsIXfa0GawPt08svCBGUzx9sfRP/2e6ZcrleUKi/SSBzovrHknYGSf -3W6VMD9ZlPOl3cJHIE69SrFbOqlaLMk3zCXcqPvHA/057GGiV+lNa9ZLyvuWiBDj -yZapc/ONLx9G23j5VpilnpvkcjSj0NS+sX9hCI5xe31yUMI+WXwvENAESFc1ATYl -09aCFfrr3XIhTETl5k/hk8AB4/fbtqjtyToqyBTdQM2FTIwhToDg79hkhI3Zqi7c -8DBru5lEeTMOFn5iDD1vH0J7XYRemOFCA+HL9TAhLk9HKXZ8KD1o135qUN8T0tU+ -pFepqaC5S0vn4Yukm87qoetbY2+kZ+4G2cRFVgfIA7+3Fm+p4d+bwwNElt9HaoHr -lkhSwkgCBbeKX0txqG4qfpTBE6tO14G7Ra3X7wrPH1+s5sBrSE1k47SWpNeqpv3X -NJ4GASNTrnLwwfe1NMzI6UGo/189BRfhrfuyHbH/SpGoVZrrmS3NUUmvew7PubYz -0XaKFEYW2o08tHS5vZA+ -=a5V4 +iQJ8BAEBCgBmBQJVfxwXXxSAAAAAAC4AKGlzc3Vlci1mcHJAbm90YXRpb25zLm9w +ZW5wZ3AuZmlmdGhob3JzZW1hbi5uZXQ0QUU0N0I4NzFERUI0MTJFN0EyODE0NUFF +OTQwMkE3OUIwMzUyOUEyAAoJEOlAKnmwNSmiyjsP/1DbINCTZ4Elv73+xLIQ/PVQ +97A7UzJyQW2SOA65Y0fcu47GYylW2QycY7bgEQN6JgbdKKYT9kMcdCshlBGddAqz +YiEZzGc4j64RdzglPK+uD6XRGomO9z80oLGLwOGeRM/ixNFFS15mRB62KDvWoWIY +3A9HqxulpdKBZC3gxpEHCf/MUnut4traSjgtc2LbZDCYNrIZAZSyjOlgjWyoEW/v +JLOco7wXQKnQeWuBXHptU0UOwWNRx3lcfoVGy0r64KaYVYDeluhy1ivsLGH4UVRA +y3xO5YfTZXxkFJjPrVzodkj1Zh5G1VKgdTxlZR0J8rXQul8pHoQhZ65NMr1Y17+u +SK2ITwER+bUU/tMWzUw9KCL0SCn0aAUg38nAshWjUELxmOHei0YOp6Hh73AmcxFf +H27r/ymIp2UnywLxN19dMLWeIJQrSXILqT9pGhsLt0wzl95f2VYJTQCO1V6Wdo0v +fWaTEX0Xi59oUXbdLvSPERNWW/DheRTtpOG37ALtwvRjyYwthpExlnjCLyBVDImw +FNh9sWJoOBdNZgtxTVt/Dwgklp0dS9GMjE+I4gFu45/JdXPJslBqr9p9fhc00lXD +dHkEbSzQEzKzmhzZPo+UOrRSW3rL7NryuxGMl/MhzMFv8S9cuyVnVUA7Rb6E+9Ol +jJcK+12Wm+ZtGgvdDuc6 +=Bpsa -----END PGP SIGNATURE----- diff --git a/sci-chemistry/openbabel-python/metadata.xml b/sci-chemistry/openbabel-python/metadata.xml index 62809327b326..2fec701db8fc 100644 --- a/sci-chemistry/openbabel-python/metadata.xml +++ b/sci-chemistry/openbabel-python/metadata.xml @@ -9,4 +9,7 @@ search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. This package enables to access OpenBabel library from Python programs. </longdescription> + <upstream> + <remote-id type="sourceforge">openbabel</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-chemistry/openbabel/Manifest b/sci-chemistry/openbabel/Manifest index 637a748c8bce..0ed569cd9b7b 100644 --- a/sci-chemistry/openbabel/Manifest +++ b/sci-chemistry/openbabel/Manifest @@ -10,23 +10,23 @@ DIST openbabel-2.3.2.tar.gz 20509105 SHA256 4eaca26679aa6cc85ebf96af19191472ac63 EBUILD openbabel-2.2.3.ebuild 2180 SHA256 9b0e0be77041683ca870113f54eab4464cfdbde5b50cb7a473668fa067772b56 SHA512 843922aaf5412ca1a5891f0694592269c8eb44dacda345c51911fcf55b3727a5ad687602c5ff47fb81e8cb13e67a7e04e4f7baada09a2139e3e5a5e05fca95c2 WHIRLPOOL 4f89b451b0e6fbd9e2fe3fa6d3abe44cbc8fa1070fec22e4ab7c594326d8523fa6c06cdf6dcf86f21c5730ad0549ceb3d4404e5d899913327d3247728a4b60bf EBUILD openbabel-2.3.2.ebuild 1990 SHA256 e3d7724f5b2bd92347f37bb00e89036b8417138148757e825de3a4c365e3108e SHA512 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name="pdb2pka">Install experimental pdb2pka interface</flag> </use> + <upstream> + <remote-id