Rename all patches, add support for desktop icon, drop nosplash patch and add launch option

Package-Manager: portage-2.2.0_alpha86/cvs/Linux x86_64

17 files changed, 64 insertions, 206 deletions

diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog
index ca714f689b81..753435a0a288 100644
--- a/sci-chemistry/pymol/ChangeLog
+++ b/sci-chemistry/pymol/ChangeLog
@@ -1,6 +1,21 @@
 # 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 1.82 2012/02/13 22:09:19 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/ChangeLog,v 1.83 2012/02/14 08:18:11 jlec Exp $
+
+  14 Feb 2012; Justin Lecher <jlec@gentoo.org> -files/1.2.2-data-path.patch,
+  -files/1.2.1/pymol-1.2.1-data-path.patch, -files/1.2.2-prefix.patch,
+  -files/1.2.1/pymol-1.2.1-shaders.patch, -files/1.3.0-vmd.patch,
+  -pymol-1.2.3-r1.ebuild, -files/1.4.1-data-path.patch,
+  pymol-1.3.1_pre3925-r1.ebuild, -files/1.4.1-shaders.patch,
+  pymol-1.4.1.ebuild, -files/1.4-shaders.patch,
+  +files/pymol-1.2.2-data-path.patch, +files/pymol-1.4.1-data-path.patch,
+  -files/1.4-vmd.patch, +files/pymol-1.3.0-vmd.patch,
+  +files/pymol-1.4.1-shaders.patch, -files/1.4.1-web.patch,
+  +files/pymol-1.2.2-prefix.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-nosplash.patch:
+  Rename all patches, add support for desktop icon, drop nosplash patch and add
+  launch option
 
 *pymol-1.5.0.1 (13 Feb 2012)
 
diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
index 00d4c6b482d3..4623e641689a 100644
--- a/sci-chemistry/pymol/Manifest
+++ b/sci-chemistry/pymol/Manifest
@@ -2,40 +2,36 @@
 Hash: SHA512
 
