[arch-commits] Commit in pymol/repos (16 files)
Evgeniy Alekseev
arcanis at archlinux.org
Mon Oct 10 11:09:39 UTC 2016
Date: Monday, October 10, 2016 @ 11:09:38
Author: arcanis
Revision: 191856
archrelease: copy trunk to community-i686, community-x86_64
Added:
pymol/repos/community-i686/ChangeLog
(from rev 191855, pymol/trunk/ChangeLog)
pymol/repos/community-i686/PKGBUILD
(from rev 191855, pymol/trunk/PKGBUILD)
pymol/repos/community-i686/apbstools_tcltk8.6.patch
(from rev 191855, pymol/trunk/apbstools_tcltk8.6.patch)
pymol/repos/community-i686/pymol-38899.patch
(from rev 191855, pymol/trunk/pymol-38899.patch)
pymol/repos/community-x86_64/ChangeLog
(from rev 191855, pymol/trunk/ChangeLog)
pymol/repos/community-x86_64/PKGBUILD
(from rev 191855, pymol/trunk/PKGBUILD)
pymol/repos/community-x86_64/apbstools_tcltk8.6.patch
(from rev 191855, pymol/trunk/apbstools_tcltk8.6.patch)
pymol/repos/community-x86_64/pymol-38899.patch
(from rev 191855, pymol/trunk/pymol-38899.patch)
Deleted:
pymol/repos/community-i686/ChangeLog
pymol/repos/community-i686/PKGBUILD
pymol/repos/community-i686/apbstools_tcltk8.6.patch
pymol/repos/community-i686/pymol-38899.patch
pymol/repos/community-x86_64/ChangeLog
pymol/repos/community-x86_64/PKGBUILD
pymol/repos/community-x86_64/apbstools_tcltk8.6.patch
pymol/repos/community-x86_64/pymol-38899.patch
-------------------------------------------+
/ChangeLog | 82 ++++
/PKGBUILD | 122 ++++++
/apbstools_tcltk8.6.patch | 212 +++++++++++
/pymol-38899.patch | 502 ++++++++++++++++++++++++++++
community-i686/ChangeLog | 38 --
community-i686/PKGBUILD | 61 ---
community-i686/apbstools_tcltk8.6.patch | 106 -----
community-i686/pymol-38899.patch | 251 --------------
community-x86_64/ChangeLog | 38 --
community-x86_64/PKGBUILD | 61 ---
community-x86_64/apbstools_tcltk8.6.patch | 106 -----
community-x86_64/pymol-38899.patch | 251 --------------
12 files changed, 918 insertions(+), 912 deletions(-)
Deleted: community-i686/ChangeLog
===================================================================
--- community-i686/ChangeLog 2016-10-10 11:09:14 UTC (rev 191855)
+++ community-i686/ChangeLog 2016-10-10 11:09:38 UTC (rev 191856)
@@ -1,38 +0,0 @@
-1.8.2.1-2
-glew-2.0 rebuild
-
-1.8.2.1-1:
-upstream update
-
-1.8.2.0-2:
-drop install file, use pacman hooks instead
-
-1.8.2.0-1:
-upstream update
-
-1.8.0.0.r4144-1:
-upstream update
-
-1.8.0.0-1:
-upstream update
-
-1.7.6.0-1:
-upstream update
-
-1.7.4.0-2:
-glew rebuild
-
-1.7.4.0-1:
-upstream update
-
-1.7.2.1-2:
-fix dep list
-
-1.7.2.1-1:
-upstream update
-
-1.7.2.0-2:
-glew rebuild
-
-1.7.2.0-1:
-upstream update
Copied: pymol/repos/community-i686/ChangeLog (from rev 191855, pymol/trunk/ChangeLog)
===================================================================
--- community-i686/ChangeLog (rev 0)
+++ community-i686/ChangeLog 2016-10-10 11:09:38 UTC (rev 191856)
@@ -0,0 +1,41 @@
+1.8.4.0-1:
+upstream update
+
+1.8.2.1-2
+glew-2.0 rebuild
+
+1.8.2.1-1:
+upstream update
+
+1.8.2.0-2:
+drop install file, use pacman hooks instead
+
+1.8.2.0-1:
+upstream update
+
+1.8.0.0.r4144-1:
+upstream update
+
+1.8.0.0-1:
+upstream update
+
+1.7.6.0-1:
+upstream update
+
+1.7.4.0-2:
+glew rebuild
+
+1.7.4.0-1:
+upstream update
+
+1.7.2.1-2:
+fix dep list
+
+1.7.2.1-1:
+upstream update
+
+1.7.2.0-2:
+glew rebuild
+
+1.7.2.0-1:
+upstream update
Deleted: community-i686/PKGBUILD
===================================================================
--- community-i686/PKGBUILD 2016-10-10 11:09:14 UTC (rev 191855)
+++ community-i686/PKGBUILD 2016-10-10 11:09:38 UTC (rev 191856)
@@ -1,61 +0,0 @@
-# $Id$
-# Maintainer: Evgeniy Alekseev <arcanis at archlinux dot org>
-# Contributor: graysky
-# Contributor: Tomasz Żok <tomasz dot zok at gmail dot com>
-
-pkgname=pymol
-pkgver=1.8.2.1
-pkgrel=2
-pkgdesc="Molecular visualization system on an Open Source foundation"
-arch=('i686' 'x86_64')
-url="http://pymol.org/"
-license=('custom')
-depends=('glew' 'glut' 'libgl' 'libxml2' 'python2-numpy' 'python2-pmw' 'tcsh')
-makedepends=('desktop-file-utils' 'gendesk')
-source=("http://downloads.sourceforge.net/project/pymol/pymol/1.8/pymol-v${pkgver}.tar.bz2"
- ${pkgname}.png::"https://c.fsdn.com/allura/p/pymol/icon"
- "${pkgname}-38899.patch"
- "apbstools_tcltk8.6.patch")
-md5sums=('7b6b61f8b314a9ad204f9df6212bf505'
- '0e9df23150d39cbcb8f79c38ce2a52e5'
- '1f8152c4604ba2939b24e25a022937ca'
- '138550367b74fd62a7c7bc48d339eb2d')
-changelog=ChangeLog
-
-prepare() {
- # create desktop file
- gendesk -f -n --pkgname "${pkgname}" --pkgdesc "${pkgdesc}" \
- --name="PyMOL Molecular Graphics System" \
- --categories="Science;Chemistry"
-
- # suppress non-zero exit code that breaks makepkg
- sed -i '/sys.exit/ s,2,0,' "${srcdir}/pymol/setup.py"
- # change python to python2
- find "${pkgname}" -name '*.py' -type f -exec \
- sed -i 's|env python|env python2|g' {} \;
- find "${pkgname}/test" -type f -exec \
- sed -i 's|bin/python|bin/python2|g' {} \;
- # fix FS#38899
- patch -p0 -i "${pkgname}-38899.patch"
- mv "${srcdir}/${pkgname}/modules/web" "${srcdir}/${pkgname}/modules/pymolweb"
- # fix FS#39526
- cd "${srcdir}/${pkgname}"
- patch -p0 -i "${srcdir}/apbstools_tcltk8.6.patch"
-}
-
-build() {
- cd "${srcdir}/${pkgname}"
- # required c++11
- export CPPFLAGS="$CPPFLAGS -std=c++11"
- python2 setup.py build
-}
-
-package() {
- cd "${srcdir}/${pkgname}"
- python2 setup.py install --prefix=/usr --root="${pkgdir}"
- install -Dm644 "LICENSE" "${pkgdir}/usr/share/licenses/${pkgname}/LICENSE"
- install -Dm644 "${srcdir}/pymol.desktop" "${pkgdir}/usr/share/applications/pymol.desktop"
- install -Dm644 "${srcdir}/pymol.png" "${pkgdir}/usr/share/pixmaps/pymol.png"
-}
-
-# vim:set ts=2 sw=2 et:
Copied: pymol/repos/community-i686/PKGBUILD (from rev 191855, pymol/trunk/PKGBUILD)
===================================================================
--- community-i686/PKGBUILD (rev 0)
+++ community-i686/PKGBUILD 2016-10-10 11:09:38 UTC (rev 191856)
@@ -0,0 +1,61 @@
+# $Id$
+# Maintainer: Evgeniy Alekseev <arcanis at archlinux dot org>
+# Contributor: graysky
+# Contributor: Tomasz Żok <tomasz dot zok at gmail dot com>
+
+pkgname=pymol
+pkgver=1.8.4.0
+pkgrel=1
+pkgdesc="Molecular visualization system on an Open Source foundation"
+arch=('i686' 'x86_64')
+url="http://pymol.org/"
+license=('custom')
+depends=('glew' 'glut' 'libgl' 'libxml2' 'python2-numpy' 'python2-pmw' 'tcsh')
+makedepends=('desktop-file-utils' 'gendesk')
+source=("http://downloads.sourceforge.net/project/pymol/pymol/1.8/pymol-v${pkgver}.tar.bz2"
+ ${pkgname}.png::"https://c.fsdn.com/allura/p/pymol/icon"
+ "${pkgname}-38899.patch"
+ "apbstools_tcltk8.6.patch")
+md5sums=('85451c40abc0a359a5ed91abd363b2c2'
+ '0e9df23150d39cbcb8f79c38ce2a52e5'
+ '1f8152c4604ba2939b24e25a022937ca'
+ '138550367b74fd62a7c7bc48d339eb2d')
+changelog=ChangeLog
+
+prepare() {
+ # create desktop file
+ gendesk -f -n --pkgname "${pkgname}" --pkgdesc "${pkgdesc}" \
+ --name="PyMOL Molecular Graphics System" \
+ --categories="Science;Chemistry"
+
+ # suppress non-zero exit code that breaks makepkg
+ sed -i '/sys.exit/ s,2,0,' "${srcdir}/pymol/setup.py"
+ # change python to python2
+ find "${pkgname}" -name '*.py' -type f -exec \
+ sed -i 's|env python|env python2|g' {} \;
+ find "${pkgname}/test" -type f -exec \
+ sed -i 's|bin/python|bin/python2|g' {} \;
+ # fix FS#38899
+ patch -p0 -i "${pkgname}-38899.patch"
+ mv "${srcdir}/${pkgname}/modules/web" "${srcdir}/${pkgname}/modules/pymolweb"
+ # fix FS#39526
+ cd "${srcdir}/${pkgname}"
+ patch -p0 -i "${srcdir}/apbstools_tcltk8.6.patch"
+}
+
+build() {
+ cd "${srcdir}/${pkgname}"
+ # required c++11
+ export CPPFLAGS="$CPPFLAGS -std=c++11"
+ python2 setup.py build
+}
+
+package() {
+ cd "${srcdir}/${pkgname}"
+ python2 setup.py install --prefix=/usr --root="${pkgdir}"
+ install -Dm644 "LICENSE" "${pkgdir}/usr/share/licenses/${pkgname}/LICENSE"
+ install -Dm644 "${srcdir}/pymol.desktop" "${pkgdir}/usr/share/applications/pymol.desktop"
+ install -Dm644 "${srcdir}/pymol.png" "${pkgdir}/usr/share/pixmaps/pymol.png"
+}
+
+# vim:set ts=2 sw=2 et:
Deleted: community-i686/apbstools_tcltk8.6.patch
===================================================================
--- community-i686/apbstools_tcltk8.6.patch 2016-10-10 11:09:14 UTC (rev 191855)
+++ community-i686/apbstools_tcltk8.6.patch 2016-10-10 11:09:38 UTC (rev 191856)
@@ -1,106 +0,0 @@
---- modules/pmg_tk/startup/apbs_tools.py.orig 2014-05-14 01:07:32.000000000 +0400
-+++ modules/pmg_tk/startup/apbs_tools.py 2014-05-14 01:15:35.090032827 +0400
-@@ -612,7 +612,8 @@
- # Set up the Main page
- page = self.notebook.add('Main')
- group = Pmw.Group(page,tag_text='Main options')
-- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
-+ #group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
-+ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
- self.selection = Pmw.EntryField(group.interior(),
- labelpos='w',
- label_text='Selection to use: ',
-@@ -856,7 +864,8 @@
- page.grid_columnconfigure(5,weight=1)
- page = self.notebook.add('Program Locations')
- group = Pmw.Group(page,tag_text='Locations')
-- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
-+ #group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
-+ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
- def quickFileValidation(s):
- if s == '': return Pmw.PARTIAL
- elif os.path.isfile(s): return Pmw.OK
-@@ -955,7 +964,8 @@
-
- page = self.notebook.add('Temp File Locations')
- group = Pmw.Group(page,tag_text='Locations')
-- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
-+ #group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
-+ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
- self.pymol_generated_pqr_filename = Pmw.EntryField(group.interior(),
- labelpos = 'w',
- label_pyclass = FileDialogButtonClassFactory.get(self.setPymolGeneratedPqrFilename),
-@@ -1003,17 +1013,20 @@
- page = self.notebook.add('Visualization (1)')
- group = VisualizationGroup(page,tag_text='Visualization',visgroup_num=1)
- self.visualization_group_1 = group
-- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
-+ #group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
-+ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
-
- page = self.notebook.add('Visualization (2)')
- group = VisualizationGroup(page,tag_text='Visualization',visgroup_num=2)
- self.visualization_group_2 = group
-- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
-+ #group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
-+ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
-
- # Create a couple of other empty pages
- page = self.notebook.add('About')
- group = Pmw.Group(page, tag_text='About PyMOL APBS Tools')
-- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
-+ #group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
-+ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
- text = """This plugin integrates PyMOL (http://PyMOL.org/) with APBS (http://www.poissonboltzmann.org/apbs/).
