4 files changed, 76 insertions, 40 deletions

diff --git a/biology/pymol/Makefile b/biology/pymol/Makefile
index dd1f70fa088a..33484a174424 100644
--- a/biology/pymol/Makefile
+++ b/biology/pymol/Makefile
@@ -18,25 +18,25 @@ RUN_DEPENDS=	${PYNUMERIC} \
 LIB_DEPENDS=	png.6:${PORTSDIR}/graphics/png \
 		freetype.9:${PORTSDIR}/print/freetype2
 
-VERSION=	1.4.1
-SVNREVISION=	3946
+VERSION=	1.5.0.1
+SVNREVISION=	3978
 
 USE_BZIP2=	yes
 WRKSRC=		${WRKDIR}/pymol-${PORTVERSION}
 USE_GL=		glut glew
 USE_GMAKE=	yes
 USE_PYTHON=	yes
-PLIST_SUB=	PYTHON_VER=${PYTHON_VER}
+PLIST_SUB=	PYMOL_VER=${VERSION} PYTHON_VER=${PYTHON_VER}
 
 pre-build:
 	@${REINPLACE_CMD} -e "s+%%LOCALBASE%%+${LOCALBASE}+"  ${WRKSRC}/setup.py
 
+#do build process actually installs some files, so omitted.
 do-build:
-	@cd ${BUILD_WRKSRC}; ${SETENV} ${MAKE_ENV} ${PYTHON_CMD} ${PYSETUP} build
 
 do-install:
-	@(cd ${BUILD_WRKSRC}; ${SETENV} ${MAKE_ENV} ${PYTHON_CMD} ${PYSETUP} install \
-	; ${SETENV} ${MAKE_ENV} ${PYTHON_CMD} setup2.py install)
+	@(cd ${BUILD_WRKSRC}; ${SETENV} ${MAKE_ENV} ${PYTHON_CMD} ${PYSETUP} install)
+	@(cd ${BUILD_WRKSRC}; ${SETENV} ${MAKE_ENV} ${PYTHON_CMD} setup2.py install)
 	@${INSTALL_SCRIPT} ${WRKSRC}/pymol ${PREFIX}/bin/pymol
 
