svn commit: r456763 - in head: . science science/py-pymol science/py-pymol/files
Yuri Victorovich
yuri at FreeBSD.org
Tue Dec 19 19:49:19 UTC 2017
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 at FreeBSD.org
-COMMENT= Free and Open-Source molecular modeling system
+MAINTAINER= yuri at 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%%
%%PYTHON_SITELIBDIR%%/chempy/sdf.py
%%PYTHON_SITELIBDIR%%/chempy/sdf.pyc
+%%PYTHON_SITELIBDIR%%/chempy/sdf.%%PYTHON_PYOEXTENSION%%
%%PYTHON_SITELIBDIR%%/chempy/solvate.py
%%PYTHON_SITELIBDIR%%/chempy/solvate.pyc
+%%PYTHON_SITELIBDIR%%/chempy/solvate.%%PYTHON_PYOEXTENSION%%
%%PYTHON_SITELIBDIR%%/chempy/tinker/__init__.py
%%PYTHON_SITELIBDIR%%/chempy/tinker/__init__.pyc
+%%PYTHON_SITELIBDIR%%/chempy/tinker/__init__.%%PYTHON_PYOEXTENSION%%
%%PYTHON_SITELIBDIR%%/chempy/tinker/amber.py
%%PYTHON_SITELIBDIR%%/chempy/tinker/amber.pyc
+%%PYTHON_SITELIBDIR%%/chempy/tinker/amber.%%PYTHON_PYOEXTENSION%%
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%%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/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
%%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
@@ -433,9 +583,6 @@ bin/pymol
%%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
@@ -726,129 +873,130 @@ bin/pymol
%%PYTHON_SITELIBDIR%%/pymol/pymol_path/test/win.py
%%PYTHON_SITELIBDIR%%/pymol/querying.py
%%PYTHON_SITELIBDIR%%/pymol/querying.pyc
+%%PYTHON_SITELIBDIR%%/pymol/querying.%%PYTHON_PYOEXTENSION%%
%%PYTHON_SITELIBDIR%%/pymol/rpc.py
%%PYTHON_SITELIBDIR%%/pymol/rpc.pyc
+%%PYTHON_SITELIBDIR%%/pymol/rpc.%%PYTHON_PYOEXTENSION%%
%%PYTHON_SITELIBDIR%%/pymol/selecting.py
%%PYTHON_SITELIBDIR%%/pymol/selecting.pyc
+%%PYTHON_SITELIBDIR%%/pymol/selecting.%%PYTHON_PYOEXTENSION%%
%%PYTHON_SITELIBDIR%%/pymol/selector.py
%%PYTHON_SITELIBDIR%%/pymol/selector.pyc
+%%PYTHON_SITELIBDIR%%/pymol/selector.%%PYTHON_PYOEXTENSION%%
%%PYTHON_SITELIBDIR%%/pymol/setting.py
%%PYTHON_SITELIBDIR%%/pymol/setting.pyc
+%%PYTHON_SITELIBDIR%%/pymol/setting.%%PYTHON_PYOEXTENSION%%
%%PYTHON_SITELIBDIR%%/pymol/shortcut.py
%%PYTHON_SITELIBDIR%%/pymol/shortcut.pyc
+%%PYTHON_SITELIBDIR%%/pymol/shortcut.%%PYTHON_PYOEXTENSION%%
%%PYTHON_SITELIBDIR%%/pymol/util.py
%%PYTHON_SITELIBDIR%%/pymol/util.pyc
+%%PYTHON_SITELIBDIR%%/pymol/util.%%PYTHON_PYOEXTENSION%%
%%PYTHON_SITELIBDIR%%/pymol/vfont.py
%%PYTHON_SITELIBDIR%%/pymol/vfont.pyc
+%%PYTHON_SITELIBDIR%%/pymol/vfont.%%PYTHON_PYOEXTENSION%%
%%PYTHON_SITELIBDIR%%/pymol/viewing.py
%%PYTHON_SITELIBDIR%%/pymol/viewing.pyc
+%%PYTHON_SITELIBDIR%%/pymol/viewing.%%PYTHON_PYOEXTENSION%%
%%PYTHON_SITELIBDIR%%/pymol/wizard/__init__.py
%%PYTHON_SITELIBDIR%%/pymol/wizard/__init__.pyc
