Version Bump

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

11 files changed, 464 insertions, 14 deletions

diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog
index adab98470532..ca714f689b81 100644
--- a/sci-chemistry/pymol/ChangeLog
+++ b/sci-chemistry/pymol/ChangeLog
@@ -1,6 +1,15 @@
 # ChangeLog for sci-chemistry/pymol
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/ChangeLog,v 1.81 2011/06/02 08:39:41 jlec Exp $
+# 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 $
+
+*pymol-1.5.0.1 (13 Feb 2012)
+
+  13 Feb 2012; Justin Lecher <jlec@gentoo.org> +pymol-1.5.0.1.ebuild,
+  +files/pymol-1.5.0.1-data-path.patch, +files/pymol-1.5.0.1-flags.patch,
+  +files/pymol-1.5.0.1-nosplash.patch, +files/pymol-1.5.0.1-prefix.patch,
+  +files/pymol-1.5.0.1-setup.py.patch, +files/pymol-1.5.0.1-vmd.patch,
+  +files/pymol-1.5.0.1-web.patch, metadata.xml:
+  Version Bump
 
   02 Jun 2011; Justin Lecher <jlec@gentoo.org> +files/1.4.1-web.patch,
   pymol-1.4.1.ebuild, metadata.xml:
diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
index aaed1a9ed2c0..00d4c6b482d3 100644
--- a/sci-chemistry/pymol/Manifest
+++ b/sci-chemistry/pymol/Manifest
@@ -1,5 +1,5 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
+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
@@ -15,18 +15,27 @@ AUX 1.4.1-web.patch 550 RMD160 fc15b0e428b9376a9d7f2e87d06035555ceab2fe SHA1 06d
 AUX pymol-0.99_rc10-data-path.patch 2969 RMD160 608e0e936fccf0860f6b5269e6739c839fcd32ea SHA1 7a3585d14431b7840eff8f6ee0a5d8324049ff77 SHA256 10c97c3d4d2f620a2884a812a6997f2cf8472f2e0c589c2630a4d0bcf67656de
 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-1.5.0.1-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
-MISC ChangeLog 365 RMD160 7e92122533ba27a74b2a6a5fb896942e6af9f46b SHA1 c8351ec6aeef475604719c615f2c707371f67af7 SHA256 07ff7156ca6f37fbc8a2fabceb20710ed64b8edfa32c5bde77478fe1678aa9ae
-MISC metadata.xml 564 RMD160 4fe4285d22edbd5b83021ff1f05d3a487fa8e6b2 SHA1 d3282e321144e2f741a91ac39fdbcfcff326a92d SHA256 ff58b5f1bc713939fec5fd635bc944ff310967c4e4ba40f83d458bbb2600c511
+EBUILD pymol-1.5.0.1.ebuild 2611 RMD160 d1f989ee5e98c71d8180dd902b7f900d2854d88e SHA1 d10ea7118f372c8f5e82a24ea375f4c658212a9e SHA256 bc16cb480522eec37bfeb901f31f749e370dca31765bccce790e86e00a8b3962
+MISC ChangeLog 748 RMD160 f81a7a71a263a10a37d42d1ac15b83bf0c49d66c SHA1 815274b61ad85f50cd1d5147ea8b45907de735b8 SHA256 208f0acca90c1dbc978bd3c2829cf0128f6705bbb08be830bfba6919a20d018d
+MISC metadata.xml 569 RMD160 edfb6f78a19d49eb7f18fb0d8336a0c5f97c3f34 SHA1 c75951bdda3dcb4564d23b873e30773bc9ed7fc7 SHA256 6f2b2746c7b2182262554076f11159b11d671695c40509bf7014c7546d719ff2
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.17 (GNU/Linux)
+Version: GnuPG v2.0.18 (GNU/Linux)
 
