sci-chemistry/pymol: Drop old

(Portage version: 2.2.15/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!)

33 files changed, 18 insertions, 2905 deletions

diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog
index 759cabd6e6b1..41ba243c0ccc 100644
--- a/sci-chemistry/pymol/ChangeLog
+++ b/sci-chemistry/pymol/ChangeLog
@@ -1,6 +1,23 @@
 # ChangeLog for sci-chemistry/pymol
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/ChangeLog,v 1.125 2015/01/22 08:14:25 pinkbyte Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/ChangeLog,v 1.126 2015/01/22 09:06:49 jlec Exp $
+
+  22 Jan 2015; Justin Lecher <jlec@gentoo.org> -pymol-1.5.0.3-r1.ebuild,
+  -pymol-1.5.0.3-r2.ebuild, -pymol-1.6.0_rc1.ebuild, -pymol-1.6.0.0.ebuild,
+  -pymol-1.6.0.0-r1.ebuild, -pymol-1.6.0.0-r2.ebuild, -pymol-1.7.0.0.ebuild,
+  -pymol-1.7.0.4.ebuild, -pymol-1.7.0.4-r1.ebuild, -pymol-1.7.1.1.ebuild,
+  -pymol-1.7.1.3.ebuild, -pymol-1.7.2.0.ebuild, -pymol-1.7.2.1.ebuild,
+  -pymol-1.7.3.0.ebuild, -pymol-1.7.3.1.ebuild, -pymol-1.7.3.2.ebuild,
+  -pymol-1.7.3.4.ebuild, -files/pymol-1.5.0.1-data-path.patch,
+  -files/pymol-1.5.0.1-flags.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,
+  -files/pymol-1.5.0.3-prefix.patch, -files/pymol-1.5.0.3-web.patch,
+  -files/pymol-1.6.0.0-bg_rgb.patch, -files/pymol-1.6.0.0-labels.patch,
+  -files/pymol-1.6.0.0-stereo.patch,
+  -files/pymol-1.7.0.4-fix-broken-label-scaling-on-Linux.patch,
+  -files/pymol-9999-listing.patch, -files/1.2.1/nosplash-gentoo.patch,
+  -files/pymol-9999-options.patch, metadata.xml:
+  Drop old
 
   22 Jan 2015; Sergey Popov <pinkbyte@gentoo.org> pymol-1.5.0.3-r1.ebuild:
   Drop to ~ppc, wrt bug #507142
diff --git a/sci-chemistry/pymol/files/1.2.1/nosplash-gentoo.patch b/sci-chemistry/pymol/files/1.2.1/nosplash-gentoo.patch
deleted file mode 100644
index 3125b285696c..000000000000
--- a/sci-chemistry/pymol/files/1.2.1/nosplash-gentoo.patch
+++ /dev/null
@@ -1,9 +0,0 @@
---- modules/pymol/invocation.py	2009-06-25 17:26:27.000000000 +0200
-+++ modules/pymol/invocation.py.new	2009-06-25 17:41:57.000000000 +0200
-@@ -395,6 +395,4 @@
-         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)")
-         
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
deleted file mode 100644
index a2b09bb9eee3..000000000000
--- a/sci-chemistry/pymol/files/pymol-1.5.0.1-data-path.patch
+++ /dev/null
@@ -1,151 +0,0 @@
- 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 |    8 ++++----
- 7 files changed, 19 insertions(+), 19 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
-@@ -52,8 +52,8 @@ class Mutagenesis(Wizard):
-         
-         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
-@@ -217,8 +217,8 @@ class Mutagenesis(Wizard):
-     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
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
deleted file mode 100644
index 9bdba45f3b1f..000000000000
--- a/sci-chemistry/pymol/files/pymol-1.5.0.1-flags.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 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-setup.py.patch b/sci-chemistry/pymol/files/pymol-1.5.0.1-setup.py.patch
deleted file mode 100644
index 076d6907a183..000000000000
--- a/sci-chemistry/pymol/files/pymol-1.5.0.1-setup.py.patch
+++ /dev/null
@@ -1,39 +0,0 @@
- 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
deleted file mode 100644
index cf47082efb2b..000000000000
--- a/sci-chemistry/pymol/files/pymol-1.5.0.1-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 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
deleted file mode 100644
index fe61f0264f0b..000000000000
--- a/sci-chemistry/pymol/files/pymol-1.5.0.1-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 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/files/pymol-1.5.0.3-prefix.patch b/sci-chemistry/pymol/files/pymol-1.5.0.3-prefix.patch
deleted file mode 100644
index 9b0bad342e19..000000000000
--- a/sci-chemistry/pymol/files/pymol-1.5.0.3-prefix.patch
+++ /dev/null
@@ -1,57 +0,0 @@
-Index: setup.py
-===================================================================
---- setup.py	(revision 3983)
-+++ setup.py	(working copy)
-@@ -1,4 +1,4 @@
--#!/usr/bin/env python
-+#!@GENTOO_PORTAGE_EPREFIX@/usr/bin/env python
- #
- # This script only applies if you are performing a Python Distutils-based
- # installation of PyMOL.
-@@ -35,7 +35,7 @@
- 	      "modules/cealign/src/tnt" ]
-     libs=["glut32","opengl32","glu32","png"]
-     pyogl_libs = ["glut32","opengl32","glu32"]
--    lib_dirs=["/usr/lib/w32api"]
-+    lib_dirs=["@GENTOO_PORTAGE_EPREFIX@/usr/lib/w32api"]
-     def_macros=[("_PYMOL_MODULE",None),
-                 ("CYGWIN",None),
-                 ("_PYMOL_LIBPNG",None)]
-@@ -87,7 +87,7 @@
-                   "/sw/include/freetype2/freetype",
-                   "/sw/include/freetype2",
-                   "/sw/include",
--                  "/usr/X11/include",
-+                  "@GENTOO_PORTAGE_EPREFIX@/usr/X11/include",
- 		  "modules/cealign/src",
- 		  "modules/cealign/src/tnt",
- 		  #"contrib/uiuc/plugins/include/",
-@@ -114,8 +114,8 @@
-         ext_comp_args=[]
-         ext_link_args=[
-                        "-L/sw/lib", "-lpng",
--                       "/usr/X11/lib/libGL.dylib",
--                       "/usr/X11/lib/libGLU.dylib",
-+                       "@GENTOO_PORTAGE_EPREFIX@/usr/X11/lib/libGL.dylib",
-+                       "@GENTOO_PORTAGE_EPREFIX@/usr/X11/lib/libGLU.dylib",
-                        "-lfreeglut",
-                        "-lglew",
-                        "-L/sw/lib/freetype219/lib", "-lfreetype"
-@@ -221,7 +221,7 @@
-                  "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",
-@@ -242,7 +242,7 @@
-                    "GLU",
-                    "glut",
-                    "GLEW"]
--    lib_dirs = [ "/usr/X11R6/lib64", ]
-+    lib_dirs = [ "@GENTOO_PORTAGE_EPREFIX@/usr/X11R6/lib64", ]
-     def_macros = [ ("_PYMOL_MODULE",None),
-                    ("_PYMOL_INLINE",None),
-                    ("_PYMOL_FREETYPE",None),
diff --git a/sci-chemistry/pymol/files/pymol-1.5.0.3-web.patch b/sci-chemistry/pymol/files/pymol-1.5.0.3-web.patch
deleted file mode 100644
index 4f48140169cc..000000000000
--- a/sci-chemistry/pymol/files/pymol-1.5.0.3-web.patch
+++ /dev/null
@@ -1,16 +0,0 @@
-Index: setup.py
-===================================================================
---- setup.py	(revision 3983)
-+++ setup.py	(working copy)
-@@ -292,10 +292,7 @@
-                  'pymol/opengl/glu',
-                  'pymol/opengl/glut',
-                  'pymol/wizard',
--                 'pymol2',
--                 'web',
--                 'web/examples',
--                 'web/javascript', ],
-+                 'pymol2', ],
-     ext_modules = [
-         Extension("pymol._cmd", [
-                 "modules/cealign/src/ccealignmodule.cpp",
diff --git a/sci-chemistry/pymol/files/pymol-1.6.0.0-bg_rgb.patch b/sci-chemistry/pymol/files/pymol-1.6.0.0-bg_rgb.patch
deleted file mode 100644
index 39fcbc019bbe..000000000000
--- a/sci-chemistry/pymol/files/pymol-1.6.0.0-bg_rgb.patch
+++ /dev/null
@@ -1,254 +0,0 @@
-Index: pymol/setup.py
-===================================================================
---- pymol/setup.py	(revision 4031)
-+++ pymol/setup.py	(revision 4032)
-@@ -123,10 +123,10 @@
-                 out.write('"%s" "%s"' % (python_exe, pymol_file))
-                 out.write(' %1 %2 %3 %4 %5 %6 %7 %8 %9' + os.linesep)
-             else:
--                out.write('#!/bin/sh' + os.linesep)
-+                out.write('#!/bin/bash' + os.linesep)
-                 if sys.platform.startswith('darwin'):
--                    out.write('if [ "$DISPLAY" == "" ]; then DISPLAY=":0.0"; export DISPLAY; fi' + os.linesep)
--                out.write('PYMOL_PATH="%s"; export PYMOL_PATH' % pymol_path + os.linesep)
-+                    out.write('[ "$DISPLAY" == "" ] && export DISPLAY=":0.0"' + os.linesep)
-+                out.write('export PYMOL_PATH="%s"' % pymol_path + os.linesep)
-                 out.write('"%s" "%s" "$@"' % (python_exe, pymol_file) + os.linesep)
- 
-         os.chmod(launch_script, 0755)
-@@ -135,12 +135,16 @@
- 
- #============================================================================
- 
-+# should be something like (build_base + "/generated"), but that's only
-+# known to build and install instances
-+generated_dir = os.path.join(os.environ.get("PYMOL_BLD", "build"), "generated")
-+
- import create_shadertext
- create_shadertext.create_shadertext(
-         "data/shaders",
-         "shadertext.txt",
--        "generated/include/ShaderText.h",
--        "generated/src/ShaderText.c")
-+        generated_dir + "/ShaderText.h",
-+        generated_dir + "/ShaderText.c")
- 
- pymol_src_dirs = [
-     "ov/src",
-@@ -152,12 +156,10 @@
-     "layer5",
-     "modules/cealign/src",
-     "modules/cealign/src/tnt",
--    'generated/src',
--    'generated/include',
-+    generated_dir,
- ]
- 
- def_macros = [
--    ("_PYMOL_MODULE", None),
- ]
- 
- libs = []
-@@ -226,27 +228,32 @@
- 
-     for prefix in prefix_path:
-         inc_dirs += filter(os.path.isdir, [prefix + s for s in ["/include", "/include/freetype2"]])
--        lib_dirs += filter(os.path.isdir, [prefix + s for s in ["/lib"]])
-+        lib_dirs += filter(os.path.isdir, [prefix + s for s in ["/lib64", "/lib"]])
- 
-     glut = posix_find_lib(['glut', 'freeglut'], lib_dirs)
--    for _libs in (libs, pyogl_libs):
--        _libs += ["GL", "GLU", "GLEW", glut]
- 
--    ext_comp_args = ["-ffast-math", "-funroll-loops", "-O3", "-fcommon"]
-+    libs += ["GLEW"]
-+    pyogl_libs += ["GL", "GLU", glut]
- 
-+    libs += pyogl_libs
-+
-+    ext_comp_args += ["-ffast-math", "-funroll-loops", "-O3", "-fcommon"]
-+
- def get_pymol_version():
-     return re.findall(r'_PyMOL_VERSION "(.*)"', open('layer0/Version.h').read())[0]
- 
- def get_sources(subdirs, suffixes=('.c', '.cpp')):