-
- Documentation may be found at
-@@ -2271,7 +2284,8 @@
- self.update_buttonbox = Pmw.ButtonBox(self.mm_group.interior(), padx=0)
- self.update_buttonbox.pack(side=LEFT)
- self.update_buttonbox.add('Update',command=self.refresh)
-- self.mm_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=TOP)
-+ #self.mm_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=TOP)
-+ self.mm_group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
-
- self.ms_group = Pmw.Group(self.interior(),tag_text='Molecular Surface')
- self.ms_buttonbox = Pmw.ButtonBox(self.ms_group.interior(), padx=0)
-@@ -2322,7 +2336,8 @@
- bars = (self.mol_surf_low,self.mol_surf_middle,self.mol_surf_high)
- Pmw.alignlabels(bars)
- for bar in bars: bar.pack(side=LEFT)
-- self.ms_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT)
-+ #self.ms_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT)
-+ self.ms_group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
-
- self.fl_group = Pmw.Group(self.interior(),tag_text='Field Lines')
- self.fl_buttonbox = Pmw.ButtonBox(self.fl_group.interior(), padx=0)
-@@ -2337,7 +2352,8 @@
- text = """Follows same coloring as surface.""",
- )
- label.pack()
-- self.fl_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=TOP)
-+ #self.fl_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=TOP)
-+ self.fl_group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
-
- self.pi_group = Pmw.Group(self.interior(),tag_text='Positive Isosurface')
- self.pi_buttonbox = Pmw.ButtonBox(self.pi_group.interior(), padx=0)
-@@ -2356,7 +2372,8 @@
- entryfield_validate = {'validator' : 'real', 'min':0}
- )
- self.pos_surf_val.pack(side=LEFT)
-- self.pi_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT)
-+ #self.pi_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT)
-+ self.pi_group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
-
- self.ni_group = Pmw.Group(self.interior(),tag_text='Negative Isosurface')
- self.ni_buttonbox = Pmw.ButtonBox(self.ni_group.interior(), padx=0)
-@@ -2375,7 +2392,8 @@
- entryfield_validate = {'validator' : 'real', 'max':0}
- )
- self.neg_surf_val.pack(side=LEFT)
-- self.ni_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT)
-+ #self.ni_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT)
-+ self.ni_group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
-
-
-
Copied: pymol/repos/community-i686/apbstools_tcltk8.6.patch (from rev 191855, pymol/trunk/apbstools_tcltk8.6.patch)
===================================================================
--- community-i686/apbstools_tcltk8.6.patch (rev 0)
+++ community-i686/apbstools_tcltk8.6.patch 2016-10-10 11:09:38 UTC (rev 191856)
@@ -0,0 +1,106 @@
+--- modules/pmg_tk/startup/apbs_tools.py.orig 2014-05-14 01:07:32.000000000 +0400
++++ modules/pmg_tk/startup/apbs_tools.py 2014-05-14 01:15:35.090032827 +0400
+@@ -612,7 +612,8 @@
+ # Set up the Main page
+ page = self.notebook.add('Main')
+ group = Pmw.Group(page,tag_text='Main options')
+- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
++ #group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
++ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
+ self.selection = Pmw.EntryField(group.interior(),
+ labelpos='w',
+ label_text='Selection to use: ',
+@@ -856,7 +864,8 @@
+ page.grid_columnconfigure(5,weight=1)
+ page = self.notebook.add('Program Locations')
+ group = Pmw.Group(page,tag_text='Locations')
+- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
++ #group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
++ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
+ def quickFileValidation(s):
+ if s == '': return Pmw.PARTIAL
+ elif os.path.isfile(s): return Pmw.OK
+@@ -955,7 +964,8 @@
+
+ page = self.notebook.add('Temp File Locations')
+ group = Pmw.Group(page,tag_text='Locations')
+- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
++ #group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
++ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
+ self.pymol_generated_pqr_filename = Pmw.EntryField(group.interior(),
+ labelpos = 'w',
+ label_pyclass = FileDialogButtonClassFactory.get(self.setPymolGeneratedPqrFilename),
+@@ -1003,17 +1013,20 @@
+ page = self.notebook.add('Visualization (1)')
+ group = VisualizationGroup(page,tag_text='Visualization',visgroup_num=1)
+ self.visualization_group_1 = group
+- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
++ #group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
++ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
+
+ page = self.notebook.add('Visualization (2)')
+ group = VisualizationGroup(page,tag_text='Visualization',visgroup_num=2)
+ self.visualization_group_2 = group
+- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
++ #group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
++ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
+
+ # Create a couple of other empty pages
+ page = self.notebook.add('About')
+ group = Pmw.Group(page, tag_text='About PyMOL APBS Tools')
+- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
++ #group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
++ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
+ text = """This plugin integrates PyMOL (http://PyMOL.org/) with APBS (http://www.poissonboltzmann.org/apbs/).
+
+ Documentation may be found at
+@@ -2271,7 +2284,8 @@
+ self.update_buttonbox = Pmw.ButtonBox(self.mm_group.interior(), padx=0)
+ self.update_buttonbox.pack(side=LEFT)
+ self.update_buttonbox.add('Update',command=self.refresh)
+- self.mm_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=TOP)
++ #self.mm_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=TOP)
++ self.mm_group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
+
+ self.ms_group = Pmw.Group(self.interior(),tag_text='Molecular Surface')
+ self.ms_buttonbox = Pmw.ButtonBox(self.ms_group.interior(), padx=0)
+@@ -2322,7 +2336,8 @@
+ bars = (self.mol_surf_low,self.mol_surf_middle,self.mol_surf_high)
+ Pmw.alignlabels(bars)
+ for bar in bars: bar.pack(side=LEFT)
+- self.ms_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT)
++ #self.ms_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT)
++ self.ms_group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
+
+ self.fl_group = Pmw.Group(self.interior(),tag_text='Field Lines')
+ self.fl_buttonbox = Pmw.ButtonBox(self.fl_group.interior(), padx=0)
+@@ -2337,7 +2352,8 @@
+ text = """Follows same coloring as surface.""",
+ )
+ label.pack()
+- self.fl_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=TOP)
++ #self.fl_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=TOP)
++ self.fl_group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
+
+ self.pi_group = Pmw.Group(self.interior(),tag_text='Positive Isosurface')
+ self.pi_buttonbox = Pmw.ButtonBox(self.pi_group.interior(), padx=0)
+@@ -2356,7 +2372,8 @@
+ entryfield_validate = {'validator' : 'real', 'min':0}
+ )
+ self.pos_surf_val.pack(side=LEFT)
+- self.pi_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT)
++ #self.pi_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT)
++ self.pi_group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
+
+ self.ni_group = Pmw.Group(self.interior(),tag_text='Negative Isosurface')
+ self.ni_buttonbox = Pmw.ButtonBox(self.ni_group.interior(), padx=0)
+@@ -2375,7 +2392,8 @@
+ entryfield_validate = {'validator' : 'real', 'max':0}
+ )
+ self.neg_surf_val.pack(side=LEFT)
+- self.ni_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT)
++ #self.ni_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT)
++ self.ni_group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
+
+
+
Deleted: community-i686/pymol-38899.patch
===================================================================
--- community-i686/pymol-38899.patch 2016-10-10 11:09:14 UTC (rev 191855)
+++ community-i686/pymol-38899.patch 2016-10-10 11:09:38 UTC (rev 191856)
@@ -1,251 +0,0 @@
-diff -ruN pymol.orig/modules/pymol/importing.py pymol/modules/pymol/importing.py
---- pymol.orig/modules/pymol/importing.py 2014-01-15 00:02:55.000000000 +0400
-+++ pymol/modules/pymol/importing.py 2014-02-14 10:19:11.275591741 +0400
-@@ -473,7 +473,7 @@
- def _processPWG(fname,_self=cmd):
- r = DEFAULT_ERROR
- try:
-- from web.pymolhttpd import PymolHttpd
-+ from pymolweb.pymolhttpd import PymolHttpd
- browser_flag = 0
- launch_flag = 0
- report_url = None
-diff -ruN pymol.orig/modules/web/examples/content/SOP.html pymol/modules/web/examples/content/SOP.html
---- pymol.orig/modules/web/examples/content/SOP.html 2014-01-15 00:02:58.000000000 +0400
-+++ pymol/modules/web/examples/content/SOP.html 2014-02-14 10:19:11.275591741 +0400
-@@ -49,7 +49,7 @@
- The first seven
- <a href="../index.html#sample01" target="_blank"> sample applications</a>
- are implemented like this, residing in folders at
--<code>$PYMOL_PATH/modules/web/examples/sample[0-7]</code> There
-+<code>$PYMOL_PATH/modules/pymolweb/examples/sample[0-7]</code> There
- may be future PyMOL web applications delivered with new versions of
- PyMOL. Of course, you are free to write your own PyMOL web
- applications and store them on each user's machine, or perhaps on a
-diff -ruN pymol.orig/modules/web/examples/content/pwg.html pymol/modules/web/examples/content/pwg.html
---- pymol.orig/modules/web/examples/content/pwg.html 2014-01-15 00:02:58.000000000 +0400
-+++ pymol/modules/web/examples/content/pwg.html 2014-02-14 10:19:11.275591741 +0400
-@@ -58,13 +58,13 @@
-
- <p>In contrast, the PWG file which launches the Sample 01 application is:</p>
- <pre>
--root $PYMOL_PATH/modules/web/examples/sample01/htdocs
-+root $PYMOL_PATH/modules/pymolweb/examples/sample01/htdocs
- browser
- </pre>
-
- <p>which tells PyMOL to (1) launch its internal web server on a
- dynamically assigned port with a root content directory of
--$PYMOL_PATH/modules/web/examples/sample01/htdocs and (2) open
-+$PYMOL_PATH/modules/pymolweb/examples/sample01/htdocs and (2) open
- up a local browser window pointing at that server instance. The
- assumption in this scenario is that this newly-opened web page will be
- responsible for sending requests to the PyMOL server (and thus, will
-diff -ruN pymol.orig/modules/web/examples/content/running.html pymol/modules/web/examples/content/running.html
---- pymol.orig/modules/web/examples/content/running.html 2014-01-15 00:02:58.000000000 +0400
-+++ pymol/modules/web/examples/content/running.html 2014-02-14 10:19:11.278925074 +0400
-@@ -36,7 +36,7 @@
-
- <p>The main index file with sample application links is located at</p>
-
--<pre>./modules/web/examples/index.html</pre>
-+<pre>./modules/pymolweb/examples/index.html</pre>
-
- <p>If you are reading this file from within a browser, then you may
- <a href="../index.html">return to it now</a> in order to try the sample
-@@ -55,7 +55,7 @@
-
- <pre># from within the PyMOL folder
-
--cd ./modules/web/examples
-+cd ./modules/pymolweb/examples
-
- # then
-
-diff -ruN pymol.orig/modules/web/examples/content/server.html pymol/modules/web/examples/content/server.html
---- pymol.orig/modules/web/examples/content/server.html 2014-01-15 00:02:58.000000000 +0400
-+++ pymol/modules/web/examples/content/server.html 2014-02-14 10:19:11.278925074 +0400
-@@ -18,7 +18,7 @@
- browser window).</p>
-
- <p>The source code is located at
--<code>$PYMOL_PATH/modules/web/pymolhttpd.py</code>,
-+<code>$PYMOL_PATH/modules/pymolweb/pymolhttpd.py</code>,
- and this file serves as a python module that can be imported by any
- python script running inside of PyMOL. </p>
-
-@@ -33,7 +33,7 @@
- <p>Alternatively, pymolhttpd.py can be used as the start-up script
- when you launch PyMOL.</p>
-
--<pre>pymol $PYMOL_PATH/modules/web/pymolhttpd.py</pre>
-+<pre>pymol $PYMOL_PATH/modules/pymolweb/pymolhttpd.py</pre>
-
- <p>This will cause PyMOL to start serving requests on the default port
- (8080, assuming of course that the port is not already claimed by
-@@ -44,7 +44,7 @@
- <p>
- The PyMOL web server module can be imported into and launched using code like this.