-iEYEARECAAYFAk3nTFMACgkQgAnW8HDreRbfNACfdam4Wpy43+C72VatNJjGkxwG
-45cAnRRiPPDP66xxWpK4y3YDtldlLWo1
-=30Ik
+iEYEAREKAAYFAk85ihUACgkQgAnW8HDreRZVWgCgy2khVXi+gCrqb1cUGhA9AV0T
+LQ8AniIcSOH22EDfhckr3hZg9kUkrVwk
+=2ggS
 -----END PGP SIGNATURE-----
diff --git a/sci-chemistry/pymol/files/pymol-1.5.0.1-data-path.patch b/sci-chemistry/pymol/files/pymol-1.5.0.1-data-path.patch
new file mode 100644
index 000000000000..e865bfd04174
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol-1.5.0.1-data-path.patch
@@ -0,0 +1,147 @@
+ layer0/ShaderMgr.c                  |   16 ++++++++--------
+ layer1/Setting.c                    |    2 +-
+ 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 ++--
+ 7 files changed, 17 insertions(+), 17 deletions(-)
+
+diff --git a/layer0/ShaderMgr.c b/layer0/ShaderMgr.c
+index cc760ae..364277f 100644
+--- a/layer0/ShaderMgr.c
++++ b/layer0/ShaderMgr.c
+@@ -385,7 +385,7 @@ 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;
+   size_t res;
+ 
+   PRINTFB(G, FB_ShaderMgr, FB_Debugging)
+@@ -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 from disk\n" ENDFB(G);
++      " PyMOLShader_NewFromFile-Warning: PYMOL_DATA not set, cannot read shader config files from disk\n" 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 c2b8bbb..4c6fdb7 100644
+--- a/layer1/Setting.c
++++ b/layer1/Setting.c
+@@ -4375,7 +4375,7 @@ 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);
+-    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/modules/chempy/__init__.py b/modules/chempy/__init__.py
+index 23dbe45..795a223 100644
+--- a/modules/chempy/__init__.py
++++ b/modules/chempy/__init__.py
+@@ -235,7 +235,7 @@ 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 457ace7..7cc2953 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-1.5.0.1-flags.patch b/sci-chemistry/pymol/files/pymol-1.5.0.1-flags.patch
new file mode 100644
index 000000000000..9bdba45f3b1f
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol-1.5.0.1-flags.patch
@@ -0,0 +1,19 @@
+ setup.py |    5 +----
+ 1 files changed, 1 insertions(+), 4 deletions(-)
+
+diff --git a/setup.py b/setup.py
+index 2b6fa35..9c0556d 100755
+--- a/setup.py
++++ b/setup.py
+@@ -197,10 +197,7 @@ else: # linux or other unix
+                    ("_PYMOL_GL_CALLLISTS",None),
+                    ("OPENGL_ES_2",None),
+                    ]
+-    ext_comp_args = [ "-ffast-math",
+-                      "-funroll-loops",
+-                      "-O3",
+-                      "-g" ]
++    ext_comp_args = []
+     ext_link_args = []
+ 
+ 
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
new file mode 100644
index 000000000000..b296285e89ca
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol-1.5.0.1-nosplash.patch
@@ -0,0 +1,15 @@
+ 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/files/pymol-1.5.0.1-prefix.patch b/sci-chemistry/pymol/files/pymol-1.5.0.1-prefix.patch
new file mode 100644
index 000000000000..830eb8febbf5
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol-1.5.0.1-prefix.patch
@@ -0,0 +1,43 @@
+ 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/files/pymol-1.5.0.1-setup.py.patch b/sci-chemistry/pymol/files/pymol-1.5.0.1-setup.py.patch
new file mode 100644
index 000000000000..076d6907a183
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol-1.5.0.1-setup.py.patch
@@ -0,0 +1,39 @@
+ setup.py |   28 ----------------------------
+ 1 files changed, 0 insertions(+), 28 deletions(-)
+
+diff --git a/setup.py b/setup.py
+index 18866a2..705b0c5 100755
+--- a/setup.py
++++ b/setup.py
+@@ -487,31 +487,3 @@ distribution = setup ( # Distribution meta-data
+                   define_macros = def_macros
+                   )
+         ])
+-
+-# make available for setup2.py
+-try:
+-    site_packages = distribution.command_obj['install'].install_libbase
+-except KeyError:
+-    print """
+- Error: Please run, 'setup.py install' not 'setup build' or other variant.
+-
+-"""
+-    sys.exit(2)
+-
+-f = open('setup3.py', 'w')
+-print >> f, 'site_packages =', repr(site_packages)
+-f.close()
+-
+-print '''