-     return [f for d in subdirs for s in suffixes for f in glob(d + '/*' + s)]
- 
--def get_packages(base, parent='', r=[]):
-+def get_packages(base, parent='', r=None):
-     from os.path import join, exists
-+    if r is None:
-+        r = []
-     if parent:
-         r.append(parent)
-     for name in os.listdir(join(base, parent)):
-         if '.' not in name and exists(join(base, parent, name, '__init__.py')):
--            get_packages(base, join(parent, name))
-+            get_packages(base, join(parent, name), r)
-     return r
- 
- def pyogl_extension(name, sources):
-@@ -260,7 +267,10 @@
-     author    = "Schrodinger",
-     url       = "http://pymol.org",
-     contact   = "pymol-users@lists.sourceforge.net",
--    description = "PyMOL is a Python-enhanced molecular graphics tool. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies. Open Source PyMOL is free to everyone!", 
-+    description = ("PyMOL is a Python-enhanced molecular graphics tool. "
-+        "It excels at 3D visualization of proteins, small molecules, density, "
-+        "surfaces, and trajectories. It also includes molecular editing, "
-+        "ray tracing, and movies. Open Source PyMOL is free to everyone!"),
- 
-     package_dir = {'' : 'modules'},
-     packages = get_packages('modules'),
-Index: pymol/ChangeLog
-===================================================================
---- pymol/ChangeLog	(revision 4031)
-+++ pymol/ChangeLog	(revision 4032)
-@@ -2,6 +2,12 @@
- CHANGE LOG
- =========================================================================
- 
-+2013-06-18 Blaine Bell, Thomas Holder
-+
-+	* fixed loading in bg_rgb settings from old project pse files
-+
-+	* add URL support for run command
-+
- 2013-06-13 Blaine Bell <blaine.bell@schrodinger.com>
- 
- 	* fixed labels when use_shaders is 0 and show_frame_rate is on
-Index: pymol/layer1/Setting.c
-===================================================================
---- pymol/layer1/Setting.c	(revision 4031)
-+++ pymol/layer1/Setting.c	(revision 4032)
-@@ -41,6 +41,7 @@
- #include"ShaderMgr.h"
- #include"Sphere.h"
- #include"Selector.h"
-+#include"Parse.h"
- 
- static void *SettingPtr(CSetting * I, int index, ov_size size);
- 
-@@ -920,43 +921,67 @@
-         set_type = false;
-         break;
-       default:
--        if(ok)
--          switch (setting_type) {
--          case cSetting_boolean:
--          case cSetting_int:
--            ok = PConvPyIntToInt(PyList_GetItem(list, 2),
--                                 (int *) SettingPtr(I, index, sizeof(int)));
--            break;
--          case cSetting_color:
--            {
--              int color = 0;
--              ok = PConvPyIntToInt(PyList_GetItem(list, 2), &color);
--              if(ok)
--                color = ColorConvertOldSessionIndex(I->G, color);
--              *((int *) SettingPtr(I, index, sizeof(int))) = color;
--            }
--            break;
--          case cSetting_float:
--            ok = PConvPyFloatToFloat(PyList_GetItem(list, 2),
--                                     (float *) SettingPtr(I, index, sizeof(float)));
--            break;
--          case cSetting_float3:
--            ok = PConvPyListToFloatArrayInPlaceAutoZero(PyList_GetItem(list, 2),
--                                                        (float *) SettingPtr(I, index,
--                                                                             3 *
--                                                                             sizeof
--                                                                             (float)), 3);
--            break;
--          case cSetting_string:
--            ok = PConvPyStrToStrPtr(PyList_GetItem(list, 2), &str);
--            if(ok) {
--              strcpy(((char *) SettingPtr(I, index, strlen(str) + 1)), str);
--            }
--            break;
--          }
-+        if(ok){
-+	  int skip = false;
-+	  switch (index){
-+	  case cSetting_bg_rgb:
-+	  case cSetting_bg_rgb_top:
-+	  case cSetting_bg_rgb_bottom:
-+	    if (setting_type == cSetting_float3){
-+	      float vals[3];
-+	      ok = PConvPyListToFloatArrayInPlaceAutoZero(PyList_GetItem(list, 2), (float*)&vals, 3);
-+	      if (ok){
-+		SettingSet_color_from_3f(I, index, vals);
-+		setting_type = cSetting_color;
-+		skip = true;
-+	      }
-+	    } else if (setting_type == cSetting_color){
-+	      int color = 0;
-+	      ok = PConvPyIntToInt(PyList_GetItem(list, 2), &color);
-+	      if(ok)
-+		color = ColorConvertOldSessionIndex(I->G, color);
-+	      *((int *) SettingPtr(I, index, sizeof(int))) = color;
-+	    }
-+	  }
-+	  if (!skip){
-+	    switch (setting_type) {
-+	    case cSetting_boolean:
-+	    case cSetting_int:
-+	      ok = PConvPyIntToInt(PyList_GetItem(list, 2),
-+				   (int *) SettingPtr(I, index, sizeof(int)));
-+	      break;
-+	    case cSetting_color:
-+	      {
-+		int color = 0;
-+		ok = PConvPyIntToInt(PyList_GetItem(list, 2), &color);
-+		if(ok)
-+		  color = ColorConvertOldSessionIndex(I->G, color);
-+		*((int *) SettingPtr(I, index, sizeof(int))) = color;
-+	      }
-+	      break;
-+	    case cSetting_float:
-+	      ok = PConvPyFloatToFloat(PyList_GetItem(list, 2),
-+				       (float *) SettingPtr(I, index, sizeof(float)));
-+	      break;
-+	    case cSetting_float3:
-+	      ok = PConvPyListToFloatArrayInPlaceAutoZero(PyList_GetItem(list, 2),
-+							  (float *) SettingPtr(I, index,
-+									       3 *
-+									       sizeof
-+									       (float)), 3);
-+	      break;
-+	    case cSetting_string:
-+	      ok = PConvPyStrToStrPtr(PyList_GetItem(list, 2), &str);
-+	      if(ok) {
-+		strcpy(((char *) SettingPtr(I, index, strlen(str) + 1)), str);
-+	      }
-+	      break;
-+	    }
-+	  }
-+	}
-       }
-       if(ok && set_type)
--        I->info[index].type = setting_type;
-+	I->info[index].type = setting_type;
-     }
-   }
-   return (ok);
-Index: pymol/modules/pymol/parsing.py
-===================================================================
---- pymol/modules/pymol/parsing.py	(revision 4031)
-+++ pymol/modules/pymol/parsing.py	(revision 4032)
-@@ -437,6 +437,15 @@
- 
-     # launching routines
- 
-+    def execfile(filename, global_ns, local_ns):
-+        if '://' in filename:
-+            import pymol.internal as pi
-+            co = compile(pi.file_read(filename), filename, 'exec')
-+            exec(co, global_ns, local_ns)
-+        else:
-+            import __builtin__ as b
-+            b.execfile(filename, global_ns, local_ns)
-+
-     def run_file(file,global_ns,local_ns):
-         pymol.__script__ = file
-         try:
diff --git a/sci-chemistry/pymol/files/pymol-1.6.0.0-labels.patch b/sci-chemistry/pymol/files/pymol-1.6.0.0-labels.patch
deleted file mode 100644
index 170ab2edcd95..000000000000
--- a/sci-chemistry/pymol/files/pymol-1.6.0.0-labels.patch
+++ /dev/null
@@ -1,372 +0,0 @@
-Index: pymol/ChangeLog
-===================================================================
---- pymol/ChangeLog	(revision 4030)
-+++ pymol/ChangeLog	(revision 4031)
-@@ -2,6 +2,16 @@
- CHANGE LOG
- =========================================================================
- 
-+2013-06-13 Blaine Bell <blaine.bell@schrodinger.com>
-+
-+	* fixed labels when use_shaders is 0 and show_frame_rate is on
-+
-+2013-06-12 Thomas Holder <thomas.holder@schrodinger.com>
-+
-+	* update APBS Tools plugin
-+
-+	* fix spectrumany when minimum/maximum are provided
-+
- 2013-06-11 Blaine Bell <blaine.bell@schrodinger.com>
- 
- 	* Open Source PyMOL v1.6.0.0
-Index: pymol/layer1/Character.c
-===================================================================
---- pymol/layer1/Character.c	(revision 4030)
-+++ pymol/layer1/Character.c	(revision 4031)
-@@ -276,16 +276,16 @@
- 	    rec->extent[2], rec->extent[1],
- 	    rec->extent[2], rec->extent[3]
- 	  };	
--	  glEnableClientState(GL_VERTEX_ARRAY);
--	  glEnableClientState(GL_TEXTURE_COORD_ARRAY);
--#ifdef OPENGL_ES_1
--	  glClientActiveTexture(GL_TEXTURE1);
--#endif
--	  glVertexPointer(3, GL_FLOAT, 0, vertexVals);    
--	  glTexCoordPointer(2, GL_FLOAT, 0, texVals);
--	  glDrawArrays(GL_TRIANGLE_STRIP, 0, 4);
--	  glDisableClientState(GL_VERTEX_ARRAY);
--	  glDisableClientState(GL_TEXTURE_COORD_ARRAY);
-+	  glBegin(GL_QUADS);
-+	  glTexCoord2f(rec->extent[0], rec->extent[1]);
-+	  glVertex3f(v0[0], v0[1], v0[2]);
-+	  glTexCoord2f(rec->extent[0], rec->extent[3]);
-+	  glVertex3f(v0[0], v1[1], v0[2]);
-+	  glTexCoord2f(rec->extent[2], rec->extent[3]);
-+	  glVertex3f(v1[0], v1[1], v0[2]);
-+	  glTexCoord2f(rec->extent[2], rec->extent[1]);
-+	  glVertex3f(v1[0], v0[1], v0[2]);
-+	  glEnd();
- 	}
-       }
-     }
-Index: pymol/modules/pymol/__init__.py
-===================================================================
---- pymol/modules/pymol/__init__.py	(revision 4030)
-+++ pymol/modules/pymol/__init__.py	(revision 4031)
-@@ -252,9 +252,11 @@
-         # auto-detect bundled FREEMOL (if present)
-         
-         if not os.environ.has_key("FREEMOL"):
--            test_path = os.path.join(os.environ['PYMOL_PATH'],"freemol")
--            if os.path.isdir(test_path):
--                os.environ['FREEMOL'] = test_path
-+            for test_path in ['freemol', 'ext']:
-+                test_path = os.path.join(os.environ['PYMOL_PATH'], test_path)
-+                if os.path.isdir(test_path):
-+                    os.environ['FREEMOL'] = test_path
-+                    break
-                 
-         # include FREEMOL's libpy in sys.path (if present)
-         
-@@ -339,9 +341,6 @@
-             elif vendor.startswith('Parallels'):
-                 if renderer[0:8]=='Parallel':
-                     pass
--                    # this was critical for older Parallels
--                    # but actually slows down current versions
--                    # cmd.set('texture_fonts',1) 
- 
-             elif vendor.startswith('ATI'):
-                 if renderer[0:17]=='FireGL2 / FireGL3':  # obsolete ?
