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Date:      Tue, 19 Dec 2017 19:49:17 +0000 (UTC)
From:      Yuri Victorovich <yuri@FreeBSD.org>
To:        ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org
Subject:   svn commit: r456763 - in head: . science science/py-pymol science/py-pymol/files
Message-ID:  <201712191949.vBJJnHjl084883@repo.freebsd.org>

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Author: yuri
Date: Tue Dec 19 19:49:17 2017
New Revision: 456763
URL: https://svnweb.freebsd.org/changeset/ports/456763

Log:
  Re-added port: science/py-pymol: OpenGL based molecular visualization system (existed 2002/08/13-2014/09/01, deleted in r366862)
  
  Approved by:	adamw (mentor)
  Differential Revision:	https://reviews.freebsd.org/D12902

Added:
  head/science/py-pymol/
     - copied from r366861, head/biology/pymol/
  head/science/py-pymol/files/patch-create__shadertext.py   (contents, props changed)
Modified:
  head/MOVED
  head/science/Makefile
  head/science/py-pymol/Makefile
  head/science/py-pymol/distinfo
  head/science/py-pymol/files/patch-setup.py
  head/science/py-pymol/pkg-descr
  head/science/py-pymol/pkg-plist

Modified: head/MOVED
==============================================================================
--- head/MOVED	Tue Dec 19 19:02:51 2017	(r456762)
+++ head/MOVED	Tue Dec 19 19:49:17 2017	(r456763)
@@ -6474,7 +6474,6 @@ audio/liquidsoap||2014-09-01|Not staged
 benchmarks/spec-sfs||2014-09-01|Not staged
 biology/blast||2014-09-01|Not staged
 biology/embassy||2014-09-01|Not staged
-biology/pymol||2014-09-01|Not staged
 cad/scv||2014-09-01|Not staged
 cad/systemc||2014-09-01|Not staged
 chinese/cmexfonts||2014-09-01|Not staged

Modified: head/science/Makefile
==============================================================================
--- head/science/Makefile	Tue Dec 19 19:02:51 2017	(r456762)
+++ head/science/Makefile	Tue Dec 19 19:49:17 2017	(r456763)
@@ -170,6 +170,7 @@
     SUBDIR += py-pupynere
     SUBDIR += py-pyaixi
     SUBDIR += py-pydicom
+    SUBDIR += py-pymol
     SUBDIR += py-pysal
     SUBDIR += py-pyteomics
     SUBDIR += py-pyteomics.biolccc

Modified: head/science/py-pymol/Makefile
==============================================================================
--- head/biology/pymol/Makefile	Mon Sep  1 11:12:56 2014	(r366861)
+++ head/science/py-pymol/Makefile	Tue Dec 19 19:49:17 2017	(r456763)
@@ -2,48 +2,36 @@
 # $FreeBSD$
 
 PORTNAME=	pymol
-PORTVERSION=	${VERSION}.${SVNREVISION}
-PORTREVISION=	3
-CATEGORIES=	biology python
-MASTER_SITES=	${MASTER_SITE_LOCAL:S|%SUBDIR%|maho/pymol|}
+DISTVERSIONPREFIX=	v
+DISTVERSION=	1.8.6.0
+CATEGORIES=	science biology python
+MASTER_SITES=	SF/pymol/pymol/1.8/
+PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
 
-MAINTAINER=	ports@FreeBSD.org
-COMMENT=	Free and Open-Source molecular modeling system
+MAINTAINER=	yuri@FreeBSD.org
+COMMENT=	OpenGL-based molecular visualization system
 
-BUILD_DEPENDS=	${PYNUMERIC}
-RUN_DEPENDS=	${PYNUMERIC} \
-		${PYTHON_SITELIBDIR}/Pmw:${PORTSDIR}/x11-toolkits/py-Pmw
-LIB_DEPENDS=	libpng15.so:${PORTSDIR}/graphics/png \
-		libfreetype.so:${PORTSDIR}/print/freetype2
+LICENSE=	PyMOL
+LICENSE_NAME=	Open-Source PyMOL Copyright
+LICENSE_FILE=	${WRKSRC}/LICENSE
+LICENSE_PERMS=	dist-mirror dist-sell pkg-mirror pkg-sell auto-accept
 
-VERSION=	1.5.0.1
-SVNREVISION=	3978
+RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}msgpack-python>0:devel/py-msgpack-python@${FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}Pmw>0:x11-toolkits/py-Pmw@${FLAVOR}
+LIB_DEPENDS=	libfreetype.so:print/freetype2 \
+		libpng16.so:graphics/png \
+		libmsgpackc.so:devel/msgpack
 