+- After running:
+-
+-     python setup.py install
+-     
+- Please run, to complete the installation:
+-
+-     python setup2.py install
+-
+- To uninstall PyMOL, run:
+-
+-     python setup2.py uninstall
+-'''
diff --git a/sci-chemistry/pymol/files/pymol-1.5.0.1-vmd.patch b/sci-chemistry/pymol/files/pymol-1.5.0.1-vmd.patch
new file mode 100644
index 000000000000..cf47082efb2b
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol-1.5.0.1-vmd.patch
@@ -0,0 +1,36 @@
+ setup.py |    8 ++++----
+ 1 files changed, 4 insertions(+), 4 deletions(-)
+
+diff --git a/setup.py b/setup.py
+index 366d552..ce0d271 100755
+--- a/setup.py
++++ b/setup.py
+@@ -161,8 +161,8 @@ else: # linux or other unix
+                  "layer5",
+                  "/usr/include/freetype2",
+               # 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",
+                  "generated/include",
+@@ -190,7 +190,7 @@ else: # linux or other unix
+                    # Numeric Python support                    
+                    #                ("_PYMOL_NUMPY",None),
+                    # VMD plugin support           
+-                   #               ("_PYMOL_VMD_PLUGINS",None)
++                                  ("_PYMOL_VMD_PLUGINS",None),
+                    ("_PYMOL_CGO_DRAWARRAYS",None),
+                    ("_PYMOL_CGO_DRAWBUFFERS",None),
+                    ("_CGO_DRAWARRAYS",None),
+@@ -354,7 +354,7 @@ distribution = 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-1.5.0.1-web.patch b/sci-chemistry/pymol/files/pymol-1.5.0.1-web.patch
new file mode 100644
index 000000000000..fe61f0264f0b
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol-1.5.0.1-web.patch
@@ -0,0 +1,19 @@
+ setup.py |    5 +----
+ 1 files changed, 1 insertions(+), 4 deletions(-)
+
+diff --git a/setup.py b/setup.py
+index 18866a2..366d552 100755
+--- a/setup.py
++++ b/setup.py
+@@ -229,10 +229,7 @@ distribution = 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/metadata.xml b/sci-chemistry/pymol/metadata.xml
index bf11e08cfb39..d7cc1df353d3 100644
--- a/sci-chemistry/pymol/metadata.xml
+++ b/sci-chemistry/pymol/metadata.xml
@@ -1,15 +1,15 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-<herd>sci-chemistry</herd>
-<maintainer>
+	<herd>sci-chemistry</herd>
+	<maintainer>
 		<email>jlec@gentoo.org</email>
-</maintainer>
-<use>
+	</maintainer>
+	<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>
+	</use>
 </pkgmetadata>
diff --git a/sci-chemistry/pymol/pymol-1.5.0.1.ebuild b/sci-chemistry/pymol/pymol-1.5.0.1.ebuild
new file mode 100644
index 000000000000..829d4fad273d
--- /dev/null
+++ b/sci-chemistry/pymol/pymol-1.5.0.1.ebuild
@@ -0,0 +1,114 @@
+# 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 $
+
+EAPI=4
+
+PYTHON_DEPEND="2:2.7"
+SUPPORT_PYTHON_ABIS="1"
+RESTRICT_PYTHON_ABIS="2.4 2.5 2.6 3.*"
+PYTHON_USE_WITH="tk"
+PYTHON_MODNAME="${PN} chempy pmg_tk pmg_wx"
+
+inherit eutils distutils prefix versionator
+
+DESCRIPTION="A Python-extensible molecular graphics system."
+HOMEPAGE="http://pymol.sourceforge.net/"
+SRC_URI="mirror://sourceforge/project/${PN}/${PN}/${PV}/${PN}-v${PV}.tar.bz2"
+
+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}"/${P}-prefix.patch && \
+		eprefixify setup.py
+
+	# Turn off splash screen.  Please do make a project contribution
+	# if you are able though. #299020
+	epatch "${FILESDIR}"/${P}-nosplash.patch
+
+	use vmd && epatch "${FILESDIR}"/${P}-vmd.patch
+
+	if use numpy; then
+		sed \
+			-e '/PYMOL_NUMPY/s:^#::g' \
+			-i setup.py || die
+	fi
+
+	rm ./modules/pmg_tk/startup/apbs_tools.py || die
+
+	echo "site_packages = \'$(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
+	$(PYTHON -f) -O \${PYMOL_PATH}/__init__.py \$*
+	EOF
+
+	dobin "${T}"/pymol
+
+	insinto /usr/share/pymol
+	doins -r test data scripts
+
+	insinto /usr/share/pymol/examples
+	doins -r examples
+
+	dodoc DEVELOPERS README
+}
+
+pkg_postinst() {
+	elog "\t USE=shaders was removed,"
+	elog "please use pymol config settings"
+	elog "\t set use_shaders, 1"
+	distutils_pkg_postinst
+}