sci-chemistry/pymol: Add fix for OSX prefix and keyword ~x64-macos ~x86-macos; #437324; Drop old

Package-Manager: portage-2.2.0_alpha128/cvs/Linux x86_64

21 files changed, 27 insertions, 1164 deletions

diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog
index 79f7b86ee3db..a631c3445016 100644
--- a/sci-chemistry/pymol/ChangeLog
+++ b/sci-chemistry/pymol/ChangeLog
@@ -1,6 +1,18 @@
 # ChangeLog for sci-chemistry/pymol
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/ChangeLog,v 1.94 2012/09/23 07:50:50 phajdan.jr Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/ChangeLog,v 1.95 2012/10/06 12:02:10 jlec Exp $
+
+  06 Oct 2012; Justin Lecher <jlec@gentoo.org>
+  -files/pymol-0.99_rc10-data-path.patch, -files/pymol-1.2.2-data-path.patch,
+  -files/pymol-1.2.2-prefix.patch, -files/pymol-1.2.2-shaders.patch,
+  -files/pymol-1.2.2-vmd.patch, -files/pymol-1.3.0-vmd.patch,
+  -pymol-1.3.1_pre3925-r1.ebuild, -pymol-1.4.1.ebuild,
+  -files/pymol-1.4.1-data-path.patch, -files/pymol-1.4.1-shaders.patch,
+  -files/pymol-1.4.1-web.patch, -files/pymol-1.4-shaders.patch,
+  -files/pymol-1.4-vmd.patch, -pymol-1.5.0.1.ebuild,
+  -files/pymol-1.5.0.1-prefix.patch, -pymol-1.5.0.2.ebuild,
+  -pymol-1.5.0.3.ebuild, pymol-1.5.0.3-r1.ebuild, metadata.xml:
+  Add fix for OSX prefix and keyword ~x64-macos ~x86-macos; #437324; Drop old
 
   23 Sep 2012; Pawel Hajdan jr <phajdan.jr@gentoo.org> pymol-1.5.0.3-r1.ebuild:
   x86 stable wrt bug #431120
diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
index 65b0a747c382..0994afd4019d 100644
--- a/sci-chemistry/pymol/Manifest
+++ b/sci-chemistry/pymol/Manifest
@@ -2,43 +2,23 @@
 Hash: SHA256
 
 AUX 1.2.1/nosplash-gentoo.patch 485 SHA256 acf8ef1d53719c1b4158b0f49250e8ed7c3aa4c870ef7ce4bdbc8ec97f591e27 SHA512 a47022fb97e176ca9f6abbab9a738cf3d59a6d7257d867ffdc7091fb726e24089e7e1523a902524e1f77eab7453c0ca2163716c365f1f8c3b5d58a0820d07828 WHIRLPOOL c80681a27ab1d99404e9d7ce94fe07a639e3c971a75177bd0c3232a45540e69d08f614c5ca72dbadfa4a066029581936f06cc8919ab375c1ddf3b66fd56f05de
-AUX pymol-0.99_rc10-data-path.patch 2969 SHA256 10c97c3d4d2f620a2884a812a6997f2cf8472f2e0c589c2630a4d0bcf67656de SHA512 2a640ea0375e4d4e3abf00c81e60a063ba77b68fc459607635e432b023289fef40a4bbd737fb0db2ff50e1372b85c9d6c076a1ba4b33dfa38bb41f6fb60b8a93 WHIRLPOOL e26e7484d16dcf5cb83489765d533650b882c3597a98dd776d40d5349165daf7e2bb4ccb1e06d607a2e65449d760c6e9b6c5b53e772a31a9b3efb1c0a944ef01
-AUX pymol-1.2.2-data-path.patch 3361 SHA256 da9dfec59b09b2fd6bad5f0188589a0d04c28296651add308acd35d159f60947 SHA512 21778124727e8419f56e0ebd74abc4287fabf5e21d4c365695b9ffd78b56204c7ffae9b3d3026f457b9b290c5abc35fba712369eaaaf17ac02e185a5f284486f WHIRLPOOL f43fde51d1cb3591844869982e68f743fe7fd1f42693ad28a96ad5e39fcab90c6665187666652fa0f3687af4ba46da9e4b797e18e892f255657ea02c93cad014
-AUX pymol-1.2.2-prefix.patch 1183 SHA256 35b14c60163517debfdeae52b3be00bc0fc6ab96c58d2bf3efb65e22728522d4 SHA512 e730ad36a3835e2ef82cf40f0d6cdceddafd3fb7317bb37cf1e3a1fed7c9bb5ba4791820c89d2c7ce9a95e1fda106331f63e9cb5c5955bc3b5a360ac0be1df05 WHIRLPOOL dfb2d335f7efcb4b4627d2086c1b89ee27cedd245e2ebfea8cc2763ff5336d63cc010d71d44b70024e59a98481ab68cd55d2042ddd9cf23ae96763d02d33bb82
-AUX pymol-1.2.2-shaders.patch 441 SHA256 c15e5c5d2a6b53b96c6a7fe0b717ac0f7d85c90aca3e5b02c8d8c34b9038cb68 SHA512 7df930bf13fac8d2f0b390c117e87f6691b1bcd0e5c920fec91073de8a85ec91275fc081b2b36a4123e4dac5ebec87ff434048b361e889f6a1be73d046c138ca WHIRLPOOL 2de27db21db0949570bbe8362cdf152963cacd305a985aec637eee1263f3f343b2ca73fa74df1a63882899baf7c4beb109b279e3f2566049b2a7cbc549c721bf
-AUX pymol-1.2.2-vmd.patch 1250 SHA256 d3688f57f32912ace20a3344dc49530a48963454dcc5a9aafe45d4b6be269525 SHA512 f62a901c20dd83a5a611cafa51cbcb78d23348ed149a8bfbdaeb09c24cc3c8f8b6f90ef38dc99fdf2314b2e4663d0388681507efa0ba526efc3c49059f48048f WHIRLPOOL 5093d9cbd05cc096705a79259f7f04b412b64349bd14e8cd3fc554bc233b7ac64f02886d0baf7929d5980c15ebb8f19ffd003fc6bfcd5064fb4d52a524004f94
-AUX pymol-1.3.0-vmd.patch 1286 SHA256 79f13530928bf00b6469a6fe473d1e743e22b25edd2a4ad6d53762ccac9ff318 SHA512 50d06a2a238e32a1d6d215c4f1e3d3e3ebdfee97a34159de05ebca88debe0eec541c1b038c41eb97a149bb0c7676aefb3feeefa5b0a4d37f1fbc02f0e06de905 WHIRLPOOL cf3cf5b121e71c7b305191677e54e96a3c1674d1a528ee656b8dd05c501509966e846811cba6efb0ca2d3982dbfab066d605e52d1ffc55555537bf307ba90c7d
-AUX pymol-1.4-shaders.patch 2851 SHA256 bcd30eb9e18195d5d05d902df4497abfc6b786e9f4e418e9c71ebb1c3dca0bf1 SHA512 c094b08148067f8c65856734f96f1335c6fc50278c68c6d5f74177d9c3b25409890904746a2a7a0cadfd186de0afd9038048db5179a11778796e950bddc8d3b2 WHIRLPOOL 9cff5800d43332fcd87747173e000a3d6a044d237c6cf263e296302dca4f53196f894886a84a9aad2dd3d31879314b3fa1142f1f142e80e38a333ba2d76d4a66
-AUX pymol-1.4-vmd.patch 1414 SHA256 320436783d1cfa4f94bd4fe57af4bdf7d3d200c951938d127d77b75d77bef7f0 SHA512 73955480e5ea8d537cb1a913c9f8bc13e92e8dedbcf46f0a3fead717c116cff339db31c2e4473bfa82868abaef7c4473072d5a86ab475770f670f86cff4e2f63 WHIRLPOOL 51510faa5cdc9867ae6fe8bccc5a92c505493574e33a89284cc5368b46aef07c8b5bf96b6505cff3f886859ec7379f55dda133a5a38d7955f6b16c0af0a656b0
-AUX pymol-1.4.1-data-path.patch 3898 SHA256 911f69cb428f91a284102580b73f771648f6a1a059a53c1bcc31c51ab492b010 SHA512 fd2d9f3bfe484afce929a623ff7188a6cfbeabaebb0ef3637b4f3e76a709656b53d47aba8f82bb77d3a55ea716825c1759bc02b252d850a57385f4cc2c309466 WHIRLPOOL 90a5a01f35e0adba55e25fe6577cdc646145fa498ef0b9332294953a4ceb892680cec3f635d4865b3bdcb7d28b9cf4a70e8e8836adde13737bd18ddb758d3189
-AUX pymol-1.4.1-shaders.patch 2507 SHA256 b0cbb5bc81bb8f85bef8cbb6cd76f91b02b076ef5798075e152626becf3b5ae5 SHA512 0a0d04ee858da3738ee9d164a6534746a2b787c53807f11c936d64a6ec6b1bfd50fcdac7c60c3278243063c4aa329b4a4dc9668df9e415464ac8a39a14cc5946 WHIRLPOOL a47da0a893fcaa24c86c9cfd87a7d08e32d2cc0ed1acfc53ebd52d9f17ce5064d9ad817f680937ce85e5cb02cdc82766aaeda0dbe3d938f2bb7365b3a26dfea5
-AUX pymol-1.4.1-web.patch 550 SHA256 2545245c4c18c96faf76e0ba4a754402cb2081e56f945da1732b63fddda4fb2b SHA512 d4a5c55be2e3411bd3f016cb8df3d259bca2fe3cc3e6e4868a6afa3a459cf442c98a0a83313a82660a377cf7d96218ef42c0c175c3fb167f056b9139216f95e5 WHIRLPOOL ee9f8b994385ae4e8880d19148621e7a2e4201845deea535e5864020f382358c136d131918cfc79e56e7a0aaa4b7c1acbe5b805f0a769bc50411d9cb1e0cb8e2
 AUX pymol-1.5.0.1-data-path.patch 6765 SHA256 ad3ba9a519cc2a97c37868ce4d27a9868710be0dd32687327abd920c57db8661 SHA512 df17c40757012cffa4e63a740b9548b4b07bd81a691896c174850713fce8ec4a80bd6a035a03343c04e433ae9d09706c2d3e2b13d16d0fc6049708100025951d WHIRLPOOL b9f46b71f1c803b1c00976672a94984b786bc2b2d94c6dc10769c09113ece255bf14c0540cd106fa3c835b77cb51a34759507a3ec4674d5d307d467696a56565
 AUX pymol-1.5.0.1-flags.patch 521 SHA256 7a92d5ea975dcef50ea9614b87c56d7b4f1b976210608800413a80de98c69a3f SHA512 70b2b4c210e7e32c0ed039ab38fba6acd1f3bb0c7f67c68c7040ff9017b853e46bdf40de92b67c9cb4754cbc0ef43df8abaec25e3fae606d40aa43a9f5f22e44 WHIRLPOOL a9f0503bbdd97b10c2c458f7f07d4be26cc4e50d48110adc7b77bc2a5dc85323de757b17ad14795363140a52201ca999389d927350b9b0418699fb156fcfabe6