 AUX 1.2.1/nosplash-gentoo.patch 485 RMD160 3b3d85ffe14a253e54c4ff89b210cf35effe7aee SHA1 627affce7ee9763e308cf6dee70b831e09bd829d SHA256 acf8ef1d53719c1b4158b0f49250e8ed7c3aa4c870ef7ce4bdbc8ec97f591e27
-AUX 1.2.1/pymol-1.2.1-data-path.patch 1585 RMD160 e8d505a25869f0abd7b1ef77e1176c5fe7b2a312 SHA1 89464b3780fc48bd239c0e0662dbd1d61665984f SHA256 c89862e631b7bb0e05426ad0550be51501380d4522820a7600708d5290e5dfa8
-AUX 1.2.1/pymol-1.2.1-shaders.patch 442 RMD160 db5ee361cd1e253b9aa012098d08eb7873d95da3 SHA1 881d25514bc744d6f12b5f30bfa1709ed45dba05 SHA256 48042a9baf28c35a55204f646f14eddcf5093e17f518d7de2ffc50cbb7914dda
-AUX 1.2.2-data-path.patch 3361 RMD160 ece520d476cc13a312ba3976902fda9dedf7758d SHA1 3a03308d74372bf8fe62cbe804711bdb58895f8d SHA256 da9dfec59b09b2fd6bad5f0188589a0d04c28296651add308acd35d159f60947
-AUX 1.2.2-prefix.patch 1183 RMD160 25a3e3fb1639e0c5cc93928b4fcba412a3e9b371 SHA1 3c61c3552a579a48883c61b646f05ce1f059744e SHA256 35b14c60163517debfdeae52b3be00bc0fc6ab96c58d2bf3efb65e22728522d4
-AUX 1.3.0-vmd.patch 1286 RMD160 3587dbf9664747de1d10ad0039773ef9451f7488 SHA1 79dd6e0881edb905b5e098646e1de40224bcf6a6 SHA256 79f13530928bf00b6469a6fe473d1e743e22b25edd2a4ad6d53762ccac9ff318
-AUX 1.4-shaders.patch 2851 RMD160 3e2f6e8a3c930d1e11e99760e619767ed4d71718 SHA1 8b214a10dfedf7e3cb55c7c77eaff95b7478e5e5 SHA256 bcd30eb9e18195d5d05d902df4497abfc6b786e9f4e418e9c71ebb1c3dca0bf1
-AUX 1.4-vmd.patch 1414 RMD160 c7de92c73a0f91e6f95a7208b912cb6105f6d972 SHA1 51515e11cbaed06407238c0e900091174db1ff26 SHA256 320436783d1cfa4f94bd4fe57af4bdf7d3d200c951938d127d77b75d77bef7f0
-AUX 1.4.1-data-path.patch 3898 RMD160 842548be0710bb4f80791fdb98654b36cb777e84 SHA1 f3dedae4a97ee4916ca7ce4733506d6b8221e79f SHA256 911f69cb428f91a284102580b73f771648f6a1a059a53c1bcc31c51ab492b010
-AUX 1.4.1-shaders.patch 2507 RMD160 2dea0805fcc8a993d7f5fa8668257be860c7d5e8 SHA1 4548f93fbe92a511dc0d2425c86402a776567cb4 SHA256 b0cbb5bc81bb8f85bef8cbb6cd76f91b02b076ef5798075e152626becf3b5ae5
-AUX 1.4.1-web.patch 550 RMD160 fc15b0e428b9376a9d7f2e87d06035555ceab2fe SHA1 06db70ef92ce981715cde9ac1578291b653341d9 SHA256 2545245c4c18c96faf76e0ba4a754402cb2081e56f945da1732b63fddda4fb2b
 AUX pymol-0.99_rc10-data-path.patch 2969 RMD160 608e0e936fccf0860f6b5269e6739c839fcd32ea SHA1 7a3585d14431b7840eff8f6ee0a5d8324049ff77 SHA256 10c97c3d4d2f620a2884a812a6997f2cf8472f2e0c589c2630a4d0bcf67656de
+AUX pymol-1.2.2-data-path.patch 3361 RMD160 ece520d476cc13a312ba3976902fda9dedf7758d SHA1 3a03308d74372bf8fe62cbe804711bdb58895f8d SHA256 da9dfec59b09b2fd6bad5f0188589a0d04c28296651add308acd35d159f60947
+AUX pymol-1.2.2-prefix.patch 1183 RMD160 25a3e3fb1639e0c5cc93928b4fcba412a3e9b371 SHA1 3c61c3552a579a48883c61b646f05ce1f059744e SHA256 35b14c60163517debfdeae52b3be00bc0fc6ab96c58d2bf3efb65e22728522d4
 AUX pymol-1.2.2-shaders.patch 441 RMD160 c0d9e177f701a015aec192b2bdf6b1df31e8de16 SHA1 5651438459920b74040330ec0b7d9ea14e63818c SHA256 c15e5c5d2a6b53b96c6a7fe0b717ac0f7d85c90aca3e5b02c8d8c34b9038cb68
 AUX pymol-1.2.2-vmd.patch 1250 RMD160 fa5064d842099cd43e951278220b80fba170c5ec SHA1 2381931650169a841cf41fd38a1b870c0a896745 SHA256 d3688f57f32912ace20a3344dc49530a48963454dcc5a9aafe45d4b6be269525