-Index: pymol/modules/pymol/preset.py
-===================================================================
---- pymol/modules/pymol/preset.py	(revision 4030)
-+++ pymol/modules/pymol/preset.py	(revision 4031)
-@@ -21,7 +21,7 @@
- 
- tmp_sele = "_p_tmp"
- 
--prot_and_dna_sele = "(resn ALA+CYS+CYX+ASP+GLU+PHE+GLY+HIS+HID+HIE+HIP+HISE+HISD+HISP+ILE+LYS+LEU+MET+MSE+ASN+PRO+GLN+ARG+SER+THR+VAL+TRP+TYR+A+C+T+G+U)"
-+prot_and_dna_sele = "(resn ALA+CYS+CYX+ASP+GLU+PHE+GLY+HIS+HID+HIE+HIP+HISE+HISD+HISP+ILE+LYS+LEU+MET+MSE+ASN+PRO+GLN+ARG+SER+THR+VAL+TRP+TYR+A+C+T+G+U+DA+DC+DT+DG+DU+DI)"
- wat_sele = "(resn WAT,H2O,HOH,TIP)"
- ion_sele = "(resn CA,HG,K,NA,ZN,MG,CL)"
- solv_sele = "("+wat_sele+"|"+ion_sele+")"
-Index: pymol/modules/pymol/cmd.py
-===================================================================
---- pymol/modules/pymol/cmd.py	(revision 4030)
-+++ pymol/modules/pymol/cmd.py	(revision 4031)
-@@ -310,8 +310,7 @@
-         selection_sc = lambda sc=Shortcut,gn=get_names:sc(gn('public')+['all'])
-         object_sc = lambda sc=Shortcut,gn=get_names:sc(gn('objects'))
-         map_sc = lambda sc=Shortcut,gnot=get_names_of_type:sc(gnot('object:map'))
--        contour_sc =  lambda sc=Shortcut,gnot=get_names_of_type:sc(
--            gnot('object:mesh')+gnot('object:surface'))
-+        contour_sc =  lambda sc=Shortcut,gnot=get_names_of_type:sc(gnot('object:mesh')+gnot('object:surface'))
-         group_sc = lambda sc=Shortcut,gnot=get_names_of_type:sc(gnot('object:group'))
-         
-         # Table for argument autocompletion
-Index: pymol/modules/pymol/viewing.py
-===================================================================
---- pymol/modules/pymol/viewing.py	(revision 4030)
-+++ pymol/modules/pymol/viewing.py	(revision 4031)
-@@ -1393,9 +1393,9 @@
-                 if action=='clear':
-                     for key in pymol._scene_dict.keys():
-                         # free selections
--                        list = pymol._scene_dict[key]
--                        if len(list)>3:
--                            colorection = list[3]
-+                        scene_list = pymol._scene_dict[key]
-+                        if len(scene_list)>3:
-+                            colorection = scene_list[3]
-                             if colorection!=None:
-                                 _self.del_colorection(colorection,key) 
-                         name = "_scene_"+key+"_*"
-@@ -1427,6 +1427,8 @@
-                         print "Error: scene '%s' not found."%key
-                     elif new_key==None:
-                         print "Error: must provide the 'new_key' argument"
-+                    elif new_key == key:
-+                        print "scene: '%s' not changed" % key
-                     else:
-                         new_scene_order = []
-                         for a in pymol._scene_order:
-@@ -1443,9 +1445,9 @@
-                             if name in valid_names:
-                                 new_name = "_scene_"+new_key+"_"+rep_name
-                                 _self.set_name(name,new_name)
--                        list = pymol._scene_dict[new_key]
--                        if len(list)>3:
--                            _self.set_colorection_name(list[3],key,new_key)
-+                        scene_list = pymol._scene_dict[new_key]
-+                        if len(scene_list)>3:
-+                            _self.set_colorection_name(scene_list[3],key,new_key)
-                         print" scene: '%s' renamed to '%s'."%(key,new_key)
-                         pymol._scene_dict_sc.rebuild( pymol._scene_dict.keys())
-                         _self.set("session_changed",1,quiet=1)
-@@ -1464,29 +1466,29 @@
-                     _self.set("scenes_changed",1,quiet=1);
-                     key = pymol._scene_dict_sc.auto_err(key,'scene')
-                     _self.set('scene_current_name', key, quiet=1)               
--                    list = pymol._scene_dict[key]
--                    ll = len(list)
-+                    scene_list = pymol._scene_dict[key]
-+                    ll = len(scene_list)
-                     if (ll>1) and (active):
--                        if list[1]!=None:
-+                        if scene_list[1]!=None:
-                             _self.disable()
-                             _self.deselect()
--                            _self.set_vis(list[1])
-+                            _self.set_vis(scene_list[1])
-                     if (ll>2) and (frame):
--                        if list[2]!=None:
-+                        if scene_list[2]!=None:
-                             if not _self.get_movie_playing(): # don't set frame when movie is already playing
--                                if _self.get_frame()!=list[2]: # only set the frame when it isn't already correct
--                                    _self.frame(list[2],scene=1) # let frame know that it is being set by a scene
-+                                if _self.get_frame()!=scene_list[2]: # only set the frame when it isn't already correct
-+                                    _self.frame(scene_list[2],scene=1) # let frame know that it is being set by a scene
-                             else:
-                                 _self.set_frame(1,10) # seek scene
-                     if (ll>3) and (color):
--                        if list[3]!=None:
--                            _self.set_colorection(list[3],key)
-+                        if scene_list[3]!=None:
-+                            _self.set_colorection(scene_list[3],key)
-                     if (ll>4) and (rep):
--                        if list[4]==None:
-+                        if scene_list[4]==None:
-                             rep = 0
-                     if (ll>5) and (message==None):
--                        if list[5]!=None:
--                            message=list[5]
-+                        if scene_list[5]!=None:
-+                            message=scene_list[5]
-                     if rep!=0:
-                         _self.hide("(all)")
-                         valid_names = _self.get_names("all")
-@@ -1521,8 +1523,8 @@
-                     if replace_flag and not mess_flag:
-                         _self.wizard()
-                     if (ll>0) and (view):
--                        if list[0]!=None:
--                            _self.set_view(list[0],animate,quiet,hand)
-+                        if scene_list[0]!=None:
-+                            _self.set_view(scene_list[0],animate,quiet,hand)
-                     if not quiet and _feedback(fb_module.scene,fb_mask.actions,_self): # redundant
-                         print " scene: \"%s\" recalled."%key
-                 elif (action=='store') or (action=='update'):
-@@ -1535,11 +1537,11 @@
-                     if not pymol._scene_dict.has_key(key):
-                         pymol._scene_dict_sc.append(key)
-                     else: # get rid of existing one (if exists)
--                        list = pymol._scene_dict[key]
--                        if (action=='update') and (message==None) and len(list)>5:
-+                        scene_list = pymol._scene_dict[key]
-+                        if (action=='update') and (message==None) and len(scene_list)>5:
-                             message = pymol._scene_dict[key][5]
--                        if len(list)>3:
--                            colorection = list[3]
-+                        if len(scene_list)>3:
-+                            colorection = scene_list[3]
-                             if colorection!=None:
-                                 _self.del_colorection(colorection,key) # important -- free RAM
-                         name = "_scene_"+key+"_*"
-@@ -1575,9 +1577,9 @@
-                         key = setting.get("scene_current_name",_self=_self)
-                     key = pymol._scene_dict_sc.auto_err(key,'scene')
-                     if pymol._scene_dict.has_key(key):
--                        list = pymol._scene_dict[key]
--                        if len(list)>3:
--                            colorection = list[3]
-+                        scene_list = pymol._scene_dict[key]
-+                        if len(scene_list)>3:
-+                            colorection = scene_list[3]
-                             if colorection!=None:
-                                 _self.del_colorection(colorection,key) # important -- free RAM
-                         lst = _scene_validate_list(_self)
-@@ -2573,7 +2575,7 @@
-             v = e_it.next()
-             if v is None:
-                 return False
--            v = (float(v) - minimum) / val_range * (n_colors - 1)
-+            v = min(1.0, max(0.0, (float(v) - minimum) / val_range)) * (n_colors - 1)
-             i = min(int(v), n_colors - 2)
-             p = v - i
-             rgb = [int(255 * (col_tuples[i+1][j] * p + col_tuples[i][j] * (1.0 - p)))
-Index: pymol/modules/pymol/checking.py
-===================================================================
---- pymol/modules/pymol/checking.py	(revision 4030)
-+++ pymol/modules/pymol/checking.py	(revision 4031)
-@@ -1,6 +1,9 @@
- 
- import types
--import cmd
-+try:
-+    import cmd
-+except:
-+    cmd = None
- 
- def _raising(code=-1,_self=cmd):
-     # WARNING: internal routine, subject to change
-Index: pymol/modules/pymol/shortcut.py
-===================================================================
---- pymol/modules/pymol/shortcut.py	(revision 4030)
-+++ pymol/modules/pymol/shortcut.py	(revision 4031)
-@@ -15,7 +15,10 @@
- if __name__=='pymol.shortcut' or __name__=='shortcut':
-     
-     import copy
--    from pymol.checking import is_string, is_list
-+    try:
-+        from pymol.checking import is_string, is_list
-+    except:
-+        from checking import is_string, is_list
-     
-     def mkabbr(a, m=1):
-         b = a.split('_')
-Index: pymol/modules/pymol/editing.py
-===================================================================
---- pymol/modules/pymol/editing.py	(revision 4030)
-+++ pymol/modules/pymol/editing.py	(revision 4031)
-@@ -400,13 +400,15 @@
-         if _self._raising(r,_self): raise pymol.CmdException            
-         return r
- 
--    def push_undo(selection, state=0, _self=cmd):
-+    def push_undo(selection, just_coordinates=1, finish_undo=0, add_objects=0, delete_objects=0, state=0, _self=cmd):
-         '''
- DESCRIPTION
- 
-     "push_undo" stores the current conformations of objects in the
-     selection onto their individual undo rings.
- 
-+    Notice: This command is only partly implemented in open-source PyMOL.
-+
- USAGE
- 
-     push_undo (all)
-Index: pymol/modules/pmg_tk/skins/normal/__init__.py
-===================================================================
---- pymol/modules/pmg_tk/skins/normal/__init__.py	(revision 4030)
-+++ pymol/modules/pmg_tk/skins/normal/__init__.py	(revision 4031)
-@@ -106,19 +106,6 @@
-         self.app.destroycomponent('commandframe')
-         
-     def createMessageBar(self):
--        # Create the message bar area for help and status messages.
--#        frame = self.app.createcomponent('bottomtray', (), None,
--#                                     Frame,(self.app._hull,), relief=SUNKEN)
--#        self.__messageBar = self.app.createcomponent('messagebar',
--#                                                  (), None,
--#                                                 Pmw.MessageBar, 
--#                                                 (frame,),
--#                                                 #entry_width = 40,
--#                                                 entry_relief=SUNKEN,
--#                                                 entry_bd=1,
--#                                                 labelpos=None)
--#        self.__messageBar.pack(side=LEFT, expand=NO, fill=X)
--
-         self.messageBar = Pmw.MessageBar(self.commandFrame, entry_width = 25,
-              entry_relief='sunken', entry_borderwidth=1) #, labelpos = 'w')
- 
-@@ -139,7 +126,6 @@
-         self.balloon.configure(statuscommand = self.messageBar.helpmessage)
- 
-     def destroyMessageBar(self):
--
-         self.messageBar.destroy()
-         
-     def get_current_session_file(self):
-@@ -465,27 +451,6 @@
-         self.entry.bind('<Home>',lambda e,s=self: s.cmd.do("cmd._special(106,0,0)"))
-         self.entry.bind('<End>',lambda e,s=self: s.cmd.do("cmd._special(107,0,0)"))
- 
--# obviated by changes made to the X11 OpenGL Window      
--#        if sys.platform=='darwin':
--#            if self.app.pymol.invocation.options.external_gui==3: # PyMOLX11Hybrid focus kludge
--#                self.root.bind_all('<Leave>',lambda e,s=self: s.focus_out(e)) 
--#                self.root.bind_all('<Enter>',lambda e,s=self: s.focus_in(e))
--
--#    def focus_in(self,event): # PyMOLX11Hybrid focus kludge
--#        if self.refocus_entry:
--#            self.cmd.do("_ cmd.window('defocus')") # deactivate MacPyMOL OpenGL window
--#            self.refocus_entry = 0
--#            self.entry.focus_set()
--
--#    def focus_out(self,event): # PyMOLX11Hybrid focus kludge
--#        # necessary so that the OpenGL portion of
--#        # PyMOLX11Hybrid can exhibit click-through behavior        
--#        if id(event.widget) == id(self.root):
--#            if ((event.y>event.widget.winfo_height())):
--#                self.root.focus_set() # (return cursor to entry window)
--#                self.cmd.do("_ cmd.window('focus')") # activate MacPyMOL OpenGL window
--#                self.refocus_entry = 1
--
-     def update_feedback(self):
-         if self.focus_entry:
-             self.focus_entry=0
-@@ -981,18 +946,16 @@
-             self.cmd.save(sfile,quiet=0)
- 
-     def file_save_mpeg(self):
--        ok = 1
-         try:
-             from freemol import mpeg_encode
-             if not mpeg_encode.validate():
--                ok = 0
-                 print "produce-error: Unable to validate freemol.mpeg_encode"
-+                raise
-         except:
--            ok = 0
--            pass
--        if not ok:
-             tkMessageBox.showerror("Error",
-                 "MPEG encoder missing.\nThe FreeMOL add-ons may not be installed.")