- <pre>
--from web import pymolhttpd
-+from pymolweb import pymolhttpd
- httpd = pymolhttpd.PymolHttpd("htdocs", 8080)
- httpd.start()
- </pre>
-diff -ruN pymol.orig/modules/web/examples/index.html pymol/modules/web/examples/index.html
---- pymol.orig/modules/web/examples/index.html 2014-01-15 00:02:58.000000000 +0400
-+++ pymol/modules/web/examples/index.html 2014-02-14 10:19:11.288925075 +0400
-@@ -156,7 +156,7 @@
- services interface!</p>
-
- <p>The code for the applications above is located inside a series of folders located at:
--<pre>$PYMOL_PATH/modules/web/examples/sample*</pre></p>
-+<pre>$PYMOL_PATH/modules/pymolweb/examples/sample*</pre></p>
-
- </body>
- </html>
-diff -ruN pymol.orig/modules/web/examples/sample01/htdocs/api.html pymol/modules/web/examples/sample01/htdocs/api.html
---- pymol.orig/modules/web/examples/sample01/htdocs/api.html 2014-01-15 00:02:56.000000000 +0400
-+++ pymol/modules/web/examples/sample01/htdocs/api.html 2014-02-14 10:19:11.288925075 +0400
-@@ -9,9 +9,9 @@
- </ul><hr><p>Please click the link(s) below before testing methods in this section (in order).</p><pre><a target="result" href="/apply/pymol.cmd.reinitialize">/apply/pymol.cmd.reinitialize</a></pre>
-
- <ul><li><p><font face="Courier" size="2"><b>load</b></font>
--<i>filename, object, state, format, finish, discrete, quiet, multiplex, zoom, partial</i><pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb</a></pre>
-+<i>filename, object, state, format, finish, discrete, quiet, multiplex, zoom, partial</i><pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb</a></pre>
-
--<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/map.ccp4">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/map.ccp4</a></pre>
-+<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/map.ccp4">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/map.ccp4</a></pre>
-
- </p></li>
- <li><p><font face="Courier" size="2"><b>enable</b></font>
-@@ -38,7 +38,7 @@
- </p></li>
- </ul><hr><p>Please click the link(s) below before testing methods in this section (in order).</p><pre><a target="result" href="/apply/pymol.cmd.reinitialize">/apply/pymol.cmd.reinitialize</a></pre>
-
--<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb</a></pre>
-+<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb</a></pre>
-
- <ul><li><p><font face="Courier" size="2"><b>color</b></font>
- <i>color, selection, quiet, flags</i><pre><a target="result" href="/apply/pymol.cmd.color?color=yellow&selection=elem c">/apply/pymol.cmd.color?color=yellow&selection=elem c</a></pre>
-@@ -118,9 +118,9 @@
- </p></li>
- </ul><hr><p>Please click the link(s) below before testing methods in this section (in order).</p><pre><a target="result" href="/apply/pymol.cmd.reinitialize">/apply/pymol.cmd.reinitialize</a></pre>
-
--<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb</a></pre>
-+<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb</a></pre>
-
--<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/map.ccp4">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/map.ccp4</a></pre>
-+<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/map.ccp4">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/map.ccp4</a></pre>
-
- <ul><li><p><font face="Courier" size="2"><b>isomesh</b></font>
- <i>name, map, level, selection, buffer, state, carve, source_state, quiet</i><pre><a target="result" href="/apply/pymol.cmd.isomesh?name=mesh&map=map&level=1.0">/apply/pymol.cmd.isomesh?name=mesh&map=map&level=1.0</a></pre>
-@@ -142,7 +142,7 @@
- </p></li>
- </ul><hr><p>Please click the link(s) below before testing methods in this section (in order).</p><pre><a target="result" href="/apply/pymol.cmd.reinitialize">/apply/pymol.cmd.reinitialize</a></pre>
-
--<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb</a></pre>
-+<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb</a></pre>
-
- <ul><li><p><font face="Courier" size="2"><b>show</b></font>
- <i>representation, selection</i><pre><a target="result" href="/apply/pymol.cmd.show?representation=sticks">/apply/pymol.cmd.show?representation=sticks</a></pre>
-@@ -174,7 +174,7 @@
- </p></li>
- </ul><hr><p>Please click the link(s) below before testing methods in this section (in order).</p><pre><a target="result" href="/apply/pymol.cmd.reinitialize">/apply/pymol.cmd.reinitialize</a></pre>
-
--<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb</a></pre>
-+<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb</a></pre>
-
- <ul><li><p><font face="Courier" size="2"><b>show_as</b></font>
- <i>representation, selection</i><pre><a target="result" href="/apply/pymol.cmd.show_as?representation=spheres">/apply/pymol.cmd.show_as?representation=spheres</a></pre>
-@@ -224,7 +224,7 @@
- </p></li>
- </ul><hr><p>Please click the link(s) below before testing methods in this section (in order).</p><pre><a target="result" href="/apply/pymol.cmd.reinitialize">/apply/pymol.cmd.reinitialize</a></pre>
-
--<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb</a></pre>
-+<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb</a></pre>
-
- <ul><li><p><font face="Courier" size="2"><b>super</b></font>
- <i>mobile, target, cutoff, cycles, gap, extend, max_gap, object, matrix, mobile_state, target_state, quiet, max_skip, transform, reset, seq, radius, scale, base, coord, expect, window, ante</i><pre><a target="result" href="/apply/pymol.cmd.create?name=helix1&selection=polymer and 5-17/">/apply/pymol.cmd.create?name=helix1&selection=polymer and 5-17/</a></pre>
-diff -ruN pymol.orig/modules/web/examples/sample01/start.pwg pymol/modules/web/examples/sample01/start.pwg
---- pymol.orig/modules/web/examples/sample01/start.pwg 2014-01-15 00:02:56.000000000 +0400
-+++ pymol/modules/web/examples/sample01/start.pwg 2014-02-14 10:19:11.288925075 +0400
-@@ -1,2 +1,2 @@
--root $PYMOL_PATH/modules/web/examples/sample01/htdocs
-+root $PYMOL_PATH/modules/pymolweb/examples/sample01/htdocs
- browser
-diff -ruN pymol.orig/modules/web/examples/sample02/start.pwg pymol/modules/web/examples/sample02/start.pwg
---- pymol.orig/modules/web/examples/sample02/start.pwg 2014-01-15 00:02:56.000000000 +0400
-+++ pymol/modules/web/examples/sample02/start.pwg 2014-02-14 10:19:11.292258408 +0400
-@@ -1,2 +1,2 @@
--root $PYMOL_PATH/modules/web/examples/sample02/htdocs
-+root $PYMOL_PATH/modules/pymolweb/examples/sample02/htdocs
- browser
-diff -ruN pymol.orig/modules/web/examples/sample03/start.pwg pymol/modules/web/examples/sample03/start.pwg
---- pymol.orig/modules/web/examples/sample03/start.pwg 2014-01-15 00:02:56.000000000 +0400
-+++ pymol/modules/web/examples/sample03/start.pwg 2014-02-14 10:19:11.292258408 +0400
-@@ -1,2 +1,2 @@
--root $PYMOL_PATH/modules/web/examples/sample03/htdocs
-+root $PYMOL_PATH/modules/pymolweb/examples/sample03/htdocs
- browser
-diff -ruN pymol.orig/modules/web/examples/sample04/htdocs/pdbshow.js pymol/modules/web/examples/sample04/htdocs/pdbshow.js
---- pymol.orig/modules/web/examples/sample04/htdocs/pdbshow.js 2014-01-15 00:02:56.000000000 +0400
-+++ pymol/modules/web/examples/sample04/htdocs/pdbshow.js 2014-02-14 10:19:11.292258408 +0400
-@@ -12,7 +12,7 @@
- function get_protein(a) {
- // load protein, unless already loaded
- if (load_state[a] == undefined) {
-- load = "load?filename=$PYMOL_PATH/modules/web/examples/data/" + a + ".pdb.gz" + zoom;
-+ load = "load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/" + a + ".pdb.gz" + zoom;
- cmd(load);
- zoom = "&zoom=0"; // subsequent loads shold not zoom
- cmd("orient?selection=bymol organic and elem n&animate=2");
-diff -ruN pymol.orig/modules/web/examples/sample04/start.pwg pymol/modules/web/examples/sample04/start.pwg
---- pymol.orig/modules/web/examples/sample04/start.pwg 2014-01-15 00:02:56.000000000 +0400
-+++ pymol/modules/web/examples/sample04/start.pwg 2014-02-14 10:19:11.292258408 +0400
-@@ -1,2 +1,2 @@
--root $PYMOL_PATH/modules/web/examples/sample04/htdocs
-+root $PYMOL_PATH/modules/pymolweb/examples/sample04/htdocs
- browser
-diff -ruN pymol.orig/modules/web/examples/sample05/htdocs/index.html pymol/modules/web/examples/sample05/htdocs/index.html
---- pymol.orig/modules/web/examples/sample05/htdocs/index.html 2014-01-15 00:02:57.000000000 +0400
-+++ pymol/modules/web/examples/sample05/htdocs/index.html 2014-02-14 10:19:11.292258408 +0400
-@@ -108,7 +108,7 @@
-
- function loadPDB(code)
- {
-- return cmd('load?filename=$PYMOL_PATH/modules/web/examples/data/'+code+'.pdb');
-+ return cmd('load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/'+code+'.pdb');
- }
-
- </script>
-diff -ruN pymol.orig/modules/web/examples/sample05/start.pwg pymol/modules/web/examples/sample05/start.pwg
---- pymol.orig/modules/web/examples/sample05/start.pwg 2014-01-15 00:02:57.000000000 +0400
-+++ pymol/modules/web/examples/sample05/start.pwg 2014-02-14 10:19:11.292258408 +0400
-@@ -1,2 +1,2 @@
--root $PYMOL_PATH/modules/web/examples/sample05/htdocs
-+root $PYMOL_PATH/modules/pymolweb/examples/sample05/htdocs
- browser
-diff -ruN pymol.orig/modules/web/examples/sample06/start.pwg pymol/modules/web/examples/sample06/start.pwg
---- pymol.orig/modules/web/examples/sample06/start.pwg 2014-01-15 00:02:57.000000000 +0400
-+++ pymol/modules/web/examples/sample06/start.pwg 2014-02-14 10:19:11.292258408 +0400
-@@ -1,3 +1,3 @@
--root $PYMOL_PATH/modules/web/examples/sample06/htdocs
-+root $PYMOL_PATH/modules/pymolweb/examples/sample06/htdocs
- browser
- logging 0
-diff -ruN pymol.orig/modules/web/examples/sample07/start.pwg pymol/modules/web/examples/sample07/start.pwg
---- pymol.orig/modules/web/examples/sample07/start.pwg 2014-01-15 00:02:57.000000000 +0400
-+++ pymol/modules/web/examples/sample07/start.pwg 2014-02-14 10:19:11.295591741 +0400
-@@ -1,2 +1,2 @@
--root $PYMOL_PATH/modules/web/examples/sample07/htdocs
-+root $PYMOL_PATH/modules/pymolweb/examples/sample07/htdocs
- browser
-diff -ruN pymol.orig/modules/web/examples/sample08/start.pwg pymol/modules/web/examples/sample08/start.pwg
---- pymol.orig/modules/web/examples/sample08/start.pwg 2014-01-15 00:02:57.000000000 +0400
-+++ pymol/modules/web/examples/sample08/start.pwg 2014-02-14 10:19:11.295591741 +0400
-@@ -1,3 +1,3 @@
--root $PYMOL_PATH/modules/web/examples/sample08/htdocs
-+root $PYMOL_PATH/modules/pymolweb/examples/sample08/htdocs
- browser
- logging 0
\ No newline at end of file
Copied: pymol/repos/community-i686/pymol-38899.patch (from rev 191855, pymol/trunk/pymol-38899.patch)
===================================================================
--- community-i686/pymol-38899.patch (rev 0)
+++ community-i686/pymol-38899.patch 2016-10-10 11:09:38 UTC (rev 191856)
@@ -0,0 +1,251 @@
+diff -ruN pymol.orig/modules/pymol/importing.py pymol/modules/pymol/importing.py
+--- pymol.orig/modules/pymol/importing.py 2014-01-15 00:02:55.000000000 +0400
++++ pymol/modules/pymol/importing.py 2014-02-14 10:19:11.275591741 +0400
+@@ -473,7 +473,7 @@
+ def _processPWG(fname,_self=cmd):
+ r = DEFAULT_ERROR
+ try:
+- from web.pymolhttpd import PymolHttpd
++ from pymolweb.pymolhttpd import PymolHttpd
+ browser_flag = 0
+ launch_flag = 0
+ report_url = None
+diff -ruN pymol.orig/modules/web/examples/content/SOP.html pymol/modules/web/examples/content/SOP.html
+--- pymol.orig/modules/web/examples/content/SOP.html 2014-01-15 00:02:58.000000000 +0400
++++ pymol/modules/web/examples/content/SOP.html 2014-02-14 10:19:11.275591741 +0400
+@@ -49,7 +49,7 @@
+ The first seven
+ <a href="../index.html#sample01" target="_blank"> sample applications</a>
+ are implemented like this, residing in folders at
+-<code>$PYMOL_PATH/modules/web/examples/sample[0-7]</code> There
++<code>$PYMOL_PATH/modules/pymolweb/examples/sample[0-7]</code> There
+ may be future PyMOL web applications delivered with new versions of
+ PyMOL. Of course, you are free to write your own PyMOL web
+ applications and store them on each user's machine, or perhaps on a
+diff -ruN pymol.orig/modules/web/examples/content/pwg.html pymol/modules/web/examples/content/pwg.html
+--- pymol.orig/modules/web/examples/content/pwg.html 2014-01-15 00:02:58.000000000 +0400
++++ pymol/modules/web/examples/content/pwg.html 2014-02-14 10:19:11.275591741 +0400
+@@ -58,13 +58,13 @@
+
+ <p>In contrast, the PWG file which launches the Sample 01 application is:</p>
+ <pre>
+-root $PYMOL_PATH/modules/web/examples/sample01/htdocs
++root $PYMOL_PATH/modules/pymolweb/examples/sample01/htdocs
+ browser
+ </pre>
+
+ <p>which tells PyMOL to (1) launch its internal web server on a
+ dynamically assigned port with a root content directory of
+-$PYMOL_PATH/modules/web/examples/sample01/htdocs and (2) open
++$PYMOL_PATH/modules/pymolweb/examples/sample01/htdocs and (2) open
+ up a local browser window pointing at that server instance. The
+ assumption in this scenario is that this newly-opened web page will be
+ responsible for sending requests to the PyMOL server (and thus, will
+diff -ruN pymol.orig/modules/web/examples/content/running.html pymol/modules/web/examples/content/running.html
+--- pymol.orig/modules/web/examples/content/running.html 2014-01-15 00:02:58.000000000 +0400
++++ pymol/modules/web/examples/content/running.html 2014-02-14 10:19:11.278925074 +0400
+@@ -36,7 +36,7 @@
+
+ <p>The main index file with sample application links is located at</p>
+
+-<pre>./modules/web/examples/index.html</pre>
++<pre>./modules/pymolweb/examples/index.html</pre>
+
+ <p>If you are reading this file from within a browser, then you may
+ <a href="../index.html">return to it now</a> in order to try the sample
+@@ -55,7 +55,7 @@
+
+ <pre># from within the PyMOL folder
+
+-cd ./modules/web/examples
++cd ./modules/pymolweb/examples
+
+ # then
+
+diff -ruN pymol.orig/modules/web/examples/content/server.html pymol/modules/web/examples/content/server.html
+--- pymol.orig/modules/web/examples/content/server.html 2014-01-15 00:02:58.000000000 +0400
++++ pymol/modules/web/examples/content/server.html 2014-02-14 10:19:11.278925074 +0400
+@@ -18,7 +18,7 @@
+ browser window).</p>
+
+ <p>The source code is located at
+-<code>$PYMOL_PATH/modules/web/pymolhttpd.py</code>,
++<code>$PYMOL_PATH/modules/pymolweb/pymolhttpd.py</code>,
+ and this file serves as a python module that can be imported by any
+ python script running inside of PyMOL. </p>
+
+@@ -33,7 +33,7 @@
+ <p>Alternatively, pymolhttpd.py can be used as the start-up script
+ when you launch PyMOL.</p>
+
+-<pre>pymol $PYMOL_PATH/modules/web/pymolhttpd.py</pre>
++<pre>pymol $PYMOL_PATH/modules/pymolweb/pymolhttpd.py</pre>
+
+ <p>This will cause PyMOL to start serving requests on the default port
+ (8080, assuming of course that the port is not already claimed by
+@@ -44,7 +44,7 @@
+ <p>
+ The PyMOL web server module can be imported into and launched using code like this.