 #maintainance
diff --git a/biology/pymol/distinfo b/biology/pymol/distinfo
index 8472777d7006..509273172d80 100644
--- a/biology/pymol/distinfo
+++ b/biology/pymol/distinfo
@@ -1,2 +1,2 @@
-SHA256 (pymol-1.4.1.3946.tar.bz2) = 0b505ed6275fa1aeec6036830d28c8ee5feedfd67bcac7def873f0481f2cb558
-SIZE (pymol-1.4.1.3946.tar.bz2) = 9038319
+SHA256 (pymol-1.5.0.1.3978.tar.bz2) = 76ff4a6bc126f3fd4dccb62c2345fea3b2a007ecc687d89f7fe21b8f5a0496fc
+SIZE (pymol-1.5.0.1.3978.tar.bz2) = 9730397
diff --git a/biology/pymol/files/patch-setup.py b/biology/pymol/files/patch-setup.py
index d81c647b7d31..105d89d8a732 100644
--- a/biology/pymol/files/patch-setup.py
+++ b/biology/pymol/files/patch-setup.py
@@ -1,21 +1,31 @@
---- setup.py.bak	2010-09-16 10:45:18.000000000 +0900
-+++ setup.py	2010-09-16 10:51:57.000000000 +0900
-@@ -127,7 +127,8 @@
-     inc_dirs=["ov/src",
-               "layer0","layer1","layer2",
-               "layer3","layer4","layer5",
--              "/usr/include/freetype2",
-+              "%%LOCALBASE%%/include",
-+              "%%LOCALBASE%%/include/freetype2",
- #                 "/users/warren/ext/include",
- # VMD plugin support
- #              "contrib/uiuc/plugins/include",
-@@ -139,7 +140,7 @@
-           ]	
-     pyogl_libs = ["GL","GLU","glut"]
-     lib_dirs=[
--        "/usr/X11R6/lib",
-+         "%%LOCALBASE%%/lib",
- #        "/users/warren/pymol/ext/lib"
-         ]
-     def_macros=[("_PYMOL_MODULE",None),
+--- setup.py	2012-02-14 04:02:02.000000000 +0900
++++ setup.py	2012-02-15 13:09:38.000000000 +0900
+@@ -159,7 +159,8 @@
+                  "layer3",
+                  "layer4",
+                  "layer5",
+-                 "/usr/include/freetype2",
++                 "%%LOCALBASE%%/include/freetype2",
++                 "%%LOCALBASE%%/include",
+               # VMD plugin support
+               #              "contrib/uiuc/plugins/include",
+               #              "contrib/uiuc/plugins/molfile_plugin/src",
+@@ -181,7 +181,7 @@
+                    "GLU",
+                    "glut",
+                    "GLEW"]
+-    lib_dirs = [ "/usr/X11R6/lib64", ]
++    lib_dirs = [ "%%LOCALBASE%%/lib", ]
+     def_macros = [ ("_PYMOL_MODULE",None),
+                    ("_PYMOL_INLINE",None),
+                    ("_PYMOL_FREETYPE",None),
+@@ -201,7 +202,7 @@
+                       "-funroll-loops",
+                       "-O3",
+                       "-g" ]
+-    ext_link_args = []
++    ext_link_args = [ "-L%%LOCALBASE%%/lib" ]
+ 
+ 
+ distribution = setup ( # Distribution meta-data
+
diff --git a/biology/pymol/pkg-plist b/biology/pymol/pkg-plist
index 4c01bb24eb22..fb7eabf7b538 100644
--- a/biology/pymol/pkg-plist
+++ b/biology/pymol/pkg-plist
@@ -114,6 +114,8 @@ bin/pymol
 %%PYTHON_SITELIBDIR%%/pmg_tk/Demo.pyc
 %%PYTHON_SITELIBDIR%%/pmg_tk/PMGApp.py
 %%PYTHON_SITELIBDIR%%/pmg_tk/PMGApp.pyc
+%%PYTHON_SITELIBDIR%%/pmg_tk/PyMOLMapLoad.py
+%%PYTHON_SITELIBDIR%%/pmg_tk/PyMOLMapLoad.pyc
 %%PYTHON_SITELIBDIR%%/pmg_tk/SetEditor.py
 %%PYTHON_SITELIBDIR%%/pmg_tk/SetEditor.pyc
 %%PYTHON_SITELIBDIR%%/pmg_tk/Setting.py
@@ -122,21 +124,21 @@ bin/pymol
 %%PYTHON_SITELIBDIR%%/pmg_tk/__init__.pyc
 %%PYTHON_SITELIBDIR%%/pmg_tk/skins/__init__.py
 %%PYTHON_SITELIBDIR%%/pmg_tk/skins/__init__.pyc
-%%PYTHON_SITELIBDIR%%/pmg_tk/skins/normal/__init__.py
-%%PYTHON_SITELIBDIR%%/pmg_tk/skins/normal/__init__.pyc
-%%PYTHON_SITELIBDIR%%/pmg_tk/skins/normal/SimpleColorChooser.py
-%%PYTHON_SITELIBDIR%%/pmg_tk/skins/normal/SimpleColorChooser.pyc