-WRKSRC=		${WRKDIR}/pymol-${PORTVERSION}
-USE_GL=		glut glew
-USES=		gmake tar:bzip2
-USE_PYTHON=	yes
-PLIST_SUB=	PYMOL_VER=${VERSION} PYTHON_VER=${PYTHON_VER}
+WRKSRC=		${WRKDIR}/pymol
 
-NO_STAGE=	yes
-pre-build:
-	@${REINPLACE_CMD} -e "s+%%LOCALBASE%%+${LOCALBASE}+"  ${WRKSRC}/setup.py
+USES=		compiler:c++11-lang python shebangfix tar:bz2
+USE_GL=		gl glew glu glut
+USE_GNOME=	libxml2
+USE_PYTHON=	distutils concurrent  # autoplist is broken: https://sourceforge.net/p/pymol/bugs/189
+SHEBANG_FILES=	test/show test/run test/cyg
 
-#do build process actually installs some files, so omitted.
-do-build:
-
-do-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
-do-fetch-svn:
-	#svn ls https://pymol.svn.sourceforge.net/svnroot/pymol/tags
-	#http://pymol.svn.sourceforge.net/viewvc/pymol/trunk/
-	${RM} -rf pymol-${VERSION}.${SVNREVISION}
-	svn -r ${SVNREVISION} export http://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol pymol-${VERSION}.${SVNREVISION}
-	tar cvfj pymol-${VERSION}.${SVNREVISION}.tar.bz2 pymol-${VERSION}.${SVNREVISION}
-	scp pymol-${VERSION}.${SVNREVISION}.tar.bz2 freefall.freebsd.org:public_distfiles/pymol/
+post-install:
+	@${STRIP_CMD} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/pymol/_cmd.so
+	@${STRIP_CMD} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/chempy/champ/_champ.so
 
 .include <bsd.port.mk>

Modified: head/science/py-pymol/distinfo
==============================================================================
--- head/biology/pymol/distinfo	Mon Sep  1 11:12:56 2014	(r366861)
+++ head/science/py-pymol/distinfo	Tue Dec 19 19:49:17 2017	(r456763)
@@ -1,2 +1,3 @@
-SHA256 (pymol-1.5.0.1.3978.tar.bz2) = 76ff4a6bc126f3fd4dccb62c2345fea3b2a007ecc687d89f7fe21b8f5a0496fc
-SIZE (pymol-1.5.0.1.3978.tar.bz2) = 9730397
+TIMESTAMP = 1509591135
+SHA256 (pymol-v1.8.6.0.tar.bz2) = 7eaaf90ac1e1be0969291cdb1154b3631b5b6403cce1d697133d90cd37a3c565
+SIZE (pymol-v1.8.6.0.tar.bz2) = 8717164

Added: head/science/py-pymol/files/patch-create__shadertext.py
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/science/py-pymol/files/patch-create__shadertext.py	Tue Dec 19 19:49:17 2017	(r456763)
@@ -0,0 +1,34 @@
+--- create_shadertext.py.orig	2017-03-09 18:16:07 UTC
++++ create_shadertext.py
+@@ -93,19 +93,20 @@ def create_shadertext(shaderdir, shaderd
+ 
+ def create_buildinfo(outputdir, pymoldir='.'):
+ 
+-    try:
+-        sha = Popen(['git', 'rev-parse', 'HEAD'], cwd=pymoldir,
+-                stdout=PIPE).stdout.read().strip().decode()
+-    except OSError:
+-        sha = ''
++    #try:
++    #    sha = Popen(['git', 'rev-parse', 'HEAD'], cwd=pymoldir,
++    #            stdout=PIPE).stdout.read().strip().decode()
++    #except OSError:
++    #    sha = ''
++    sha = 'n/a'
+ 
+     rev = 0
+-    try:
+-        for line in Popen(['svn', 'info'], cwd=pymoldir, stdout=PIPE).stdout:
+-            if line.startswith(b'Last Changed Rev'):
+-                rev = int(line.split()[3])
+-    except OSError:
+-        pass
++    #try:
++    #    for line in Popen(['svn', 'info'], cwd=pymoldir, stdout=PIPE).stdout:
++    #        if line.startswith(b'Last Changed Rev'):
++    #            rev = int(line.split()[3])
++    #except OSError:
++    #    pass
+ 
+     with openw(os.path.join(outputdir, 'PyMOLBuildInfo.h')) as out:
+         print('''