-+            return
-+
-         else:
-             sfile = asksaveasfilename(defaultextension = _def_ext(".mpg"),
-                                       initialdir = self.initialdir,
diff --git a/sci-chemistry/pymol/files/pymol-1.6.0.0-stereo.patch b/sci-chemistry/pymol/files/pymol-1.6.0.0-stereo.patch
deleted file mode 100644
index 6d0f2e16833d..000000000000
--- a/sci-chemistry/pymol/files/pymol-1.6.0.0-stereo.patch
+++ /dev/null
@@ -1,72 +0,0 @@
-From 4920977eeeebdc944a824e2c589272324ea5e74e Mon Sep 17 00:00:00 2001
-From: speleo3 <speleo3@21428953-86e3-433d-9a34-2224224d0fc8>
-Date: Mon, 15 Jul 2013 14:01:10 +0000
-Subject: [PATCH] fixed flickering ortho problems on some machines
-
-git-svn-id: svn://svn.code.sf.net/p/pymol/code/trunk@4034 21428953-86e3-433d-9a34-2224224d0fc8
----
- pymol/ChangeLog      |  4 ++++
- pymol/layer1/Ortho.c | 26 ++++++++++++++++++++------
- 2 files changed, 24 insertions(+), 6 deletions(-)
-
-diff --git a/pymol/layer1/Ortho.c b/pymol/layer1/Ortho.c
-index 4d79114..9dd5d45 100644
---- a/pymol/layer1/Ortho.c
-+++ b/pymol/layer1/Ortho.c
-@@ -1517,7 +1517,7 @@ void OrthoDoDraw(PyMOLGlobals * G, int render_mode)
-   int overlay, text;
-   int rightSceneMargin;
-   int internal_feedback;
--  int times = 1;
-+  int times = 1, origtimes = 0;
-   int double_pump = false;
-   float *bg_color;
-   int skip_prompt = 0;
-@@ -1627,6 +1627,7 @@ void OrthoDoDraw(PyMOLGlobals * G, int render_mode)
- 
-     SceneGLClearColor(0.0, 0.0, 0.0, 1.0);
- 
-+    origtimes = times;
-     while(times--) {
- 
-       switch (times) {
-@@ -1678,7 +1679,7 @@ void OrthoDoDraw(PyMOLGlobals * G, int render_mode)
- 	  } else {
- 	    OrthoRenderCGO(G);
- 	    OrthoPopMatrix(G);
--	    return;
-+	    continue;
- 	  }
- 	}
-       }
-@@ -1925,10 +1926,23 @@ void OrthoDoDraw(PyMOLGlobals * G, int render_mode)
- 	CGOStop(I->orthoCGO);
- 	I->orthoCGO->use_shader = true;
-       }
--
--      OrthoPushMatrix(G);
--      OrthoRenderCGO(G);
--      OrthoPopMatrix(G);
-+      
-+      while(origtimes--){
-+	switch (origtimes){
-+	case 1:
-+	  OrthoDrawBuffer(G, GL_BACK_LEFT);
-+	  break;
-+	case 0:
-+	  if(double_pump) {
-+	    OrthoDrawBuffer(G, GL_BACK_RIGHT);
-+	  } else
-+	    OrthoDrawBuffer(G, GL_BACK);
-+	  break;
-+	}
-+	OrthoPushMatrix(G);
-+	OrthoRenderCGO(G);
-+	OrthoPopMatrix(G);
-+      }
-     }
-   }
- 
--- 
-1.8.3.2
-
diff --git a/sci-chemistry/pymol/files/pymol-1.7.0.4-fix-broken-label-scaling-on-Linux.patch b/sci-chemistry/pymol/files/pymol-1.7.0.4-fix-broken-label-scaling-on-Linux.patch
deleted file mode 100644
index 359a3bc9c78c..000000000000
--- a/sci-chemistry/pymol/files/pymol-1.7.0.4-fix-broken-label-scaling-on-Linux.patch
+++ /dev/null
@@ -1,79 +0,0 @@
-From 5c744d0dcf3ae717ce774e07e24812a543f4a866 Mon Sep 17 00:00:00 2001
-From: speleo3 <speleo3@21428953-86e3-433d-9a34-2224224d0fc8>
-Date: Mon, 10 Mar 2014 15:50:16 +0000
-Subject: [PATCH] fix broken label scaling on Linux
-
-- label scaling became distorted on window resizing
-- minor readability update in label.vs (no change)
-
-
-git-svn-id: svn://svn.code.sf.net/p/pymol/code/trunk@4069 21428953-86e3-433d-9a34-2224224d0fc8
----
- pymol/data/shaders/label.vs | 17 ++++++++---------
- pymol/layer1/Scene.c        | 10 ----------
- 2 files changed, 8 insertions(+), 19 deletions(-)
-
-diff --git a/pymol/data/shaders/label.vs b/pymol/data/shaders/label.vs
-index b179530..58d9dad 100644
---- a/pymol/data/shaders/label.vs
-+++ b/pymol/data/shaders/label.vs
-@@ -21,16 +21,15 @@ uniform float fog_enabled; // actually bool
- 
- void main()
- {
--  vec4 transformedPosition = gl_ModelViewProjectionMatrix * attr_worldpos;
--  transformedPosition.xyz = transformedPosition.xyz/transformedPosition.w;
--  transformedPosition.w = 1.;
--  transformedPosition.xy = transformedPosition.xy + attr_screenworldoffset.xy/(screenSize*screenOriginVertexScale);
--  transformedPosition.z = transformedPosition.z + attr_screenworldoffset.z/(screenSize.x*screenOriginVertexScale);
--  transformedPosition.x = transformedPosition.x + aspectRatioAdjustment * attr_screenoffset.x * 2./screenSize.x;
--  transformedPosition.y = transformedPosition.y + attr_screenoffset.y * 2./screenSize.y;
--  gl_Position = transformedPosition;
-+  vec4 pos = gl_ModelViewProjectionMatrix * attr_worldpos;
-+  pos /= pos.w;
-+  pos.xyz += attr_screenworldoffset / (screenSize.xyx * screenOriginVertexScale);
-+  pos.xy += attr_screenoffset.xy * 2. / screenSize * vec2(aspectRatioAdjustment, 1.);
-+
-+  gl_Position = pos;
-   textureLookup = attr_texcoords;
--  normalizedViewCoordinate = (gl_Position.xyz/gl_Position.w) / 2.0 + 0.5;
-+  normalizedViewCoordinate = pos.xyz / 2.0 + 0.5;
-+
-   if (fog_enabled > 0.5) {
-     vec3 eye_pos = vec3(gl_ModelViewMatrix * attr_worldpos);
-     fog = max(0.0, (gl_Fog.end - abs(eye_pos.z)) * gl_Fog.scale);
-diff --git a/pymol/layer1/Scene.c b/pymol/layer1/Scene.c
-index 639f737..59ee89e 100644
---- a/pymol/layer1/Scene.c
-+++ b/pymol/layer1/Scene.c
-@@ -1972,13 +1972,8 @@ void SceneGetImageSize(PyMOLGlobals * G, int *width, int *height)
- void SceneGetImageSizeFast(PyMOLGlobals * G, int *width, int *height)
- {
-   register CScene *I = G->Scene;
--  if(I->Image) {
--    *width = I->Image->width;
--    *height = I->Image->height;
--  } else {
-     *width = I->Width;
-     *height = I->Height;
--  }
- }
- void SceneGetImageSizeFastAdjustForGrid(PyMOLGlobals * G, int *width, int *height){
-   register CScene *I = G->Scene;
-@@ -1986,13 +1981,8 @@ void SceneGetImageSizeFastAdjustForGrid(PyMOLGlobals * G, int *width, int *heigh
-     *width = I->grid.cur_viewport_size[0];
-     *height = I->grid.cur_viewport_size[1];
-   } else {
--    if(I->Image) {
--      *width = I->Image->width;
--      *height = I->Image->height;
--    } else {
-       *width = I->Width;
-       *height = I->Height;
--    }
-   }
- }
- 
--- 
-1.9.0
-
diff --git a/sci-chemistry/pymol/files/pymol-9999-listing.patch b/sci-chemistry/pymol/files/pymol-9999-listing.patch
deleted file mode 100644
index 1b4039c560a6..000000000000
--- a/sci-chemistry/pymol/files/pymol-9999-listing.patch
+++ /dev/null
@@ -1,17 +0,0 @@
- pymol/modules/pymol/plugins/repository.py | 3 ++-
- 1 file changed, 2 insertions(+), 1 deletion(-)
-
-diff --git a/pymol/modules/pymol/plugins/repository.py b/pymol/modules/pymol/plugins/repository.py
-index 9697f68..9820fac 100644
---- a/pymol/modules/pymol/plugins/repository.py
-+++ b/pymol/modules/pymol/plugins/repository.py
-@@ -182,7 +182,8 @@ class GithubRepository(HttpRepository):
- 
-     def fetchjson(self, url):
-         handle = urlopen('https://api.github.com' + url)
--        return eval(handle.read())
-+        ret = handle.read().replace("false", "False")
-+        return eval(ret)
- 
- class LocalRepository(Repository):
-     def __init__(self, url):
diff --git a/sci-chemistry/pymol/files/pymol-9999-options.patch b/sci-chemistry/pymol/files/pymol-9999-options.patch
deleted file mode 100644
index ce05e172e6bb..000000000000
--- a/sci-chemistry/pymol/files/pymol-9999-options.patch
+++ /dev/null
@@ -1,15 +0,0 @@
- pymol/setup.py | 1 +
- 1 file changed, 1 insertion(+)
-
-diff --git a/pymol/setup.py b/pymol/setup.py
-index c446d6c..b7b353b 100644
---- a/pymol/setup.py
-+++ b/pymol/setup.py
-@@ -51,6 +51,7 @@ def CCompiler_compile(self, sources, output_dir=None, macros=None,
- class options:
-     osx_frameworks = False
-     jobs = int(os.getenv('JOBS', 0))
-+    no_libxml = False
- 
- try:
-     import argparse
diff --git a/sci-chemistry/pymol/metadata.xml b/sci-chemistry/pymol/metadata.xml
index 14ad67b8fdda..ace2d8e58ce8 100644
--- a/sci-chemistry/pymol/metadata.xml
+++ b/sci-chemistry/pymol/metadata.xml
@@ -7,8 +7,6 @@
   </maintainer>
   <use>
     <flag name="apbs">Install the apbs plugin</flag>
-    <flag name="numpy">Compile numpy support</flag>
-    <flag name="vmd">Enable vmd module for trajectories</flag>
     <flag name="web">Install Pymodule needed for web app support</flag>
   </use>
 </pkgmetadata>
diff --git a/sci-chemistry/pymol/pymol-1.5.0.3-r1.ebuild b/sci-chemistry/pymol/pymol-1.5.0.3-r1.ebuild
deleted file mode 100644
index 1a0e65335a5c..000000000000
--- a/sci-chemistry/pymol/pymol-1.5.0.3-r1.ebuild
+++ /dev/null
@@ -1,127 +0,0 @@
-# Copyright 1999-2015 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 1.13 2015/01/22 08:14:25 pinkbyte 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="${PN} chempy pmg_tk pmg_wx"
-
-inherit distutils eutils fdo-mime prefix versionator
-
-DESCRIPTION="A Python-extensible molecular graphics system"
-HOMEPAGE="http://www.pymol.org/"
-SRC_URI="
-	http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz
-	http://dev.gentoo.org/~jlec/distfiles/${PN}-icons.tar.xz"
-
-LICENSE="PSF-2.2"
-SLOT="0"
-KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-IUSE="apbs numpy vmd web"
-
-DEPEND="
-	dev-python/numpy
-	dev-python/pmw:0
-	media-libs/freetype:2
-	media-libs/glew
-	media-libs/libpng
-	media-video/mpeg-tools
-	sys-libs/zlib
-	media-libs/freeglut
-	apbs? (
-		sci-chemistry/apbs
-		sci-chemistry/pdb2pqr
-		sci-chemistry/pymol-apbs-plugin
-	)
-	web? ( !dev-python/webpy )"
-RDEPEND="${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 = \'$(python_get_sitedir -f)\'" > setup3.py || die
-
-	sed \
-		-e "s:/opt/local:${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
-}
-
-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" "MimeType=chemical/x-pdb;"
-}
-
-pkg_postinst() {
-	elog "\t USE=shaders was removed,"
-	elog "please use pymol config settings (~/.pymolrc)"
-	elog "\t set use_shaders, 1"
-	elog "in case of crashes, please deactivate this experimental feature by setting"
-	elog "\t set use_shaders, 0"
-	elog "\t set sphere_mode, 0"
-	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-r2.ebuild b/sci-chemistry/pymol/pymol-1.5.0.3-r2.ebuild
deleted file mode 100644
index c6a0cf553459..000000000000
--- a/sci-chemistry/pymol/pymol-1.5.0.3-r2.ebuild
+++ /dev/null
@@ -1,120 +0,0 @@
-# Copyright 1999-2014 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-r2.ebuild,v 1.5 2014/05/01 12:18:46 jlec Exp $
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-PYTHON_REQ_USE="tk"
-
-inherit distutils-r1 fdo-mime prefix versionator
-
-DESCRIPTION="A Python-extensible molecular graphics system"
-HOMEPAGE="http://www.pymol.org/"
-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 ~x64-macos ~x86-macos"
-IUSE="apbs numpy vmd web"
-
-DEPEND="
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-python/pmw[${PYTHON_USEDEP}]
-	media-libs/freetype:2
-	media-libs/glew
-	media-libs/libpng
-	media-video/mpeg-tools
-	sys-libs/zlib
-	media-libs/freeglut
-	apbs? (
-		sci-chemistry/apbs
-		sci-chemistry/pdb2pqr
-		sci-chemistry/pymol-apbs-plugin
-	)
-	web? ( !dev-python/webpy )"
-RDEPEND="${DEPEND}"
-
-python_prepare_all() {
-	local PATCHES=(
-		"${FILESDIR}"/${PN}-1.5.0.1-setup.py.patch
-		"${FILESDIR}"/${PN}-1.5.0.1-data-path.patch
-		"${FILESDIR}"/${PN}-1.5.0.1-flags.patch
-		"${FILESDIR}"/${P}-prefix.patch
-		)
-
-	use web || PATCHES+=( "${FILESDIR}"/${P}-web.patch )
-	use vmd && PATCHES+=( "${FILESDIR}"/${PN}-1.5.0.1-vmd.patch )
-
-	if use numpy; then
-		sed \
-			-e '/PYMOL_NUMPY/s:^#::g' \
-			-i setup.py || die
-	fi
-
-	rm ./modules/pmg_tk/startup/apbs_tools.py || die
-
-	python_export python2_7 EPYTHON PYTHON_SITEDIR
-	echo "site_packages = \'$(python_get_sitedir)\'" > setup3.py || die
-
-	sed \
-		-e "s:/opt/local:${EPREFIX}/usr:g" \
-		-e '/ext_comp_args/s:\[.*\]:[]:g' \
-		-i setup.py || die
-
-	distutils-r1_python_prepare_all
-
-	eprefixify setup.py
-}
-
-python_install_all() {
-	distutils-r1_python_install_all
-
-	python_export python2_7 EPYTHON
-
-	# These environment variables should not go in the wrapper script, or else
-	# it will be impossible to use the PyMOL libraries from Python.