+ <pre>
+-from web import pymolhttpd
++from pymolweb import pymolhttpd
+ httpd = pymolhttpd.PymolHttpd("htdocs", 8080)
+ httpd.start()
+ </pre>
+diff -ruN pymol.orig/modules/web/examples/index.html pymol/modules/web/examples/index.html
+--- pymol.orig/modules/web/examples/index.html 2014-01-15 00:02:58.000000000 +0400
++++ pymol/modules/web/examples/index.html 2014-02-14 10:19:11.288925075 +0400
+@@ -156,7 +156,7 @@
+ services interface!</p>
+
+ <p>The code for the applications above is located inside a series of folders located at:
+-<pre>$PYMOL_PATH/modules/web/examples/sample*</pre></p>
++<pre>$PYMOL_PATH/modules/pymolweb/examples/sample*</pre></p>
+
+ </body>
+ </html>
+diff -ruN pymol.orig/modules/web/examples/sample01/htdocs/api.html pymol/modules/web/examples/sample01/htdocs/api.html
+--- pymol.orig/modules/web/examples/sample01/htdocs/api.html 2014-01-15 00:02:56.000000000 +0400
++++ pymol/modules/web/examples/sample01/htdocs/api.html 2014-02-14 10:19:11.288925075 +0400
+@@ -9,9 +9,9 @@
+ </ul><hr><p>Please click the link(s) below before testing methods in this section (in order).</p><pre><a target="result" href="/apply/pymol.cmd.reinitialize">/apply/pymol.cmd.reinitialize</a></pre>
+
+ <ul><li><p><font face="Courier" size="2"><b>load</b></font>
+-<i>filename, object, state, format, finish, discrete, quiet, multiplex, zoom, partial</i><pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb</a></pre>
++<i>filename, object, state, format, finish, discrete, quiet, multiplex, zoom, partial</i><pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb</a></pre>
+
+-<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/map.ccp4">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/map.ccp4</a></pre>
++<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/map.ccp4">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/map.ccp4</a></pre>
+
+ </p></li>
+ <li><p><font face="Courier" size="2"><b>enable</b></font>
+@@ -38,7 +38,7 @@
+ </p></li>
+ </ul><hr><p>Please click the link(s) below before testing methods in this section (in order).</p><pre><a target="result" href="/apply/pymol.cmd.reinitialize">/apply/pymol.cmd.reinitialize</a></pre>
+
+-<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb</a></pre>
++<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb</a></pre>
+
+ <ul><li><p><font face="Courier" size="2"><b>color</b></font>
+ <i>color, selection, quiet, flags</i><pre><a target="result" href="/apply/pymol.cmd.color?color=yellow&selection=elem c">/apply/pymol.cmd.color?color=yellow&selection=elem c</a></pre>
+@@ -118,9 +118,9 @@
+ </p></li>
+ </ul><hr><p>Please click the link(s) below before testing methods in this section (in order).</p><pre><a target="result" href="/apply/pymol.cmd.reinitialize">/apply/pymol.cmd.reinitialize</a></pre>
+
+-<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb</a></pre>
++<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb</a></pre>
+
+-<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/map.ccp4">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/map.ccp4</a></pre>
++<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/map.ccp4">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/map.ccp4</a></pre>
+
+ <ul><li><p><font face="Courier" size="2"><b>isomesh</b></font>
+ <i>name, map, level, selection, buffer, state, carve, source_state, quiet</i><pre><a target="result" href="/apply/pymol.cmd.isomesh?name=mesh&map=map&level=1.0">/apply/pymol.cmd.isomesh?name=mesh&map=map&level=1.0</a></pre>
+@@ -142,7 +142,7 @@
+ </p></li>
+ </ul><hr><p>Please click the link(s) below before testing methods in this section (in order).</p><pre><a target="result" href="/apply/pymol.cmd.reinitialize">/apply/pymol.cmd.reinitialize</a></pre>
+
+-<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb</a></pre>
++<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb</a></pre>
+
+ <ul><li><p><font face="Courier" size="2"><b>show</b></font>
+ <i>representation, selection</i><pre><a target="result" href="/apply/pymol.cmd.show?representation=sticks">/apply/pymol.cmd.show?representation=sticks</a></pre>
+@@ -174,7 +174,7 @@
+ </p></li>
+ </ul><hr><p>Please click the link(s) below before testing methods in this section (in order).</p><pre><a target="result" href="/apply/pymol.cmd.reinitialize">/apply/pymol.cmd.reinitialize</a></pre>
+
+-<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb</a></pre>
++<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb</a></pre>
+
+ <ul><li><p><font face="Courier" size="2"><b>show_as</b></font>
+ <i>representation, selection</i><pre><a target="result" href="/apply/pymol.cmd.show_as?representation=spheres">/apply/pymol.cmd.show_as?representation=spheres</a></pre>
+@@ -224,7 +224,7 @@
+ </p></li>
+ </ul><hr><p>Please click the link(s) below before testing methods in this section (in order).</p><pre><a target="result" href="/apply/pymol.cmd.reinitialize">/apply/pymol.cmd.reinitialize</a></pre>
+
+-<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb</a></pre>
++<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb</a></pre>
+
+ <ul><li><p><font face="Courier" size="2"><b>super</b></font>
+ <i>mobile, target, cutoff, cycles, gap, extend, max_gap, object, matrix, mobile_state, target_state, quiet, max_skip, transform, reset, seq, radius, scale, base, coord, expect, window, ante</i><pre><a target="result" href="/apply/pymol.cmd.create?name=helix1&selection=polymer and 5-17/">/apply/pymol.cmd.create?name=helix1&selection=polymer and 5-17/</a></pre>
+diff -ruN pymol.orig/modules/web/examples/sample01/start.pwg pymol/modules/web/examples/sample01/start.pwg
+--- pymol.orig/modules/web/examples/sample01/start.pwg 2014-01-15 00:02:56.000000000 +0400
++++ pymol/modules/web/examples/sample01/start.pwg 2014-02-14 10:19:11.288925075 +0400
+@@ -1,2 +1,2 @@
+-root $PYMOL_PATH/modules/web/examples/sample01/htdocs
++root $PYMOL_PATH/modules/pymolweb/examples/sample01/htdocs
+ browser
+diff -ruN pymol.orig/modules/web/examples/sample02/start.pwg pymol/modules/web/examples/sample02/start.pwg
+--- pymol.orig/modules/web/examples/sample02/start.pwg 2014-01-15 00:02:56.000000000 +0400
++++ pymol/modules/web/examples/sample02/start.pwg 2014-02-14 10:19:11.292258408 +0400
+@@ -1,2 +1,2 @@
+-root $PYMOL_PATH/modules/web/examples/sample02/htdocs
++root $PYMOL_PATH/modules/pymolweb/examples/sample02/htdocs
+ browser
+diff -ruN pymol.orig/modules/web/examples/sample03/start.pwg pymol/modules/web/examples/sample03/start.pwg
+--- pymol.orig/modules/web/examples/sample03/start.pwg 2014-01-15 00:02:56.000000000 +0400
++++ pymol/modules/web/examples/sample03/start.pwg 2014-02-14 10:19:11.292258408 +0400
+@@ -1,2 +1,2 @@
+-root $PYMOL_PATH/modules/web/examples/sample03/htdocs
++root $PYMOL_PATH/modules/pymolweb/examples/sample03/htdocs
+ browser
+diff -ruN pymol.orig/modules/web/examples/sample04/htdocs/pdbshow.js pymol/modules/web/examples/sample04/htdocs/pdbshow.js
+--- pymol.orig/modules/web/examples/sample04/htdocs/pdbshow.js 2014-01-15 00:02:56.000000000 +0400
++++ pymol/modules/web/examples/sample04/htdocs/pdbshow.js 2014-02-14 10:19:11.292258408 +0400
+@@ -12,7 +12,7 @@
+ function get_protein(a) {
+ // load protein, unless already loaded
+ if (load_state[a] == undefined) {
+- load = "load?filename=$PYMOL_PATH/modules/web/examples/data/" + a + ".pdb.gz" + zoom;
++ load = "load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/" + a + ".pdb.gz" + zoom;
+ cmd(load);
+ zoom = "&zoom=0"; // subsequent loads shold not zoom
+ cmd("orient?selection=bymol organic and elem n&animate=2");
+diff -ruN pymol.orig/modules/web/examples/sample04/start.pwg pymol/modules/web/examples/sample04/start.pwg
+--- pymol.orig/modules/web/examples/sample04/start.pwg 2014-01-15 00:02:56.000000000 +0400
++++ pymol/modules/web/examples/sample04/start.pwg 2014-02-14 10:19:11.292258408 +0400
+@@ -1,2 +1,2 @@
+-root $PYMOL_PATH/modules/web/examples/sample04/htdocs
++root $PYMOL_PATH/modules/pymolweb/examples/sample04/htdocs
+ browser
+diff -ruN pymol.orig/modules/web/examples/sample05/htdocs/index.html pymol/modules/web/examples/sample05/htdocs/index.html
+--- pymol.orig/modules/web/examples/sample05/htdocs/index.html 2014-01-15 00:02:57.000000000 +0400
++++ pymol/modules/web/examples/sample05/htdocs/index.html 2014-02-14 10:19:11.292258408 +0400
+@@ -108,7 +108,7 @@
+
+ function loadPDB(code)
+ {
+- return cmd('load?filename=$PYMOL_PATH/modules/web/examples/data/'+code+'.pdb');
++ return cmd('load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/'+code+'.pdb');
+ }
+
+ </script>
+diff -ruN pymol.orig/modules/web/examples/sample05/start.pwg pymol/modules/web/examples/sample05/start.pwg
+--- pymol.orig/modules/web/examples/sample05/start.pwg 2014-01-15 00:02:57.000000000 +0400
++++ pymol/modules/web/examples/sample05/start.pwg 2014-02-14 10:19:11.292258408 +0400
+@@ -1,2 +1,2 @@
+-root $PYMOL_PATH/modules/web/examples/sample05/htdocs
++root $PYMOL_PATH/modules/pymolweb/examples/sample05/htdocs
+ browser
+diff -ruN pymol.orig/modules/web/examples/sample06/start.pwg pymol/modules/web/examples/sample06/start.pwg
+--- pymol.orig/modules/web/examples/sample06/start.pwg 2014-01-15 00:02:57.000000000 +0400
++++ pymol/modules/web/examples/sample06/start.pwg 2014-02-14 10:19:11.292258408 +0400
+@@ -1,3 +1,3 @@
+-root $PYMOL_PATH/modules/web/examples/sample06/htdocs
++root $PYMOL_PATH/modules/pymolweb/examples/sample06/htdocs
+ browser
+ logging 0
+diff -ruN pymol.orig/modules/web/examples/sample07/start.pwg pymol/modules/web/examples/sample07/start.pwg
+--- pymol.orig/modules/web/examples/sample07/start.pwg 2014-01-15 00:02:57.000000000 +0400
++++ pymol/modules/web/examples/sample07/start.pwg 2014-02-14 10:19:11.295591741 +0400