Modified: head/science/py-pymol/files/patch-setup.py
==============================================================================
--- head/biology/pymol/files/patch-setup.py	Mon Sep  1 11:12:56 2014	(r366861)
+++ head/science/py-pymol/files/patch-setup.py	Tue Dec 19 19:49:17 2017	(r456763)
@@ -1,31 +1,22 @@
---- 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" ]
+--- setup.py.orig	2017-03-09 18:16:07 UTC
++++ setup.py
+@@ -52,6 +52,8 @@ try:
+             "keyword support.")
+     parser.add_argument('--help-distutils', action="store_true",
+             help="show help for distutils options and exit")
++    parser.add_argument('--single-version-externally-managed', action="store_true",
++            help="single-version-externally-managed")
+     options, sys.argv[1:] = parser.parse_known_args(namespace=options)
+ except ImportError:
+     print("argparse not available")
+@@ -318,8 +320,8 @@ else: # unix style (linux, mac, ...)
  
+     # optimization currently causes a clang segfault on OS X 10.9 when
+     # compiling layer2/RepCylBond.cpp
+-    if sys.platform != 'darwin':
+-        ext_comp_args += ["-O3"]
++    #if sys.platform != 'darwin':
++    #    ext_comp_args += ["-O3"]
  
- distribution = setup ( # Distribution meta-data
-
+ def get_pymol_version():
+     return re.findall(r'_PyMOL_VERSION "(.*)"', open('layer0/Version.h').read())[0]

Modified: head/science/py-pymol/pkg-descr
==============================================================================
--- head/biology/pymol/pkg-descr	Mon Sep  1 11:12:56 2014	(r366861)
+++ head/science/py-pymol/pkg-descr	Tue Dec 19 19:49:17 2017	(r456763)
@@ -1,9 +1,9 @@
-PyMOL is a molecular graphics system with an embedded Python interpreter
-designed for real-time visualization and rapid generation of
-high-quality molecular graphics images and animations. It is fully extensible
-and available free to everyone via the "Python" license.
-PyMOL can be used to create images and animations with unprecedented ease.
-It can also perform many other valuable tasks (such as editing PDB files)
-to assist you in your research.
+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!
 
-WWW: http://pymol.sourceforge.net/
+This version represents the community-supported open source distribution
+of the closed source commercial product PyMOL.
+
+WWW: https://www.pymol.org