+AUX pymol-1.3.0-vmd.patch 1286 RMD160 3587dbf9664747de1d10ad0039773ef9451f7488 SHA1 79dd6e0881edb905b5e098646e1de40224bcf6a6 SHA256 79f13530928bf00b6469a6fe473d1e743e22b25edd2a4ad6d53762ccac9ff318
+AUX pymol-1.4-shaders.patch 2851 RMD160 3e2f6e8a3c930d1e11e99760e619767ed4d71718 SHA1 8b214a10dfedf7e3cb55c7c77eaff95b7478e5e5 SHA256 bcd30eb9e18195d5d05d902df4497abfc6b786e9f4e418e9c71ebb1c3dca0bf1
+AUX pymol-1.4-vmd.patch 1414 RMD160 c7de92c73a0f91e6f95a7208b912cb6105f6d972 SHA1 51515e11cbaed06407238c0e900091174db1ff26 SHA256 320436783d1cfa4f94bd4fe57af4bdf7d3d200c951938d127d77b75d77bef7f0
+AUX pymol-1.4.1-data-path.patch 3898 RMD160 842548be0710bb4f80791fdb98654b36cb777e84 SHA1 f3dedae4a97ee4916ca7ce4733506d6b8221e79f SHA256 911f69cb428f91a284102580b73f771648f6a1a059a53c1bcc31c51ab492b010
+AUX pymol-1.4.1-shaders.patch 2507 RMD160 2dea0805fcc8a993d7f5fa8668257be860c7d5e8 SHA1 4548f93fbe92a511dc0d2425c86402a776567cb4 SHA256 b0cbb5bc81bb8f85bef8cbb6cd76f91b02b076ef5798075e152626becf3b5ae5
+AUX pymol-1.4.1-web.patch 550 RMD160 fc15b0e428b9376a9d7f2e87d06035555ceab2fe SHA1 06db70ef92ce981715cde9ac1578291b653341d9 SHA256 2545245c4c18c96faf76e0ba4a754402cb2081e56f945da1732b63fddda4fb2b
 AUX pymol-1.5.0.1-data-path.patch 6577 RMD160 42fa714d39bd36398505db2430e29330a72c2454 SHA1 a126b73c983ffa1ac16fba0a9146f6349fef9e53 SHA256 5a0f5f4fb0308b750cfbca5007683363102a6675be9ae93466dcb53177375c61
 AUX pymol-1.5.0.1-flags.patch 521 RMD160 0a8788c55de42a24f97c96594f7065fcd26e1469 SHA1 9405af5a709bc626524bb5730f6c08e2f5c4aa1b SHA256 7a92d5ea975dcef50ea9614b87c56d7b4f1b976210608800413a80de98c69a3f
-AUX pymol-1.5.0.1-nosplash.patch 721 RMD160 d488b2e17690eaf12a4bdcae804303ae0ef4ad90 SHA1 82bb5b5611f450ee019c8655a3caf509908fcc39 SHA256 3a0819a9f0cb6934f3edc1de0d6c13ce640217a968ca5681260470fdf64d4796
 AUX pymol-1.5.0.1-prefix.patch 1746 RMD160 2bab80e0881a7180887a0259121c46fd09b73b67 SHA1 ae54823d5eb48e3dcfc57d5635b25df9728703ef SHA256 95ccc4b626ff1a6bd21da6825e647740bcda8c003ca4cf10a1bcd3940b562247
 AUX pymol-1.5.0.1-setup.py.patch 893 RMD160 3060484fe43632743eec4503d8b73cff28d9b3a4 SHA1 01353b2578867a413b31a6b063f5ca561a218ddb SHA256 3a03cb19878a772caff5c6931ff7bb1fdcd022147ec0e8a23593d4ae61cf1593
 AUX pymol-1.5.0.1-vmd.patch 1723 RMD160 7e0d0677d3dd498bfdf47e2055720d365a97ec37 SHA1 03157e315ad840bf129b02dede3cc45ebd12fcd4 SHA256 9a31ff39838484ce0df7658b896b8da137740871901bdc66db5dc4c46c293e50
 AUX pymol-1.5.0.1-web.patch 634 RMD160 8c7c2bec3dae9c154f11ae5436a63fa99f2bce39 SHA1 6b68a4220a6ce4058ceb5b10e88a0ed397d1966e SHA256 7c30f0c030c3f2e30cbd1f37c58910592a71ee2d5c5a351130e0bde13104c49e
-DIST pymol-1.2.3.tar.gz 8281001 RMD160 125b4827b1ee5708ed28ac5bd8988a75b707ce4f SHA1 435dccba925298fa4865980a7139edcb8748accc SHA256 7d85e3e818ba357fa6df0db2248ef5555f84394559790e88e7003d602a20ab9f
 DIST pymol-1.3.1_pre3925-r1.tar.gz 8185909 RMD160 fcd6bdcedda369af7d51c41fc708c69a878b1aa1 SHA1 990b1acd0d5c84f7b93dc1c9a550f95b74c67e4b SHA256 74d3a3dd1972e2f47458e80c3d157871c361ad81119c76d1edd40b5e491cb50e
 DIST pymol-1.4.1.tar.xz 6831544 RMD160 6478b14215d0c502bff3bdec0cae3c903a9004e0 SHA1 d4da217ebf2c059f4712f564b55daa81a839b259 SHA256 af020e3103360defa3749ed31c16938a00032d4c2bf40f8455c746919aeaffd6