+%%PYTHON_SITELIBDIR%%/pymol/wizard/__init__.%%PYTHON_PYOEXTENSION%%
%%PYTHON_SITELIBDIR%%/pymol/wizard/annotation.py
%%PYTHON_SITELIBDIR%%/pymol/wizard/annotation.pyc
+%%PYTHON_SITELIBDIR%%/pymol/wizard/annotation.%%PYTHON_PYOEXTENSION%%
%%PYTHON_SITELIBDIR%%/pymol/wizard/appearance.py
%%PYTHON_SITELIBDIR%%/pymol/wizard/appearance.pyc
+%%PYTHON_SITELIBDIR%%/pymol/wizard/appearance.%%PYTHON_PYOEXTENSION%%
%%PYTHON_SITELIBDIR%%/pymol/wizard/benchmark.py
%%PYTHON_SITELIBDIR%%/pymol/wizard/benchmark.pyc
+%%PYTHON_SITELIBDIR%%/pymol/wizard/benchmark.%%PYTHON_PYOEXTENSION%%
%%PYTHON_SITELIBDIR%%/pymol/wizard/box.py
%%PYTHON_SITELIBDIR%%/pymol/wizard/box.pyc
+%%PYTHON_SITELIBDIR%%/pymol/wizard/box.%%PYTHON_PYOEXTENSION%%
%%PYTHON_SITELIBDIR%%/pymol/wizard/charge.py
%%PYTHON_SITELIBDIR%%/pymol/wizard/charge.pyc
+%%PYTHON_SITELIBDIR%%/pymol/wizard/charge.%%PYTHON_PYOEXTENSION%%
%%PYTHON_SITELIBDIR%%/pymol/wizard/cleanup.py
%%PYTHON_SITELIBDIR%%/pymol/wizard/cleanup.pyc
+%%PYTHON_SITELIBDIR%%/pymol/wizard/cleanup.%%PYTHON_PYOEXTENSION%%
+%%PYTHON_SITELIBDIR%%/pymol/wizard/command.py
+%%PYTHON_SITELIBDIR%%/pymol/wizard/command.pyc
+%%PYTHON_SITELIBDIR%%/pymol/wizard/command.%%PYTHON_PYOEXTENSION%%
%%PYTHON_SITELIBDIR%%/pymol/wizard/demo.py
%%PYTHON_SITELIBDIR%%/pymol/wizard/demo.pyc
+%%PYTHON_SITELIBDIR%%/pymol/wizard/demo.%%PYTHON_PYOEXTENSION%%
%%PYTHON_SITELIBDIR%%/pymol/wizard/density.py
%%PYTHON_SITELIBDIR%%/pymol/wizard/density.pyc
+%%PYTHON_SITELIBDIR%%/pymol/wizard/density.%%PYTHON_PYOEXTENSION%%
%%PYTHON_SITELIBDIR%%/pymol/wizard/distance.py
%%PYTHON_SITELIBDIR%%/pymol/wizard/distance.pyc
+%%PYTHON_SITELIBDIR%%/pymol/wizard/distance.%%PYTHON_PYOEXTENSION%%
%%PYTHON_SITELIBDIR%%/pymol/wizard/dragging.py
%%PYTHON_SITELIBDIR%%/pymol/wizard/dragging.pyc
+%%PYTHON_SITELIBDIR%%/pymol/wizard/dragging.%%PYTHON_PYOEXTENSION%%
%%PYTHON_SITELIBDIR%%/pymol/wizard/fedora.py
%%PYTHON_SITELIBDIR%%/pymol/wizard/fedora.pyc
+%%PYTHON_SITELIBDIR%%/pymol/wizard/fedora.%%PYTHON_PYOEXTENSION%%
%%PYTHON_SITELIBDIR%%/pymol/wizard/filter.py
%%PYTHON_SITELIBDIR%%/pymol/wizard/filter.pyc
+%%PYTHON_SITELIBDIR%%/pymol/wizard/filter.%%PYTHON_PYOEXTENSION%%
%%PYTHON_SITELIBDIR%%/pymol/wizard/label.py
%%PYTHON_SITELIBDIR%%/pymol/wizard/label.pyc
+%%PYTHON_SITELIBDIR%%/pymol/wizard/label.%%PYTHON_PYOEXTENSION%%
%%PYTHON_SITELIBDIR%%/pymol/wizard/measurement.py
%%PYTHON_SITELIBDIR%%/pymol/wizard/measurement.pyc
+%%PYTHON_SITELIBDIR%%/pymol/wizard/measurement.%%PYTHON_PYOEXTENSION%%
%%PYTHON_SITELIBDIR%%/pymol/wizard/message.py
%%PYTHON_SITELIBDIR%%/pymol/wizard/message.pyc
+%%PYTHON_SITELIBDIR%%/pymol/wizard/message.%%PYTHON_PYOEXTENSION%%
%%PYTHON_SITELIBDIR%%/pymol/wizard/mutagenesis.py
%%PYTHON_SITELIBDIR%%/pymol/wizard/mutagenesis.pyc