 %%PYTHON_SITELIBDIR%%/pmg_tk/skins/normal/ColorMap.py
 %%PYTHON_SITELIBDIR%%/pmg_tk/skins/normal/ColorMap.pyc
 %%PYTHON_SITELIBDIR%%/pmg_tk/skins/normal/ColorRampModel.py
 %%PYTHON_SITELIBDIR%%/pmg_tk/skins/normal/ColorRampModel.pyc
 %%PYTHON_SITELIBDIR%%/pmg_tk/skins/normal/ModalWindow.py
 %%PYTHON_SITELIBDIR%%/pmg_tk/skins/normal/ModalWindow.pyc
+%%PYTHON_SITELIBDIR%%/pmg_tk/skins/normal/SimpleColorChooser.py
+%%PYTHON_SITELIBDIR%%/pmg_tk/skins/normal/SimpleColorChooser.pyc
+%%PYTHON_SITELIBDIR%%/pmg_tk/skins/normal/__init__.py
+%%PYTHON_SITELIBDIR%%/pmg_tk/skins/normal/__init__.pyc
 %%PYTHON_SITELIBDIR%%/pmg_tk/skins/normal/builder.py
 %%PYTHON_SITELIBDIR%%/pmg_tk/skins/normal/builder.pyc
 %%PYTHON_SITELIBDIR%%/pmg_tk/skins/normal/hist.py
-%%PYTHON_SITELIBDIR%%/pmg_tk/skins/normal/volume.py
 %%PYTHON_SITELIBDIR%%/pmg_tk/skins/normal/hist.pyc
+%%PYTHON_SITELIBDIR%%/pmg_tk/skins/normal/volume.py
 %%PYTHON_SITELIBDIR%%/pmg_tk/skins/normal/volume.pyc
 %%PYTHON_SITELIBDIR%%/pmg_tk/startup/__init__.py
 %%PYTHON_SITELIBDIR%%/pmg_tk/startup/__init__.pyc
@@ -146,7 +148,7 @@ bin/pymol
 %%PYTHON_SITELIBDIR%%/pmg_tk/startup/remote_pdb_load.pyc
 %%PYTHON_SITELIBDIR%%/pmg_wx/__init__.py
 %%PYTHON_SITELIBDIR%%/pmg_wx/__init__.pyc
-%%PYTHON_SITELIBDIR%%/pymol-1.4.0-py%%PYTHON_VER%%.egg-info
+%%PYTHON_SITELIBDIR%%/pymol-%%PYMOL_VER%%-py%%PYTHON_VER%%.egg-info
 %%PYTHON_SITELIBDIR%%/pymol/__init__.py
 %%PYTHON_SITELIBDIR%%/pymol/__init__.pyc
 %%PYTHON_SITELIBDIR%%/pymol/_cmd.so
@@ -170,6 +172,8 @@ bin/pymol
 %%PYTHON_SITELIBDIR%%/pymol/computing.pyc
 %%PYTHON_SITELIBDIR%%/pymol/constants.py
 %%PYTHON_SITELIBDIR%%/pymol/constants.pyc
+%%PYTHON_SITELIBDIR%%/pymol/constants_palette.py
+%%PYTHON_SITELIBDIR%%/pymol/constants_palette.pyc
 %%PYTHON_SITELIBDIR%%/pymol/contrib/__init__.py
 %%PYTHON_SITELIBDIR%%/pymol/contrib/__init__.pyc
 %%PYTHON_SITELIBDIR%%/pymol/controlling.py
@@ -192,10 +196,10 @@ bin/pymol
 %%PYTHON_SITELIBDIR%%/pymol/fitting.pyc
 %%PYTHON_SITELIBDIR%%/pymol/gui.py
 %%PYTHON_SITELIBDIR%%/pymol/gui.pyc
-%%PYTHON_SITELIBDIR%%/pymol/helping.py
-%%PYTHON_SITELIBDIR%%/pymol/helping.pyc
 %%PYTHON_SITELIBDIR%%/pymol/headering.py
 %%PYTHON_SITELIBDIR%%/pymol/headering.pyc
+%%PYTHON_SITELIBDIR%%/pymol/helping.py
+%%PYTHON_SITELIBDIR%%/pymol/helping.pyc
 %%PYTHON_SITELIBDIR%%/pymol/importing.py
 %%PYTHON_SITELIBDIR%%/pymol/importing.pyc
 %%PYTHON_SITELIBDIR%%/pymol/internal.py
@@ -405,14 +409,33 @@ bin/pymol
 %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc7.gif
 %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc7.xbm
 %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/pymol/cmyk.png
+%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/pymol/hsv.ppm
+%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/pymol/incentive_splash.png
 %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/pymol/matrices/BLOSUM62
 %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/pymol/splash.old.png
-%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/pymol/hsv.ppm
+%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/pymol/splash.png
+%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/pymol/splash_edu.png
+%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/cylinder.fs
+%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/cylinder.vs
+%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/cylinder_no_ff.fs
 %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/default.fs