-DIST pymol-v1.5.0.1.tar.bz2 9731413 RMD160 fc9b5586778ee5a4b8ba0ae12797abfbbc01ced1 SHA1 924fcc29c7b41498d54c17824b3ae80671b32aa0 SHA256 dfcad84ed2abc7c265faa0a5d3be30833ff49be1f80d1602e483119b742c1a09
-EBUILD pymol-1.2.3-r1.ebuild 2640 RMD160 4bcb32f90a2bf09989eb26cac13ad3721ceb75ee SHA1 ea316d2d72403eb25a42fee514f9c071f6d56ded SHA256 b8f23630086279243568e51c847823f7067f7004db1bea7d06f9c9b1202e7147
-EBUILD pymol-1.3.1_pre3925-r1.ebuild 2669 RMD160 299d49ebe4982c9a49a86666050b66b8ecaae081 SHA1 a7b4c84ea4bc6fb62e2c553fda8f1c2c5ea3c97b SHA256 ea03bdb373644f5d1e5c07659699cd27127f1db7e7273afb1e803dee77f7b8b6
-EBUILD pymol-1.4.1.ebuild 2776 RMD160 971f76d309bb8f947b00f92ba356f1cb6675151b SHA1 238785f471947c606624eb12ed62e0e7bced1156 SHA256 a052173856bb283cefdb1bc11ab1cbc959ff59433de936271a35e86f139743d3
-EBUILD pymol-1.5.0.1.ebuild 2611 RMD160 d1f989ee5e98c71d8180dd902b7f900d2854d88e SHA1 d10ea7118f372c8f5e82a24ea375f4c658212a9e SHA256 bc16cb480522eec37bfeb901f31f749e370dca31765bccce790e86e00a8b3962
-MISC ChangeLog 748 RMD160 f81a7a71a263a10a37d42d1ac15b83bf0c49d66c SHA1 815274b61ad85f50cd1d5147ea8b45907de735b8 SHA256 208f0acca90c1dbc978bd3c2829cf0128f6705bbb08be830bfba6919a20d018d
+DIST pymol-v1.5.0.1.tar.bz2 9695855 RMD160 1e5fd51299f2bbe0249a9a07117c068af49ec095 SHA1 b59ff50437d34f21ca8ffd007a600de4df684073 SHA256 16c0cfbacbbd967b23654dd3708ef6ba877ab2a6c0985ff806a17186427de49c
+DIST pymol.xpm.tar 10240 RMD160 86b01bbe6aa8bf0251a982718d343c61c781c6e3 SHA1 af1ae2c9e2479efcd600c7ba01313b5dd7ef5b87 SHA256 813c450b5acc399387ddc33cc2d747c02afb515e1c3f216be7f7284a09e64819
+EBUILD pymol-1.3.1_pre3925-r1.ebuild 2680 RMD160 889337459cad09db150cfbed5eb401cc98458e80 SHA1 a4919150db3ddbbf6b37c86eaf0ffea1dca38430 SHA256 23bc8e2ff6dfa130235e45325ad0e77e86273fb79f5da866ef9443cdb68fbcb6
+EBUILD pymol-1.4.1.ebuild 2784 RMD160 f9f0859cea1c94752a4b82e28160d0b6439a3a52 SHA1 3fe2324dd20ee7e60026dc2db3821bf08129d393 SHA256 84f720bb5ad5690e3f373b86b53708943b93c2d4237cbc5998b1b094d91596ae
+EBUILD pymol-1.5.0.1.ebuild 2784 RMD160 374ed8b0982076515a86771735588e141840d4af SHA1 c4729eed0ba548500440cdd351a7ac303cfd7fae SHA256 e50c3cb2e2cefc167e7e73f2aae7402add9b3e47147d2c74c35740e65a739bce
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 MISC metadata.xml 569 RMD160 edfb6f78a19d49eb7f18fb0d8336a0c5f97c3f34 SHA1 c75951bdda3dcb4564d23b873e30773bc9ed7fc7 SHA256 6f2b2746c7b2182262554076f11159b11d671695c40509bf7014c7546d719ff2
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diff --git a/sci-chemistry/pymol/files/1.2.1/pymol-1.2.1-data-path.patch b/sci-chemistry/pymol/files/1.2.1/pymol-1.2.1-data-path.patch
deleted file mode 100644
index 86c3fe1f1c27..000000000000
--- a/sci-chemistry/pymol/files/1.2.1/pymol-1.2.1-data-path.patch
+++ /dev/null
@@ -1,30 +0,0 @@
-diff -arNu -uarN pymol/modules/pymol/commanding.py pymol.new/modules/pymol/commanding.py
---- pymol/modules/pymol/commanding.py	2009-03-31 12:43:14.585834066 +0200
-+++ pymol.new/modules/pymol/commanding.py	2009-03-31 12:44:26.436354330 +0200
-@@ -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:
-diff -arNu -uarN pymol/modules/pymol/importing.py pymol.new/modules/pymol/importing.py
---- pymol/modules/pymol/importing.py	2009-03-31 12:43:14.546250540 +0200
-+++ pymol.new/modules/pymol/importing.py	2009-03-31 12:44:48.876657949 +0200
-@@ -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' }
-         
diff --git a/sci-chemistry/pymol/files/1.2.1/pymol-1.2.1-shaders.patch b/sci-chemistry/pymol/files/1.2.1/pymol-1.2.1-shaders.patch
deleted file mode 100644
index 06f75682344f..000000000000
--- a/sci-chemistry/pymol/files/1.2.1/pymol-1.2.1-shaders.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- pymol-1.2_rc1/setup.py.old  2009-07-17 00:05:10.339203020 -0500
-+++ pymol-1.2_rc1/setup.py      2009-07-17 00:09:03.375274561 -0500
-@@ -138,6 +138,7 @@
-                 ("_PYMOL_INLINE",None),
-                 ("_PYMOL_FREETYPE",None),
-                 ("_PYMOL_LIBPNG",None),
-+                ("_PYMOL_OPENGL_SHADERS",None),
- # Numeric Python support                    
- #                ("_PYMOL_NUMPY",None),
- # VMD plugin support   
diff --git a/sci-chemistry/pymol/files/1.2.2-data-path.patch b/sci-chemistry/pymol/files/pymol-1.2.2-data-path.patch
index cf1bf59af0c6..cf1bf59af0c6 100644
--- a/sci-chemistry/pymol/files/1.2.2-data-path.patch
+++ b/sci-chemistry/pymol/files/pymol-1.2.2-data-path.patch
diff --git a/sci-chemistry/pymol/files/1.2.2-prefix.patch b/sci-chemistry/pymol/files/pymol-1.2.2-prefix.patch
index 211881435123..211881435123 100644
--- a/sci-chemistry/pymol/files/1.2.2-prefix.patch
+++ b/sci-chemistry/pymol/files/pymol-1.2.2-prefix.patch
diff --git a/sci-chemistry/pymol/files/1.3.0-vmd.patch b/sci-chemistry/pymol/files/pymol-1.3.0-vmd.patch
index 0f34a02ea01b..0f34a02ea01b 100644
--- a/sci-chemistry/pymol/files/1.3.0-vmd.patch
+++ b/sci-chemistry/pymol/files/pymol-1.3.0-vmd.patch
diff --git a/sci-chemistry/pymol/files/1.4-shaders.patch b/sci-chemistry/pymol/files/pymol-1.4-shaders.patch
index 853ebff9da81..853ebff9da81 100644
--- a/sci-chemistry/pymol/files/1.4-shaders.patch
+++ b/sci-chemistry/pymol/files/pymol-1.4-shaders.patch
diff --git a/sci-chemistry/pymol/files/1.4-vmd.patch b/sci-chemistry/pymol/files/pymol-1.4-vmd.patch
index 2fd909ffd540..2fd909ffd540 100644
--- a/sci-chemistry/pymol/files/1.4-vmd.patch
+++ b/sci-chemistry/pymol/files/pymol-1.4-vmd.patch
diff --git a/sci-chemistry/pymol/files/1.4.1-data-path.patch b/sci-chemistry/pymol/files/pymol-1.4.1-data-path.patch
index 903714cd223a..903714cd223a 100644
--- a/sci-chemistry/pymol/files/1.4.1-data-path.patch
+++ b/sci-chemistry/pymol/files/pymol-1.4.1-data-path.patch
diff --git a/sci-chemistry/pymol/files/1.4.1-shaders.patch b/sci-chemistry/pymol/files/pymol-1.4.1-shaders.patch
index 2caac2dc4bce..2caac2dc4bce 100644
--- a/sci-chemistry/pymol/files/1.4.1-shaders.patch
+++ b/sci-chemistry/pymol/files/pymol-1.4.1-shaders.patch
diff --git a/sci-chemistry/pymol/files/1.4.1-web.patch b/sci-chemistry/pymol/files/pymol-1.4.1-web.patch
index 2d6957df594d..2d6957df594d 100644
--- a/sci-chemistry/pymol/files/1.4.1-web.patch
+++ b/sci-chemistry/pymol/files/pymol-1.4.1-web.patch
diff --git a/sci-chemistry/pymol/files/pymol-1.5.0.1-nosplash.patch b/sci-chemistry/pymol/files/pymol-1.5.0.1-nosplash.patch