+%%PYTHON_SITELIBDIR%%/pymol/wizard/mutagenesis.%%PYTHON_PYOEXTENSION%%
%%PYTHON_SITELIBDIR%%/pymol/wizard/pair_fit.py
%%PYTHON_SITELIBDIR%%/pymol/wizard/pair_fit.pyc
+%%PYTHON_SITELIBDIR%%/pymol/wizard/pair_fit.%%PYTHON_PYOEXTENSION%%
%%PYTHON_SITELIBDIR%%/pymol/wizard/pseudoatom.py
%%PYTHON_SITELIBDIR%%/pymol/wizard/pseudoatom.pyc
+%%PYTHON_SITELIBDIR%%/pymol/wizard/pseudoatom.%%PYTHON_PYOEXTENSION%%
%%PYTHON_SITELIBDIR%%/pymol/wizard/renaming.py
%%PYTHON_SITELIBDIR%%/pymol/wizard/renaming.pyc
+%%PYTHON_SITELIBDIR%%/pymol/wizard/renaming.%%PYTHON_PYOEXTENSION%%
%%PYTHON_SITELIBDIR%%/pymol/wizard/sculpting.py
%%PYTHON_SITELIBDIR%%/pymol/wizard/sculpting.pyc
+%%PYTHON_SITELIBDIR%%/pymol/wizard/sculpting.%%PYTHON_PYOEXTENSION%%
%%PYTHON_SITELIBDIR%%/pymol/wizard/security.py
%%PYTHON_SITELIBDIR%%/pymol/wizard/security.pyc
+%%PYTHON_SITELIBDIR%%/pymol/wizard/security.%%PYTHON_PYOEXTENSION%%
%%PYTHON_SITELIBDIR%%/pymol/wizard/stereodemo.py
%%PYTHON_SITELIBDIR%%/pymol/wizard/stereodemo.pyc
+%%PYTHON_SITELIBDIR%%/pymol/wizard/stereodemo.%%PYTHON_PYOEXTENSION%%
%%PYTHON_SITELIBDIR%%/pymol/wizard/toggle.py
%%PYTHON_SITELIBDIR%%/pymol/wizard/toggle.pyc
+%%PYTHON_SITELIBDIR%%/pymol/wizard/toggle.%%PYTHON_PYOEXTENSION%%
%%PYTHON_SITELIBDIR%%/pymol/wizarding.py
%%PYTHON_SITELIBDIR%%/pymol/wizarding.pyc
+%%PYTHON_SITELIBDIR%%/pymol/wizarding.%%PYTHON_PYOEXTENSION%%
%%PYTHON_SITELIBDIR%%/pymol/xray.py
%%PYTHON_SITELIBDIR%%/pymol/xray.pyc
+%%PYTHON_SITELIBDIR%%/pymol/xray.%%PYTHON_PYOEXTENSION%%
%%PYTHON_SITELIBDIR%%/pymol/xwin.py
%%PYTHON_SITELIBDIR%%/pymol/xwin.pyc
+%%PYTHON_SITELIBDIR%%/pymol/xwin.%%PYTHON_PYOEXTENSION%%
+%%PYTHON_SITELIBDIR%%/pymol2/__init__.py
+%%PYTHON_SITELIBDIR%%/pymol2/__init__.pyc
+%%PYTHON_SITELIBDIR%%/pymol2/__init__.%%PYTHON_PYOEXTENSION%%
+%%PYTHON_SITELIBDIR%%/pymol2/cmd2.py
+%%PYTHON_SITELIBDIR%%/pymol2/cmd2.pyc
+%%PYTHON_SITELIBDIR%%/pymol2/cmd2.%%PYTHON_PYOEXTENSION%%
%%PYTHON_SITELIBDIR%%/web/__init__.py
%%PYTHON_SITELIBDIR%%/web/__init__.pyc
+%%PYTHON_SITELIBDIR%%/web/__init__.%%PYTHON_PYOEXTENSION%%
%%PYTHON_SITELIBDIR%%/web/examples/__init__.py
%%PYTHON_SITELIBDIR%%/web/examples/__init__.pyc
+%%PYTHON_SITELIBDIR%%/web/examples/__init__.%%PYTHON_PYOEXTENSION%%
%%PYTHON_SITELIBDIR%%/web/examples/justhttpd.py
%%PYTHON_SITELIBDIR%%/web/examples/justhttpd.pyc
+%%PYTHON_SITELIBDIR%%/web/examples/justhttpd.%%PYTHON_PYOEXTENSION%%
%%PYTHON_SITELIBDIR%%/web/pymolhttpd.py
%%PYTHON_SITELIBDIR%%/web/pymolhttpd.pyc
- at dirrm %%PYTHON_SITELIBDIR%%/web/examples
- at dirrm %%PYTHON_SITELIBDIR%%/web
- at dirrm %%PYTHON_SITELIBDIR%%/pymol/wizard
- at dirrm %%PYTHON_SITELIBDIR%%/pymol/pymol_path/test/ref
- at dirrm %%PYTHON_SITELIBDIR%%/pymol/pymol_path/test/inp