-AUX pymol-1.5.0.1-prefix.patch 1746 SHA256 95ccc4b626ff1a6bd21da6825e647740bcda8c003ca4cf10a1bcd3940b562247 SHA512 d7cc14ab9ce6a0e3f56a5511f4249a457c28c639760a42990f4e8e6c66731f263a751a2b2295a683c68e085188005e445e8a938fde2e372238c39df8014b8fc0 WHIRLPOOL 3d84e3d21a4542044ada9d124d4db451a98c0037acce9315ab0768a725fcec792b436418dd0531fab3d8dad624a9ac6044c1a7403bdd86c1c2c4bd316141723a
 AUX pymol-1.5.0.1-setup.py.patch 893 SHA256 3a03cb19878a772caff5c6931ff7bb1fdcd022147ec0e8a23593d4ae61cf1593 SHA512 9a4d985c981a727bb8ff7b5fc8b088dd9b774bf0f6addfe3d3517850629f103dcdd3e4ba03016bcbd127f10d93c9b844b78e826d090c7a601d535801fb74ab2e WHIRLPOOL 5bcfe9b4c095c8636d34c841764d421c980d9ff2a78f09e06049d99287d4b7c019ead5b9f0d5f9b830424c020db33fc1240d01203dc090a04ec69c3587d2b33f
 AUX pymol-1.5.0.1-vmd.patch 1723 SHA256 9a31ff39838484ce0df7658b896b8da137740871901bdc66db5dc4c46c293e50 SHA512 18e4d9d87e668be8309e6c28e2345041373ac6b26441d3dc329494f2809603fdebd6b43613609618aa5a0e61cb6cd49dcb003e2642375726a9b1cb057f87850c WHIRLPOOL a7b5e0c4e1fbe092eeaa546fab865f038dc403ce4830f09f126d99999b2c9b739fed893766651fe50b56a7cd7d7344d99d4032ceea0f9507927bf10c482613b8
 AUX pymol-1.5.0.1-web.patch 634 SHA256 7c30f0c030c3f2e30cbd1f37c58910592a71ee2d5c5a351130e0bde13104c49e SHA512 98da13dcf6d652a55edfa702ecd2e304b525833cf13380f87185a8710aeac5529a9284f83146e5fd80d2ca3b15c174ddc666a931f2a643ca4c80333f00fb9d3a WHIRLPOOL 8ff57da3a02d5d6fea9fab91fe11bc18c361e563145853166a2793285fd87490859089a1a3c46488b5703f801f805bc3b3720ae6f9bbabfd0bc33d89804c00d2
 AUX pymol-1.5.0.3-prefix.patch 2278 SHA256 d4bb54dd667011747cf4f201cc4c0ac84ed6eb59cb066c374d6f89097a3914cc SHA512 bce01e7eb890863f43be482e7eeae8100002c5e27ea935dfd36f3867b80f734a41d7f723e33e39574bb6ff0547d16febf637d44fd0371c68897d6b6f61d6ecec WHIRLPOOL 4a74ea99bf6620e1c37b6a3c1382de6d1f5b97ca97d7fbeddb3207172dfbbda1bd3bf90ea6072627e5595014c7760c2d15378b67a67f3ecc0cefc9fff84e9eac
 AUX pymol-1.5.0.3-web.patch 545 SHA256 559fbf42497c33a0ec844a11d7cd89178a8e0bae437df71a4408b891857ef9b3 SHA512 272a516e8d2780bd5b74e852c9d06c27f8dd645e3c68b17bba1931d0d59af55637bc0565447642539b3b0e73b82e5392c13e51171aa3a2ebf42d717fabf4bce2 WHIRLPOOL 95a5bf25a068da437dd2c04fb22b9b4216646f9b0bd0c3ce333428a5eccc090005a0e6b4fd50279ba22df9a754acb9b61fdec07dfb7a134e3d966e0e8e14cb88
-DIST pymol-1.3.1_pre3925-r1.tar.gz 8185909 SHA256 74d3a3dd1972e2f47458e80c3d157871c361ad81119c76d1edd40b5e491cb50e SHA512 e830806e1a47891a3c9dad51eb56dd5d2b7210eb2d06f06b5b206e0872430e62288b8a1874bb7e030c74031dae8bc536b50fa1d9d00b669c2c9faedb27dfb187 WHIRLPOOL 348071d2e4cdba16e32b2deb26282ed0a812224de96e071a0f83d2151383aba684ed7dbe22b5f3e69af4e8152b09cce8500b533c4a4d73895579f84fad287c6b
-DIST pymol-1.4.1.tar.xz 6831544 SHA256 af020e3103360defa3749ed31c16938a00032d4c2bf40f8455c746919aeaffd6 SHA512 904850e2c0c3ce53429ff6a76b15cc9e693afbcbd9e40ab98f00b2fbd576e1e954ba4872a80d5eea83184ce306d16684fb3236655b4147b125dd0d401855ab16 WHIRLPOOL 0bee723c8547e385b88d261e873212521907a4c27b8f6a03a96de5c2a73e5b22c6578cc55882ba293073b81217178e3d464d6d47c8e825a3fcb0fc59b9639512
-DIST pymol-1.5.0.2.tar.xz 7389704 SHA256 22761608a0f7f815b7399830050ec759b2ada8edfe1700e2f299047d0e9254fc SHA512 6e823733b1687806eff7598c696ebae090b7689f5b25e0c03d860dbe894233aadd68926f0fefc2313fec7a5ca656292c1319580044f5b60000c67254bc2cb0ce WHIRLPOOL 146cc14fad25b4716cf690c1dccc8f8d14791b5bd55a2ec3c22ee87cbdebf228ea7d46a23b7e933bc1b6873af3dcaf202d69743999f2fec4ec80577f570dd9e0
 DIST pymol-1.5.0.3.tar.xz 7412080 SHA256 b304c2839bc944bd2619403474d36cb846b372ba281c8f05931d3f155a0aec7a SHA512 a3f1dd3089fa4158840f2cb8c3848ef70284d1f859429cfab6ac9b00f649d7274a3ac7697a7fb4996d7643068a916f9ad7b1952c5ff27003cedcc7c89e795485 WHIRLPOOL 82788bf6fce52d76ff00d1d7243e8f3962027b4512addaf0fc2f881aaf5f0da6582cb3b3b56a178ed36572947273a999be3d67ba49845eb887da6cf242c5b5f3
 DIST pymol-icons.tar.xz 38100 SHA256 03500f28256f67abfbb7d08b798b11aaa208f0ae1473ef2a7205b3c012ddb06a SHA512 5af51014d4fcbc85ef1fecd7667224709c9305b9b72bfdfd89ece2b4420fa8a81bf8c85fcc5903e2a670f44403f12764808f6a16ef42f111bbd0e7ed8e412d54 WHIRLPOOL 6104d378928c56b39f8cbe29184629b73f87da09e81e41ddc08b9b291876f1a30ccaf9ec257f47798c6d03253816f80c14567073c419fa48dd1520fa3fa58ecd
-DIST pymol-v1.5.0.1.tar.bz2 9695855 SHA256 16c0cfbacbbd967b23654dd3708ef6ba877ab2a6c0985ff806a17186427de49c SHA512 f44cccacd5a9cc6e9af8707b3033773f9bb15d09b7cd0fe8634a6277673ffc09dc9e5122fd614283c60fe1b89d2b4add1f4402aee4c96f0fa4487b0f7f6c1033 WHIRLPOOL 708c5db7cc9c4bba8dedd8af189a9c76a3356f04d6351b94509bab2a340c2f59d3610e3cc0483442c382d46ae9705e4a054e2d432b152a7a32e53b96daa351cc
-EBUILD pymol-1.3.1_pre3925-r1.ebuild 2698 SHA256 f6f88b0f0715096f6ad6ee74033b0f71c2f47d77ed02d05eb97b78fb10bcc2eb SHA512 34d0b7146c4bb291dafb160c9d442d062d85f31bc4279b228b8798b050bb07521e8b7c0b01f3e3215de27529fa2bd6bef0d3351ce7efaa8ad0427e4f601ab69c WHIRLPOOL 51a99df6b8c41e42c9f8c4fe500d3ba53827422bdb8e0a686516eec9d9b0e3ce31da332afe607f21fd7334037fa7cc88e10f8f7ab627c6b4826ecd0789441f0a
-EBUILD pymol-1.4.1.ebuild 2807 SHA256 c4713c5d289c6a00093a2c89afb918c5411de8dee91082fe22fc708b38463067 SHA512 77e50d6556f0581c98ab2793fea5290c8ed093702084daea5ece78c31a3858580fcc11b6eb81635ccce3f02faba3e122bf74a13eea33b586d4fe526ab4482b13 WHIRLPOOL fd3bc7bccf2721655ccf4c0f7b782a64fab92900ac0adf29b5892111f4a6d2c43c496e39cbc4888e7627c80c37a3275c3ea0fdaa229e47dc5750b9a92a8ae211
-EBUILD pymol-1.5.0.1.ebuild 2821 SHA256 6fea4c284b949c3f6bf0e697026fc5113f76651fb155f4f9829340ac21169686 SHA512 658b4a5260e3a2d852dd4785c9f09c049e732197e217dce098aec5afe7a5a1fc6d6fcdb0e63c78fd47339d360cabe518688604b2edeebb749783fb77a081d3fe WHIRLPOOL 32735f7c9cae06b39e12235a362e5ec12bfe2c932f9258ce8f83736da07cbed090777795abbfe7a5a5a520df8a42deab92fdc0b929c9857f0eeb140cda2e0f60
-EBUILD pymol-1.5.0.2.ebuild 2835 SHA256 46039b68a11bb4a17edf0ff7cdff2446e46c39197b1558d67e6655323dd114ff SHA512 c045b2ba6f6bf2ab03590bffedc44f5976a71e6787f350f637dbc4d44311c1a2c1acbed951fa9b21c85fdb9536115108d5afc0d0b39dd89ba330c8cf0b65ecee WHIRLPOOL 7d24fe8128d0d444d880878b41c88bc1ec5312b76543e9082246ad06a77baa5ca3bed488a1033db313541537e55a6568dcbe0331063f8db85f1ec0fdbed312c0
-EBUILD pymol-1.5.0.3-r1.ebuild 2979 SHA256 711178cf020071bafa9d0117113f4e600caa83c5de66bc9d264e8786180062af SHA512 739cd927594333f1c90ebc62c06cf2da8c4784c449b0ce1d66803af7d95753fdc215eb6bf3834f5459ed056a92a59cffb3eb78d4a116cd5a2f3d34ed070bb9bd WHIRLPOOL 1cfb86ed82a5f5495246475562f96de9f147ace027b2715867182b4838132154cde1ce8f15ea8aba7bdf483d9860a7029cccd7ccec4508c01cd4972473a5ed7b
-EBUILD pymol-1.5.0.3.ebuild 2817 SHA256 fa1b7433628e2473997c033504db72842a460370753cc901f506f390bb0cc610 SHA512 30368f1e57cd51a4a62e76a3c6631635f8f5256f12f5dc7b16f2c1aed3e3e4a730126993a13b3302d13f272b70c5cea5b993809ecd65931633632fc9c86b54e7 WHIRLPOOL 61acdd0dff47bb551db974f1a04c5b68689746e569eeed7eeff1e40191e006f90588f36fff4a03c75e586f53fe8c1895a81677cca797ede049dd5f56558d3408
-MISC ChangeLog 3199 SHA256 b2369951bbeb8ea668eec0f0d934b1a993eaf919905fee474a9043e475ffa919 SHA512 9fb5cfb42394f6b196d3b242a81561f29f44d78d6706203ca663c44e58cb5810c78c5d97f212778f9c7d69bce41b1184bda500d988c2fcf4009c3fbdf8f92c1a WHIRLPOOL b492b783af2764a24361d8b0c65817b81dc6f2b90074baa778c7bfc6fa94927da3ae08edc1ed4a5deb28bcdef0c06de0b2dbe7d172bdab31f2d0c5f57d40ffe8