-	cat >> "${T}"/20pymol <<- EOF
-		PYMOL_PATH="$(python_get_sitedir)/${PN}"
-		PYMOL_DATA="${EPREFIX}/usr/share/pymol/data"
-		PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts"
-	EOF
-
-	doenvd "${T}"/20pymol
-
-	cat >> "${T}"/pymol <<- EOF
-	#!/bin/sh
-	${EPYTHON} -O \${PYMOL_PATH}/__init__.py -q \$*
-	EOF
-
-	dobin "${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" "MimeType=chemical/x-pdb;"
-}
-
-pkg_postinst() {
-	elog "\t USE=shaders was removed,"
-	elog "please use pymol config settings (~/.pymolrc)"
-	elog "\t set use_shaders, 1"
-	elog "in case of crashes, please deactivate this experimental feature by setting"
-	elog "\t set use_shaders, 0"
-	elog "\t set sphere_mode, 0"
-	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-1.6.0.0-r1.ebuild b/sci-chemistry/pymol/pymol-1.6.0.0-r1.ebuild
deleted file mode 100644
index 0c21fbfb9a67..000000000000
--- a/sci-chemistry/pymol/pymol-1.6.0.0-r1.ebuild
+++ /dev/null
@@ -1,98 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-1.6.0.0-r1.ebuild,v 1.3 2014/05/01 12:18:46 jlec Exp $
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-PYTHON_REQ_USE="tk"
-
-inherit distutils-r1 fdo-mime versionator
-
-DESCRIPTION="A Python-extensible molecular graphics system"
-HOMEPAGE="http://www.pymol.org/"
-SRC_URI="
-	mirror://sourceforge/project/${PN}/${PN}/$(get_version_component_range 1-2)/${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 ~x64-macos ~x86-macos"
-IUSE="apbs web"
-
-DEPEND="
-	dev-python/pmw[${PYTHON_USEDEP}]
-	media-libs/freetype:2
-	media-libs/glew
-	media-libs/libpng
-	media-video/mpeg-tools
-	sys-libs/zlib
-	media-libs/freeglut
-	apbs? (
-		sci-chemistry/apbs
-		sci-chemistry/pdb2pqr
-		sci-chemistry/pymol-apbs-plugin
-	)
-	web? ( !dev-python/webpy )"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/${PN}
-
-PATCHES=(
-	"${FILESDIR}"/${P}-labels.patch
-	"${FILESDIR}"/${P}-bg_rgb.patch
-	)
-
-python_prepare_all() {
-	distutils-r1_python_prepare_all
-	sed \
-		-e "s:\"/usr:\"${EPREFIX}/usr:g" \
-		-e "/ext_comp_args/s:=\[.*\]$:= \[\]:g" \
-		-i setup.py || die
-
-	rm ./modules/pmg_tk/startup/apbs_tools.py || die
-
-	sed \
-		-e "s:/opt/local:${EPREFIX}/usr:g" \
-		-e '/ext_comp_args/s:\[.*\]:[]:g' \
-		-i setup.py || die
-}
-
-python_install() {
-	distutils-r1_python_install --pymol-path="${EPREFIX}/usr/share/pymol"
-}
-
-python_install_all() {
-	distutils-r1_python_install_all
-
-	python_export python2_7 EPYTHON
-
-	# These environment variables should not go in the wrapper script, or else
-	# it will be impossible to use the PyMOL libraries from Python.
-	cat >> "${T}"/20pymol <<- EOF
-		PYMOL_PATH="$(python_get_sitedir)/${PN}"
-		PYMOL_DATA="${EPREFIX}/usr/share/pymol/data"
-		PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts"
-	EOF
-
-	doenvd "${T}"/20pymol
-
-	doicon "${WORKDIR}"/${PN}.{xpm,png}
-	make_desktop_entry pymol PyMol ${PN} "Graphics;Education;Science;Chemistry" "MimeType=chemical/x-pdb;"
-
-	if ! use web; then
-		rm -rf "${D}/$(python_get_sitedir)/web" || die
-	fi
-
-	rm -f "${ED}"/usr/share/${PN}/LICENSE || die
-}
-
-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-1.6.0.0-r2.ebuild b/sci-chemistry/pymol/pymol-1.6.0.0-r2.ebuild
deleted file mode 100644
index 1c14915b82ce..000000000000
--- a/sci-chemistry/pymol/pymol-1.6.0.0-r2.ebuild
+++ /dev/null
@@ -1,99 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-1.6.0.0-r2.ebuild,v 1.3 2014/05/01 12:18:46 jlec Exp $
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-PYTHON_REQ_USE="tk"
-
-inherit distutils-r1 fdo-mime versionator
-
-DESCRIPTION="A Python-extensible molecular graphics system"
-HOMEPAGE="http://www.pymol.org/"
-SRC_URI="
-	mirror://sourceforge/project/${PN}/${PN}/$(get_version_component_range 1-2)/${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 ~x64-macos ~x86-macos"
-IUSE="apbs web"
-
-DEPEND="
-	dev-python/pmw[${PYTHON_USEDEP}]
-	media-libs/freetype:2
-	media-libs/glew
-	media-libs/libpng
-	media-video/mpeg-tools
-	sys-libs/zlib
-	media-libs/freeglut
-	apbs? (
-		sci-chemistry/apbs
-		sci-chemistry/pdb2pqr
-		sci-chemistry/pymol-apbs-plugin
-	)
-	web? ( !dev-python/webpy )"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/${PN}
-
-PATCHES=(
-	"${FILESDIR}"/${P}-labels.patch
-	"${FILESDIR}"/${P}-bg_rgb.patch
-	"${FILESDIR}"/${P}-stereo.patch
-	)
-
-python_prepare_all() {
-	distutils-r1_python_prepare_all
-	sed \
-		-e "s:\"/usr:\"${EPREFIX}/usr:g" \
-		-e "/ext_comp_args/s:=\[.*\]$:= \[\]:g" \
-		-i setup.py || die
-
-	rm ./modules/pmg_tk/startup/apbs_tools.py || die
-
-	sed \
-		-e "s:/opt/local:${EPREFIX}/usr:g" \
-		-e '/ext_comp_args/s:\[.*\]:[]:g' \
-		-i setup.py || die
-}
-
-python_install() {
-	distutils-r1_python_install --pymol-path="${EPREFIX}/usr/share/pymol"
-}
-
-python_install_all() {
-	distutils-r1_python_install_all
-
-	python_export python2_7 EPYTHON
-
-	# These environment variables should not go in the wrapper script, or else
-	# it will be impossible to use the PyMOL libraries from Python.
-	cat >> "${T}"/20pymol <<- EOF
-		PYMOL_PATH="$(python_get_sitedir)/${PN}"
-		PYMOL_DATA="${EPREFIX}/usr/share/pymol/data"
-		PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts"
-	EOF
-
-	doenvd "${T}"/20pymol
-
-	doicon "${WORKDIR}"/${PN}.{xpm,png}
-	make_desktop_entry pymol PyMol ${PN} "Graphics;Education;Science;Chemistry" "MimeType=chemical/x-pdb;"
-
-	if ! use web; then
-		rm -rf "${D}/$(python_get_sitedir)/web" || die
-	fi
-
-	rm -f "${ED}"/usr/share/${PN}/LICENSE || die
-}
-
-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-1.6.0.0.ebuild b/sci-chemistry/pymol/pymol-1.6.0.0.ebuild
deleted file mode 100644
index bbc3ac50b0e0..000000000000
--- a/sci-chemistry/pymol/pymol-1.6.0.0.ebuild
+++ /dev/null
@@ -1,94 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-1.6.0.0.ebuild,v 1.3 2014/05/01 12:18:46 jlec Exp $
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-PYTHON_REQ_USE="tk"
-
-inherit distutils-r1 fdo-mime versionator
-
-DESCRIPTION="A Python-extensible molecular graphics system"
-HOMEPAGE="http://www.pymol.org/"
-SRC_URI="
-	mirror://sourceforge/project/${PN}/${PN}/$(get_version_component_range 1-2)/${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 ~x64-macos ~x86-macos"
-IUSE="apbs web"
-
-DEPEND="
-	dev-python/pmw[${PYTHON_USEDEP}]
-	media-libs/freetype:2
-	media-libs/glew
-	media-libs/libpng
-	media-video/mpeg-tools
-	sys-libs/zlib
-	media-libs/freeglut
-	apbs? (
-		sci-chemistry/apbs
-		sci-chemistry/pdb2pqr
-		sci-chemistry/pymol-apbs-plugin
-	)
-	web? ( !dev-python/webpy )"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/${PN}
-
-python_prepare_all() {
-	sed \
-		-e "s:\"/usr:\"${EPREFIX}/usr:g" \
-		-e "/ext_comp_args/s:=\[.*\]$:= \[\]:g" \
-		-i setup.py || die
-
-	rm ./modules/pmg_tk/startup/apbs_tools.py || die
-
-	sed \
-		-e "s:/opt/local:${EPREFIX}/usr:g" \
-		-e '/ext_comp_args/s:\[.*\]:[]:g' \
-		-i setup.py || die
-
-	distutils-r1_python_prepare_all
-}
-
-python_install() {
-	distutils-r1_python_install --pymol-path="${EPREFIX}/usr/share/pymol"
-}
-
-python_install_all() {
-	distutils-r1_python_install_all
-
-	python_export python2_7 EPYTHON
-
-	# These environment variables should not go in the wrapper script, or else
-	# it will be impossible to use the PyMOL libraries from Python.
-	cat >> "${T}"/20pymol <<- EOF
-		PYMOL_PATH="$(python_get_sitedir)/${PN}"
-		PYMOL_DATA="${EPREFIX}/usr/share/pymol/data"
-		PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts"
-	EOF
-
-	doenvd "${T}"/20pymol
-
-	doicon "${WORKDIR}"/${PN}.{xpm,png}
-	make_desktop_entry pymol PyMol ${PN} "Graphics;Education;Science;Chemistry" "MimeType=chemical/x-pdb;"
-
-	if ! use web; then
-		rm -rf "${D}/$(python_get_sitedir)/web" || die
-	fi
-
-	rm -f "${ED}"/usr/share/${PN}/LICENSE || die
-}
-
-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-1.6.0_rc1.ebuild b/sci-chemistry/pymol/pymol-1.6.0_rc1.ebuild
deleted file mode 100644
index 7c41c54fc1af..000000000000
--- a/sci-chemistry/pymol/pymol-1.6.0_rc1.ebuild
+++ /dev/null
@@ -1,92 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-1.6.0_rc1.ebuild,v 1.3 2014/05/01 12:18:46 jlec Exp $
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-PYTHON_REQ_USE="tk"
-
-inherit distutils-r1 fdo-mime versionator
-
-DESCRIPTION="A Python-extensible molecular graphics system"
-HOMEPAGE="http://www.pymol.org/"
-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 ~x64-macos ~x86-macos"
-IUSE="apbs web"
-
-DEPEND="
-	dev-python/pmw[${PYTHON_USEDEP}]
-	media-libs/freetype:2
-	media-libs/glew
-	media-libs/libpng
-	media-video/mpeg-tools
-	sys-libs/zlib
-	media-libs/freeglut
-	apbs? (
-		sci-chemistry/apbs
-		sci-chemistry/pdb2pqr
-		sci-chemistry/pymol-apbs-plugin
-	)
-	web? ( !dev-python/webpy )"
-RDEPEND="${DEPEND}"
-
-python_prepare_all() {
-	sed \
-		-e "s:\"/usr:\"${EPREFIX}/usr:g" \
-		-e "/ext_comp_args/s:=\[.*\]$:= \[\]:g" \
-		-i setup.py || die
-
-	rm ./modules/pmg_tk/startup/apbs_tools.py || die
-
-	sed \
-		-e "s:/opt/local:${EPREFIX}/usr:g" \
-		-e '/ext_comp_args/s:\[.*\]:[]:g' \
-		-i setup.py || die
-
-	distutils-r1_python_prepare_all
-}
-
-python_install() {
-	distutils-r1_python_install --pymol-path="${EPREFIX}/usr/share/pymol"
-}
-
-python_install_all() {
-	distutils-r1_python_install_all
-
-	python_export python2_7 EPYTHON
-
-	# These environment variables should not go in the wrapper script, or else
-	# it will be impossible to use the PyMOL libraries from Python.