 %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/default.vs
+%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/default_es.fs
+%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/default_es.vs
+%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/default_es2.fs
+%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/default_es2.vs
+%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/shadertext.txt
+%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/sphere.fs
+%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/sphere.vs
+%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/sphere_arb_fs.fs
+%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/sphere_arb_vs.vs
+%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/spheredirect.vs
 %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/volume.fs
 %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/volume.vs
 %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/tut/1hpv.pdb
+%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/xray/atomformfactor2.dat
+%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/xray/atomformfactor5.dat
+%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/xray/spgbase.dat
 %%PYTHON_SITELIBDIR%%/pymol/pymol_path/examples/chempy/generate_amber.py
 %%PYTHON_SITELIBDIR%%/pymol/pymol_path/examples/chempy/generate_mmff.py
 %%PYTHON_SITELIBDIR%%/pymol/pymol_path/examples/cookbook/area_diff.pml
@@ -449,6 +472,7 @@ bin/pymol
 %%PYTHON_SITELIBDIR%%/pymol/pymol_path/examples/devel/chempy_model03.py
 %%PYTHON_SITELIBDIR%%/pymol/pymol_path/examples/devel/click_ordered_list.py
 %%PYTHON_SITELIBDIR%%/pymol/pymol_path/examples/devel/count_molecules.py
+%%PYTHON_SITELIBDIR%%/pymol/pymol_path/examples/devel/demo.sdf
 %%PYTHON_SITELIBDIR%%/pymol/pymol_path/examples/devel/extend_demo01.py
 %%PYTHON_SITELIBDIR%%/pymol/pymol_path/examples/devel/gl01.py
 %%PYTHON_SITELIBDIR%%/pymol/pymol_path/examples/devel/gl02.py
@@ -520,6 +544,7 @@ bin/pymol
 %%PYTHON_SITELIBDIR%%/pymol/pymol_path/test/dat/small03.mol2
 %%PYTHON_SITELIBDIR%%/pymol/pymol_path/test/dat/tiny.pdb
 %%PYTHON_SITELIBDIR%%/pymol/pymol_path/test/dat/water.pdb
+%%PYTHON_SITELIBDIR%%/pymol/pymol_path/test/headerTest.py
 %%PYTHON_SITELIBDIR%%/pymol/pymol_path/test/inp/B01.py
 %%PYTHON_SITELIBDIR%%/pymol/pymol_path/test/inp/B02.py
 %%PYTHON_SITELIBDIR%%/pymol/pymol_path/test/inp/B03.py
@@ -773,12 +798,12 @@ bin/pymol
 %%PYTHON_SITELIBDIR%%/pymol/xwin.pyc
 %%PYTHON_SITELIBDIR%%/web/__init__.py
 %%PYTHON_SITELIBDIR%%/web/__init__.pyc
-%%PYTHON_SITELIBDIR%%/web/pymolhttpd.py
-%%PYTHON_SITELIBDIR%%/web/pymolhttpd.pyc
 %%PYTHON_SITELIBDIR%%/web/examples/__init__.py
 %%PYTHON_SITELIBDIR%%/web/examples/__init__.pyc
 %%PYTHON_SITELIBDIR%%/web/examples/justhttpd.py
 %%PYTHON_SITELIBDIR%%/web/examples/justhttpd.pyc
+%%PYTHON_SITELIBDIR%%/web/pymolhttpd.py
+%%PYTHON_SITELIBDIR%%/web/pymolhttpd.pyc
 @dirrm %%PYTHON_SITELIBDIR%%/web/examples
 @dirrm %%PYTHON_SITELIBDIR%%/web
 @dirrm %%PYTHON_SITELIBDIR%%/pymol/wizard
@@ -795,6 +820,7 @@ bin/pymol
 @dirrm %%PYTHON_SITELIBDIR%%/pymol/pymol_path/examples/cookbook
 @dirrm %%PYTHON_SITELIBDIR%%/pymol/pymol_path/examples/chempy
 @dirrm %%PYTHON_SITELIBDIR%%/pymol/pymol_path/examples
+@dirrm %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/xray
 @dirrm %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/tut
 @dirrm %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders
 @dirrm %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/pymol/matrices