-MISC metadata.xml 569 SHA256 6f2b2746c7b2182262554076f11159b11d671695c40509bf7014c7546d719ff2 SHA512 3d8783ff6a1da73ae10d9c4b9600034045eb601d5a87755205a4d7f4cd44ccdc6dec27365f6631036689dcf05d62f440b9fda4e053b53c26fa0f018d9f176737 WHIRLPOOL 04ce89b34118d29bdbffb42556b607d295dd875e49c130aa11f3a2f14796c16bcef3d120d2f8b0b2ee123f2dd9e6102aa344bebb2f925b2ea1fe094aad447187
+EBUILD pymol-1.5.0.3-r1.ebuild 3101 SHA256 39c25812b8a12eda5a867fdf51efb8ae553e0f796a25337bbdca748abc5b8e93 SHA512 45aec912566664f5fe05094c0a7aeb672d297f36d2e95a1d0e63725af77da8c1455f2c5fbbf39918447b34f7bf3d04c5bd2b40d0b5b16aa516fdc7779fe79136 WHIRLPOOL 6164ea4147e992e2b691d41b5922b0ebbba10f4744d751d40d7d4bcf2615ea1aedaec4c1b2fd1b5b4729eb6cb528f757fda1fdb8f10501a2f96a4ecd99200314
+MISC ChangeLog 3896 SHA256 4414a8d48903c426845f51c6a91a5b35e74ddaab99b5517e8c385226363069c0 SHA512 ae67a04f0f10341b63c6dae7d8ff13fb9a6976ae7f125aaa65ffa15e9aa02271dfc5c43bb425c1e5621133b6ffa2ed259d376a5c12e97f4f199bf1b3b3628764 WHIRLPOOL d972e6021d24a31c1ffd4b14f624fb19ef5e64cdf44174287bff2972dcbf0bc8c4c1330ff7cb59c97397cdb73a2d1ec735db492cdcb391d299d92a48bf782b1c
+MISC metadata.xml 476 SHA256 d7e097dacd164bc559c12edbfb8f6fac907212ec1717f03b2169e23a4a24d3a9 SHA512 43ccdb6332400f9474f2aa2e804b19d7800096ee4274db0b1754f3fbcb4ce1bf06a0c0aa742558d172c870136f3b0671faa54ba0bb452398ec8531f4c2af17e4 WHIRLPOOL c5baebb3f8796c4e1d1a409c02bc36524b72857e84367cfb2f7b857e7f709bd26bca477bafbe2d676dd06bf61db6cc02c012fe7addfc03f33809bd342d0e69e8
 -----BEGIN PGP SIGNATURE-----
 Version: GnuPG v2.0.19 (GNU/Linux)
+Comment: GPGTools - http://gpgtools.org
 
-iEYEAREIAAYFAlBev2EACgkQuUQtlDBCeQIjmwCcDT3jmYvAgj+sht5t5Cuc/ecV
-sJoAn2uo+LqF+Rm2EDkTeOFMblPFUOO5
-=zAUk
+iEYEAREIAAYFAlBwHcYACgkQgAnW8HDreRbiRQCfRG6KqomUDXLecn4JWs4fjyrE
+XNYAn0BY77ddXL9yPcoC2j5aw2Cb2XHI
+=Fvbp
 -----END PGP SIGNATURE-----
diff --git a/sci-chemistry/pymol/files/pymol-0.99_rc10-data-path.patch b/sci-chemistry/pymol/files/pymol-0.99_rc10-data-path.patch
deleted file mode 100644
index 286489ff8d58..000000000000
--- a/sci-chemistry/pymol/files/pymol-0.99_rc10-data-path.patch
+++ /dev/null
@@ -1,64 +0,0 @@
---- pymol-0.99rc8/modules/pymol/commanding.py	2007-04-18 02:11:48.000000000 -0400
-+++ commanding.py	2007-04-24 02:17:53.000000000 -0400
-@@ -129,11 +129,11 @@
-                 unlock(0)
-             r = DEFAULT_SUCCESS
-             if show_splash==1: # generic / open-source
--                png_path = cmd.exp_path("$PYMOL_PATH/data/pymol/splash.png")
-+                png_path = cmd.exp_path("$PYMOL_DATA/pymol/splash.png")
-             elif show_splash==2: # evaluation builds
--                png_path = cmd.exp_path("$PYMOL_PATH/data/pymol/epymol.png")
-+                png_path = cmd.exp_path("$PYMOL_DATA/pymol/epymol.png")
-             else: # incentive builds
--                png_path = cmd.exp_path("$PYMOL_PATH/data/pymol/ipymol.png")
-+                png_path = cmd.exp_path("$PYMOL_DATA/pymol/ipymol.png")
-             if os.path.exists(png_path):
-                 cmd.do("_ cmd.load_png('%s',0,quiet=1)"%png_path)
-         else:
---- pymol-0.99rc8/modules/pymol/fitting.py	2007-04-18 02:11:48.000000000 -0400
-+++ fitting.py	2007-04-24 02:18:07.000000000 -0400
-@@ -61,7 +61,7 @@
-         r = DEFAULT_ERROR
-         source = selector.process(source)
-         target = selector.process(target)
--        mfile = cmd.exp_path("$PYMOL_PATH/data/pymol/matrices/"+matrix)
-+        mfile = cmd.exp_path("$PYMOL_DATA/pymol/matrices/"+matrix)
-         if object==None: object=''
-         try:
-             lock()
---- pymol-0.99rc8/modules/pymol/importing.py	2007-04-18 02:11:47.000000000 -0400
-+++ importing.py	2007-04-24 02:18:46.000000000 -0400
-@@ -177,7 +177,7 @@
-         r = DEFAULT_ERROR
-         
-         
--        tables = { 'cmyk' : "$PYMOL_PATH/data/pymol/cmyk.png",
-+        tables = { 'cmyk' : "$PYMOL_DATA/pymol/cmyk.png",
-                       'pymol' : 'pymol',
-                       'rgb' : 'rgb' }
- 
---- pymol-0.99rc8/modules/pymol/wizard/mutagenesis.py	2007-04-18 02:11:50.000000000 -0400
-+++ mutagenesis.py	2007-04-24 04:08:44.000000000 -0400
-@@ -35,8 +35,8 @@
- 
-         self.dep = default_dep
- 
--        self.ind_library = io.pkl.fromFile(os.environ['PYMOL_PATH']+
--                                           "/data/chempy/sidechains/sc_bb_ind.pkl")
-+        self.ind_library = io.pkl.fromFile(os.environ['PYMOL_DATA']+
-+                                           "/chempy/sidechains/sc_bb_ind.pkl")
-         self.load_library()
-         self.status = 0 # 0 no selection, 1 mutagenizing
-         self.bump_check = 1
-@@ -108,8 +108,8 @@
-     def load_library(self):
-         if self.dep == 'dep':
-             if not hasattr(self,'dep_library'):
--                self.dep_library = io.pkl.fromFile(os.environ['PYMOL_PATH']+
--                                           "/data/chempy/sidechains/sc_bb_dep.pkl")
-+                self.dep_library = io.pkl.fromFile(os.environ['PYMOL_DATA']+
-+                                           "/chempy/sidechains/sc_bb_dep.pkl")
-             
-     def set_mode(self,mode):
-         if mode in self.modes:
-
diff --git a/sci-chemistry/pymol/files/pymol-1.2.2-data-path.patch b/sci-chemistry/pymol/files/pymol-1.2.2-data-path.patch
deleted file mode 100644
index cf1bf59af0c6..000000000000
--- a/sci-chemistry/pymol/files/pymol-1.2.2-data-path.patch
+++ /dev/null
@@ -1,75 +0,0 @@
-Index: modules/pymol/importing.py
-===================================================================
---- modules/pymol/importing.py	(revision 3889)
-+++ modules/pymol/importing.py	(working copy)
-@@ -191,7 +191,7 @@
-     '''
-         r = DEFAULT_ERROR
-         
--        tables = { 'cmyk' : "$PYMOL_PATH/data/pymol/cmyk.png",
-+        tables = { 'cmyk' : "$PYMOL_DATA/pymol/cmyk.png",
-                    'pymol' : 'pymol',
-                    'rgb' : 'rgb',
-                    'greyscale': 'greyscale' }
-Index: modules/pymol/wizard/mutagenesis.py
-===================================================================
---- modules/pymol/wizard/mutagenesis.py	(revision 3889)
-+++ modules/pymol/wizard/mutagenesis.py	(working copy)
-@@ -53,8 +53,8 @@
- 
-         self.dep = default_dep
- 
--        self.ind_library = io.pkl.fromFile(os.environ['PYMOL_PATH']+
--                                           "/data/chempy/sidechains/sc_bb_ind.pkl")
-+        self.ind_library = io.pkl.fromFile(os.environ['PYMOL_DATA']+
-+                                           "/chempy/sidechains/sc_bb_ind.pkl")
-         self.load_library()
-         self.status = 0 # 0 no selection, 1 mutagenizing
-         self.bump_check = 1
-@@ -218,8 +218,8 @@
-     def load_library(self):
-         if self.dep == 'dep':
-             if not hasattr(self,'dep_library'):
--                self.dep_library = io.pkl.fromFile(os.environ['PYMOL_PATH']+
--                                           "/data/chempy/sidechains/sc_bb_dep.pkl")
