diff options
Diffstat (limited to 'community/pymol/pymol-38899.patch')
| -rw-r--r-- | community/pymol/pymol-38899.patch | 251 |
1 files changed, 251 insertions, 0 deletions
diff --git a/community/pymol/pymol-38899.patch b/community/pymol/pymol-38899.patch new file mode 100644 index 000000000..8e4baf416 --- /dev/null +++ b/community/pymol/pymol-38899.patch @@ -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
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