deleted file mode 100644
index b296285e89ca..000000000000
--- a/sci-chemistry/pymol/files/pymol-1.5.0.1-nosplash.patch
+++ /dev/null
@@ -1,15 +0,0 @@
- modules/pymol/invocation.py |    2 --
- 1 files changed, 0 insertions(+), 2 deletions(-)
-
-diff --git a/modules/pymol/invocation.py b/modules/pymol/invocation.py
-index de47849..c5f4487 100644
---- a/modules/pymol/invocation.py
-+++ b/modules/pymol/invocation.py
-@@ -397,7 +397,5 @@ if __name__=='pymol.invocation':
-         if loaded_something and (options.after_load_script!=""):
-             options.deferred.append(options.after_load_script)
-         options.deferred.extend(final_actions)
--        if options.show_splash and not options.no_gui and not restricted:
--            options.deferred.insert(0,"_do__ cmd.splash(1)")
-         if options.full_screen:
-             options.deferred.append("_do__ full_screen on")
diff --git a/sci-chemistry/pymol/pymol-1.2.3-r1.ebuild b/sci-chemistry/pymol/pymol-1.2.3-r1.ebuild
deleted file mode 100644
index 30dd9790aeda..000000000000
--- a/sci-chemistry/pymol/pymol-1.2.3-r1.ebuild
+++ /dev/null
@@ -1,106 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-1.2.3-r1.ebuild,v 1.9 2010/09/19 19:32:44 jlec Exp $
-
-EAPI="3"
-
-SUPPORT_PYTHON_ABIS="1"
-PYTHON_DEPEND="2:2.6"
-PYTHON_USE_WITH="tk"
-REV="3891"
-
-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} -> ${P}.tar.gz"
-
-LICENSE="PSF-2.2"
-SLOT="0"
-KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux"
-IUSE="apbs numpy shaders vmd"
-
-DEPEND="
-		dev-python/numpy
-		dev-python/pmw
-		media-libs/freetype:2
-		media-libs/libpng
-		media-video/mpeg-tools
-		sys-libs/zlib
-		media-libs/freeglut
-		apbs? (
-			dev-libs/maloc
-			sci-chemistry/apbs
-			sci-chemistry/pdb2pqr
-			sci-chemistry/pymol-apbs-plugin
-		)"
-RDEPEND="${DEPEND}"
-RESTRICT_PYTHON_ABIS="3.* 2.4 2.5"
-
-S="${WORKDIR}"/${PN}
-
-src_prepare() {
-	epatch "${FILESDIR}"/1.2.2-data-path.patch
-
-	epatch "${FILESDIR}"/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}"/${PN}-1.2.2-vmd.patch
-
-	use numpy && \
-		sed \
-			-e '/PYMOL_NUMPY/s:^#::g' \
-			-i setup.py
-
-	rm ./modules/pmg_tk/startup/apbs_tools.py || die
-
-	# python 3.* fix
-	# sed '452,465d' -i setup.py
-	distutils_src_prepare
-}
-
-src_configure() {
-	:
-}
-
-src_install() {
-	distutils_src_install
-
-	# These environment variables should not go in the wrapper script, or else
-	# it will be impossible to use the PyMOL libraries from Python.
-	cat >> "${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."
-
-#	rm "${D}"$(python_get_sitedir)/pmg_tk/startup/apbs_tools.py
-}
diff --git a/sci-chemistry/pymol/pymol-1.3.1_pre3925-r1.ebuild b/sci-chemistry/pymol/pymol-1.3.1_pre3925-r1.ebuild
index 49210fa0f430..047cb181440a 100644
--- a/sci-chemistry/pymol/pymol-1.3.1_pre3925-r1.ebuild
+++ b/sci-chemistry/pymol/pymol-1.3.1_pre3925-r1.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2011 Gentoo Foundation
+# 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 1.3 2011/05/24 18:44:14 phajdan.jr Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-1.3.1_pre3925-r1.ebuild,v 1.4 2012/02/14 08:18:11 jlec Exp $
 