-+                self.dep_library = io.pkl.fromFile(os.environ['PYMOL_DATA']+
-+                                           "/chempy/sidechains/sc_bb_dep.pkl")
-             
-     def set_mode(self,mode):
-         cmd=self.cmd
-Index: modules/pymol/commanding.py
-===================================================================
---- modules/pymol/commanding.py	(revision 3889)
-+++ modules/pymol/commanding.py	(working copy)
-@@ -219,11 +219,11 @@
-                 _self.unlock(0,_self)
-             r = DEFAULT_SUCCESS
-             if show_splash==1: # generic / open-source
--                png_path = _self.exp_path("$PYMOL_PATH/data/pymol/splash.png")
-+                png_path = _self.exp_path("$PYMOL_DATA/pymol/splash.png")
-             elif show_splash==2: # evaluation builds
--                png_path = _self.exp_path("$PYMOL_PATH/data/pymol/epymol.png")
-+                png_path = _self.exp_path("$PYMOL_DATA/pymol/epymol.png")
-             else: # incentive builds
--                png_path = _self.exp_path("$PYMOL_PATH/data/pymol/ipymol.png")
-+                png_path = _self.exp_path("$PYMOL_DATA/pymol/ipymol.png")
-             if os.path.exists(png_path):
-                 _self.do("_ cmd.load_png('%s',0,quiet=1)"%png_path)
-         else:
-Index: modules/chempy/tinker/__init__.py
-===================================================================
---- modules/chempy/tinker/__init__.py	(revision 3889)
-+++ modules/chempy/tinker/__init__.py	(working copy)
-@@ -145,9 +145,9 @@
-     bin_path = ''
-     params_path = ''
- 
--if os.environ.has_key('PYMOL_PATH'):
--    pymol_path = os.environ['PYMOL_PATH']
--    test_path = pymol_path + '/data/chempy/tinker/'
-+if os.environ.has_key('PYMOL_DATA'):
-+    pymol_path = os.environ['PYMOL_DATA']
-+    test_path = pymol_path + '/chempy/tinker/'
-     if os.path.exists(test_path):
-         params_path = test_path
- 
diff --git a/sci-chemistry/pymol/files/pymol-1.2.2-prefix.patch b/sci-chemistry/pymol/files/pymol-1.2.2-prefix.patch
deleted file mode 100644
index 211881435123..000000000000
--- a/sci-chemistry/pymol/files/pymol-1.2.2-prefix.patch
+++ /dev/null
@@ -1,31 +0,0 @@
-diff --git a/setup.py b/setup.py
-index 197f827..b39c129 100644
---- a/setup.py
-+++ b/setup.py
-@@ -112,7 +112,7 @@ elif sys.platform=='darwin':
-                     ]
-         ext_comp_args=[]
-         ext_link_args=[
--	               "-L/usr/X11R6/lib", "-lGL", "-lXxf86vm",
-+	               "-L@GENTOO_PORTAGE_EPREFIX@/usr/lib", "-lGL", "-lXxf86vm",
-                    "-L"+EXT+"/lib", "-lpng", "-lglut", "-lfreetype"
-                    ]
- #============================================================================
-@@ -120,7 +120,7 @@ else: # linux or other unix
-     inc_dirs=["ov/src",
-               "layer0","layer1","layer2",
-               "layer3","layer4","layer5",
--              "/usr/include/freetype2",
-+              "@GENTOO_PORTAGE_EPREFIX@/usr/include/freetype2",
- #                 "/users/warren/ext/include",
- # VMD plugin support
- #              "contrib/uiuc/plugins/include",
-@@ -131,7 +131,7 @@ else: # linux or other unix
-           ]	
-     pyogl_libs = ["GL","GLU","glut"]
-     lib_dirs=[
--        "/usr/X11R6/lib",
-+        "@GENTOO_PORTAGE_EPREFIX@/usr/lib",
- #        "/users/warren/pymol/ext/lib"
-         ]
-     def_macros=[("_PYMOL_MODULE",None),
diff --git a/sci-chemistry/pymol/files/pymol-1.2.2-shaders.patch b/sci-chemistry/pymol/files/pymol-1.2.2-shaders.patch
deleted file mode 100644
index 7d0c35d83893..000000000000
--- a/sci-chemistry/pymol/files/pymol-1.2.2-shaders.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- setup.py.old	2009-10-03 01:01:22.444881137 -0500
-+++ setup.py	2009-10-03 01:01:41.580752440 -0500
-@@ -139,7 +139,7 @@
-                 ("_PYMOL_FREETYPE",None),
-                 ("_PYMOL_LIBPNG",None),
- # OpenGL shaders
--#               ("_PYMOL_OPENGL_SHADERS",None),
-+               ("_PYMOL_OPENGL_SHADERS",None),
- # Numeric Python support                    
- #                ("_PYMOL_NUMPY",None),
- # VMD plugin support           
diff --git a/sci-chemistry/pymol/files/pymol-1.2.2-vmd.patch b/sci-chemistry/pymol/files/pymol-1.2.2-vmd.patch
deleted file mode 100644
index 1355abe22093..000000000000
--- a/sci-chemistry/pymol/files/pymol-1.2.2-vmd.patch
+++ /dev/null
@@ -1,33 +0,0 @@
-Index: setup.py
-===================================================================
---- setup.py	(revision 3887)
-+++ setup.py	(working copy)
-@@ -123,8 +123,8 @@
-               "/usr/include/freetype2",
- #                 "/users/warren/ext/include",
- # VMD plugin support
--#              "contrib/uiuc/plugins/include",
--#              "contrib/uiuc/plugins/molfile_plugin/src",
-+              "contrib/uiuc/plugins/include",
-+              "contrib/uiuc/plugins/molfile_plugin/src",
-               ]
-     libs=["GL","GLU","glut","png","z","freetype",
- #          "Xxf86vm"
-@@ -143,7 +143,7 @@
- # Numeric Python support                    
- #                ("_PYMOL_NUMPY",None),
- # VMD plugin support           
--#               ("_PYMOL_VMD_PLUGINS",None)
-+               ("_PYMOL_VMD_PLUGINS",None)
-                 ]
-     ext_comp_args=["-ffast-math","-funroll-loops","-O3"]
-     ext_link_args=[]
-@@ -290,7 +290,7 @@
-     "layer5/main.c"
- # VMD plugin support
-     # switch the 0 to 1 to activate the additional source code
--    ] + 0 * [
-+    ] + 1 * [
- # (incomplete support -- only TRJ, TRR, XTC, DCD so far...)
-     'contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c',
-     'contrib/uiuc/plugins/molfile_plugin/src/avsplugin.cpp',
diff --git a/sci-chemistry/pymol/files/pymol-1.3.0-vmd.patch b/sci-chemistry/pymol/files/pymol-1.3.0-vmd.patch
deleted file mode 100644
index 0f34a02ea01b..000000000000
--- a/sci-chemistry/pymol/files/pymol-1.3.0-vmd.patch
+++ /dev/null
@@ -1,33 +0,0 @@
-Index: setup.py
-===================================================================
---- setup.py	(revision 3908)
-+++ setup.py	(working copy)
-@@ -130,8 +130,8 @@
-               "/usr/include/freetype2",
- #                 "/users/warren/ext/include",
- # VMD plugin support
--#              "contrib/uiuc/plugins/include",
--#              "contrib/uiuc/plugins/molfile_plugin/src",
-+              "contrib/uiuc/plugins/include",
-+              "contrib/uiuc/plugins/molfile_plugin/src",
-               "modules/cealign/src",
- 	      "modules/cealign/src/tnt", ]
-     libs=["GL","GLU","glut","png","z","freetype",
-@@ -151,7 +151,7 @@
- # Numeric Python support                    
- #                ("_PYMOL_NUMPY",None),
- # VMD plugin support           
--#               ("_PYMOL_VMD_PLUGINS",None)
-+               ("_PYMOL_VMD_PLUGINS",None)
-                 ]
-     ext_comp_args=["-ffast-math","-funroll-loops","-O3"]
-     ext_link_args=[]
-@@ -299,7 +299,7 @@
-     "layer5/main.c"
- # VMD plugin support
-     # switch the 0 to 1 to activate the additional source code
--    ] + 0 * [
-+    ] + 1 * [
- # (incomplete support -- only TRJ, TRR, XTC, DCD so far...)