-	cat >> "${T}"/20pymol <<- EOF
-		PYMOL_PATH="$(python_get_sitedir)/${PN}"
-		PYMOL_DATA="${EPREFIX}/usr/share/pymol/data"
-		PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts"
-	EOF
-
-	doenvd "${T}"/20pymol
-
-	doicon "${WORKDIR}"/${PN}.{xpm,png}
-	make_desktop_entry pymol PyMol ${PN} "Graphics;Education;Science;Chemistry" "MimeType=chemical/x-pdb;"
-
-	if ! use web; then
-		rm -rf "${D}/$(python_get_sitedir)/web" || die
-	fi
-
-	rm -f "${ED}"/usr/share/${PN}/LICENSE || die
-}
-
-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-1.7.0.0.ebuild b/sci-chemistry/pymol/pymol-1.7.0.0.ebuild
deleted file mode 100644
index 73702b3569c6..000000000000
--- a/sci-chemistry/pymol/pymol-1.7.0.0.ebuild
+++ /dev/null
@@ -1,97 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-1.7.0.0.ebuild,v 1.4 2014/05/01 12:18:46 jlec Exp $
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-PYTHON_REQ_USE="tk"
-
-inherit distutils-r1 fdo-mime versionator
-
-DESCRIPTION="A Python-extensible molecular graphics system"
-HOMEPAGE="http://www.pymol.org/"
-SRC_URI="
-	mirror://sourceforge/project/${PN}/${PN}/$(get_version_component_range 1-2)/${PN}-v${PV}.tar.bz2
-	http://dev.gentoo.org/~jlec/distfiles/${P}.png.xz"
-
-LICENSE="PSF-2.2"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-IUSE="apbs web"
-
-DEPEND="
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-python/pmw[${PYTHON_USEDEP}]
-	dev-python/pyopengl[${PYTHON_USEDEP}]
-	media-libs/freetype:2
-	media-libs/glew
-	media-libs/libpng
-	media-video/mpeg-tools
-	sys-libs/zlib
-	media-libs/freeglut
-	apbs? (
-		sci-chemistry/apbs
-		sci-chemistry/pdb2pqr
-		sci-chemistry/pymol-apbs-plugin[${PYTHON_USEDEP}]
-	)
-	web? ( !dev-python/webpy[${PYTHON_USEDEP}] )"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/${PN}
-
-python_prepare_all() {
-	sed \
-		-e "s:\"/usr:\"${EPREFIX}/usr:g" \
-		-e "/ext_comp_args/s:=\[.*\]$:= \[\]:g" \
-		-e "/import/s:argparse:argparseX:g" \
-		-i setup.py || die
-
-	rm ./modules/pmg_tk/startup/apbs_tools.py || die
-
-	sed \
-		-e "s:/opt/local:${EPREFIX}/usr:g" \
-		-e '/ext_comp_args/s:\[.*\]:[]:g' \
-		-i setup.py || die
-
-	distutils-r1_python_prepare_all
-}
-
-python_install() {
-	distutils-r1_python_install --pymol-path="${EPREFIX}/usr/share/pymol"
-}
-
-python_install_all() {
-	distutils-r1_python_install_all
-
-	python_export python2_7 EPYTHON
-
-	# These environment variables should not go in the wrapper script, or else
-	# it will be impossible to use the PyMOL libraries from Python.
-	cat >> "${T}"/20pymol <<- EOF
-		PYMOL_PATH="$(python_get_sitedir)/${PN}"
-		PYMOL_DATA="${EPREFIX}/usr/share/pymol/data"
-		PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts"
-	EOF
-
-	doenvd "${T}"/20pymol
-
-	newicon "${WORKDIR}"/${P}.png ${PN}.png
-	make_desktop_entry pymol PyMol ${PN} "Graphics;Education;Science;Chemistry" "MimeType=chemical/x-pdb;"
-
-	if ! use web; then
-		rm -rf "${D}/$(python_get_sitedir)/web" || die
-	fi
-
-	rm -f "${ED}"/usr/share/${PN}/LICENSE || die
-}
-
-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-1.7.0.4-r1.ebuild b/sci-chemistry/pymol/pymol-1.7.0.4-r1.ebuild
deleted file mode 100644
index 1e13a976cbee..000000000000
--- a/sci-chemistry/pymol/pymol-1.7.0.4-r1.ebuild
+++ /dev/null
@@ -1,103 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-1.7.0.4-r1.ebuild,v 1.2 2014/05/01 12:18:46 jlec Exp $
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-PYTHON_REQ_USE="tk"
-
-inherit distutils-r1 fdo-mime versionator
-
-DESCRIPTION="A Python-extensible molecular graphics system"
-HOMEPAGE="http://www.pymol.org/"
-SRC_URI="
-	http://dev.gentoo.org/~jlec/distfiles/${PN}-1.7.0.0.png.xz
-	http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz
-"
-#	mirror://sourceforge/project/${PN}/${PN}/$(get_version_component_range 1-2)/${PN}-v${PV}.tar.bz2
-
-LICENSE="PSF-2.2"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-IUSE="apbs web"
-
-DEPEND="
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-python/pmw[${PYTHON_USEDEP}]
-	dev-python/pyopengl[${PYTHON_USEDEP}]
-	media-libs/freetype:2
-	media-libs/glew
-	media-libs/libpng
-	media-video/mpeg-tools
-	sys-libs/zlib
-	media-libs/freeglut
-	apbs? (
-		sci-chemistry/apbs
-		sci-chemistry/pdb2pqr
-		sci-chemistry/pymol-apbs-plugin[${PYTHON_USEDEP}]
-	)
-	web? ( !dev-python/webpy[${PYTHON_USEDEP}] )"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/${P}/${PN}
-
-PATCHES=(
-	"${FILESDIR}"/${P}-fix-broken-label-scaling-on-Linux.patch
-)
-
-python_prepare_all() {
-	sed \
-		-e "s:\"/usr:\"${EPREFIX}/usr:g" \
-		-e "/ext_comp_args/s:=\[.*\]$:= \[\]:g" \
-		-e "/import/s:argparse:argparseX:g" \
-		-i setup.py || die
-
-	rm ./modules/pmg_tk/startup/apbs_tools.py || die
-
-	sed \
-		-e "s:/opt/local:${EPREFIX}/usr:g" \
-		-e '/ext_comp_args/s:\[.*\]:[]:g' \
-		-i setup.py || die
-
-	distutils-r1_python_prepare_all
-}
-
-python_install() {
-	distutils-r1_python_install --pymol-path="${EPREFIX}/usr/share/pymol"
-}
-
-python_install_all() {
-	distutils-r1_python_install_all
-
-	python_export python2_7 EPYTHON
-
-	# These environment variables should not go in the wrapper script, or else
-	# it will be impossible to use the PyMOL libraries from Python.
-	cat >> "${T}"/20pymol <<- EOF
-		PYMOL_PATH="$(python_get_sitedir)/${PN}"
-		PYMOL_DATA="${EPREFIX}/usr/share/pymol/data"
-		PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts"
-	EOF
-
-	doenvd "${T}"/20pymol
-
-	newicon "${WORKDIR}"/${PN}-1.7.0.0.png ${PN}.png
-	make_desktop_entry pymol PyMol ${PN} "Graphics;Education;Science;Chemistry" "MimeType=chemical/x-pdb;"
-
-	if ! use web; then
-		rm -rf "${D}/$(python_get_sitedir)/web" || die
-	fi
-
-	rm -f "${ED}"/usr/share/${PN}/LICENSE || die
-}
-
-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-1.7.0.4.ebuild b/sci-chemistry/pymol/pymol-1.7.0.4.ebuild
deleted file mode 100644
index fb556c9d126a..000000000000
--- a/sci-chemistry/pymol/pymol-1.7.0.4.ebuild
+++ /dev/null
@@ -1,99 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-1.7.0.4.ebuild,v 1.2 2014/05/01 12:18:46 jlec Exp $
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-PYTHON_REQ_USE="tk"
-
-inherit distutils-r1 fdo-mime versionator
-
-DESCRIPTION="A Python-extensible molecular graphics system"
-HOMEPAGE="http://www.pymol.org/"
-SRC_URI="
-	http://dev.gentoo.org/~jlec/distfiles/${PN}-1.7.0.0.png.xz
-	http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz
-"
-#	mirror://sourceforge/project/${PN}/${PN}/$(get_version_component_range 1-2)/${PN}-v${PV}.tar.bz2
-
-LICENSE="PSF-2.2"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-IUSE="apbs web"
-
-DEPEND="
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-python/pmw[${PYTHON_USEDEP}]
-	dev-python/pyopengl[${PYTHON_USEDEP}]
-	media-libs/freetype:2
-	media-libs/glew
-	media-libs/libpng
-	media-video/mpeg-tools
-	sys-libs/zlib
-	media-libs/freeglut
-	apbs? (
-		sci-chemistry/apbs
-		sci-chemistry/pdb2pqr
-		sci-chemistry/pymol-apbs-plugin[${PYTHON_USEDEP}]
-	)
-	web? ( !dev-python/webpy[${PYTHON_USEDEP}] )"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/${P}/${PN}
-
-python_prepare_all() {
-	sed \
-		-e "s:\"/usr:\"${EPREFIX}/usr:g" \
-		-e "/ext_comp_args/s:=\[.*\]$:= \[\]:g" \
-		-e "/import/s:argparse:argparseX:g" \
-		-i setup.py || die
-
-	rm ./modules/pmg_tk/startup/apbs_tools.py || die
-
-	sed \
-		-e "s:/opt/local:${EPREFIX}/usr:g" \
-		-e '/ext_comp_args/s:\[.*\]:[]:g' \
-		-i setup.py || die
-
-	distutils-r1_python_prepare_all
-}
-
-python_install() {
-	distutils-r1_python_install --pymol-path="${EPREFIX}/usr/share/pymol"
-}
-
-python_install_all() {
-	distutils-r1_python_install_all
-
-	python_export python2_7 EPYTHON
-
-	# These environment variables should not go in the wrapper script, or else
-	# it will be impossible to use the PyMOL libraries from Python.
-	cat >> "${T}"/20pymol <<- EOF
-		PYMOL_PATH="$(python_get_sitedir)/${PN}"
-		PYMOL_DATA="${EPREFIX}/usr/share/pymol/data"
-		PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts"
-	EOF
-
-	doenvd "${T}"/20pymol
-
-	newicon "${WORKDIR}"/${PN}-1.7.0.0.png ${PN}.png
-	make_desktop_entry pymol PyMol ${PN} "Graphics;Education;Science;Chemistry" "MimeType=chemical/x-pdb;"
-
-	if ! use web; then
-		rm -rf "${D}/$(python_get_sitedir)/web" || die
-	fi
-
-	rm -f "${ED}"/usr/share/${PN}/LICENSE || die
-}
-
-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-1.7.1.1.ebuild b/sci-chemistry/pymol/pymol-1.7.1.1.ebuild
deleted file mode 100644
index f1b65e9caca3..000000000000
--- a/sci-chemistry/pymol/pymol-1.7.1.1.ebuild
+++ /dev/null
@@ -1,99 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-1.7.1.1.ebuild,v 1.2 2014/05/01 12:18:46 jlec Exp $
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-PYTHON_REQ_USE="tk"
-
-inherit distutils-r1 fdo-mime versionator
-
-DESCRIPTION="A Python-extensible molecular graphics system"
-HOMEPAGE="http://www.pymol.org/"
-SRC_URI="
-	http://dev.gentoo.org/~jlec/distfiles/${PN}-1.7.0.0.png.xz
-	http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz
-"
-#	mirror://sourceforge/project/${PN}/${PN}/$(get_version_component_range 1-2)/${PN}-v${PV}.tar.bz2
-
-LICENSE="PSF-2.2"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-IUSE="apbs web"
-
-DEPEND="
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-python/pmw[${PYTHON_USEDEP}]
-	dev-python/pyopengl[${PYTHON_USEDEP}]
-	media-libs/freetype:2
-	media-libs/glew
-	media-libs/libpng
-	media-video/mpeg-tools
-	sys-libs/zlib
-	media-libs/freeglut
-	apbs? (
-		sci-chemistry/apbs
-		sci-chemistry/pdb2pqr
-		sci-chemistry/pymol-apbs-plugin[${PYTHON_USEDEP}]
-	)
-	web? ( !dev-python/webpy[${PYTHON_USEDEP}] )"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/${P}/${PN}
-
-python_prepare_all() {
-	sed \
-		-e "s:\"/usr:\"${EPREFIX}/usr:g" \
-		-e "/ext_comp_args/s:=\[.*\]$:= \[\]:g" \
-		-e "/import/s:argparse:argparseX:g" \
-		-i setup.py || die
-
-	rm ./modules/pmg_tk/startup/apbs_tools.py || die
-
-	sed \
-		-e "s:/opt/local:${EPREFIX}/usr:g" \
-		-e '/ext_comp_args/s:\[.*\]:[]:g' \
-		-i setup.py || die
-
-	distutils-r1_python_prepare_all
-}
-
-python_install() {
-	distutils-r1_python_install --pymol-path="${EPREFIX}/usr/share/pymol"
-}
-
-python_install_all() {
-	distutils-r1_python_install_all
-
-	python_export python2_7 EPYTHON
-
-	# These environment variables should not go in the wrapper script, or else
-	# it will be impossible to use the PyMOL libraries from Python.