Modified: head/science/py-pymol/pkg-plist
==============================================================================
--- head/biology/pymol/pkg-plist	Mon Sep  1 11:12:56 2014	(r366861)
+++ head/science/py-pymol/pkg-plist	Tue Dec 19 19:49:17 2017	(r456763)
@@ -1,257 +1,392 @@
 bin/pymol
 %%PYTHON_SITELIBDIR%%/chempy/__init__.py
 %%PYTHON_SITELIBDIR%%/chempy/__init__.pyc
+%%PYTHON_SITELIBDIR%%/chempy/__init__.%%PYTHON_PYOEXTENSION%%
 %%PYTHON_SITELIBDIR%%/chempy/arc.py
 %%PYTHON_SITELIBDIR%%/chempy/arc.pyc
+%%PYTHON_SITELIBDIR%%/chempy/arc.%%PYTHON_PYOEXTENSION%%
 %%PYTHON_SITELIBDIR%%/chempy/bmin/__init__.py
 %%PYTHON_SITELIBDIR%%/chempy/bmin/__init__.pyc
+%%PYTHON_SITELIBDIR%%/chempy/bmin/__init__.%%PYTHON_PYOEXTENSION%%
 %%PYTHON_SITELIBDIR%%/chempy/bmin/commands.py
 %%PYTHON_SITELIBDIR%%/chempy/bmin/commands.pyc
+%%PYTHON_SITELIBDIR%%/chempy/bmin/commands.%%PYTHON_PYOEXTENSION%%
 %%PYTHON_SITELIBDIR%%/chempy/bmin/realtime.py
 %%PYTHON_SITELIBDIR%%/chempy/bmin/realtime.pyc
+%%PYTHON_SITELIBDIR%%/chempy/bmin/realtime.%%PYTHON_PYOEXTENSION%%
 %%PYTHON_SITELIBDIR%%/chempy/bmin/state.py
 %%PYTHON_SITELIBDIR%%/chempy/bmin/state.pyc
+%%PYTHON_SITELIBDIR%%/chempy/bmin/state.%%PYTHON_PYOEXTENSION%%
 %%PYTHON_SITELIBDIR%%/chempy/bmin/util.py
 %%PYTHON_SITELIBDIR%%/chempy/bmin/util.pyc
+%%PYTHON_SITELIBDIR%%/chempy/bmin/util.%%PYTHON_PYOEXTENSION%%
 %%PYTHON_SITELIBDIR%%/chempy/bond_amber.py
 %%PYTHON_SITELIBDIR%%/chempy/bond_amber.pyc
+%%PYTHON_SITELIBDIR%%/chempy/bond_amber.%%PYTHON_PYOEXTENSION%%
 %%PYTHON_SITELIBDIR%%/chempy/bond_mmff.py
 %%PYTHON_SITELIBDIR%%/chempy/bond_mmff.pyc
+%%PYTHON_SITELIBDIR%%/chempy/bond_mmff.%%PYTHON_PYOEXTENSION%%
 %%PYTHON_SITELIBDIR%%/chempy/bonds.py
 %%PYTHON_SITELIBDIR%%/chempy/bonds.pyc
+%%PYTHON_SITELIBDIR%%/chempy/bonds.%%PYTHON_PYOEXTENSION%%
 %%PYTHON_SITELIBDIR%%/chempy/brick.py
 %%PYTHON_SITELIBDIR%%/chempy/brick.pyc
+%%PYTHON_SITELIBDIR%%/chempy/brick.%%PYTHON_PYOEXTENSION%%
 %%PYTHON_SITELIBDIR%%/chempy/cc1.py
 %%PYTHON_SITELIBDIR%%/chempy/cc1.pyc
+%%PYTHON_SITELIBDIR%%/chempy/cc1.%%PYTHON_PYOEXTENSION%%
 %%PYTHON_SITELIBDIR%%/chempy/cex.py
 %%PYTHON_SITELIBDIR%%/chempy/cex.pyc
+%%PYTHON_SITELIBDIR%%/chempy/cex.%%PYTHON_PYOEXTENSION%%
 %%PYTHON_SITELIBDIR%%/chempy/champ/__init__.py
 %%PYTHON_SITELIBDIR%%/chempy/champ/__init__.pyc
+%%PYTHON_SITELIBDIR%%/chempy/champ/__init__.%%PYTHON_PYOEXTENSION%%
 %%PYTHON_SITELIBDIR%%/chempy/champ/_champ.so
 %%PYTHON_SITELIBDIR%%/chempy/champ/amber99.py
 %%PYTHON_SITELIBDIR%%/chempy/champ/amber99.pyc
+%%PYTHON_SITELIBDIR%%/chempy/champ/amber99.%%PYTHON_PYOEXTENSION%%
 %%PYTHON_SITELIBDIR%%/chempy/champ/assign.py
 %%PYTHON_SITELIBDIR%%/chempy/champ/assign.pyc
+%%PYTHON_SITELIBDIR%%/chempy/champ/assign.%%PYTHON_PYOEXTENSION%%
 %%PYTHON_SITELIBDIR%%/chempy/champ/formal_charges.py
 %%PYTHON_SITELIBDIR%%/chempy/champ/formal_charges.pyc
+%%PYTHON_SITELIBDIR%%/chempy/champ/formal_charges.%%PYTHON_PYOEXTENSION%%
 %%PYTHON_SITELIBDIR%%/chempy/charge.py
 %%PYTHON_SITELIBDIR%%/chempy/charge.pyc
+%%PYTHON_SITELIBDIR%%/chempy/charge.%%PYTHON_PYOEXTENSION%%
 %%PYTHON_SITELIBDIR%%/chempy/cif.py
 %%PYTHON_SITELIBDIR%%/chempy/cif.pyc