-     'contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c',
-     'contrib/uiuc/plugins/molfile_plugin/src/avsplugin.cpp',
diff --git a/sci-chemistry/pymol/files/pymol-1.4-shaders.patch b/sci-chemistry/pymol/files/pymol-1.4-shaders.patch
deleted file mode 100644
index 853ebff9da81..000000000000
--- a/sci-chemistry/pymol/files/pymol-1.4-shaders.patch
+++ /dev/null
@@ -1,62 +0,0 @@
- layer0/ShaderMgr.c |   16 ++++++++--------
- layer1/Setting.c   |    2 +-
- 2 files changed, 9 insertions(+), 9 deletions(-)
-
-diff --git a/layer0/ShaderMgr.c b/layer0/ShaderMgr.c
-index 929167f..ecb4130 100644
---- a/layer0/ShaderMgr.c
-+++ b/layer0/ShaderMgr.c
-@@ -386,7 +386,7 @@ int CShaderMgr_ShadersPresent(CShaderMgr * I)
- char * CShaderMgr_ReadShaderFromDisk(PyMOLGlobals * G, const char * fileName) {
-   FILE* f;
-   long size;
--  char* buffer = NULL, *p, *pymol_path, *shader_path, *fullFile;
-+  char* buffer = NULL, *p, *pymol_data, *shader_path, *fullFile;
- 
-   PRINTFB(G, FB_ShaderMgr, FB_Debugging)
-     "CShaderMgr_ReadShaderFromDisk: fileName='%s'\n", fileName
-@@ -398,16 +398,16 @@ char * CShaderMgr_ReadShaderFromDisk(PyMOLGlobals * G, const char * fileName) {
-     return NULL;
-   }
-   
--  pymol_path = getenv("PYMOL_PATH");
--  if (!pymol_path){
-+  pymol_data = getenv("PYMOL_DATA");
-+  if (!pymol_data){
-     PRINTFB(G, FB_ShaderMgr, FB_Warnings)
--      " PyMOLShader_NewFromFile-Warning: PYMOL_PATH not set, cannot read shader config files (%s) from disk\n", fileName ENDFB(G);
-+      " PyMOLShader_NewFromFile-Warning: PYMOL_DATA not set, cannot read shader config files (%s) from disk\n", fileName ENDFB(G);
-     return NULL;
-   }
-   /* make this a setting */
--  shader_path = "/data/shaders/";
--  fullFile = malloc( sizeof(char) * (strlen(pymol_path)+strlen(shader_path)+strlen(fileName)+1));
--  fullFile = strcpy(fullFile, pymol_path);
-+  shader_path = "/shaders/";
-+  fullFile = malloc( sizeof(char) * (strlen(pymol_data)+strlen(shader_path)+strlen(fileName)+1));
-+  fullFile = strcpy(fullFile, pymol_data);
-   fullFile = strcat(fullFile, shader_path);
-   fullFile = strcat(fullFile, fileName);
- 
-@@ -416,7 +416,7 @@ char * CShaderMgr_ReadShaderFromDisk(PyMOLGlobals * G, const char * fileName) {
- 
-   if (!f) {
-     PRINTFB(G, FB_ShaderMgr, FB_Errors)
--      " PyMOLShader_NewFromFile-Error: Unable to open file '%s' PYMOL_PATH='%s'\n", fullFile, pymol_path ENDFB(G);
-+      " PyMOLShader_NewFromFile-Error: Unable to open file '%s' PYMOL_DATA='%s'\n", fullFile, pymol_data ENDFB(G);
-     return NULL;
-   } else {
-     PRINTFB(G, FB_ShaderMgr, FB_Blather)
-diff --git a/layer1/Setting.c b/layer1/Setting.c
-index 3aa0b8d..f9b5789 100644
---- a/layer1/Setting.c
-+++ b/layer1/Setting.c
-@@ -3956,7 +3956,7 @@ void SettingInitGlobal(PyMOLGlobals * G, int alloc, int reset_gui, int use_defau
-     set_b(I, cSetting_line_use_shader, 1);
-     set_b(I, cSetting_sphere_use_shader, 1);
-     set_b(I, cSetting_use_shaders, 0);  /* disable by default until optimized shaders present; doesn't effect vol */
--    set_s(I, cSetting_shader_path, "data/shaders");
-+    set_s(I, cSetting_shader_path, "shaders");
-     set_i(I, cSetting_volume_bit_depth, 8);
-     set_color(I, cSetting_volume_color, "-1");
-     set_f(I, cSetting_volume_layers, 256);
diff --git a/sci-chemistry/pymol/files/pymol-1.4-vmd.patch b/sci-chemistry/pymol/files/pymol-1.4-vmd.patch
deleted file mode 100644
index 2fd909ffd540..000000000000
--- a/sci-chemistry/pymol/files/pymol-1.4-vmd.patch
+++ /dev/null
@@ -1,36 +0,0 @@
- setup.py |    8 ++++----
- 1 files changed, 4 insertions(+), 4 deletions(-)
-
-diff --git a/setup.py b/setup.py
-index b0f4dad..4ec5145 100644
---- a/setup.py
-+++ b/setup.py
-@@ -132,8 +132,8 @@ else: # linux or other unix
-               "/usr/include/freetype2",
- #                 "/users/warren/ext/include",
- # VMD plugin support
--#              "contrib/uiuc/plugins/include",
--#              "contrib/uiuc/plugins/molfile_plugin/src",
-+              "contrib/uiuc/plugins/include",
-+              "contrib/uiuc/plugins/molfile_plugin/src",
-               "modules/cealign/src",
- 	      "modules/cealign/src/tnt", ]
-     libs=["GL","GLU","glut","png","z","freetype", "GLEW",
-@@ -153,7 +153,7 @@ else: # linux or other unix
- # Numeric Python support                    
- #                ("_PYMOL_NUMPY",None),
- # VMD plugin support           
--#               ("_PYMOL_VMD_PLUGINS",None)
-+               ("_PYMOL_VMD_PLUGINS",None),
- 		("NO_MMLIBS",None),
-                 ]
-     ext_comp_args=["-ffast-math","-funroll-loops","-O3"]
-@@ -307,7 +307,7 @@ setup ( # Distribution meta-data
-     "layer5/main.c"
- # VMD plugin support
-     # switch the 0 to 1 to activate the additional source code
--    ] + 0 * [
-+    ] + 1 * [
- # (incomplete support -- only TRJ, TRR, XTC, DCD so far...)
-     'contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c',
-     'contrib/uiuc/plugins/molfile_plugin/src/avsplugin.cpp',
diff --git a/sci-chemistry/pymol/files/pymol-1.4.1-data-path.patch b/sci-chemistry/pymol/files/pymol-1.4.1-data-path.patch
deleted file mode 100644
index 903714cd223a..000000000000
--- a/sci-chemistry/pymol/files/pymol-1.4.1-data-path.patch
+++ /dev/null
@@ -1,87 +0,0 @@
- modules/chempy/__init__.py          |    2 +-
- modules/chempy/tinker/__init__.py   |    2 +-
- modules/pymol/commanding.py         |    6 +++---
- modules/pymol/importing.py          |    2 +-
- modules/pymol/wizard/mutagenesis.py |    4 ++--
- 5 files changed, 8 insertions(+), 8 deletions(-)
-
-diff --git a/modules/chempy/__init__.py b/modules/chempy/__init__.py
-index 998e8f8..02fe156 100644
---- a/modules/chempy/__init__.py
-+++ b/modules/chempy/__init__.py
-@@ -229,7 +229,7 @@ if os.environ.has_key('CHEMPY_DATA'):  #
- elif os.environ.has_key('PYMOL_DATA'):
-     path = os.environ['PYMOL_DATA'] + '/chempy/'
- elif os.environ.has_key('PYMOL_PATH'):
--    path = os.environ['PYMOL_PATH'] + '/data/chempy/'   
-+    path = os.environ['PYMOL_PATH'] + '/chempy/'   
- elif os.environ.has_key('FREEMOL_MODULES'):
-     path = os.environ['FREEMOL_MODULES'] + '/chempy/'
- else:
-diff --git a/modules/chempy/tinker/__init__.py b/modules/chempy/tinker/__init__.py
-index a2d8eb1..1e48f81 100644
---- a/modules/chempy/tinker/__init__.py
-+++ b/modules/chempy/tinker/__init__.py
-@@ -147,7 +147,7 @@ else:
- 
- if os.environ.has_key('PYMOL_PATH'):
-     pymol_path = os.environ['PYMOL_PATH']
--    test_path = pymol_path + '/data/chempy/tinker/'
-+    test_path = pymol_path + '/chempy/tinker/'
-     if os.path.exists(test_path):
-         params_path = test_path
- 
-diff --git a/modules/pymol/commanding.py b/modules/pymol/commanding.py
-index 5a202d0..5cb27a6 100644
---- a/modules/pymol/commanding.py
-+++ b/modules/pymol/commanding.py
-@@ -219,11 +219,11 @@ USAGE
-                 _self.unlock(0,_self)
-             r = DEFAULT_SUCCESS
-             if show_splash==1: # generic / open-source
--                png_path = _self.exp_path("$PYMOL_PATH/data/pymol/splash.png")
-+                png_path = _self.exp_path("$PYMOL_DATA/pymol/splash.png")
-             elif show_splash==2: # evaluation builds
--                png_path = _self.exp_path("$PYMOL_PATH/data/pymol/epymol.png")
-+                png_path = _self.exp_path("$PYMOL_DATA/pymol/epymol.png")
-             else: # incentive builds
--                png_path = _self.exp_path("$PYMOL_PATH/data/pymol/ipymol.png")
-+                png_path = _self.exp_path("$PYMOL_DATA/pymol/ipymol.png")
-             if os.path.exists(png_path):
-                 _self.do("_ cmd.load_png('%s',0,quiet=1)"%png_path)
-         else:
-diff --git a/modules/pymol/importing.py b/modules/pymol/importing.py
-index 1ccf986..72ae9f3 100644
---- a/modules/pymol/importing.py
-+++ b/modules/pymol/importing.py
-@@ -191,7 +191,7 @@ SEE ALSO
-     '''
-         r = DEFAULT_ERROR
-         
--        tables = { 'cmyk' : "$PYMOL_PATH/data/pymol/cmyk.png",
-+        tables = { 'cmyk' : "$PYMOL_DATA/pymol/cmyk.png",
-                    'pymol' : 'pymol',
-                    'rgb' : 'rgb',
-                    'greyscale': 'greyscale' }
-diff --git a/modules/pymol/wizard/mutagenesis.py b/modules/pymol/wizard/mutagenesis.py
-index 8a5250d..6c1b26c 100644
---- a/modules/pymol/wizard/mutagenesis.py
-+++ b/modules/pymol/wizard/mutagenesis.py
-@@ -53,7 +53,7 @@ class Mutagenesis(Wizard):
-         self.dep = default_dep
- 
-         self.ind_library = io.pkl.fromFile(os.environ['PYMOL_PATH']+
--                                           "/data/chempy/sidechains/sc_bb_ind.pkl")
-+                                           "/chempy/sidechains/sc_bb_ind.pkl")
-         self.load_library()
-         self.status = 0 # 0 no selection, 1 mutagenizing
-         self.bump_check = 1
-@@ -218,7 +218,7 @@ class Mutagenesis(Wizard):
-         if self.dep == 'dep':
-             if not hasattr(self,'dep_library'):