type="github">Electrostatics/apbs-pdb2pqr</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-chemistry/psi/Manifest b/sci-chemistry/psi/Manifest index 41f8f947a619..f6cbf4e6c89e 100644 --- a/sci-chemistry/psi/Manifest +++ b/sci-chemistry/psi/Manifest @@ -1,5 +1,5 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA256 +Hash: SHA512 AUX 3.4.0-destdir.patch 1320 SHA256 17909af7b5dff643ef8ea134bf4468cd361457ba9192a1f9155a5870470af7a6 SHA512 cacd44ce2b5d0a1d7ccc2c2bb0429973b3d5d7cf145bc99ea5cbbbe693bef3bb624641761f93ba7f275f1d41fce0b14f15134167071fff4bce0542429d4d1098 WHIRLPOOL 3589a0e751d2ce2321b9495191be831d78997044bc15a07a38aecc29df08b40c0cbe4038593ede60872de3f45c441d765887b6395f546e4d9a4bd25fb378fdc0 AUX 3.4.0-dont-build-libint.patch 432 SHA256 2bceacc5e924b033b2ef774df789cb5cd11278452da7ea2aad5d51d3b7a8d43c SHA512 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b/sci-chemistry/pymol-plugins-bni-tools/metadata.xml index c0432fefe855..c4982f1db5fb 100644 --- a/sci-chemistry/pymol-plugins-bni-tools/metadata.xml +++ b/sci-chemistry/pymol-plugins-bni-tools/metadata.xml @@ -6,4 +6,7 @@ <email>jlec@gentoo.org</email> <name>Justin Lecher (jlec)</name> </maintainer> + <upstream> + <remote-id type="sourceforge">bni-tools</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-chemistry/pymol-plugins-dynamics/Manifest b/sci-chemistry/pymol-plugins-dynamics/Manifest index 1d61b1ed6757..2f26d2b3da8f 100644 --- a/sci-chemistry/pymol-plugins-dynamics/Manifest +++ b/sci-chemistry/pymol-plugins-dynamics/Manifest @@ -1,26 +1,26 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA256 +Hash: SHA512 DIST pymol-plugins-dynamics-1.2.0.tar.gz 725163 SHA256 edf9bddbbce41ee5319bfd0b28d6e0b0eba56e8b2d8a300d510be8ff5894704f SHA512 7e8d62ea58cb88348136fccd132d9a1faaa3474c0a0f821e729ced777620e2083b1b0606d79fc75802755c96c5eb0b90e08b00e5c865ecbaaee2b837f56987de WHIRLPOOL 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type="github">tomaszmakarewicz/Dynamics</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-chemistry/pymol-plugins-psico/Manifest b/sci-chemistry/pymol-plugins-psico/Manifest index e1c960a8ebcf..73ce887bc48c 100644 --- a/sci-chemistry/pymol-plugins-psico/Manifest +++ b/sci-chemistry/pymol-plugins-psico/Manifest @@ -4,23 +4,23 @@ Hash: SHA512 DIST pymol-plugins-psico-3.1.tar.gz 76136 SHA256 07bfb0cfc1ca4720180de0b462a8c210e933bfc75cec9823d8c89fa2007ce651 SHA512 b0f57049ea6fc290a5abd48e0c98d4fda3c3f947898597b80e11cb3ab9ac14038aade0a016b21a525bf0ab4cf68e3be35c64b8ec34422268058414c20a755b0e WHIRLPOOL 7f64fc7fbded6a5eeb1940725b7ab3488e9c94a1587040a8f072a5e38319a640fbcf9d71cb57d97cdd7ca83de0298a0d839221f3a850601785db869a0ce2e2ea EBUILD pymol-plugins-psico-3.1-r1.ebuild 1166 SHA256 4df8db9839be3667e6984ea27f97aa5370816a74a28dfeecd3eda94679ca4b75 SHA512 9ae90a4c7c380c81db02dce05944af7e1d3bb103bd4e75e41bf2a2f219c6e12f023c059749b002afe5cd54a85a2c041f1265636896d3ccce949473d044aa22f4 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