+@@ -1,2 +1,2 @@
+-root $PYMOL_PATH/modules/web/examples/sample07/htdocs
++root $PYMOL_PATH/modules/pymolweb/examples/sample07/htdocs
+ browser
+diff -ruN pymol.orig/modules/web/examples/sample08/start.pwg pymol/modules/web/examples/sample08/start.pwg
+--- pymol.orig/modules/web/examples/sample08/start.pwg 2014-01-15 00:02:57.000000000 +0400
++++ pymol/modules/web/examples/sample08/start.pwg 2014-02-14 10:19:11.295591741 +0400
+@@ -1,3 +1,3 @@
+-root $PYMOL_PATH/modules/web/examples/sample08/htdocs
++root $PYMOL_PATH/modules/pymolweb/examples/sample08/htdocs
+ browser
+ logging 0
\ No newline at end of file
Deleted: community-x86_64/ChangeLog
===================================================================
--- community-x86_64/ChangeLog 2016-10-10 11:09:14 UTC (rev 191855)
+++ community-x86_64/ChangeLog 2016-10-10 11:09:38 UTC (rev 191856)
@@ -1,38 +0,0 @@
-1.8.2.1-2
-glew-2.0 rebuild
-
-1.8.2.1-1:
-upstream update
-
-1.8.2.0-2:
-drop install file, use pacman hooks instead
-
-1.8.2.0-1:
-upstream update
-
-1.8.0.0.r4144-1:
-upstream update
-
-1.8.0.0-1:
-upstream update
-
-1.7.6.0-1:
-upstream update
-
-1.7.4.0-2:
-glew rebuild
-
-1.7.4.0-1:
-upstream update
-
-1.7.2.1-2:
-fix dep list
-
-1.7.2.1-1:
-upstream update
-
-1.7.2.0-2:
-glew rebuild
-
-1.7.2.0-1:
-upstream update
Copied: pymol/repos/community-x86_64/ChangeLog (from rev 191855, pymol/trunk/ChangeLog)
===================================================================
--- community-x86_64/ChangeLog (rev 0)
+++ community-x86_64/ChangeLog 2016-10-10 11:09:38 UTC (rev 191856)
@@ -0,0 +1,41 @@
+1.8.4.0-1:
+upstream update
+
+1.8.2.1-2
+glew-2.0 rebuild
+
+1.8.2.1-1:
+upstream update
+
+1.8.2.0-2:
+drop install file, use pacman hooks instead
+
+1.8.2.0-1:
+upstream update
+
+1.8.0.0.r4144-1:
+upstream update
+
+1.8.0.0-1:
+upstream update
+
+1.7.6.0-1:
+upstream update
+
+1.7.4.0-2:
+glew rebuild
+
+1.7.4.0-1:
+upstream update
+
+1.7.2.1-2:
+fix dep list
+
+1.7.2.1-1:
+upstream update
+
+1.7.2.0-2:
+glew rebuild
+
+1.7.2.0-1:
+upstream update
Deleted: community-x86_64/PKGBUILD
===================================================================
--- community-x86_64/PKGBUILD 2016-10-10 11:09:14 UTC (rev 191855)
+++ community-x86_64/PKGBUILD 2016-10-10 11:09:38 UTC (rev 191856)
@@ -1,61 +0,0 @@
-# $Id$
-# Maintainer: Evgeniy Alekseev <arcanis at archlinux dot org>
-# Contributor: graysky
-# Contributor: Tomasz Żok <tomasz dot zok at gmail dot com>
-
-pkgname=pymol
-pkgver=1.8.2.1
-pkgrel=2
-pkgdesc="Molecular visualization system on an Open Source foundation"
-arch=('i686' 'x86_64')
-url="http://pymol.org/"
-license=('custom')
-depends=('glew' 'glut' 'libgl' 'libxml2' 'python2-numpy' 'python2-pmw' 'tcsh')
-makedepends=('desktop-file-utils' 'gendesk')
-source=("http://downloads.sourceforge.net/project/pymol/pymol/1.8/pymol-v${pkgver}.tar.bz2"
- ${pkgname}.png::"https://c.fsdn.com/allura/p/pymol/icon"
- "${pkgname}-38899.patch"
- "apbstools_tcltk8.6.patch")
-md5sums=('7b6b61f8b314a9ad204f9df6212bf505'
- '0e9df23150d39cbcb8f79c38ce2a52e5'
- '1f8152c4604ba2939b24e25a022937ca'
- '138550367b74fd62a7c7bc48d339eb2d')
-changelog=ChangeLog
-
-prepare() {
- # create desktop file
- gendesk -f -n --pkgname "${pkgname}" --pkgdesc "${pkgdesc}" \
- --name="PyMOL Molecular Graphics System" \
- --categories="Science;Chemistry"
-
- # suppress non-zero exit code that breaks makepkg
- sed -i '/sys.exit/ s,2,0,' "${srcdir}/pymol/setup.py"
- # change python to python2
- find "${pkgname}" -name '*.py' -type f -exec \
- sed -i 's|env python|env python2|g' {} \;
- find "${pkgname}/test" -type f -exec \
- sed -i 's|bin/python|bin/python2|g' {} \;
- # fix FS#38899
- patch -p0 -i "${pkgname}-38899.patch"
- mv "${srcdir}/${pkgname}/modules/web" "${srcdir}/${pkgname}/modules/pymolweb"
- # fix FS#39526
- cd "${srcdir}/${pkgname}"
- patch -p0 -i "${srcdir}/apbstools_tcltk8.6.patch"
-}
-
-build() {
- cd "${srcdir}/${pkgname}"
- # required c++11
- export CPPFLAGS="$CPPFLAGS -std=c++11"
- python2 setup.py build
-}
-
-package() {
- cd "${srcdir}/${pkgname}"
- python2 setup.py install --prefix=/usr --root="${pkgdir}"
- install -Dm644 "LICENSE" "${pkgdir}/usr/share/licenses/${pkgname}/LICENSE"
- install -Dm644 "${srcdir}/pymol.desktop" "${pkgdir}/usr/share/applications/pymol.desktop"
- install -Dm644 "${srcdir}/pymol.png" "${pkgdir}/usr/share/pixmaps/pymol.png"
-}
-
-# vim:set ts=2 sw=2 et:
Copied: pymol/repos/community-x86_64/PKGBUILD (from rev 191855, pymol/trunk/PKGBUILD)
===================================================================
--- community-x86_64/PKGBUILD (rev 0)
+++ community-x86_64/PKGBUILD 2016-10-10 11:09:38 UTC (rev 191856)
@@ -0,0 +1,61 @@
+# $Id$
+# Maintainer: Evgeniy Alekseev <arcanis at archlinux dot org>
+# Contributor: graysky
+# Contributor: Tomasz Żok <tomasz dot zok at gmail dot com>
+
+pkgname=pymol
+pkgver=1.8.4.0
+pkgrel=1
+pkgdesc="Molecular visualization system on an Open Source foundation"
+arch=('i686' 'x86_64')
+url="http://pymol.org/"
+license=('custom')
+depends=('glew' 'glut' 'libgl' 'libxml2' 'python2-numpy' 'python2-pmw' 'tcsh')
+makedepends=('desktop-file-utils' 'gendesk')
+source=("http://downloads.sourceforge.net/project/pymol/pymol/1.8/pymol-v${pkgver}.tar.bz2"
+ ${pkgname}.png::"https://c.fsdn.com/allura/p/pymol/icon"
+ "${pkgname}-38899.patch"
+ "apbstools_tcltk8.6.patch")
+md5sums=('85451c40abc0a359a5ed91abd363b2c2'
+ '0e9df23150d39cbcb8f79c38ce2a52e5'
+ '1f8152c4604ba2939b24e25a022937ca'
+ '138550367b74fd62a7c7bc48d339eb2d')
+changelog=ChangeLog
+
+prepare() {
+ # create desktop file
+ gendesk -f -n --pkgname "${pkgname}" --pkgdesc "${pkgdesc}" \
+ --name="PyMOL Molecular Graphics System" \
+ --categories="Science;Chemistry"
+
+ # suppress non-zero exit code that breaks makepkg
+ sed -i '/sys.exit/ s,2,0,' "${srcdir}/pymol/setup.py"
+ # change python to python2
+ find "${pkgname}" -name '*.py' -type f -exec \
+ sed -i 's|env python|env python2|g' {} \;
+ find "${pkgname}/test" -type f -exec \
+ sed -i 's|bin/python|bin/python2|g' {} \;
+ # fix FS#38899
+ patch -p0 -i "${pkgname}-38899.patch"
+ mv "${srcdir}/${pkgname}/modules/web" "${srcdir}/${pkgname}/modules/pymolweb"
+ # fix FS#39526
+ cd "${srcdir}/${pkgname}"
+ patch -p0 -i "${srcdir}/apbstools_tcltk8.6.patch"
+}
+
+build() {
+ cd "${srcdir}/${pkgname}"
+ # required c++11
+ export CPPFLAGS="$CPPFLAGS -std=c++11"
+ python2 setup.py build
+}
+
+package() {
+ cd "${srcdir}/${pkgname}"
+ python2 setup.py install --prefix=/usr --root="${pkgdir}"
+ install -Dm644 "LICENSE" "${pkgdir}/usr/share/licenses/${pkgname}/LICENSE"
+ install -Dm644 "${srcdir}/pymol.desktop" "${pkgdir}/usr/share/applications/pymol.desktop"
+ install -Dm644 "${srcdir}/pymol.png" "${pkgdir}/usr/share/pixmaps/pymol.png"
+}
+
+# vim:set ts=2 sw=2 et:
Deleted: community-x86_64/apbstools_tcltk8.6.patch
===================================================================
--- community-x86_64/apbstools_tcltk8.6.patch 2016-10-10 11:09:14 UTC (rev 191855)
+++ community-x86_64/apbstools_tcltk8.6.patch 2016-10-10 11:09:38 UTC (rev 191856)
@@ -1,106 +0,0 @@
---- modules/pmg_tk/startup/apbs_tools.py.orig 2014-05-14 01:07:32.000000000 +0400
-+++ modules/pmg_tk/startup/apbs_tools.py 2014-05-14 01:15:35.090032827 +0400
-@@ -612,7 +612,8 @@
- # Set up the Main page
- page = self.notebook.add('Main')
- group = Pmw.Group(page,tag_text='Main options')
-- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
-+ #group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
-+ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
- self.selection = Pmw.EntryField(group.interior(),
- labelpos='w',
- label_text='Selection to use: ',
-@@ -856,7 +864,8 @@
- page.grid_columnconfigure(5,weight=1)
- page = self.notebook.add('Program Locations')
- group = Pmw.Group(page,tag_text='Locations')
-- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
-+ #group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
-+ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
- def quickFileValidation(s):
- if s == '': return Pmw.PARTIAL
- elif os.path.isfile(s): return Pmw.OK
-@@ -955,7 +964,8 @@
-
- page = self.notebook.add('Temp File Locations')
- group = Pmw.Group(page,tag_text='Locations')
-- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
-+ #group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
-+ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
- self.pymol_generated_pqr_filename = Pmw.EntryField(group.interior(),
- labelpos = 'w',
- label_pyclass = FileDialogButtonClassFactory.get(self.setPymolGeneratedPqrFilename),
-@@ -1003,17 +1013,20 @@
- page = self.notebook.add('Visualization (1)')
- group = VisualizationGroup(page,tag_text='Visualization',visgroup_num=1)
- self.visualization_group_1 = group
-- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
-+ #group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
-+ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
-
- page = self.notebook.add('Visualization (2)')
- group = VisualizationGroup(page,tag_text='Visualization',visgroup_num=2)
- self.visualization_group_2 = group
-- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
-+ #group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
-+ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
-
- # Create a couple of other empty pages
- page = self.notebook.add('About')
- group = Pmw.Group(page, tag_text='About PyMOL APBS Tools')
-- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
-+ #group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
-+ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
- text = """This plugin integrates PyMOL (http://PyMOL.org/) with APBS (http://www.poissonboltzmann.org/apbs/).
