Date: Thursday, August 3, 2017 @ 19:49:59 Author: felixonmars Revision: 247908
archrelease: copy trunk to community-staging-i686, community-staging-x86_64 Added: pymol/repos/community-staging-i686/ pymol/repos/community-staging-i686/ChangeLog (from rev 247906, pymol/trunk/ChangeLog) pymol/repos/community-staging-i686/PKGBUILD (from rev 247906, pymol/trunk/PKGBUILD) pymol/repos/community-staging-i686/apbstools_tcltk8.6.patch (from rev 247906, pymol/trunk/apbstools_tcltk8.6.patch) pymol/repos/community-staging-i686/pymol-38899.patch (from rev 247906, pymol/trunk/pymol-38899.patch) pymol/repos/community-staging-x86_64/ pymol/repos/community-staging-x86_64/ChangeLog (from rev 247906, pymol/trunk/ChangeLog) pymol/repos/community-staging-x86_64/PKGBUILD (from rev 247906, pymol/trunk/PKGBUILD) pymol/repos/community-staging-x86_64/apbstools_tcltk8.6.patch (from rev 247906, pymol/trunk/apbstools_tcltk8.6.patch) pymol/repos/community-staging-x86_64/pymol-38899.patch (from rev 247906, pymol/trunk/pymol-38899.patch) ---------------------------------------------------+ community-staging-i686/ChangeLog | 48 +++ community-staging-i686/PKGBUILD | 61 ++++ community-staging-i686/apbstools_tcltk8.6.patch | 106 ++++++++ community-staging-i686/pymol-38899.patch | 251 ++++++++++++++++++++ community-staging-x86_64/ChangeLog | 48 +++ community-staging-x86_64/PKGBUILD | 61 ++++ community-staging-x86_64/apbstools_tcltk8.6.patch | 106 ++++++++ community-staging-x86_64/pymol-38899.patch | 251 ++++++++++++++++++++ 8 files changed, 932 insertions(+) Copied: pymol/repos/community-staging-i686/ChangeLog (from rev 247906, pymol/trunk/ChangeLog) =================================================================== --- community-staging-i686/ChangeLog (rev 0) +++ community-staging-i686/ChangeLog 2017-08-03 19:49:59 UTC (rev 247908) @@ -0,0 +1,48 @@ +1.8.6.0-2: +rollback to python2 (see FS#53654) + +1.8.6.0-1: +* upstream update +* use python3 instead of python2 + +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 Copied: pymol/repos/community-staging-i686/PKGBUILD (from rev 247906, pymol/trunk/PKGBUILD) =================================================================== --- community-staging-i686/PKGBUILD (rev 0) +++ community-staging-i686/PKGBUILD 2017-08-03 19:49:59 UTC (rev 247908) @@ -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=1.8.6.0 +pkgrel=3 +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' 'msgpack-c') +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=('dc317a4046d653417ac6d4a984176e26' + '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-staging-i686/apbstools_tcltk8.6.patch (from rev 247906, pymol/trunk/apbstools_tcltk8.6.patch) =================================================================== --- community-staging-i686/apbstools_tcltk8.6.patch (rev 0) +++ community-staging-i686/apbstools_tcltk8.6.patch 2017-08-03 19:49:59 UTC (rev 247908) @@ -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)) + + + Copied: pymol/repos/community-staging-i686/pymol-38899.patch (from rev 247906, pymol/trunk/pymol-38899.patch) =================================================================== --- community-staging-i686/pymol-38899.patch (rev 0) +++ community-staging-i686/pymol-38899.patch 2017-08-03 19:49:59 UTC (rev 247908) @@ -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 Copied: pymol/repos/community-staging-x86_64/ChangeLog (from rev 247906, pymol/trunk/ChangeLog) =================================================================== --- community-staging-x86_64/ChangeLog (rev 0) +++ community-staging-x86_64/ChangeLog 2017-08-03 19:49:59 UTC (rev 247908) @@ -0,0 +1,48 @@ +1.8.6.0-2: +rollback to python2 (see FS#53654) + +1.8.6.0-1: +* upstream update +* use python3 instead of python2 + +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 Copied: pymol/repos/community-staging-x86_64/PKGBUILD (from rev 247906, pymol/trunk/PKGBUILD) =================================================================== --- community-staging-x86_64/PKGBUILD (rev 0) +++ community-staging-x86_64/PKGBUILD 2017-08-03 19:49:59 UTC (rev 247908) @@ -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=1.8.6.0 +pkgrel=3 +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' 'msgpack-c') +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=('dc317a4046d653417ac6d4a984176e26' + '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-staging-x86_64/apbstools_tcltk8.6.patch (from rev 247906, pymol/trunk/apbstools_tcltk8.6.patch) =================================================================== --- community-staging-x86_64/apbstools_tcltk8.6.patch (rev 0) +++ community-staging-x86_64/apbstools_tcltk8.6.patch 2017-08-03 19:49:59 UTC (rev 247908) @@ -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)) + + + Copied: pymol/repos/community-staging-x86_64/pymol-38899.patch (from rev 247906, pymol/trunk/pymol-38899.patch) =================================================================== --- community-staging-x86_64/pymol-38899.patch (rev 0) +++ community-staging-x86_64/pymol-38899.patch 2017-08-03 19:49:59 UTC (rev 247908) @@ -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