-                 self.dep_library = io.pkl.fromFile(os.environ['PYMOL_PATH']+
--                                           "/data/chempy/sidechains/sc_bb_dep.pkl")
-+                                           "/chempy/sidechains/sc_bb_dep.pkl")
-             
-     def set_mode(self,mode):
-         cmd=self.cmd
diff --git a/sci-chemistry/pymol/files/pymol-1.4.1-shaders.patch b/sci-chemistry/pymol/files/pymol-1.4.1-shaders.patch
deleted file mode 100644
index 2caac2dc4bce..000000000000
--- a/sci-chemistry/pymol/files/pymol-1.4.1-shaders.patch
+++ /dev/null
@@ -1,58 +0,0 @@
-Index: layer0/ShaderMgr.c
-===================================================================
---- layer0/ShaderMgr.c	(revision 3945)
-+++ layer0/ShaderMgr.c	(working copy)
-@@ -400,7 +400,7 @@
- char * CShaderMgr_ReadShaderFromDisk(PyMOLGlobals * G, const char * fileName) {
-   FILE* f;
-   long size;
--  char* buffer = NULL, *p, *pymol_path, *shader_path, *fullFile;
-+  char* buffer = NULL, *p, *pymol_data, *shader_path, *fullFile;
- 
-   PRINTFB(G, FB_ShaderMgr, FB_Debugging)
-     "CShaderMgr_ReadShaderFromDisk: fileName='%s'\n", fileName
-@@ -412,16 +412,16 @@
-     return NULL;
-   }
-   
--  pymol_path = getenv("PYMOL_PATH");
--  if (!pymol_path){
-+  pymol_data = getenv("PYMOL_DATA");
-+  if (!pymol_data){
-     PRINTFB(G, FB_ShaderMgr, FB_Warnings)
--      " PyMOLShader_NewFromFile-Warning: PYMOL_PATH not set, cannot read shader config files from disk\n", fileName ENDFB(G);
-+      " PyMOLShader_NewFromFile-Warning: PYMOL_DATA not set, cannot read shader config files from disk\n", fileName ENDFB(G);
-     return NULL;
-   }
-   /* make this a setting */
--  shader_path = "/data/shaders/";
--  fullFile = malloc( sizeof(char) * (strlen(pymol_path)+strlen(shader_path)+strlen(fileName)+1));
--  fullFile = strcpy(fullFile, pymol_path);
-+  shader_path = "/shaders/";
-+  fullFile = malloc( sizeof(char) * (strlen(pymol_data)+strlen(shader_path)+strlen(fileName)+1));
-+  fullFile = strcpy(fullFile, pymol_data);
-   fullFile = strcat(fullFile, shader_path);
-   fullFile = strcat(fullFile, fileName);
- 
-@@ -430,7 +430,7 @@
- 
-   if (!f) {
-     PRINTFB(G, FB_ShaderMgr, FB_Errors)
--      " PyMOLShader_NewFromFile-Error: Unable to open file '%s' PYMOL_PATH='%s'\n", fullFile, pymol_path ENDFB(G);
-+      " PyMOLShader_NewFromFile-Error: Unable to open file '%s' PYMOL_DATA='%s'\n", fullFile, pymol_data ENDFB(G);
-     return NULL;
-   } else {
-     PRINTFB(G, FB_ShaderMgr, FB_Blather)
-Index: layer1/Setting.c
-===================================================================
---- layer1/Setting.c	(revision 3945)
-+++ layer1/Setting.c	(working copy)
-@@ -3990,7 +3990,7 @@
-     set_b(I, cSetting_line_use_shader, 1);
-     set_b(I, cSetting_sphere_use_shader, 1);
-     set_b(I, cSetting_use_shaders, 0);  /* disable by default until optimized shaders present; doesn't effect vol */
--    set_s(I, cSetting_shader_path, "data/shaders");
-+    set_s(I, cSetting_shader_path, "shaders");
-     set_i(I, cSetting_volume_bit_depth, 8);
-     set_color(I, cSetting_volume_color, "-1");
-     set_f(I, cSetting_volume_layers, 256);
diff --git a/sci-chemistry/pymol/files/pymol-1.4.1-web.patch b/sci-chemistry/pymol/files/pymol-1.4.1-web.patch
deleted file mode 100644
index 2d6957df594d..000000000000
--- a/sci-chemistry/pymol/files/pymol-1.4.1-web.patch
+++ /dev/null
@@ -1,19 +0,0 @@
- setup.py |    5 +----
- 1 files changed, 1 insertions(+), 4 deletions(-)
-
-diff --git a/setup.py b/setup.py
-index b0f4dad..94d292d 100644
---- a/setup.py
-+++ b/setup.py
-@@ -180,10 +180,7 @@ setup ( # Distribution meta-data
-                 'pymol/opengl/gl',
-                 'pymol/opengl/glu',
-                 'pymol/opengl/glut',
--                'pymol/wizard',
--		'web',
--		'web/examples',
--		'web/javascript', ],
-+                'pymol/wizard', ],
- 	ext_modules = [
-     Extension("pymol._cmd", [
-     "modules/cealign/src/ccealignmodule.cpp",
diff --git a/sci-chemistry/pymol/files/pymol-1.5.0.1-prefix.patch b/sci-chemistry/pymol/files/pymol-1.5.0.1-prefix.patch
deleted file mode 100644
index 830eb8febbf5..000000000000
--- a/sci-chemistry/pymol/files/pymol-1.5.0.1-prefix.patch
+++ /dev/null
@@ -1,43 +0,0 @@
- setup.py |    8 ++++----
- 1 files changed, 4 insertions(+), 4 deletions(-)
-
-diff --git a/setup.py b/setup.py
-index ce0d271..2b6fa35 100755
---- a/setup.py
-+++ b/setup.py
-@@ -104,7 +104,7 @@ elif sys.platform=='darwin':
-         inc_dirs=["ov/src",
-                   "layer0","layer1","layer2",
-                   "layer3","layer4","layer5", 
--                  "/usr/X11R6/include",
-+                  "@GENTOO_PORTAGE_EPREFIX@/usr/include",
-                   EXT+"/include",
-                   EXT+"/include/GL",
-                   EXT+"/include/freetype2",
-@@ -120,7 +120,7 @@ elif sys.platform=='darwin':
-                     ]
-         ext_comp_args=[]
-         ext_link_args=[
--            "-L/usr/X11R6/lib64", "-lGL", "-lXxf86vm",
-+            "-L@GENTOO_PORTAGE_EPREFIX@/usr/lib64", "-lGL", "-lXxf86vm",
-             "-L"+EXT+"/lib", "-lpng", "-lglut", "-lfreetype"
-             ]
- #============================================================================
-@@ -159,7 +159,7 @@ else: # linux or other unix
-                  "layer3",
-                  "layer4",
-                  "layer5",
--                 "/usr/include/freetype2",
-+                 "@GENTOO_PORTAGE_EPREFIX@/usr/include/freetype2",
-               # VMD plugin support
-                             "contrib/uiuc/plugins/include",
-                             "contrib/uiuc/plugins/molfile_plugin/src",
-@@ -180,7 +180,7 @@ else: # linux or other unix
-                    "GLU",
-                    "glut",
-                    "GLEW"]
--    lib_dirs = [ "/usr/X11R6/lib64", ]
-+    lib_dirs = [ "@GENTOO_PORTAGE_EPREFIX@/usr/lib64", ]
-     def_macros = [ ("_PYMOL_MODULE",None),
-                    ("_PYMOL_INLINE",None),
-                    ("_PYMOL_FREETYPE",None),
diff --git a/sci-chemistry/pymol/metadata.xml b/sci-chemistry/pymol/metadata.xml
index d7cc1df353d3..dca3a9a8c74d 100644
--- a/sci-chemistry/pymol/metadata.xml
+++ b/sci-chemistry/pymol/metadata.xml
@@ -8,7 +8,6 @@
 	<use>
 		<flag name="apbs">Install the apbs plugin</flag>
 		<flag name="numpy">Compile numpy support</flag>
-		<flag name="shaders">Build with Shaders support - good for high-end 3D video cards.</flag>
 		<flag name="vmd">Enable vmd module for trajectories</flag>
 		<flag name="web">Install Pymodule needed for web app support</flag>
 	</use>
diff --git a/sci-chemistry/pymol/pymol-1.3.1_pre3925-r1.ebuild b/sci-chemistry/pymol/pymol-1.3.1_pre3925-r1.ebuild
deleted file mode 100644
index 6429b8cbae52..000000000000
--- a/sci-chemistry/pymol/pymol-1.3.1_pre3925-r1.ebuild
+++ /dev/null
@@ -1,106 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-1.3.1_pre3925-r1.ebuild,v 1.6 2012/06/04 06:02:01 xmw Exp $
-
-EAPI="3"
-
-PYTHON_DEPEND="2:2.6"
-SUPPORT_PYTHON_ABIS="1"
-RESTRICT_PYTHON_ABIS="2.4 2.5 3.* *-jython 2.7-pypy-*"
-PYTHON_USE_WITH="tk"
-PYTHON_MODNAME="${PN} chempy pmg_tk pmg_wx"
-REV="3925"
-
-inherit eutils distutils prefix
-
-DESCRIPTION="A Python-extensible molecular graphics system"
-HOMEPAGE="http://pymol.sourceforge.net/"
-#SRC_URI="http://pymol.svn.sourceforge.net/viewvc/pymol/trunk/pymol.tar.gz?view=tar&pathrev=${REV} -> ${P}.tar.gz"
-SRC_URI="mirror://gentoo/${PF}.tar.gz"
-
-LICENSE="PSF-2.2"
-SLOT="0"
-KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux"
-IUSE="apbs numpy shaders vmd"
-
-DEPEND="
-		dev-python/numpy
-		dev-python/pmw
-		media-libs/freetype:2
-		media-libs/libpng
-		media-video/mpeg-tools
-		sys-libs/zlib
-		media-libs/freeglut
-		apbs? (
-			dev-libs/maloc
-			sci-chemistry/apbs
-			sci-chemistry/pdb2pqr
-			sci-chemistry/pymol-apbs-plugin
-		)"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/${PN}
-
-src_prepare() {
-	epatch "${FILESDIR}"/${PN}-1.2.2-data-path.patch
-
-	epatch "${FILESDIR}"/${PN}-1.2.2-prefix.patch && \
-	eprefixify setup.py
-
-	# Turn off splash screen.  Please do make a project contribution
-	# if you are able though. #299020
-	epatch "${FILESDIR}"/1.2.1/nosplash-gentoo.patch
-
-	# Respect CFLAGS
-	sed -i \
-		-e "s:\(ext_comp_args=\).*:\1[]:g" \
-		"${S}"/setup.py || die "Failed running sed on setup.py"
-
-	use shaders && epatch "${FILESDIR}"/${PN}-1.2.2-shaders.patch
-
-	use vmd && epatch "${FILESDIR}"/${PN}-1.3.0-vmd.patch
-
-	use numpy && \
-		sed \
-			-e '/PYMOL_NUMPY/s:^#::g' \
-			-i setup.py
-
-	rm ./modules/pmg_tk/startup/apbs_tools.py || die
-
-	# python 3.* fix
-	# sed '452,465d' -i setup.py
-	distutils_src_prepare
-}
-
-src_configure() {
-	:
-}
-
-src_install() {
-	distutils_src_install
-
-	# These environment variables should not go in the wrapper script, or else
-	# it will be impossible to use the PyMOL libraries from Python.
