[arch-commits] Commit in pymol/repos (10 files)

Evgeniy Alekseev arcanis at archlinux.org
Mon Mar 20 15:19:46 UTC 2017


    Date: Monday, March 20, 2017 @ 15:19:45
  Author: arcanis
Revision: 217646

archrelease: copy trunk to community-testing-i686, community-testing-x86_64

Added:
  pymol/repos/community-testing-i686/
  pymol/repos/community-testing-i686/ChangeLog
    (from rev 217644, pymol/trunk/ChangeLog)
  pymol/repos/community-testing-i686/PKGBUILD
    (from rev 217645, pymol/trunk/PKGBUILD)
  pymol/repos/community-testing-i686/apbstools_tcltk8.6.patch
    (from rev 217645, pymol/trunk/apbstools_tcltk8.6.patch)
  pymol/repos/community-testing-i686/pymol-38899.patch
    (from rev 217645, pymol/trunk/pymol-38899.patch)
  pymol/repos/community-testing-x86_64/
  pymol/repos/community-testing-x86_64/ChangeLog
    (from rev 217645, pymol/trunk/ChangeLog)
  pymol/repos/community-testing-x86_64/PKGBUILD
    (from rev 217645, pymol/trunk/PKGBUILD)
  pymol/repos/community-testing-x86_64/apbstools_tcltk8.6.patch
    (from rev 217645, pymol/trunk/apbstools_tcltk8.6.patch)
  pymol/repos/community-testing-x86_64/pymol-38899.patch
    (from rev 217645, pymol/trunk/pymol-38899.patch)

---------------------------------------------------+
 community-testing-i686/ChangeLog                  |   45 +++
 community-testing-i686/PKGBUILD                   |   56 ++++
 community-testing-i686/apbstools_tcltk8.6.patch   |  106 ++++++++
 community-testing-i686/pymol-38899.patch          |  251 ++++++++++++++++++++
 community-testing-x86_64/ChangeLog                |   45 +++
 community-testing-x86_64/PKGBUILD                 |   56 ++++
 community-testing-x86_64/apbstools_tcltk8.6.patch |  106 ++++++++
 community-testing-x86_64/pymol-38899.patch        |  251 ++++++++++++++++++++
 8 files changed, 916 insertions(+)

Copied: pymol/repos/community-testing-i686/ChangeLog (from rev 217644, pymol/trunk/ChangeLog)
===================================================================
--- community-testing-i686/ChangeLog	                        (rev 0)
+++ community-testing-i686/ChangeLog	2017-03-20 15:19:45 UTC (rev 217646)
@@ -0,0 +1,45 @@
+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-testing-i686/PKGBUILD (from rev 217645, pymol/trunk/PKGBUILD)
===================================================================
--- community-testing-i686/PKGBUILD	                        (rev 0)
+++ community-testing-i686/PKGBUILD	2017-03-20 15:19:45 UTC (rev 217646)
@@ -0,0 +1,56 @@
+# $Id$
+# 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=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' 'python-numpy' 'python-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,' "${srcdir}/pymol/setup.py"
+  # fix FS#38899
+  patch -p0 -i "${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"
+  python setup.py build
+}
+
+package() {
+  cd "${srcdir}/${pkgname}"
+  python 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-testing-i686/apbstools_tcltk8.6.patch (from rev 217645, pymol/trunk/apbstools_tcltk8.6.patch)
===================================================================
--- community-testing-i686/apbstools_tcltk8.6.patch	                        (rev 0)
+++ community-testing-i686/apbstools_tcltk8.6.patch	2017-03-20 15:19:45 UTC (rev 217646)
@@ -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-testing-i686/pymol-38899.patch (from rev 217645, pymol/trunk/pymol-38899.patch)
===================================================================
--- community-testing-i686/pymol-38899.patch	                        (rev 0)
+++ community-testing-i686/pymol-38899.patch	2017-03-20 15:19:45 UTC (rev 217646)
@@ -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-testing-x86_64/ChangeLog (from rev 217645, pymol/trunk/ChangeLog)
===================================================================
--- community-testing-x86_64/ChangeLog	                        (rev 0)
+++ community-testing-x86_64/ChangeLog	2017-03-20 15:19:45 UTC (rev 217646)
@@ -0,0 +1,45 @@
+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-testing-x86_64/PKGBUILD (from rev 217645, pymol/trunk/PKGBUILD)
===================================================================
--- community-testing-x86_64/PKGBUILD	                        (rev 0)
+++ community-testing-x86_64/PKGBUILD	2017-03-20 15:19:45 UTC (rev 217646)
@@ -0,0 +1,56 @@
+# $Id$
+# 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=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' 'python-numpy' 'python-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,' "${srcdir}/pymol/setup.py"
+  # fix FS#38899
+  patch -p0 -i "${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"
+  python setup.py build
+}
+
+package() {
+  cd "${srcdir}/${pkgname}"
+  python 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-testing-x86_64/apbstools_tcltk8.6.patch (from rev 217645, pymol/trunk/apbstools_tcltk8.6.patch)
===================================================================
--- community-testing-x86_64/apbstools_tcltk8.6.patch	                        (rev 0)
+++ community-testing-x86_64/apbstools_tcltk8.6.patch	2017-03-20 15:19:45 UTC (rev 217646)
@@ -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-testing-x86_64/pymol-38899.patch (from rev 217645, pymol/trunk/pymol-38899.patch)
===================================================================
--- community-testing-x86_64/pymol-38899.patch	                        (rev 0)
+++ community-testing-x86_64/pymol-38899.patch	2017-03-20 15:19:45 UTC (rev 217646)
@@ -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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