-
- Documentation may be found at
-@@ -2271,7 +2284,8 @@
- self.update_buttonbox = Pmw.ButtonBox(self.mm_group.interior(), padx=0)
- self.update_buttonbox.pack(side=LEFT)
- self.update_buttonbox.add('Update',command=self.refresh)
-- self.mm_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=TOP)
-+ #self.mm_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=TOP)
-+ self.mm_group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
-
- self.ms_group = Pmw.Group(self.interior(),tag_text='Molecular Surface')
- self.ms_buttonbox = Pmw.ButtonBox(self.ms_group.interior(), padx=0)
-@@ -2322,7 +2336,8 @@
- bars = (self.mol_surf_low,self.mol_surf_middle,self.mol_surf_high)
- Pmw.alignlabels(bars)
- for bar in bars: bar.pack(side=LEFT)
-- self.ms_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT)
-+ #self.ms_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT)
-+ self.ms_group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
-
- self.fl_group = Pmw.Group(self.interior(),tag_text='Field Lines')
- self.fl_buttonbox = Pmw.ButtonBox(self.fl_group.interior(), padx=0)
-@@ -2337,7 +2352,8 @@
- text = """Follows same coloring as surface.""",
- )
- label.pack()
-- self.fl_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=TOP)
-+ #self.fl_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=TOP)
-+ self.fl_group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
-
- self.pi_group = Pmw.Group(self.interior(),tag_text='Positive Isosurface')
- self.pi_buttonbox = Pmw.ButtonBox(self.pi_group.interior(), padx=0)
-@@ -2356,7 +2372,8 @@
- entryfield_validate = {'validator' : 'real', 'min':0}
- )
- self.pos_surf_val.pack(side=LEFT)
-- self.pi_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT)
-+ #self.pi_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT)
-+ self.pi_group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
-
- self.ni_group = Pmw.Group(self.interior(),tag_text='Negative Isosurface')
- self.ni_buttonbox = Pmw.ButtonBox(self.ni_group.interior(), padx=0)
-@@ -2375,7 +2392,8 @@
- entryfield_validate = {'validator' : 'real', 'max':0}
- )
- self.neg_surf_val.pack(side=LEFT)
-- self.ni_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT)
-+ #self.ni_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT)
-+ self.ni_group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
-
-
-
Copied: pymol/repos/community-x86_64/apbstools_tcltk8.6.patch (from rev 191855, pymol/trunk/apbstools_tcltk8.6.patch)
===================================================================
--- community-x86_64/apbstools_tcltk8.6.patch (rev 0)
+++ community-x86_64/apbstools_tcltk8.6.patch 2016-10-10 11:09:38 UTC (rev 191856)
@@ -0,0 +1,106 @@
+--- modules/pmg_tk/startup/apbs_tools.py.orig 2014-05-14 01:07:32.000000000 +0400
++++ modules/pmg_tk/startup/apbs_tools.py 2014-05-14 01:15:35.090032827 +0400
+@@ -612,7 +612,8 @@
+ # Set up the Main page
+ page = self.notebook.add('Main')
+ group = Pmw.Group(page,tag_text='Main options')
+- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
++ #group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
++ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
+ self.selection = Pmw.EntryField(group.interior(),
+ labelpos='w',
+ label_text='Selection to use: ',
+@@ -856,7 +864,8 @@
+ page.grid_columnconfigure(5,weight=1)
+ page = self.notebook.add('Program Locations')
+ group = Pmw.Group(page,tag_text='Locations')
+- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
++ #group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
++ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
+ def quickFileValidation(s):
+ if s == '': return Pmw.PARTIAL
+ elif os.path.isfile(s): return Pmw.OK
+@@ -955,7 +964,8 @@
+
+ page = self.notebook.add('Temp File Locations')
+ group = Pmw.Group(page,tag_text='Locations')
+- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
++ #group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
++ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
+ self.pymol_generated_pqr_filename = Pmw.EntryField(group.interior(),
+ labelpos = 'w',
+ label_pyclass = FileDialogButtonClassFactory.get(self.setPymolGeneratedPqrFilename),
+@@ -1003,17 +1013,20 @@
+ page = self.notebook.add('Visualization (1)')
+ group = VisualizationGroup(page,tag_text='Visualization',visgroup_num=1)
+ self.visualization_group_1 = group
+- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
++ #group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
++ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
+
+ page = self.notebook.add('Visualization (2)')
+ group = VisualizationGroup(page,tag_text='Visualization',visgroup_num=2)
+ self.visualization_group_2 = group
+- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
++ #group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
++ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
+
+ # Create a couple of other empty pages
+ page = self.notebook.add('About')
+ group = Pmw.Group(page, tag_text='About PyMOL APBS Tools')
+- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
++ #group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
++ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
+ text = """This plugin integrates PyMOL (http://PyMOL.org/) with APBS (http://www.poissonboltzmann.org/apbs/).
+
+ Documentation may be found at
+@@ -2271,7 +2284,8 @@
+ self.update_buttonbox = Pmw.ButtonBox(self.mm_group.interior(), padx=0)
+ self.update_buttonbox.pack(side=LEFT)
+ self.update_buttonbox.add('Update',command=self.refresh)
+- self.mm_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=TOP)
++ #self.mm_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=TOP)
++ self.mm_group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
+
+ self.ms_group = Pmw.Group(self.interior(),tag_text='Molecular Surface')
+ self.ms_buttonbox = Pmw.ButtonBox(self.ms_group.interior(), padx=0)
+@@ -2322,7 +2336,8 @@
+ bars = (self.mol_surf_low,self.mol_surf_middle,self.mol_surf_high)
+ Pmw.alignlabels(bars)
+ for bar in bars: bar.pack(side=LEFT)
+- self.ms_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT)
++ #self.ms_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT)
++ self.ms_group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
+
+ self.fl_group = Pmw.Group(self.interior(),tag_text='Field Lines')
+ self.fl_buttonbox = Pmw.ButtonBox(self.fl_group.interior(), padx=0)
+@@ -2337,7 +2352,8 @@
+ text = """Follows same coloring as surface.""",
+ )
+ label.pack()
+- self.fl_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=TOP)
++ #self.fl_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=TOP)
++ self.fl_group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
+
+ self.pi_group = Pmw.Group(self.interior(),tag_text='Positive Isosurface')
+ self.pi_buttonbox = Pmw.ButtonBox(self.pi_group.interior(), padx=0)
+@@ -2356,7 +2372,8 @@
+ entryfield_validate = {'validator' : 'real', 'min':0}
+ )
+ self.pos_surf_val.pack(side=LEFT)
+- self.pi_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT)
++ #self.pi_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT)
++ self.pi_group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
+
+ self.ni_group = Pmw.Group(self.interior(),tag_text='Negative Isosurface')
+ self.ni_buttonbox = Pmw.ButtonBox(self.ni_group.interior(), padx=0)
+@@ -2375,7 +2392,8 @@
+ entryfield_validate = {'validator' : 'real', 'max':0}
+ )
+ self.neg_surf_val.pack(side=LEFT)
+- self.ni_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT)
++ #self.ni_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT)
++ self.ni_group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
+
+
+
Deleted: community-x86_64/pymol-38899.patch
===================================================================
--- community-x86_64/pymol-38899.patch 2016-10-10 11:09:14 UTC (rev 191855)
+++ community-x86_64/pymol-38899.patch 2016-10-10 11:09:38 UTC (rev 191856)
@@ -1,251 +0,0 @@
-diff -ruN pymol.orig/modules/pymol/importing.py pymol/modules/pymol/importing.py
---- pymol.orig/modules/pymol/importing.py 2014-01-15 00:02:55.000000000 +0400
-+++ pymol/modules/pymol/importing.py 2014-02-14 10:19:11.275591741 +0400
-@@ -473,7 +473,7 @@
- def _processPWG(fname,_self=cmd):
- r = DEFAULT_ERROR
- try:
-- from web.pymolhttpd import PymolHttpd
-+ from pymolweb.pymolhttpd import PymolHttpd
- browser_flag = 0
- launch_flag = 0
- report_url = None
-diff -ruN pymol.orig/modules/web/examples/content/SOP.html pymol/modules/web/examples/content/SOP.html
---- pymol.orig/modules/web/examples/content/SOP.html 2014-01-15 00:02:58.000000000 +0400
-+++ pymol/modules/web/examples/content/SOP.html 2014-02-14 10:19:11.275591741 +0400
-@@ -49,7 +49,7 @@
- The first seven
- <a href="../index.html#sample01" target="_blank"> sample applications</a>
- are implemented like this, residing in folders at
--<code>$PYMOL_PATH/modules/web/examples/sample[0-7]</code> There
-+<code>$PYMOL_PATH/modules/pymolweb/examples/sample[0-7]</code> There
- may be future PyMOL web applications delivered with new versions of
- PyMOL. Of course, you are free to write your own PyMOL web
- applications and store them on each user's machine, or perhaps on a
-diff -ruN pymol.orig/modules/web/examples/content/pwg.html pymol/modules/web/examples/content/pwg.html
---- pymol.orig/modules/web/examples/content/pwg.html 2014-01-15 00:02:58.000000000 +0400
-+++ pymol/modules/web/examples/content/pwg.html 2014-02-14 10:19:11.275591741 +0400
-@@ -58,13 +58,13 @@
-
- <p>In contrast, the PWG file which launches the Sample 01 application is:</p>
- <pre>
--root $PYMOL_PATH/modules/web/examples/sample01/htdocs
-+root $PYMOL_PATH/modules/pymolweb/examples/sample01/htdocs
- browser
- </pre>
-
- <p>which tells PyMOL to (1) launch its internal web server on a
- dynamically assigned port with a root content directory of
--$PYMOL_PATH/modules/web/examples/sample01/htdocs and (2) open
-+$PYMOL_PATH/modules/pymolweb/examples/sample01/htdocs and (2) open
- up a local browser window pointing at that server instance. The
- assumption in this scenario is that this newly-opened web page will be
- responsible for sending requests to the PyMOL server (and thus, will
-diff -ruN pymol.orig/modules/web/examples/content/running.html pymol/modules/web/examples/content/running.html
---- pymol.orig/modules/web/examples/content/running.html 2014-01-15 00:02:58.000000000 +0400
-+++ pymol/modules/web/examples/content/running.html 2014-02-14 10:19:11.278925074 +0400
-@@ -36,7 +36,7 @@
-
- <p>The main index file with sample application links is located at</p>
-
--<pre>./modules/web/examples/index.html</pre>
-+<pre>./modules/pymolweb/examples/index.html</pre>
-
- <p>If you are reading this file from within a browser, then you may
- <a href="../index.html">return to it now</a> in order to try the sample
-@@ -55,7 +55,7 @@
-
- <pre># from within the PyMOL folder
-
--cd ./modules/web/examples
-+cd ./modules/pymolweb/examples
-
- # then
-
-diff -ruN pymol.orig/modules/web/examples/content/server.html pymol/modules/web/examples/content/server.html
---- pymol.orig/modules/web/examples/content/server.html 2014-01-15 00:02:58.000000000 +0400
-+++ pymol/modules/web/examples/content/server.html 2014-02-14 10:19:11.278925074 +0400
-@@ -18,7 +18,7 @@
- browser window).</p>
-
- <p>The source code is located at
--<code>$PYMOL_PATH/modules/web/pymolhttpd.py</code>,
-+<code>$PYMOL_PATH/modules/pymolweb/pymolhttpd.py</code>,
- and this file serves as a python module that can be imported by any
- python script running inside of PyMOL. </p>
-
-@@ -33,7 +33,7 @@
- <p>Alternatively, pymolhttpd.py can be used as the start-up script
- when you launch PyMOL.</p>
-
--<pre>pymol $PYMOL_PATH/modules/web/pymolhttpd.py</pre>
-+<pre>pymol $PYMOL_PATH/modules/pymolweb/pymolhttpd.py</pre>
-
- <p>This will cause PyMOL to start serving requests on the default port
- (8080, assuming of course that the port is not already claimed by
-@@ -44,7 +44,7 @@
- <p>
- The PyMOL web server module can be imported into and launched using code like this.