- at dirrm %%PYTHON_SITELIBDIR%%/pymol/pymol_path/test/dat
- at dirrm %%PYTHON_SITELIBDIR%%/pymol/pymol_path/test
- at dirrm %%PYTHON_SITELIBDIR%%/pymol/pymol_path/scripts/metaphorics
- at dirrm %%PYTHON_SITELIBDIR%%/pymol/pymol_path/scripts
- at dirrm %%PYTHON_SITELIBDIR%%/pymol/pymol_path/examples/package/redhat
- at dirrm %%PYTHON_SITELIBDIR%%/pymol/pymol_path/examples/package
- at dirrm %%PYTHON_SITELIBDIR%%/pymol/pymol_path/examples/launching
- at dirrm %%PYTHON_SITELIBDIR%%/pymol/pymol_path/examples/devel
- at dirrm %%PYTHON_SITELIBDIR%%/pymol/pymol_path/examples/cookbook
- at dirrm %%PYTHON_SITELIBDIR%%/pymol/pymol_path/examples/chempy
- at dirrm %%PYTHON_SITELIBDIR%%/pymol/pymol_path/examples
- at dirrm %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/xray
- at dirrm %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/tut
- at dirrm %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders
- at dirrm %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/pymol/matrices
- at dirrm %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/pymol
- at dirrm %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/pmg_tk/bitmaps/builder
- at dirrm %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/pmg_tk/bitmaps
- at dirrm %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/pmg_tk
- at dirrm %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/demo
- at dirrm %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/tinker
- at dirrm %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/sidechains
- at dirrm %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments
- at dirrm %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy
- at dirrm %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data
- at dirrm %%PYTHON_SITELIBDIR%%/pymol/pymol_path
- at dirrm %%PYTHON_SITELIBDIR%%/pymol/opengl/glut
- at dirrm %%PYTHON_SITELIBDIR%%/pymol/opengl/glu
- at dirrm %%PYTHON_SITELIBDIR%%/pymol/opengl/gl
- at dirrm %%PYTHON_SITELIBDIR%%/pymol/opengl
- at dirrm %%PYTHON_SITELIBDIR%%/pymol/contrib
- at dirrm %%PYTHON_SITELIBDIR%%/pymol
- at dirrm %%PYTHON_SITELIBDIR%%/pmg_wx
- at dirrm %%PYTHON_SITELIBDIR%%/pmg_tk/startup
- at dirrm %%PYTHON_SITELIBDIR%%/pmg_tk/skins/normal
- at dirrm %%PYTHON_SITELIBDIR%%/pmg_tk/skins
- at dirrm %%PYTHON_SITELIBDIR%%/pmg_tk
- at dirrm %%PYTHON_SITELIBDIR%%/chempy/tinker
- at dirrm %%PYTHON_SITELIBDIR%%/chempy/fragments
- at dirrm %%PYTHON_SITELIBDIR%%/chempy/fast
- at dirrm %%PYTHON_SITELIBDIR%%/chempy/champ
- at dirrm %%PYTHON_SITELIBDIR%%/chempy/bmin
- at dirrm %%PYTHON_SITELIBDIR%%/chempy
+%%PYTHON_SITELIBDIR%%/web/pymolhttpd.%%PYTHON_PYOEXTENSION%%
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