+%%PYTHON_SITELIBDIR%%/chempy/cif.%%PYTHON_PYOEXTENSION%%
 %%PYTHON_SITELIBDIR%%/chempy/cpv.py
 %%PYTHON_SITELIBDIR%%/chempy/cpv.pyc
+%%PYTHON_SITELIBDIR%%/chempy/cpv.%%PYTHON_PYOEXTENSION%%
 %%PYTHON_SITELIBDIR%%/chempy/dictdb.py
 %%PYTHON_SITELIBDIR%%/chempy/dictdb.pyc
+%%PYTHON_SITELIBDIR%%/chempy/dictdb.%%PYTHON_PYOEXTENSION%%
 %%PYTHON_SITELIBDIR%%/chempy/fast/__init__.py
 %%PYTHON_SITELIBDIR%%/chempy/fast/__init__.pyc
+%%PYTHON_SITELIBDIR%%/chempy/fast/__init__.%%PYTHON_PYOEXTENSION%%
 %%PYTHON_SITELIBDIR%%/chempy/fragments/__init__.py
 %%PYTHON_SITELIBDIR%%/chempy/fragments/__init__.pyc
+%%PYTHON_SITELIBDIR%%/chempy/fragments/__init__.%%PYTHON_PYOEXTENSION%%
 %%PYTHON_SITELIBDIR%%/chempy/gamess1.py
 %%PYTHON_SITELIBDIR%%/chempy/gamess1.pyc
+%%PYTHON_SITELIBDIR%%/chempy/gamess1.%%PYTHON_PYOEXTENSION%%
 %%PYTHON_SITELIBDIR%%/chempy/gms.py
 %%PYTHON_SITELIBDIR%%/chempy/gms.pyc
+%%PYTHON_SITELIBDIR%%/chempy/gms.%%PYTHON_PYOEXTENSION%%
 %%PYTHON_SITELIBDIR%%/chempy/hetatm.py
 %%PYTHON_SITELIBDIR%%/chempy/hetatm.pyc
+%%PYTHON_SITELIBDIR%%/chempy/hetatm.%%PYTHON_PYOEXTENSION%%
 %%PYTHON_SITELIBDIR%%/chempy/io.py
 %%PYTHON_SITELIBDIR%%/chempy/io.pyc
+%%PYTHON_SITELIBDIR%%/chempy/io.%%PYTHON_PYOEXTENSION%%
 %%PYTHON_SITELIBDIR%%/chempy/lst.py
 %%PYTHON_SITELIBDIR%%/chempy/lst.pyc
+%%PYTHON_SITELIBDIR%%/chempy/lst.%%PYTHON_PYOEXTENSION%%
 %%PYTHON_SITELIBDIR%%/chempy/mae.py
 %%PYTHON_SITELIBDIR%%/chempy/mae.pyc
+%%PYTHON_SITELIBDIR%%/chempy/mae.%%PYTHON_PYOEXTENSION%%
 %%PYTHON_SITELIBDIR%%/chempy/map.py
 %%PYTHON_SITELIBDIR%%/chempy/map.pyc
+%%PYTHON_SITELIBDIR%%/chempy/map.%%PYTHON_PYOEXTENSION%%
 %%PYTHON_SITELIBDIR%%/chempy/mass.py
 %%PYTHON_SITELIBDIR%%/chempy/mass.pyc
+%%PYTHON_SITELIBDIR%%/chempy/mass.%%PYTHON_PYOEXTENSION%%
 %%PYTHON_SITELIBDIR%%/chempy/mmd.py
 %%PYTHON_SITELIBDIR%%/chempy/mmd.pyc
+%%PYTHON_SITELIBDIR%%/chempy/mmd.%%PYTHON_PYOEXTENSION%%
+%%PYTHON_SITELIBDIR%%/chempy/mmtf/__init__.py
+%%PYTHON_SITELIBDIR%%/chempy/mmtf/__init__.pyc
+%%PYTHON_SITELIBDIR%%/chempy/mmtf/__init__.%%PYTHON_PYOEXTENSION%%
+%%PYTHON_SITELIBDIR%%/chempy/mmtf/io.py
+%%PYTHON_SITELIBDIR%%/chempy/mmtf/io.pyc
+%%PYTHON_SITELIBDIR%%/chempy/mmtf/io.%%PYTHON_PYOEXTENSION%%
 %%PYTHON_SITELIBDIR%%/chempy/models.py
 %%PYTHON_SITELIBDIR%%/chempy/models.pyc
+%%PYTHON_SITELIBDIR%%/chempy/models.%%PYTHON_PYOEXTENSION%%
 %%PYTHON_SITELIBDIR%%/chempy/mol.py
 %%PYTHON_SITELIBDIR%%/chempy/mol.pyc
+%%PYTHON_SITELIBDIR%%/chempy/mol.%%PYTHON_PYOEXTENSION%%
 %%PYTHON_SITELIBDIR%%/chempy/mol2.py
 %%PYTHON_SITELIBDIR%%/chempy/mol2.pyc
+%%PYTHON_SITELIBDIR%%/chempy/mol2.%%PYTHON_PYOEXTENSION%%
 %%PYTHON_SITELIBDIR%%/chempy/neighbor.py
 %%PYTHON_SITELIBDIR%%/chempy/neighbor.pyc
+%%PYTHON_SITELIBDIR%%/chempy/neighbor.%%PYTHON_PYOEXTENSION%%
 %%PYTHON_SITELIBDIR%%/chempy/pdb.py
 %%PYTHON_SITELIBDIR%%/chempy/pdb.pyc
+%%PYTHON_SITELIBDIR%%/chempy/pdb.%%PYTHON_PYOEXTENSION%%
 %%PYTHON_SITELIBDIR%%/chempy/pkl.py
 %%PYTHON_SITELIBDIR%%/chempy/pkl.pyc
+%%PYTHON_SITELIBDIR%%/chempy/pkl.%%PYTHON_PYOEXTENSION%%
 %%PYTHON_SITELIBDIR%%/chempy/place.py
 %%PYTHON_SITELIBDIR%%/chempy/place.pyc
+%%PYTHON_SITELIBDIR%%/chempy/place.%%PYTHON_PYOEXTENSION%%
