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

(Portage version: 2.2.0_alpha128/cvs/Linux x86_64)

20 files changed, 20 insertions, 1137 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/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
-}