 EAPI="3"
 
@@ -13,7 +13,7 @@ REV="3925"
 
 inherit eutils distutils prefix
 
-DESCRIPTION="A Python-extensible molecular graphics system."
+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"
@@ -42,9 +42,9 @@ RDEPEND="${DEPEND}"
 S="${WORKDIR}"/${PN}
 
 src_prepare() {
-	epatch "${FILESDIR}"/1.2.2-data-path.patch
+	epatch "${FILESDIR}"/${PN}-1.2.2-data-path.patch
 
-	epatch "${FILESDIR}"/1.2.2-prefix.patch && \
+	epatch "${FILESDIR}"/${PN}-1.2.2-prefix.patch && \
 	eprefixify setup.py
 
 	# Turn off splash screen.  Please do make a project contribution
@@ -58,7 +58,7 @@ src_prepare() {
 
 	use shaders && epatch "${FILESDIR}"/${PN}-1.2.2-shaders.patch
 
-	use vmd && epatch "${FILESDIR}"/1.3.0-vmd.patch
+	use vmd && epatch "${FILESDIR}"/${PN}-1.3.0-vmd.patch
 
 	use numpy && \
 		sed \
diff --git a/sci-chemistry/pymol/pymol-1.4.1.ebuild b/sci-chemistry/pymol/pymol-1.4.1.ebuild
index e52f29d26142..aad9eee68429 100644
--- a/sci-chemistry/pymol/pymol-1.4.1.ebuild
+++ b/sci-chemistry/pymol/pymol-1.4.1.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2011 Gentoo Foundation
+# 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 1.2 2011/06/02 08:39:41 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-1.4.1.ebuild,v 1.3 2012/02/14 08:18:11 jlec Exp $
 
 EAPI="3"
 
@@ -12,7 +12,7 @@ PYTHON_MODNAME="${PN} chempy pmg_tk pmg_wx"
 
 inherit eutils distutils prefix versionator
 
-DESCRIPTION="A Python-extensible molecular graphics system."
+DESCRIPTION="A Python-extensible molecular graphics system"
 HOMEPAGE="http://pymol.sourceforge.net/"
 SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz"
 