 %%PYTHON_SITELIBDIR%%/chempy/protein.py
 %%PYTHON_SITELIBDIR%%/chempy/protein.pyc
+%%PYTHON_SITELIBDIR%%/chempy/protein.%%PYTHON_PYOEXTENSION%%
 %%PYTHON_SITELIBDIR%%/chempy/protein_amber.py
 %%PYTHON_SITELIBDIR%%/chempy/protein_amber.pyc
+%%PYTHON_SITELIBDIR%%/chempy/protein_amber.%%PYTHON_PYOEXTENSION%%
 %%PYTHON_SITELIBDIR%%/chempy/protein_amber99.py
 %%PYTHON_SITELIBDIR%%/chempy/protein_amber99.pyc
+%%PYTHON_SITELIBDIR%%/chempy/protein_amber99.%%PYTHON_PYOEXTENSION%%
 %%PYTHON_SITELIBDIR%%/chempy/protein_mmff.py
 %%PYTHON_SITELIBDIR%%/chempy/protein_mmff.pyc
+%%PYTHON_SITELIBDIR%%/chempy/protein_mmff.%%PYTHON_PYOEXTENSION%%
 %%PYTHON_SITELIBDIR%%/chempy/protein_residues.py
 %%PYTHON_SITELIBDIR%%/chempy/protein_residues.pyc
+%%PYTHON_SITELIBDIR%%/chempy/protein_residues.%%PYTHON_PYOEXTENSION%%
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+%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/compute_color_for_light.fs
+%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/compute_fog_color.fs
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-%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/cylinder_no_ff.fs
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+%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/defaultscreen.fs
+%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/defaultscreen.vs
+%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/indicator.fs
+%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/indicator.vs
+%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/label.fs
+%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/label.vs
+%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/labelscreen.fs
+%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/labelscreen.vs
+%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/ramp.fs
+%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/ramp.vs
+%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/screen.fs
+%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/screen.vs
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@@ -433,9 +583,6 @@ bin/pymol
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-%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/xray/atomformfactor5.dat
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@@ -726,129 +873,130 @@ bin/pymol
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-@dirrm %%PYTHON_SITELIBDIR%%/pymol/opengl/glu
-@dirrm %%PYTHON_SITELIBDIR%%/pymol/opengl/gl
-@dirrm %%PYTHON_SITELIBDIR%%/pymol/opengl
-@dirrm %%PYTHON_SITELIBDIR%%/pymol/contrib
-@dirrm %%PYTHON_SITELIBDIR%%/pymol
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-@dirrm %%PYTHON_SITELIBDIR%%/pmg_tk/skins/normal
-@dirrm %%PYTHON_SITELIBDIR%%/pmg_tk/skins
-@dirrm %%PYTHON_SITELIBDIR%%/pmg_tk
-@dirrm %%PYTHON_SITELIBDIR%%/chempy/tinker
-@dirrm %%PYTHON_SITELIBDIR%%/chempy/fragments
-@dirrm %%PYTHON_SITELIBDIR%%/chempy/fast
-@dirrm %%PYTHON_SITELIBDIR%%/chempy/champ
-@dirrm %%PYTHON_SITELIBDIR%%/chempy/bmin
-@dirrm %%PYTHON_SITELIBDIR%%/chempy
+%%PYTHON_SITELIBDIR%%/web/pymolhttpd.%%PYTHON_PYOEXTENSION%%



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