-	cat >> "${T}"/20pymol <<- EOF
-		PYMOL_PATH="${EPREFIX}/$(python_get_sitedir -f)/${PN}"
-		PYMOL_DATA="${EPREFIX}/usr/share/pymol/data"
-		PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts"
-	EOF
-
-	doenvd "${T}"/20pymol || die "Failed to install env.d file."
-
-	cat >> "${T}"/pymol <<- EOF
-	#!/bin/sh
-	$(PYTHON -f) -O \${PYMOL_PATH}/__init__.py \$*
-	EOF
-
-	dobin "${T}"/pymol || die "Failed to install wrapper."
-
-	insinto /usr/share/pymol
-	doins -r test data scripts || die "no shared data"
-
-	insinto /usr/share/pymol/examples
-	doins -r examples || die "Failed to install docs."
-
-	dodoc DEVELOPERS README || die "Failed to install docs."
-}
diff --git a/sci-chemistry/pymol/pymol-1.4.1.ebuild b/sci-chemistry/pymol/pymol-1.4.1.ebuild
deleted file mode 100644
index 749c910d2c8e..000000000000
--- a/sci-chemistry/pymol/pymol-1.4.1.ebuild
+++ /dev/null
@@ -1,113 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-1.4.1.ebuild,v 1.4 2012/02/26 06:10:49 patrick Exp $
-
-EAPI="3"
-
-PYTHON_DEPEND="2:2.6"
-SUPPORT_PYTHON_ABIS="1"
-RESTRICT_PYTHON_ABIS="2.4 2.5 3.* *-jython 2.7-pypy-*"
-PYTHON_USE_WITH="tk"
-PYTHON_MODNAME="${PN} chempy pmg_tk pmg_wx"
-
-inherit eutils distutils prefix versionator
-
-DESCRIPTION="A Python-extensible molecular graphics system"
-HOMEPAGE="http://pymol.sourceforge.net/"
-SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz"
-
-LICENSE="PSF-2.2"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-IUSE="apbs numpy vmd web"
-
-DEPEND="
-	dev-python/numpy
-	dev-python/pmw
-	media-libs/freetype:2
-	media-libs/glew
-	media-libs/libpng
-	media-video/mpeg-tools
-	sys-libs/zlib
-	media-libs/freeglut
-	apbs? (
-		dev-libs/maloc
-		sci-chemistry/apbs
-		sci-chemistry/pdb2pqr
-		sci-chemistry/pymol-apbs-plugin
-	)
-	web? ( !dev-python/webpy )"
-RDEPEND="${DEPEND}"
-
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/${P}-data-path.patch \
-		"${FILESDIR}"/${P}-shaders.patch
-
-	use web || epatch "${FILESDIR}"/${P}-web.patch
-
-	epatch "${FILESDIR}"/${PN}-1.2.2-prefix.patch && \
-		eprefixify setup.py
-
-	# Turn off splash screen.  Please do make a project contribution
-	# if you are able though. #299020
-	epatch "${FILESDIR}"/1.2.1/nosplash-gentoo.patch
-
-	# Respect CFLAGS
-	sed -i \
-		-e "s:\(ext_comp_args=\).*:\1[]:g" \
-		"${S}"/setup.py || die "Failed running sed on setup.py"
-
-	use vmd && epatch "${FILESDIR}"/${PN}-$(get_version_component_range 1-2)-vmd.patch
-
-	use numpy && \
-		sed \
-			-e '/PYMOL_NUMPY/s:^#::g' \
-			-i setup.py
-
-	rm ./modules/pmg_tk/startup/apbs_tools.py || die
-
-	# python 3.* fix
-	# sed '452,465d' -i setup.py
-	distutils_src_prepare
-}
-
-src_configure() {
-	:
-}
-
-src_install() {
-	distutils_src_install
-
-	# These environment variables should not go in the wrapper script, or else
-	# it will be impossible to use the PyMOL libraries from Python.
-	cat >> "${T}"/20pymol <<- EOF
-		PYMOL_PATH="${EPREFIX}/$(python_get_sitedir -f)/${PN}"
-		PYMOL_DATA="${EPREFIX}/usr/share/pymol/data"
-		PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts"
-	EOF
-
-	doenvd "${T}"/20pymol || die "Failed to install env.d file."
-
-	cat >> "${T}"/pymol <<- EOF
-	#!/bin/sh
-	$(PYTHON -f) -O \${PYMOL_PATH}/__init__.py \$*
-	EOF
-
-	dobin "${T}"/pymol || die "Failed to install wrapper."
-
-	insinto /usr/share/pymol
-	doins -r test data scripts || die "no shared data"
-
-	insinto /usr/share/pymol/examples
-	doins -r examples || die "Failed to install docs."
-
-	dodoc DEVELOPERS README || die "Failed to install docs."
-}
-
-pkg_postinst() {
-	elog "\t USE=shaders was removed,"
-	elog "please use pymol config settings"
-	elog "\t set use_shaders, 1"
-	distutils_pkg_postinst
-}
diff --git a/sci-chemistry/pymol/pymol-1.5.0.1.ebuild b/sci-chemistry/pymol/pymol-1.5.0.1.ebuild
deleted file mode 100644
index 676c37917758..000000000000
--- a/sci-chemistry/pymol/pymol-1.5.0.1.ebuild
+++ /dev/null
@@ -1,122 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-1.5.0.1.ebuild,v 1.6 2012/08/12 17:41:22 jlec Exp $
-
-EAPI=4
-
-PYTHON_DEPEND="2:2.7"
-SUPPORT_PYTHON_ABIS="1"
-RESTRICT_PYTHON_ABIS="2.4 2.5 2.6 3.* *-jython 2.7-pypy-*"
-PYTHON_USE_WITH="tk"
-PYTHON_MODNAME="${PN} chempy pmg_tk pmg_wx"
-
-inherit distutils eutils fdo-mime prefix versionator
-
-DESCRIPTION="A Python-extensible molecular graphics system"
-HOMEPAGE="http://pymol.sourceforge.net/"
-SRC_URI="
-	mirror://sourceforge/project/${PN}/${PN}/${PV}/${PN}-v${PV}.tar.bz2
-	http://dev.gentoo.org/~jlec/distfiles/${PN}-icons.tar.xz"
-
-LICENSE="PSF-2.2"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-IUSE="apbs numpy vmd web"
-
-DEPEND="
-	dev-python/numpy
-	dev-python/pmw
-	media-libs/freetype:2
-	media-libs/glew
-	media-libs/libpng
-	media-video/mpeg-tools
-	sys-libs/zlib
-	media-libs/freeglut
-	apbs? (
-		dev-libs/maloc
-		sci-chemistry/apbs
-		sci-chemistry/pdb2pqr
-		sci-chemistry/pymol-apbs-plugin
-	)
-	web? ( !dev-python/webpy )"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/${PN}
-
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/${P}-setup.py.patch \
-		"${FILESDIR}"/${P}-data-path.patch \
-		"${FILESDIR}"/${P}-flags.patch
-
-	use web || epatch "${FILESDIR}"/${P}-web.patch
-
-	epatch "${FILESDIR}"/${P}-prefix.patch && \
-		eprefixify setup.py
-
-	use vmd && epatch "${FILESDIR}"/${P}-vmd.patch
-
-	if use numpy; then
-		sed \
-			-e '/PYMOL_NUMPY/s:^#::g' \
-			-i setup.py || die
-	fi
-
-	rm ./modules/pmg_tk/startup/apbs_tools.py || die
-
-	echo "site_packages = \'$(python_get_sitedir -f)\'" > setup3.py || die
-
-	# python 3.* fix
-	# sed '452,465d' -i setup.py
-	distutils_src_prepare
-}
-
-src_configure() {
-	:
-}
-
-src_install() {
-	distutils_src_install
-
-	# These environment variables should not go in the wrapper script, or else
-	# it will be impossible to use the PyMOL libraries from Python.