- <pre>
--from web import pymolhttpd
-+from pymolweb import pymolhttpd
- httpd = pymolhttpd.PymolHttpd("htdocs", 8080)
- httpd.start()
- </pre>
-diff -ruN pymol.orig/modules/web/examples/index.html pymol/modules/web/examples/index.html
---- pymol.orig/modules/web/examples/index.html 2014-01-15 00:02:58.000000000 +0400
-+++ pymol/modules/web/examples/index.html 2014-02-14 10:19:11.288925075 +0400
-@@ -156,7 +156,7 @@
- services interface!</p>
-
- <p>The code for the applications above is located inside a series of folders located at:
--<pre>$PYMOL_PATH/modules/web/examples/sample*</pre></p>
-+<pre>$PYMOL_PATH/modules/pymolweb/examples/sample*</pre></p>
-
- </body>
- </html>
-diff -ruN pymol.orig/modules/web/examples/sample01/htdocs/api.html pymol/modules/web/examples/sample01/htdocs/api.html
---- pymol.orig/modules/web/examples/sample01/htdocs/api.html 2014-01-15 00:02:56.000000000 +0400
-+++ pymol/modules/web/examples/sample01/htdocs/api.html 2014-02-14 10:19:11.288925075 +0400
-@@ -9,9 +9,9 @@
- </ul><hr><p>Please click the link(s) below before testing methods in this section (in order).</p><pre><a target="result" href="/apply/pymol.cmd.reinitialize">/apply/pymol.cmd.reinitialize</a></pre>
-
- <ul><li><p><font face="Courier" size="2"><b>load</b></font>
--<i>filename, object, state, format, finish, discrete, quiet, multiplex, zoom, partial</i><pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb</a></pre>
-+<i>filename, object, state, format, finish, discrete, quiet, multiplex, zoom, partial</i><pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb</a></pre>
-
--<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/map.ccp4">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/map.ccp4</a></pre>
-+<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/map.ccp4">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/map.ccp4</a></pre>
-
- </p></li>
- <li><p><font face="Courier" size="2"><b>enable</b></font>
-@@ -38,7 +38,7 @@
- </p></li>
- </ul><hr><p>Please click the link(s) below before testing methods in this section (in order).</p><pre><a target="result" href="/apply/pymol.cmd.reinitialize">/apply/pymol.cmd.reinitialize</a></pre>
-
--<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb</a></pre>
-+<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb</a></pre>
-
- <ul><li><p><font face="Courier" size="2"><b>color</b></font>
- <i>color, selection, quiet, flags</i><pre><a target="result" href="/apply/pymol.cmd.color?color=yellow&selection=elem c">/apply/pymol.cmd.color?color=yellow&selection=elem c</a></pre>
-@@ -118,9 +118,9 @@
- </p></li>
- </ul><hr><p>Please click the link(s) below before testing methods in this section (in order).</p><pre><a target="result" href="/apply/pymol.cmd.reinitialize">/apply/pymol.cmd.reinitialize</a></pre>
-
--<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb</a></pre>
-+<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb</a></pre>
-
--<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/map.ccp4">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/map.ccp4</a></pre>
-+<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/map.ccp4">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/map.ccp4</a></pre>
-
- <ul><li><p><font face="Courier" size="2"><b>isomesh</b></font>
- <i>name, map, level, selection, buffer, state, carve, source_state, quiet</i><pre><a target="result" href="/apply/pymol.cmd.isomesh?name=mesh&map=map&level=1.0">/apply/pymol.cmd.isomesh?name=mesh&map=map&level=1.0</a></pre>
-@@ -142,7 +142,7 @@
- </p></li>
- </ul><hr><p>Please click the link(s) below before testing methods in this section (in order).</p><pre><a target="result" href="/apply/pymol.cmd.reinitialize">/apply/pymol.cmd.reinitialize</a></pre>
-
--<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb</a></pre>
-+<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb</a></pre>
-
- <ul><li><p><font face="Courier" size="2"><b>show</b></font>
- <i>representation, selection</i><pre><a target="result" href="/apply/pymol.cmd.show?representation=sticks">/apply/pymol.cmd.show?representation=sticks</a></pre>
-@@ -174,7 +174,7 @@
- </p></li>
- </ul><hr><p>Please click the link(s) below before testing methods in this section (in order).</p><pre><a target="result" href="/apply/pymol.cmd.reinitialize">/apply/pymol.cmd.reinitialize</a></pre>
-
--<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb</a></pre>
-+<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb</a></pre>
-
- <ul><li><p><font face="Courier" size="2"><b>show_as</b></font>
- <i>representation, selection</i><pre><a target="result" href="/apply/pymol.cmd.show_as?representation=spheres">/apply/pymol.cmd.show_as?representation=spheres</a></pre>
-@@ -224,7 +224,7 @@
- </p></li>
- </ul><hr><p>Please click the link(s) below before testing methods in this section (in order).</p><pre><a target="result" href="/apply/pymol.cmd.reinitialize">/apply/pymol.cmd.reinitialize</a></pre>
-
--<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb</a></pre>
-+<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb</a></pre>
-
- <ul><li><p><font face="Courier" size="2"><b>super</b></font>
- <i>mobile, target, cutoff, cycles, gap, extend, max_gap, object, matrix, mobile_state, target_state, quiet, max_skip, transform, reset, seq, radius, scale, base, coord, expect, window, ante</i><pre><a target="result" href="/apply/pymol.cmd.create?name=helix1&selection=polymer and 5-17/">/apply/pymol.cmd.create?name=helix1&selection=polymer and 5-17/</a></pre>
-diff -ruN pymol.orig/modules/web/examples/sample01/start.pwg pymol/modules/web/examples/sample01/start.pwg
---- pymol.orig/modules/web/examples/sample01/start.pwg 2014-01-15 00:02:56.000000000 +0400
-+++ pymol/modules/web/examples/sample01/start.pwg 2014-02-14 10:19:11.288925075 +0400
-@@ -1,2 +1,2 @@
--root $PYMOL_PATH/modules/web/examples/sample01/htdocs
-+root $PYMOL_PATH/modules/pymolweb/examples/sample01/htdocs
- browser
-diff -ruN pymol.orig/modules/web/examples/sample02/start.pwg pymol/modules/web/examples/sample02/start.pwg
---- pymol.orig/modules/web/examples/sample02/start.pwg 2014-01-15 00:02:56.000000000 +0400
-+++ pymol/modules/web/examples/sample02/start.pwg 2014-02-14 10:19:11.292258408 +0400
-@@ -1,2 +1,2 @@
--root $PYMOL_PATH/modules/web/examples/sample02/htdocs
-+root $PYMOL_PATH/modules/pymolweb/examples/sample02/htdocs
- browser
-diff -ruN pymol.orig/modules/web/examples/sample03/start.pwg pymol/modules/web/examples/sample03/start.pwg
---- pymol.orig/modules/web/examples/sample03/start.pwg 2014-01-15 00:02:56.000000000 +0400
-+++ pymol/modules/web/examples/sample03/start.pwg 2014-02-14 10:19:11.292258408 +0400
-@@ -1,2 +1,2 @@
--root $PYMOL_PATH/modules/web/examples/sample03/htdocs
-+root $PYMOL_PATH/modules/pymolweb/examples/sample03/htdocs
- browser
-diff -ruN pymol.orig/modules/web/examples/sample04/htdocs/pdbshow.js pymol/modules/web/examples/sample04/htdocs/pdbshow.js
---- pymol.orig/modules/web/examples/sample04/htdocs/pdbshow.js 2014-01-15 00:02:56.000000000 +0400
-+++ pymol/modules/web/examples/sample04/htdocs/pdbshow.js 2014-02-14 10:19:11.292258408 +0400
-@@ -12,7 +12,7 @@
- function get_protein(a) {
- // load protein, unless already loaded
- if (load_state[a] == undefined) {
-- load = "load?filename=$PYMOL_PATH/modules/web/examples/data/" + a + ".pdb.gz" + zoom;
-+ load = "load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/" + a + ".pdb.gz" + zoom;
- cmd(load);
- zoom = "&zoom=0"; // subsequent loads shold not zoom
- cmd("orient?selection=bymol organic and elem n&animate=2");
-diff -ruN pymol.orig/modules/web/examples/sample04/start.pwg pymol/modules/web/examples/sample04/start.pwg
---- pymol.orig/modules/web/examples/sample04/start.pwg 2014-01-15 00:02:56.000000000 +0400
-+++ pymol/modules/web/examples/sample04/start.pwg 2014-02-14 10:19:11.292258408 +0400
-@@ -1,2 +1,2 @@
--root $PYMOL_PATH/modules/web/examples/sample04/htdocs
-+root $PYMOL_PATH/modules/pymolweb/examples/sample04/htdocs
- browser
-diff -ruN pymol.orig/modules/web/examples/sample05/htdocs/index.html pymol/modules/web/examples/sample05/htdocs/index.html
---- pymol.orig/modules/web/examples/sample05/htdocs/index.html 2014-01-15 00:02:57.000000000 +0400
-+++ pymol/modules/web/examples/sample05/htdocs/index.html 2014-02-14 10:19:11.292258408 +0400
-@@ -108,7 +108,7 @@
-
- function loadPDB(code)
- {
-- return cmd('load?filename=$PYMOL_PATH/modules/web/examples/data/'+code+'.pdb');
-+ return cmd('load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/'+code+'.pdb');
- }
-
- </script>
-diff -ruN pymol.orig/modules/web/examples/sample05/start.pwg pymol/modules/web/examples/sample05/start.pwg
---- pymol.orig/modules/web/examples/sample05/start.pwg 2014-01-15 00:02:57.000000000 +0400
-+++ pymol/modules/web/examples/sample05/start.pwg 2014-02-14 10:19:11.292258408 +0400
-@@ -1,2 +1,2 @@
--root $PYMOL_PATH/modules/web/examples/sample05/htdocs
-+root $PYMOL_PATH/modules/pymolweb/examples/sample05/htdocs
- browser
-diff -ruN pymol.orig/modules/web/examples/sample06/start.pwg pymol/modules/web/examples/sample06/start.pwg
---- pymol.orig/modules/web/examples/sample06/start.pwg 2014-01-15 00:02:57.000000000 +0400
-+++ pymol/modules/web/examples/sample06/start.pwg 2014-02-14 10:19:11.292258408 +0400
-@@ -1,3 +1,3 @@
--root $PYMOL_PATH/modules/web/examples/sample06/htdocs
-+root $PYMOL_PATH/modules/pymolweb/examples/sample06/htdocs
- browser
- logging 0
-diff -ruN pymol.orig/modules/web/examples/sample07/start.pwg pymol/modules/web/examples/sample07/start.pwg
---- pymol.orig/modules/web/examples/sample07/start.pwg 2014-01-15 00:02:57.000000000 +0400
-+++ pymol/modules/web/examples/sample07/start.pwg 2014-02-14 10:19:11.295591741 +0400
-@@ -1,2 +1,2 @@
--root $PYMOL_PATH/modules/web/examples/sample07/htdocs
-+root $PYMOL_PATH/modules/pymolweb/examples/sample07/htdocs
- browser
-diff -ruN pymol.orig/modules/web/examples/sample08/start.pwg pymol/modules/web/examples/sample08/start.pwg
---- pymol.orig/modules/web/examples/sample08/start.pwg 2014-01-15 00:02:57.000000000 +0400
-+++ pymol/modules/web/examples/sample08/start.pwg 2014-02-14 10:19:11.295591741 +0400
-@@ -1,3 +1,3 @@
--root $PYMOL_PATH/modules/web/examples/sample08/htdocs
-+root $PYMOL_PATH/modules/pymolweb/examples/sample08/htdocs
- browser
- logging 0
\ No newline at end of file
Copied: pymol/repos/community-x86_64/pymol-38899.patch (from rev 191855, pymol/trunk/pymol-38899.patch)
===================================================================
--- community-x86_64/pymol-38899.patch (rev 0)
+++ community-x86_64/pymol-38899.patch 2016-10-10 11:09:38 UTC (rev 191856)
@@ -0,0 +1,251 @@
+diff -ruN pymol.orig/modules/pymol/importing.py pymol/modules/pymol/importing.py
+--- pymol.orig/modules/pymol/importing.py 2014-01-15 00:02:55.000000000 +0400
++++ pymol/modules/pymol/importing.py 2014-02-14 10:19:11.275591741 +0400
+@@ -473,7 +473,7 @@
+ def _processPWG(fname,_self=cmd):
+ r = DEFAULT_ERROR
+ try:
+- from web.pymolhttpd import PymolHttpd
++ from pymolweb.pymolhttpd import PymolHttpd
+ browser_flag = 0
+ launch_flag = 0
+ report_url = None
+diff -ruN pymol.orig/modules/web/examples/content/SOP.html pymol/modules/web/examples/content/SOP.html
+--- pymol.orig/modules/web/examples/content/SOP.html 2014-01-15 00:02:58.000000000 +0400
++++ pymol/modules/web/examples/content/SOP.html 2014-02-14 10:19:11.275591741 +0400
+@@ -49,7 +49,7 @@
+ The first seven
+ <a href="../index.html#sample01" target="_blank"> sample applications</a>
+ are implemented like this, residing in folders at
+-<code>$PYMOL_PATH/modules/web/examples/sample[0-7]</code> There
++<code>$PYMOL_PATH/modules/pymolweb/examples/sample[0-7]</code> There
+ may be future PyMOL web applications delivered with new versions of
+ PyMOL. Of course, you are free to write your own PyMOL web
+ applications and store them on each user's machine, or perhaps on a
+diff -ruN pymol.orig/modules/web/examples/content/pwg.html pymol/modules/web/examples/content/pwg.html
+--- pymol.orig/modules/web/examples/content/pwg.html 2014-01-15 00:02:58.000000000 +0400
++++ pymol/modules/web/examples/content/pwg.html 2014-02-14 10:19:11.275591741 +0400
+@@ -58,13 +58,13 @@
+
+ <p>In contrast, the PWG file which launches the Sample 01 application is:</p>
+ <pre>
+-root $PYMOL_PATH/modules/web/examples/sample01/htdocs
++root $PYMOL_PATH/modules/pymolweb/examples/sample01/htdocs
+ browser
+ </pre>
+
+ <p>which tells PyMOL to (1) launch its internal web server on a
+ dynamically assigned port with a root content directory of
+-$PYMOL_PATH/modules/web/examples/sample01/htdocs and (2) open
++$PYMOL_PATH/modules/pymolweb/examples/sample01/htdocs and (2) open
+ up a local browser window pointing at that server instance. The
+ assumption in this scenario is that this newly-opened web page will be
+ responsible for sending requests to the PyMOL server (and thus, will
+diff -ruN pymol.orig/modules/web/examples/content/running.html pymol/modules/web/examples/content/running.html
+--- pymol.orig/modules/web/examples/content/running.html 2014-01-15 00:02:58.000000000 +0400
++++ pymol/modules/web/examples/content/running.html 2014-02-14 10:19:11.278925074 +0400
+@@ -36,7 +36,7 @@
+
+ <p>The main index file with sample application links is located at</p>
+
+-<pre>./modules/web/examples/index.html</pre>
++<pre>./modules/pymolweb/examples/index.html</pre>
+
+ <p>If you are reading this file from within a browser, then you may
+ <a href="../index.html">return to it now</a> in order to try the sample
+@@ -55,7 +55,7 @@
+
+ <pre># from within the PyMOL folder
+
+-cd ./modules/web/examples
++cd ./modules/pymolweb/examples
+
+ # then
+
+diff -ruN pymol.orig/modules/web/examples/content/server.html pymol/modules/web/examples/content/server.html
+--- pymol.orig/modules/web/examples/content/server.html 2014-01-15 00:02:58.000000000 +0400
++++ pymol/modules/web/examples/content/server.html 2014-02-14 10:19:11.278925074 +0400
+@@ -18,7 +18,7 @@
+ browser window).</p>
+
+ <p>The source code is located at
+-<code>$PYMOL_PATH/modules/web/pymolhttpd.py</code>,
++<code>$PYMOL_PATH/modules/pymolweb/pymolhttpd.py</code>,
+ and this file serves as a python module that can be imported by any
+ python script running inside of PyMOL. </p>
+
+@@ -33,7 +33,7 @@
+ <p>Alternatively, pymolhttpd.py can be used as the start-up script
+ when you launch PyMOL.</p>
+
+-<pre>pymol $PYMOL_PATH/modules/web/pymolhttpd.py</pre>
++<pre>pymol $PYMOL_PATH/modules/pymolweb/pymolhttpd.py</pre>
+
+ <p>This will cause PyMOL to start serving requests on the default port
+ (8080, assuming of course that the port is not already claimed by
+@@ -44,7 +44,7 @@
+ <p>
+ The PyMOL web server module can be imported into and launched using code like this.