-	cat >> "${T}"/20pymol <<- EOF
-		PYMOL_PATH="$(python_get_sitedir)/${PN}"
-		PYMOL_DATA="${EPREFIX}/usr/share/pymol/data"
-		PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts"
-	EOF
-
-	doenvd "${T}"/20pymol
-
-	newicon "${WORKDIR}"/${PN}-1.7.0.0.png ${PN}.png
-	make_desktop_entry pymol PyMol ${PN} "Graphics;Education;Science;Chemistry" "MimeType=chemical/x-pdb;"
-
-	if ! use web; then
-		rm -rf "${D}/$(python_get_sitedir)/web" || die
-	fi
-
-	rm -f "${ED}"/usr/share/${PN}/LICENSE || die
-}
-
-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-1.7.1.3.ebuild b/sci-chemistry/pymol/pymol-1.7.1.3.ebuild
deleted file mode 100644
index d12102f74631..000000000000
--- a/sci-chemistry/pymol/pymol-1.7.1.3.ebuild
+++ /dev/null
@@ -1,99 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-1.7.1.3.ebuild,v 1.1 2014/05/14 14:02:17 jlec Exp $
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-PYTHON_REQ_USE="tk"
-
-inherit distutils-r1 fdo-mime versionator
-
-DESCRIPTION="A Python-extensible molecular graphics system"
-HOMEPAGE="http://www.pymol.org/"
-SRC_URI="
-	http://dev.gentoo.org/~jlec/distfiles/${PN}-1.7.0.0.png.xz
-	http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz
-"
-#	mirror://sourceforge/project/${PN}/${PN}/$(get_version_component_range 1-2)/${PN}-v${PV}.tar.bz2
-
-LICENSE="PSF-2.2"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-IUSE="apbs web"
-
-DEPEND="
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-python/pmw[${PYTHON_USEDEP}]
-	dev-python/pyopengl[${PYTHON_USEDEP}]
-	media-libs/freetype:2
-	media-libs/glew
-	media-libs/libpng
-	media-video/mpeg-tools
-	sys-libs/zlib
-	media-libs/freeglut
-	apbs? (
-		sci-chemistry/apbs
-		sci-chemistry/pdb2pqr
-		sci-chemistry/pymol-apbs-plugin[${PYTHON_USEDEP}]
-	)
-	web? ( !dev-python/webpy[${PYTHON_USEDEP}] )"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/${P}/${PN}
-
-python_prepare_all() {
-	sed \
-		-e "s:\"/usr:\"${EPREFIX}/usr:g" \
-		-e "/ext_comp_args/s:=\[.*\]$:= \[\]:g" \
-		-e "/import/s:argparse:argparseX:g" \
-		-i setup.py || die
-
-	rm ./modules/pmg_tk/startup/apbs_tools.py || die
-
-	sed \
-		-e "s:/opt/local:${EPREFIX}/usr:g" \
-		-e '/ext_comp_args/s:\[.*\]:[]:g' \
-		-i setup.py || die
-
-	distutils-r1_python_prepare_all
-}
-
-python_install() {
-	distutils-r1_python_install --pymol-path="${EPREFIX}/usr/share/pymol"
-}
-
-python_install_all() {
-	distutils-r1_python_install_all
-
-	python_export python2_7 EPYTHON
-
-	# These environment variables should not go in the wrapper script, or else
-	# it will be impossible to use the PyMOL libraries from Python.
-	cat >> "${T}"/20pymol <<- EOF
-		PYMOL_PATH="$(python_get_sitedir)/${PN}"
-		PYMOL_DATA="${EPREFIX}/usr/share/pymol/data"
-		PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts"
-	EOF
-
-	doenvd "${T}"/20pymol
-
-	newicon "${WORKDIR}"/${PN}-1.7.0.0.png ${PN}.png
-	make_desktop_entry pymol PyMol ${PN} "Graphics;Education;Science;Chemistry" "MimeType=chemical/x-pdb;"
-
-	if ! use web; then
-		rm -rf "${D}/$(python_get_sitedir)/web" || die
-	fi
-
-	rm -f "${ED}"/usr/share/${PN}/LICENSE || die
-}
-
-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-1.7.2.0.ebuild b/sci-chemistry/pymol/pymol-1.7.2.0.ebuild
deleted file mode 100644
index 8ef573dcd0b5..000000000000
--- a/sci-chemistry/pymol/pymol-1.7.2.0.ebuild
+++ /dev/null
@@ -1,100 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-1.7.2.0.ebuild,v 1.1 2014/08/11 07:27:00 jlec Exp $
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-PYTHON_REQ_USE="tk"
-
-inherit distutils-r1 fdo-mime versionator
-
-DESCRIPTION="A Python-extensible molecular graphics system"
-HOMEPAGE="http://www.pymol.org/"
-SRC_URI="
-	http://dev.gentoo.org/~jlec/distfiles/${PN}-1.7.0.0.png.xz
-	http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz
-"
-#	mirror://sourceforge/project/${PN}/${PN}/$(get_version_component_range 1-2)/${PN}-v${PV}.tar.bz2
-# git archive -v --prefix=${P}/ master -o ${P}.tar.xz
-
-LICENSE="PSF-2.2"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-IUSE="apbs web"
-
-DEPEND="
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-python/pmw[${PYTHON_USEDEP}]
-	dev-python/pyopengl[${PYTHON_USEDEP}]
-	media-libs/freetype:2
-	media-libs/glew
-	media-libs/libpng
-	media-video/mpeg-tools
-	sys-libs/zlib
-	media-libs/freeglut
-	apbs? (
-		sci-chemistry/apbs
-		sci-chemistry/pdb2pqr
-		sci-chemistry/pymol-apbs-plugin[${PYTHON_USEDEP}]
-	)
-	web? ( !dev-python/webpy[${PYTHON_USEDEP}] )"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/${P}/${PN}
-
-python_prepare_all() {
-	sed \
-		-e "s:\"/usr:\"${EPREFIX}/usr:g" \
-		-e "/ext_comp_args/s:=\[.*\]$:= \[\]:g" \
-		-e "/import/s:argparse:argparseX:g" \
-		-i setup.py || die
-
-	rm ./modules/pmg_tk/startup/apbs_tools.py || die
-
-	sed \
-		-e "s:/opt/local:${EPREFIX}/usr:g" \
-		-e '/ext_comp_args/s:\[.*\]:[]:g' \
-		-i setup.py || die
-
-	distutils-r1_python_prepare_all
-}
-
-python_install() {
-	distutils-r1_python_install --pymol-path="${EPREFIX}/usr/share/pymol"
-}
-
-python_install_all() {
-	distutils-r1_python_install_all
-
-	python_export python2_7 EPYTHON
-
-	# These environment variables should not go in the wrapper script, or else
-	# it will be impossible to use the PyMOL libraries from Python.
-	cat >> "${T}"/20pymol <<- EOF
-		PYMOL_PATH="$(python_get_sitedir)/${PN}"
-		PYMOL_DATA="${EPREFIX}/usr/share/pymol/data"
-		PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts"
-	EOF
-
-	doenvd "${T}"/20pymol
-
-	newicon "${WORKDIR}"/${PN}-1.7.0.0.png ${PN}.png
-	make_desktop_entry pymol PyMol ${PN} "Graphics;Education;Science;Chemistry" "MimeType=chemical/x-pdb;"
-
-	if ! use web; then
-		rm -rf "${D}/$(python_get_sitedir)/web" || die
-	fi
-
-	rm -f "${ED}"/usr/share/${PN}/LICENSE || die
-}
-
-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-1.7.2.1.ebuild b/sci-chemistry/pymol/pymol-1.7.2.1.ebuild
deleted file mode 100644
index 800087c73243..000000000000
--- a/sci-chemistry/pymol/pymol-1.7.2.1.ebuild
+++ /dev/null
@@ -1,100 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-1.7.2.1.ebuild,v 1.1 2014/08/21 07:25:44 jlec Exp $
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-PYTHON_REQ_USE="tk"
-
-inherit distutils-r1 fdo-mime versionator
-
-DESCRIPTION="A Python-extensible molecular graphics system"
-HOMEPAGE="http://www.pymol.org/"
-SRC_URI="
-	http://dev.gentoo.org/~jlec/distfiles/${PN}-1.7.0.0.png.xz
-	http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz
-"
-#	mirror://sourceforge/project/${PN}/${PN}/$(get_version_component_range 1-2)/${PN}-v${PV}.tar.bz2
-# git archive -v --prefix=${P}/ master -o ${P}.tar.xz
-
-LICENSE="PSF-2.2"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-IUSE="apbs web"
-
-DEPEND="
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-python/pmw[${PYTHON_USEDEP}]
-	dev-python/pyopengl[${PYTHON_USEDEP}]
-	media-libs/freetype:2
-	media-libs/glew
-	media-libs/libpng
-	media-video/mpeg-tools
-	sys-libs/zlib
-	media-libs/freeglut
-	apbs? (
-		sci-chemistry/apbs
-		sci-chemistry/pdb2pqr
-		sci-chemistry/pymol-apbs-plugin[${PYTHON_USEDEP}]
-	)
-	web? ( !dev-python/webpy[${PYTHON_USEDEP}] )"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/${P}/${PN}
-
-python_prepare_all() {
-	sed \
-		-e "s:\"/usr:\"${EPREFIX}/usr:g" \
-		-e "/ext_comp_args/s:=\[.*\]$:= \[\]:g" \
-		-e "/import/s:argparse:argparseX:g" \
-		-i setup.py || die
-
-	rm ./modules/pmg_tk/startup/apbs_tools.py || die
-
-	sed \
-		-e "s:/opt/local:${EPREFIX}/usr:g" \
-		-e '/ext_comp_args/s:\[.*\]:[]:g' \
-		-i setup.py || die
-
-	distutils-r1_python_prepare_all
-}
-
-python_install() {
-	distutils-r1_python_install --pymol-path="${EPREFIX}/usr/share/pymol"
-}
-
-python_install_all() {
-	distutils-r1_python_install_all
-
-	python_export python2_7 EPYTHON
-
-	# These environment variables should not go in the wrapper script, or else
-	# it will be impossible to use the PyMOL libraries from Python.
-	cat >> "${T}"/20pymol <<- EOF
-		PYMOL_PATH="$(python_get_sitedir)/${PN}"
-		PYMOL_DATA="${EPREFIX}/usr/share/pymol/data"
-		PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts"
-	EOF
-
-	doenvd "${T}"/20pymol
-
-	newicon "${WORKDIR}"/${PN}-1.7.0.0.png ${PN}.png
-	make_desktop_entry pymol PyMol ${PN} "Graphics;Education;Science;Chemistry" "MimeType=chemical/x-pdb;"
-
-	if ! use web; then
-		rm -rf "${D}/$(python_get_sitedir)/web" || die
-	fi
-
-	rm -f "${ED}"/usr/share/${PN}/LICENSE || die
-}
-
-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-1.7.3.0.ebuild b/sci-chemistry/pymol/pymol-1.7.3.0.ebuild
deleted file mode 100644
index 9bb025baf671..000000000000
--- a/sci-chemistry/pymol/pymol-1.7.3.0.ebuild
+++ /dev/null
@@ -1,100 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-1.7.3.0.ebuild,v 1.1 2014/09/15 08:20:08 jlec Exp $
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-PYTHON_REQ_USE="tk"
-
-inherit distutils-r1 fdo-mime versionator
-
-DESCRIPTION="A Python-extensible molecular graphics system"
-HOMEPAGE="http://www.pymol.org/"
-SRC_URI="
-	http://dev.gentoo.org/~jlec/distfiles/${PN}-1.7.0.0.png.xz
-	http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz
-"
-#	mirror://sourceforge/project/${PN}/${PN}/$(get_version_component_range 1-2)/${PN}-v${PV}.tar.bz2
-# git archive -v --prefix=${P}/ master -o ${P}.tar.xz
-
-LICENSE="PSF-2.2"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-IUSE="apbs web"
-
-DEPEND="
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-python/pmw[${PYTHON_USEDEP}]
-	dev-python/pyopengl[${PYTHON_USEDEP}]
-	media-libs/freetype:2
-	media-libs/glew
-	media-libs/libpng
-	media-video/mpeg-tools
-	sys-libs/zlib
-	media-libs/freeglut
-	apbs? (
-		sci-chemistry/apbs
-		sci-chemistry/pdb2pqr
-		sci-chemistry/pymol-apbs-plugin[${PYTHON_USEDEP}]
-	)
-	web? ( !dev-python/webpy[${PYTHON_USEDEP}] )"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/${P}/${PN}
-
-python_prepare_all() {
-	sed \
-		-e "s:\"/usr:\"${EPREFIX}/usr:g" \
-		-e "/ext_comp_args/s:=\[.*\]$:= \[\]:g" \
-		-e "/import/s:argparse:argparseX:g" \
-		-i setup.py || die
-
-	rm ./modules/pmg_tk/startup/apbs_tools.py || die
-
-	sed \
-		-e "s:/opt/local:${EPREFIX}/usr:g" \
-		-e '/ext_comp_args/s:\[.*\]:[]:g' \
-		-i setup.py || die
-
-	distutils-r1_python_prepare_all
-}
-
-python_install() {
-	distutils-r1_python_install --pymol-path="${EPREFIX}/usr/share/pymol"
-}
-
-python_install_all() {
-	distutils-r1_python_install_all
-
-	python_export python2_7 EPYTHON
-
-	# These environment variables should not go in the wrapper script, or else
-	# it will be impossible to use the PyMOL libraries from Python.