-	cat >> "${T}"/20pymol <<- EOF
-		PYMOL_PATH="${EPREFIX}/$(python_get_sitedir -f)/${PN}"
-		PYMOL_DATA="${EPREFIX}/usr/share/pymol/data"
-		PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts"
-	EOF
-
-	doenvd "${T}"/20pymol
-
-	cat >> "${T}"/pymol <<- EOF
-	#!/bin/sh
-	$(PYTHON -f) -O \${PYMOL_PATH}/__init__.py -q \$*
-	EOF
-
-	dobin "${T}"/pymol
-
-	insinto /usr/share/pymol
-	doins -r test data scripts
-
-	insinto /usr/share/pymol/examples
-	doins -r examples
-
-	dodoc DEVELOPERS README
-
-	doicon "${WORKDIR}"/${PN}.{xpm,png}
-	make_desktop_entry pymol PyMol ${PN} "Graphics;Education;Science;Chemistry"
-}
-
-pkg_postinst() {
-	elog "\t USE=shaders was removed,"
-	elog "please use pymol config settings"
-	elog "\t set use_shaders, 1"
-	distutils_pkg_postinst
-	fdo-mime_desktop_database_update
-	fdo-mime_mime_database_update
-}
-
-pkg_postrm() {
-	fdo-mime_desktop_database_update
-	fdo-mime_mime_database_update
-}
diff --git a/sci-chemistry/pymol/pymol-1.5.0.2.ebuild b/sci-chemistry/pymol/pymol-1.5.0.2.ebuild
deleted file mode 100644
index 34a154d15eca..000000000000
--- a/sci-chemistry/pymol/pymol-1.5.0.2.ebuild
+++ /dev/null
@@ -1,120 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-1.5.0.2.ebuild,v 1.3 2012/08/12 17:41:22 jlec Exp $
-
-EAPI=4
-
-PYTHON_DEPEND="2:2.7"
-SUPPORT_PYTHON_ABIS="1"
-RESTRICT_PYTHON_ABIS="2.4 2.5 2.6 3.* *-jython 2.7-pypy-*"
-PYTHON_USE_WITH="tk"
-PYTHON_MODNAME="${PN} chempy pmg_tk pmg_wx"
-
-inherit distutils eutils fdo-mime prefix versionator
-
-DESCRIPTION="A Python-extensible molecular graphics system"
-HOMEPAGE="http://pymol.sourceforge.net/"
-SRC_URI="
-	http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz
-	http://dev.gentoo.org/~jlec/distfiles/${PN}-icons.tar.xz"
-
-LICENSE="PSF-2.2"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-IUSE="apbs numpy vmd web"
-
-DEPEND="
-	dev-python/numpy
-	dev-python/pmw
-	media-libs/freetype:2
-	media-libs/glew
-	media-libs/libpng
-	media-video/mpeg-tools
-	sys-libs/zlib
-	media-libs/freeglut
-	apbs? (
-		dev-libs/maloc
-		sci-chemistry/apbs
-		sci-chemistry/pdb2pqr
-		sci-chemistry/pymol-apbs-plugin
-	)
-	web? ( !dev-python/webpy )"
-RDEPEND="${DEPEND}"
-
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/${PN}-1.5.0.1-setup.py.patch \
-		"${FILESDIR}"/${PN}-1.5.0.1-data-path.patch \
-		"${FILESDIR}"/${PN}-1.5.0.1-flags.patch
-
-	use web || epatch "${FILESDIR}"/${PN}-1.5.0.1-web.patch
-
-	epatch "${FILESDIR}"/${PN}-1.5.0.1-prefix.patch && \
-		eprefixify setup.py
-
-	use vmd && epatch "${FILESDIR}"/${PN}-1.5.0.1-vmd.patch
-
-	if use numpy; then
-		sed \
-			-e '/PYMOL_NUMPY/s:^#::g' \
-			-i setup.py || die
-	fi
-
-	rm ./modules/pmg_tk/startup/apbs_tools.py || die
-
-	echo "site_packages = \'$(python_get_sitedir -f)\'" > setup3.py || die
-
-	# python 3.* fix
-	# sed '452,465d' -i setup.py
-	distutils_src_prepare
-}
-
-src_configure() {
-	:
-}
-
-src_install() {
-	distutils_src_install
-
-	# These environment variables should not go in the wrapper script, or else
-	# it will be impossible to use the PyMOL libraries from Python.
-	cat >> "${T}"/20pymol <<- EOF
-		PYMOL_PATH="${EPREFIX}/$(python_get_sitedir -f)/${PN}"
-		PYMOL_DATA="${EPREFIX}/usr/share/pymol/data"
-		PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts"
-	EOF
-
-	doenvd "${T}"/20pymol
-
-	cat >> "${T}"/pymol <<- EOF
-	#!/bin/sh
-	$(PYTHON -f) -O \${PYMOL_PATH}/__init__.py -q \$*
-	EOF
-
-	dobin "${T}"/pymol
-
-	insinto /usr/share/pymol
-	doins -r test data scripts
-
-	insinto /usr/share/pymol/examples
-	doins -r examples
-
-	dodoc DEVELOPERS README
-
-	doicon "${WORKDIR}"/${PN}.{xpm,png}
-	make_desktop_entry pymol PyMol ${PN} "Graphics;Education;Science;Chemistry"
-}
-
-pkg_postinst() {
-	elog "\t USE=shaders was removed,"
-	elog "please use pymol config settings"
-	elog "\t set use_shaders, 1"
-	distutils_pkg_postinst
-	fdo-mime_desktop_database_update
-	fdo-mime_mime_database_update
-}
-
-pkg_postrm() {
-	fdo-mime_desktop_database_update
-	fdo-mime_mime_database_update
-}
diff --git a/sci-chemistry/pymol/pymol-1.5.0.3-r1.ebuild b/sci-chemistry/pymol/pymol-1.5.0.3-r1.ebuild
index 9cf3b9cc8e0b..4f0e549c28fc 100644
--- a/sci-chemistry/pymol/pymol-1.5.0.3-r1.ebuild
+++ b/sci-chemistry/pymol/pymol-1.5.0.3-r1.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2012 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-1.5.0.3-r1.ebuild,v 1.7 2012/09/23 07:50:50 phajdan.jr Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-1.5.0.3-r1.ebuild,v 1.8 2012/10/06 12:02:10 jlec Exp $
 
 EAPI=4
 
@@ -20,7 +20,7 @@ SRC_URI="
 
 LICENSE="PSF-2.2"
 SLOT="0"
-KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux"
+KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
 IUSE="apbs numpy vmd web"
 
 DEPEND="
@@ -64,6 +64,11 @@ src_prepare() {
 
 	echo "site_packages = \'$(python_get_sitedir -f)\'" > setup3.py || die
 
+	sed \
+		-e "s:/opt/local:${EPREFIX}/usr:g" \
+		-e '/ext_comp_args/s:\[.*\]:[]:g' \
+		-i setup.py || die
+
 	# python 3.* fix
 	# sed '452,465d' -i setup.py
 	distutils_src_prepare
diff --git a/sci-chemistry/pymol/pymol-1.5.0.3.ebuild b/sci-chemistry/pymol/pymol-1.5.0.3.ebuild
deleted file mode 100644
index c12e8dbfda29..000000000000
--- a/sci-chemistry/pymol/pymol-1.5.0.3.ebuild
+++ /dev/null
@@ -1,120 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-1.5.0.3.ebuild,v 1.3 2012/08/12 17:41:22 jlec Exp $
-
-EAPI=4
-
-PYTHON_DEPEND="2:2.7"
-SUPPORT_PYTHON_ABIS="1"
-RESTRICT_PYTHON_ABIS="2.4 2.5 2.6 3.* *-jython 2.7-pypy-*"
-PYTHON_USE_WITH="tk"
-PYTHON_MODNAME="${PN} chempy pmg_tk pmg_wx"
-
-inherit distutils eutils fdo-mime prefix versionator
-
-DESCRIPTION="A Python-extensible molecular graphics system"
-HOMEPAGE="http://pymol.sourceforge.net/"
-SRC_URI="
-	http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz
-	http://dev.gentoo.org/~jlec/distfiles/${PN}-icons.tar.xz"
-
-LICENSE="PSF-2.2"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-IUSE="apbs numpy vmd web"
-
-DEPEND="
-	dev-python/numpy
-	dev-python/pmw
-	media-libs/freetype:2
-	media-libs/glew
-	media-libs/libpng
-	media-video/mpeg-tools
-	sys-libs/zlib
-	media-libs/freeglut
-	apbs? (
-		dev-libs/maloc
-		sci-chemistry/apbs
-		sci-chemistry/pdb2pqr
-		sci-chemistry/pymol-apbs-plugin
-	)
-	web? ( !dev-python/webpy )"
-RDEPEND="${DEPEND}"
-
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/${PN}-1.5.0.1-setup.py.patch \
-		"${FILESDIR}"/${PN}-1.5.0.1-data-path.patch \
-		"${FILESDIR}"/${PN}-1.5.0.1-flags.patch
-
-	use web || epatch "${FILESDIR}"/${P}-web.patch
-
-	epatch "${FILESDIR}"/${P}-prefix.patch && \
-		eprefixify setup.py
-
-	use vmd && epatch "${FILESDIR}"/${PN}-1.5.0.1-vmd.patch
-
-	if use numpy; then
-		sed \
-			-e '/PYMOL_NUMPY/s:^#::g' \
-			-i setup.py || die
-	fi
-
-	rm ./modules/pmg_tk/startup/apbs_tools.py || die
-
-	echo "site_packages = \'$(python_get_sitedir -f)\'" > setup3.py || die
-
-	# python 3.* fix
-	# sed '452,465d' -i setup.py
-	distutils_src_prepare
-}
-
-src_configure() {
-	:
-}
-
-src_install() {
-	distutils_src_install
-
-	# These environment variables should not go in the wrapper script, or else
-	# it will be impossible to use the PyMOL libraries from Python.
-	cat >> "${T}"/20pymol <<- EOF
-		PYMOL_PATH="${EPREFIX}/$(python_get_sitedir -f)/${PN}"
-		PYMOL_DATA="${EPREFIX}/usr/share/pymol/data"
-		PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts"
-	EOF
-
-	doenvd "${T}"/20pymol
-
-	cat >> "${T}"/pymol <<- EOF
-	#!/bin/sh
-	$(PYTHON -f) -O \${PYMOL_PATH}/__init__.py -q \$*
-	EOF
-
-	dobin "${T}"/pymol
-
-	insinto /usr/share/pymol
-	doins -r test data scripts
-
-	insinto /usr/share/pymol/examples
-	doins -r examples
-
-	dodoc DEVELOPERS README
-
-	doicon "${WORKDIR}"/${PN}.{xpm,png}
-	make_desktop_entry pymol PyMol ${PN} "Graphics;Education;Science;Chemistry"
-}
-
-pkg_postinst() {
-	elog "\t USE=shaders was removed,"
-	elog "please use pymol config settings"
-	elog "\t set use_shaders, 1"
-	distutils_pkg_postinst
-	fdo-mime_desktop_database_update
-	fdo-mime_mime_database_update
-}
-
-pkg_postrm() {
-	fdo-mime_desktop_database_update
-	fdo-mime_mime_database_update
-}