@@ -41,12 +41,12 @@ RDEPEND="${DEPEND}"
 
 src_prepare() {
 	epatch \
-		"${FILESDIR}"/${PV}-data-path.patch \
-		"${FILESDIR}"/${PV}-shaders.patch
+		"${FILESDIR}"/${P}-data-path.patch \
+		"${FILESDIR}"/${P}-shaders.patch
 
-	use web || epatch "${FILESDIR}"/${PV}-web.patch
+	use web || epatch "${FILESDIR}"/${P}-web.patch
 
-	epatch "${FILESDIR}"/1.2.2-prefix.patch && \
+	epatch "${FILESDIR}"/${PN}-1.2.2-prefix.patch && \
 		eprefixify setup.py
 
 	# Turn off splash screen.  Please do make a project contribution
@@ -58,7 +58,7 @@ src_prepare() {
 		-e "s:\(ext_comp_args=\).*:\1[]:g" \
 		"${S}"/setup.py || die "Failed running sed on setup.py"
 
-	use vmd && epatch "${FILESDIR}"/$(get_version_component_range 1-2)-vmd.patch
+	use vmd && epatch "${FILESDIR}"/${PN}-$(get_version_component_range 1-2)-vmd.patch
 
 	use numpy && \
 		sed \
diff --git a/sci-chemistry/pymol/pymol-1.5.0.1.ebuild b/sci-chemistry/pymol/pymol-1.5.0.1.ebuild
index 829d4fad273d..381a14bfce07 100644
--- a/sci-chemistry/pymol/pymol-1.5.0.1.ebuild
+++ b/sci-chemistry/pymol/pymol-1.5.0.1.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-1.5.0.1.ebuild,v 1.1 2012/02/13 22:09:19 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-1.5.0.1.ebuild,v 1.2 2012/02/14 08:18:11 jlec Exp $
 
 EAPI=4
 
@@ -10,11 +10,13 @@ RESTRICT_PYTHON_ABIS="2.4 2.5 2.6 3.*"
 PYTHON_USE_WITH="tk"
 PYTHON_MODNAME="${PN} chempy pmg_tk pmg_wx"
 
-inherit eutils distutils prefix versionator
+inherit distutils eutils fdo-mime prefix versionator
 
-DESCRIPTION="A Python-extensible molecular graphics system."
+DESCRIPTION="A Python-extensible molecular graphics system"
 HOMEPAGE="http://pymol.sourceforge.net/"
-SRC_URI="mirror://sourceforge/project/${PN}/${PN}/${PV}/${PN}-v${PV}.tar.bz2"
+SRC_URI="
+	mirror://sourceforge/project/${PN}/${PN}/${PV}/${PN}-v${PV}.tar.bz2
+	http://dev.gentoo.org/~jlec/distfiles/${PN}.xpm.tar"
 
 LICENSE="PSF-2.2"
 SLOT="0"
@@ -52,10 +54,6 @@ src_prepare() {
 	epatch "${FILESDIR}"/${P}-prefix.patch && \
 		eprefixify setup.py
 
-	# Turn off splash screen.  Please do make a project contribution
-	# if you are able though. #299020
-	epatch "${FILESDIR}"/${P}-nosplash.patch
-
 	use vmd && epatch "${FILESDIR}"/${P}-vmd.patch
 
 	if use numpy; then
@@ -92,7 +90,7 @@ src_install() {
 
 	cat >> "${T}"/pymol <<- EOF
 	#!/bin/sh
-	$(PYTHON -f) -O \${PYMOL_PATH}/__init__.py \$*
+	$(PYTHON -f) -O \${PYMOL_PATH}/__init__.py -q \$*
 	EOF
 
 	dobin "${T}"/pymol
@@ -104,6 +102,9 @@ src_install() {
 	doins -r examples
 
 	dodoc DEVELOPERS README
+
+	doicon "${WORKDIR}"/${PN}.xpm
+	make_desktop_entry pymol PyMol ${PN}.xpm "Graphics;Science;Chemistry"
 }
 
 pkg_postinst() {
@@ -111,4 +112,11 @@ pkg_postinst() {
 	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
 }