-	cat >> "${T}"/20pymol <<- EOF
-		PYMOL_PATH="$(python_get_sitedir)/${PN}"
-		PYMOL_DATA="${EPREFIX}/usr/share/pymol/data"
-		PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts"
-	EOF
-
-	doenvd "${T}"/20pymol
-
-	newicon "${WORKDIR}"/${PN}-1.7.0.0.png ${PN}.png
-	make_desktop_entry pymol PyMol ${PN} "Graphics;Education;Science;Chemistry" "MimeType=chemical/x-pdb;"
-
-	if ! use web; then
-		rm -rf "${D}/$(python_get_sitedir)/web" || die
-	fi
-
-	rm -f "${ED}"/usr/share/${PN}/LICENSE || die
-}
-
-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-1.7.3.1.ebuild b/sci-chemistry/pymol/pymol-1.7.3.1.ebuild
deleted file mode 100644
index 37b77d5f35be..000000000000
--- a/sci-chemistry/pymol/pymol-1.7.3.1.ebuild
+++ /dev/null
@@ -1,106 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-1.7.3.1.ebuild,v 1.1 2014/10/17 06:54:03 jlec Exp $
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-PYTHON_REQ_USE="tk"
-
-inherit distutils-r1 fdo-mime versionator
-
-DESCRIPTION="A Python-extensible molecular graphics system"
-HOMEPAGE="http://www.pymol.org/"
-SRC_URI="
-	http://dev.gentoo.org/~jlec/distfiles/${PN}-1.7.0.0.png.xz
-	http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz
-"
-#	mirror://sourceforge/project/${PN}/${PN}/$(get_version_component_range 1-2)/${PN}-v${PV}.tar.bz2
-# git archive -v --prefix=${P}/ master -o ${P}.tar.xz
-
-LICENSE="PSF-2.2"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-IUSE="apbs web"
-
-DEPEND="
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-python/pmw[${PYTHON_USEDEP}]
-	dev-python/pyopengl[${PYTHON_USEDEP}]
-	media-libs/freetype:2
-	media-libs/glew
-	media-libs/libpng
-	media-video/mpeg-tools
-	sys-libs/zlib
-	media-libs/freeglut
-	apbs? (
-		sci-chemistry/apbs
-		sci-chemistry/pdb2pqr
-		sci-chemistry/pymol-apbs-plugin[${PYTHON_USEDEP}]
-	)
-	web? ( !dev-python/webpy[${PYTHON_USEDEP}] )"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/${P}/${PN}
-
-PATCHES=(
-	"${FILESDIR}"/${P}-maeffplugin.cpp.patch
-	)
-
-python_prepare_all() {
-	sed \
-		-e "s:\"/usr:\"${EPREFIX}/usr:g" \
-		-e "/ext_comp_args.*+=/s:\[.*\]$:\[\]:g" \
-		-e "/import/s:argparse:argparseX:g" \
-		-i setup.py || die
-
-	rm ./modules/pmg_tk/startup/apbs_tools.py || die
-
-	sed \
-		-e "s:/opt/local:${EPREFIX}/usr:g" \
-		-e '/ext_comp_args/s:\[.*\]:[]:g' \
-		-i setup.py || die
-
-	distutils-r1_python_prepare_all
-}
-
-python_install() {
-	distutils-r1_python_install --pymol-path="${EPREFIX}/usr/share/pymol"
-}
-
-python_install_all() {
-	distutils-r1_python_install_all
-
-	python_export python2_7 EPYTHON
-
-	# These environment variables should not go in the wrapper script, or else
-	# it will be impossible to use the PyMOL libraries from Python.
-	cat >> "${T}"/20pymol <<- EOF
-		PYMOL_PATH="$(python_get_sitedir)/${PN}"
-		PYMOL_DATA="${EPREFIX}/usr/share/pymol/data"
-		PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts"
-	EOF
-
-	doenvd "${T}"/20pymol
-
-	newicon "${WORKDIR}"/${PN}-1.7.0.0.png ${PN}.png
-	make_desktop_entry ${PN} PyMol ${PN} \
-		"Graphics;Education;Science;Chemistry;" \
-		"MimeType=chemical/x-pdb;chemical/x-mdl-molfile;chemical/x-mol2;chemical/seq-aa-fasta;chemical/seq-na-fasta;chemical/x-xyz;chemical/x-mdl-sdf;"
-
-	if ! use web; then
-		rm -rf "${D}/$(python_get_sitedir)/web" || die
-	fi
-
-	rm -f "${ED}"/usr/share/${PN}/LICENSE || die
-}
-
-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-1.7.3.2.ebuild b/sci-chemistry/pymol/pymol-1.7.3.2.ebuild
deleted file mode 100644
index 69c5657b858b..000000000000
--- a/sci-chemistry/pymol/pymol-1.7.3.2.ebuild
+++ /dev/null
@@ -1,108 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-1.7.3.2.ebuild,v 1.2 2014/10/27 17:18:52 jlec Exp $
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-PYTHON_REQ_USE="tk"
-
-inherit distutils-r1 fdo-mime versionator
-
-DESCRIPTION="A Python-extensible molecular graphics system"
-HOMEPAGE="http://www.pymol.org/"
-SRC_URI="
-	http://dev.gentoo.org/~jlec/distfiles/${PN}-1.7.0.0.png.xz
-	http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz
-"
-#	mirror://sourceforge/project/${PN}/${PN}/$(get_version_component_range 1-2)/${PN}-v${PV}.tar.bz2
-# git archive -v --prefix=${P}/ master -o ${P}.tar.xz
-
-LICENSE="PSF-2.2"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-IUSE="apbs web"
-
-DEPEND="
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-python/pmw[${PYTHON_USEDEP}]
-	dev-python/pyopengl[${PYTHON_USEDEP}]
-	media-libs/freetype:2
-	media-libs/glew
-	media-libs/libpng
-	media-video/mpeg-tools
-	sys-libs/zlib
-	media-libs/freeglut
-	apbs? (
-		sci-chemistry/apbs[${PYTHON_USEDEP}]
-		sci-chemistry/pdb2pqr[${PYTHON_USEDEP}]
-		sci-chemistry/pymol-apbs-plugin[${PYTHON_USEDEP}]
-	)
-	web? ( !dev-python/webpy[${PYTHON_USEDEP}] )"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/${P}/${PN}
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-1.7.3.1-maeffplugin.cpp.patch
-	"${FILESDIR}"/${PN}-9999-options.patch
-	"${FILESDIR}"/${PN}-9999-listing.patch
-	)
-
-python_prepare_all() {
-	sed \
-		-e "s:\"/usr:\"${EPREFIX}/usr:g" \
-		-e "/ext_comp_args.*+=/s:\[.*\]$:\[\]:g" \
-		-e "/import/s:argparse:argparseX:g" \
-		-i setup.py || die
-
-	rm ./modules/pmg_tk/startup/apbs_tools.py || die
-
-	sed \
-		-e "s:/opt/local:${EPREFIX}/usr:g" \
-		-e '/ext_comp_args/s:\[.*\]:[]:g' \
-		-i setup.py || die
-
-	distutils-r1_python_prepare_all
-}
-
-python_install() {
-	distutils-r1_python_install --pymol-path="${EPREFIX}/usr/share/pymol"
-}
-
-python_install_all() {
-	distutils-r1_python_install_all
-
-	python_export python2_7 EPYTHON
-
-	# These environment variables should not go in the wrapper script, or else
-	# it will be impossible to use the PyMOL libraries from Python.
-	cat >> "${T}"/20pymol <<- EOF
-		PYMOL_PATH="$(python_get_sitedir)/${PN}"
-		PYMOL_DATA="${EPREFIX}/usr/share/pymol/data"
-		PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts"
-	EOF
-
-	doenvd "${T}"/20pymol
-
-	newicon "${WORKDIR}"/${PN}-1.7.0.0.png ${PN}.png
-	make_desktop_entry ${PN} PyMol ${PN} \
-		"Graphics;Education;Science;Chemistry;" \
-		"MimeType=chemical/x-pdb;chemical/x-mdl-molfile;chemical/x-mol2;chemical/seq-aa-fasta;chemical/seq-na-fasta;chemical/x-xyz;chemical/x-mdl-sdf;"
-
-	if ! use web; then
-		rm -rf "${D}/$(python_get_sitedir)/web" || die
-	fi
-
-	rm -f "${ED}"/usr/share/${PN}/LICENSE || die
-}
-
-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-1.7.3.4.ebuild b/sci-chemistry/pymol/pymol-1.7.3.4.ebuild
deleted file mode 100644
index 47092b2f997d..000000000000
--- a/sci-chemistry/pymol/pymol-1.7.3.4.ebuild
+++ /dev/null
@@ -1,106 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-1.7.3.4.ebuild,v 1.1 2014/11/21 08:57:47 jlec Exp $
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-PYTHON_REQ_USE="tk"
-
-inherit distutils-r1 fdo-mime versionator
-
-DESCRIPTION="A Python-extensible molecular graphics system"
-HOMEPAGE="http://www.pymol.org/"
-SRC_URI="
-	http://dev.gentoo.org/~jlec/distfiles/${PN}-1.7.0.0.png.xz
-	http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz
-"
-#	mirror://sourceforge/project/${PN}/${PN}/$(get_version_component_range 1-2)/${PN}-v${PV}.tar.bz2
-# git archive -v --prefix=${P}/ master -o ${P}.tar.xz
-
-LICENSE="PSF-2.2"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-IUSE="apbs web"
-
-DEPEND="
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-python/pmw[${PYTHON_USEDEP}]
-	dev-python/pyopengl[${PYTHON_USEDEP}]
-	media-libs/freetype:2
-	media-libs/glew
-	media-libs/libpng
-	media-video/mpeg-tools
-	sys-libs/zlib
-	media-libs/freeglut
-	apbs? (
-		sci-chemistry/apbs[${PYTHON_USEDEP}]
-		sci-chemistry/pdb2pqr[${PYTHON_USEDEP}]
-		sci-chemistry/pymol-apbs-plugin[${PYTHON_USEDEP}]
-	)
-	web? ( !dev-python/webpy[${PYTHON_USEDEP}] )"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/${P}/${PN}
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-1.7.3.1-maeffplugin.cpp.patch
-	)
-
-python_prepare_all() {
-	sed \
-		-e "s:\"/usr:\"${EPREFIX}/usr:g" \
-		-e "/ext_comp_args.*+=/s:\[.*\]$:\[\]:g" \
-		-e "/import/s:argparse:argparseX:g" \
-		-i setup.py || die
-
-	rm ./modules/pmg_tk/startup/apbs_tools.py || die
-
-	sed \
-		-e "s:/opt/local:${EPREFIX}/usr:g" \
-		-e '/ext_comp_args/s:\[.*\]:[]:g' \
-		-i setup.py || die
-
-	distutils-r1_python_prepare_all
-}
-
-python_install() {
-	distutils-r1_python_install --pymol-path="${EPREFIX}/usr/share/pymol"
-}
-
-python_install_all() {
-	distutils-r1_python_install_all
-
-	python_export python2_7 EPYTHON
-
-	# These environment variables should not go in the wrapper script, or else
-	# it will be impossible to use the PyMOL libraries from Python.
-	cat >> "${T}"/20pymol <<- EOF
-		PYMOL_PATH="$(python_get_sitedir)/${PN}"
-		PYMOL_DATA="${EPREFIX}/usr/share/pymol/data"
-		PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts"
-	EOF
-
-	doenvd "${T}"/20pymol
-
-	newicon "${WORKDIR}"/${PN}-1.7.0.0.png ${PN}.png
-	make_desktop_entry ${PN} PyMol ${PN} \
-		"Graphics;Education;Science;Chemistry;" \
-		"MimeType=chemical/x-pdb;chemical/x-mdl-molfile;chemical/x-mol2;chemical/seq-aa-fasta;chemical/seq-na-fasta;chemical/x-xyz;chemical/x-mdl-sdf;"
-
-	if ! use web; then
-		rm -rf "${D}/$(python_get_sitedir)/web" || die
-	fi
-
-	rm -f "${ED}"/usr/share/${PN}/LICENSE || die
-}
-
-pkg_postinst() {
-	fdo-mime_desktop_database_update
-	fdo-mime_mime_database_update
-}
-
-pkg_postrm() {
-	fdo-mime_desktop_database_update
-	fdo-mime_mime_database_update
-}