+ <pre>
+-from web import pymolhttpd
++from pymolweb import pymolhttpd
+ httpd = pymolhttpd.PymolHttpd("htdocs", 8080)
+ httpd.start()
+ </pre>
+diff -ruN pymol.orig/modules/web/examples/index.html pymol/modules/web/examples/index.html
+--- pymol.orig/modules/web/examples/index.html 2014-01-15 00:02:58.000000000 +0400
++++ pymol/modules/web/examples/index.html 2014-02-14 10:19:11.288925075 +0400
+@@ -156,7 +156,7 @@
+ services interface!</p>
+
+ <p>The code for the applications above is located inside a series of folders located at:
+-<pre>$PYMOL_PATH/modules/web/examples/sample*</pre></p>
++<pre>$PYMOL_PATH/modules/pymolweb/examples/sample*</pre></p>
+
+ </body>
+ </html>
+diff -ruN pymol.orig/modules/web/examples/sample01/htdocs/api.html pymol/modules/web/examples/sample01/htdocs/api.html
+--- pymol.orig/modules/web/examples/sample01/htdocs/api.html 2014-01-15 00:02:56.000000000 +0400
++++ pymol/modules/web/examples/sample01/htdocs/api.html 2014-02-14 10:19:11.288925075 +0400
+@@ -9,9 +9,9 @@
+ </ul><hr><p>Please click the link(s) below before testing methods in this section (in order).</p><pre><a target="result" href="/apply/pymol.cmd.reinitialize">/apply/pymol.cmd.reinitialize</a></pre>
+
+ <ul><li><p><font face="Courier" size="2"><b>load</b></font>
+-<i>filename, object, state, format, finish, discrete, quiet, multiplex, zoom, partial</i><pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb</a></pre>
++<i>filename, object, state, format, finish, discrete, quiet, multiplex, zoom, partial</i><pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb</a></pre>
+
+-<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/map.ccp4">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/map.ccp4</a></pre>
++<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/map.ccp4">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/map.ccp4</a></pre>
+
+ </p></li>
+ <li><p><font face="Courier" size="2"><b>enable</b></font>
+@@ -38,7 +38,7 @@
+ </p></li>
+ </ul><hr><p>Please click the link(s) below before testing methods in this section (in order).</p><pre><a target="result" href="/apply/pymol.cmd.reinitialize">/apply/pymol.cmd.reinitialize</a></pre>
+
+-<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb</a></pre>
++<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb</a></pre>
+
+ <ul><li><p><font face="Courier" size="2"><b>color</b></font>
+ <i>color, selection, quiet, flags</i><pre><a target="result" href="/apply/pymol.cmd.color?color=yellow&selection=elem c">/apply/pymol.cmd.color?color=yellow&selection=elem c</a></pre>
+@@ -118,9 +118,9 @@
+ </p></li>
+ </ul><hr><p>Please click the link(s) below before testing methods in this section (in order).</p><pre><a target="result" href="/apply/pymol.cmd.reinitialize">/apply/pymol.cmd.reinitialize</a></pre>
+
+-<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb</a></pre>
++<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb</a></pre>
+
+-<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/map.ccp4">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/map.ccp4</a></pre>
++<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/map.ccp4">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/map.ccp4</a></pre>
+
+ <ul><li><p><font face="Courier" size="2"><b>isomesh</b></font>
+ <i>name, map, level, selection, buffer, state, carve, source_state, quiet</i><pre><a target="result" href="/apply/pymol.cmd.isomesh?name=mesh&map=map&level=1.0">/apply/pymol.cmd.isomesh?name=mesh&map=map&level=1.0</a></pre>
+@@ -142,7 +142,7 @@
+ </p></li>
+ </ul><hr><p>Please click the link(s) below before testing methods in this section (in order).</p><pre><a target="result" href="/apply/pymol.cmd.reinitialize">/apply/pymol.cmd.reinitialize</a></pre>
+
+-<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb</a></pre>
++<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb</a></pre>
+
+ <ul><li><p><font face="Courier" size="2"><b>show</b></font>
+ <i>representation, selection</i><pre><a target="result" href="/apply/pymol.cmd.show?representation=sticks">/apply/pymol.cmd.show?representation=sticks</a></pre>
+@@ -174,7 +174,7 @@
+ </p></li>
+ </ul><hr><p>Please click the link(s) below before testing methods in this section (in order).</p><pre><a target="result" href="/apply/pymol.cmd.reinitialize">/apply/pymol.cmd.reinitialize</a></pre>
+
+-<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb</a></pre>
++<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb</a></pre>
+
+ <ul><li><p><font face="Courier" size="2"><b>show_as</b></font>
+ <i>representation, selection</i><pre><a target="result" href="/apply/pymol.cmd.show_as?representation=spheres">/apply/pymol.cmd.show_as?representation=spheres</a></pre>
+@@ -224,7 +224,7 @@
+ </p></li>
+ </ul><hr><p>Please click the link(s) below before testing methods in this section (in order).</p><pre><a target="result" href="/apply/pymol.cmd.reinitialize">/apply/pymol.cmd.reinitialize</a></pre>
+
+-<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb</a></pre>
++<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb</a></pre>
+
+ <ul><li><p><font face="Courier" size="2"><b>super</b></font>
+ <i>mobile, target, cutoff, cycles, gap, extend, max_gap, object, matrix, mobile_state, target_state, quiet, max_skip, transform, reset, seq, radius, scale, base, coord, expect, window, ante</i><pre><a target="result" href="/apply/pymol.cmd.create?name=helix1&selection=polymer and 5-17/">/apply/pymol.cmd.create?name=helix1&selection=polymer and 5-17/</a></pre>
+diff -ruN pymol.orig/modules/web/examples/sample01/start.pwg pymol/modules/web/examples/sample01/start.pwg
+--- pymol.orig/modules/web/examples/sample01/start.pwg 2014-01-15 00:02:56.000000000 +0400
++++ pymol/modules/web/examples/sample01/start.pwg 2014-02-14 10:19:11.288925075 +0400
+@@ -1,2 +1,2 @@
+-root $PYMOL_PATH/modules/web/examples/sample01/htdocs
++root $PYMOL_PATH/modules/pymolweb/examples/sample01/htdocs
+ browser
+diff -ruN pymol.orig/modules/web/examples/sample02/start.pwg pymol/modules/web/examples/sample02/start.pwg
+--- pymol.orig/modules/web/examples/sample02/start.pwg 2014-01-15 00:02:56.000000000 +0400
++++ pymol/modules/web/examples/sample02/start.pwg 2014-02-14 10:19:11.292258408 +0400
+@@ -1,2 +1,2 @@
+-root $PYMOL_PATH/modules/web/examples/sample02/htdocs
++root $PYMOL_PATH/modules/pymolweb/examples/sample02/htdocs
+ browser
+diff -ruN pymol.orig/modules/web/examples/sample03/start.pwg pymol/modules/web/examples/sample03/start.pwg
+--- pymol.orig/modules/web/examples/sample03/start.pwg 2014-01-15 00:02:56.000000000 +0400
++++ pymol/modules/web/examples/sample03/start.pwg 2014-02-14 10:19:11.292258408 +0400
+@@ -1,2 +1,2 @@
+-root $PYMOL_PATH/modules/web/examples/sample03/htdocs
++root $PYMOL_PATH/modules/pymolweb/examples/sample03/htdocs
+ browser
+diff -ruN pymol.orig/modules/web/examples/sample04/htdocs/pdbshow.js pymol/modules/web/examples/sample04/htdocs/pdbshow.js
+--- pymol.orig/modules/web/examples/sample04/htdocs/pdbshow.js 2014-01-15 00:02:56.000000000 +0400
++++ pymol/modules/web/examples/sample04/htdocs/pdbshow.js 2014-02-14 10:19:11.292258408 +0400
+@@ -12,7 +12,7 @@
+ function get_protein(a) {
+ // load protein, unless already loaded
+ if (load_state[a] == undefined) {
+- load = "load?filename=$PYMOL_PATH/modules/web/examples/data/" + a + ".pdb.gz" + zoom;
++ load = "load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/" + a + ".pdb.gz" + zoom;
+ cmd(load);
+ zoom = "&zoom=0"; // subsequent loads shold not zoom
+ cmd("orient?selection=bymol organic and elem n&animate=2");
+diff -ruN pymol.orig/modules/web/examples/sample04/start.pwg pymol/modules/web/examples/sample04/start.pwg
+--- pymol.orig/modules/web/examples/sample04/start.pwg 2014-01-15 00:02:56.000000000 +0400
++++ pymol/modules/web/examples/sample04/start.pwg 2014-02-14 10:19:11.292258408 +0400
+@@ -1,2 +1,2 @@
+-root $PYMOL_PATH/modules/web/examples/sample04/htdocs
++root $PYMOL_PATH/modules/pymolweb/examples/sample04/htdocs
+ browser
+diff -ruN pymol.orig/modules/web/examples/sample05/htdocs/index.html pymol/modules/web/examples/sample05/htdocs/index.html
+--- pymol.orig/modules/web/examples/sample05/htdocs/index.html 2014-01-15 00:02:57.000000000 +0400
++++ pymol/modules/web/examples/sample05/htdocs/index.html 2014-02-14 10:19:11.292258408 +0400
+@@ -108,7 +108,7 @@
+
+ function loadPDB(code)
+ {
+- return cmd('load?filename=$PYMOL_PATH/modules/web/examples/data/'+code+'.pdb');
++ return cmd('load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/'+code+'.pdb');
+ }
+
+ </script>
+diff -ruN pymol.orig/modules/web/examples/sample05/start.pwg pymol/modules/web/examples/sample05/start.pwg
+--- pymol.orig/modules/web/examples/sample05/start.pwg 2014-01-15 00:02:57.000000000 +0400
++++ pymol/modules/web/examples/sample05/start.pwg 2014-02-14 10:19:11.292258408 +0400
+@@ -1,2 +1,2 @@
+-root $PYMOL_PATH/modules/web/examples/sample05/htdocs
++root $PYMOL_PATH/modules/pymolweb/examples/sample05/htdocs
+ browser
+diff -ruN pymol.orig/modules/web/examples/sample06/start.pwg pymol/modules/web/examples/sample06/start.pwg
+--- pymol.orig/modules/web/examples/sample06/start.pwg 2014-01-15 00:02:57.000000000 +0400
++++ pymol/modules/web/examples/sample06/start.pwg 2014-02-14 10:19:11.292258408 +0400
+@@ -1,3 +1,3 @@
+-root $PYMOL_PATH/modules/web/examples/sample06/htdocs
++root $PYMOL_PATH/modules/pymolweb/examples/sample06/htdocs
+ browser
+ logging 0
+diff -ruN pymol.orig/modules/web/examples/sample07/start.pwg pymol/modules/web/examples/sample07/start.pwg
+--- pymol.orig/modules/web/examples/sample07/start.pwg 2014-01-15 00:02:57.000000000 +0400
++++ pymol/modules/web/examples/sample07/start.pwg 2014-02-14 10:19:11.295591741 +0400
+@@ -1,2 +1,2 @@
+-root $PYMOL_PATH/modules/web/examples/sample07/htdocs
++root $PYMOL_PATH/modules/pymolweb/examples/sample07/htdocs
+ browser
+diff -ruN pymol.orig/modules/web/examples/sample08/start.pwg pymol/modules/web/examples/sample08/start.pwg
+--- pymol.orig/modules/web/examples/sample08/start.pwg 2014-01-15 00:02:57.000000000 +0400
++++ pymol/modules/web/examples/sample08/start.pwg 2014-02-14 10:19:11.295591741 +0400
+@@ -1,3 +1,3 @@
+-root $PYMOL_PATH/modules/web/examples/sample08/htdocs
++root $PYMOL_PATH/modules/pymolweb/examples/sample08/htdocs
+ browser
+ logging 0
\ No newline at end of file
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