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Process All Files In Directory - Revision history
2024-03-29T10:08:12Z
Revision history for this page on the wiki
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https://pymolwiki.org/index.php?title=Process_All_Files_In_Directory&diff=8031&oldid=prev
Cowsandmilk at 12:54, 2 February 2010
2010-02-02T12:54:19Z
<p></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 12:54, 2 February 2010</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l95" >Line 95:</td>
<td colspan="2" class="diff-lineno">Line 95:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> cmd.select("s2","%s`%d"%b)</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> cmd.select("s2","%s`%d"%b)</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> if cmd.select("(s1|s2) and not ?skip"):</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> if cmd.select("(s1|s2) and not ?skip"):</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div> cmd.iterate("s1|s2","print '</div></td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> cmd.iterate("s1|s2","print ' ',chain,resn,resi,name")</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>',chain,resn,resi,name")</div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> print ' ',round(cmd.dist("tmp","s1","s2"),3)</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> print ' ',round(cmd.dist("tmp","s1","s2"),3)</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> cmd.select("skip","s1|s2|?skip")</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> cmd.select("skip","s1|s2|?skip")</div></td></tr>
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Cowsandmilk
https://pymolwiki.org/index.php?title=Process_All_Files_In_Directory&diff=6359&oldid=prev
Inchoate at 12:39, 30 April 2009
2009-04-30T12:39:45Z
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 12:39, 30 April 2009</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l103" >Line 103:</td>
<td colspan="2" class="diff-lineno">Line 103:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Category:Script_Library|Processing All File in Directory]]</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Category:Script_Library|Processing All File in Directory]]</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">[[Category:System_Scripts]]</ins></div></td></tr>
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Inchoate
https://pymolwiki.org/index.php?title=Process_All_Files_In_Directory&diff=3451&oldid=prev
Inchoate at 15:45, 20 January 2006
2006-01-20T15:45:34Z
<p></p>
<table class="diff diff-contentalign-left diff-editfont-monospace" data-mw="interface">
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<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 15:45, 20 January 2006</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l100" >Line 100:</td>
<td colspan="2" class="diff-lineno">Line 100:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> cmd.select("skip","s1|s2|?skip")</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> cmd.select("skip","s1|s2|?skip")</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> cmd.delete("all")</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> cmd.delete("all")</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline"></pyton></del></source></div></td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div></source></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">[[Category:Script_Library|Processing All File in Directory]]</ins></div></td></tr>
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Inchoate
https://pymolwiki.org/index.php?title=Process_All_Files_In_Directory&diff=1303&oldid=prev
Inchoate at 15:44, 20 January 2006
2006-01-20T15:44:37Z
<p></p>
<p><b>New page</b></p><div>=Explanation=<br />
For a given directory with PDB files in it, the following code will output, for each PDB, the bound disulfide bond lengths like this:<br />
<pre><br />
1alk.pdb<br />
A CYS 168 SG<br />
A CYS 178 SG<br />
1.975<br />
A CYS 286 SG<br />
A CYS 336 SG<br />
1.995<br />
B CYS 168 SG<br />
B CYS 178 SG<br />
1.996<br />
B CYS 286 SG<br />
B CYS 336 SG<br />
2.032<br />
1btu.pdb<br />
CYS 42 SG<br />
CYS 58 SG<br />
2.039<br />
CYS 136 SG<br />
CYS 201 SG<br />
2.031<br />
CYS 168 SG<br />
CYS 182 SG<br />
2.001<br />
CYS 191 SG<br />
CYS 220 SG<br />
2.019<br />
...<br />
</pre><br />
<br />
=Bound Disulfides=<br />
<source lang="python"><br />
from pymol import cmd<br />
from glob import glob<br />
<br />
for file in glob("*.pdb"):<br />
print file<br />
cmd.load(file,'prot')<br />
for a in cmd.index("elem s and bound_to elem s"):<br />
if cmd.select("s1","%s`%d"%a) and \<br />
cmd.select("s2","elem s and bound_to %s`%d"%a):<br />
if cmd.select("(s1|s2) and not ?skip"):<br />
cmd.iterate("s1|s2","print ' ',chain,resn,resi,name")<br />
print ' ',round(cmd.dist("tmp","s1","s2"),3)<br />
cmd.select("skip","s1|s2|?skip")<br />
cmd.delete("all")<br />
</source><br />
<br />
=All Sulfur Distances=<br />
Note that the above is for bonded sulfurs in disulfides. For all intra-cysteine gamma sulfur distances, you'd want to do something more like:<br />
<pre><br />
1alk.pdb<br />
A CYS 168 SG<br />
A CYS 178 SG<br />
1.975<br />
A CYS 168 SG<br />
A CYS 286 SG<br />
35.845<br />
A CYS 168 SG<br />
A CYS 336 SG<br />
35.029<br />
A CYS 168 SG<br />
B CYS 168 SG<br />
63.64<br />
A CYS 168 SG<br />
B CYS 178 SG<br />
63.775<br />
A CYS 168 SG<br />
B CYS 286 SG<br />
39.02<br />
A CYS 168 SG<br />
B CYS 336 SG<br />
39.314<br />
1btu.pdb<br />
CYS 42 SG<br />
CYS 58 SG<br />
2.039<br />
CYS 42 SG<br />
CYS 136 SG<br />
</pre><br />
<br />
<source lang="python"><br />
from pymol import cmd<br />
from glob import glob<br />
<br />
for file in glob("*.pdb"):<br />
print file<br />
cmd.load(file,'prot')<br />
for a in cmd.index("CYS/SG"):<br />
for b in cmd.index("CYS/SG"):<br />
if a[1]<b[1]:<br />
cmd.select("s1","%s`%d"%a)<br />
cmd.select("s2","%s`%d"%b)<br />
if cmd.select("(s1|s2) and not ?skip"):<br />
cmd.iterate("s1|s2","print '<br />
',chain,resn,resi,name")<br />
print ' ',round(cmd.dist("tmp","s1","s2"),3)<br />
cmd.select("skip","s1|s2|?skip")<br />
cmd.delete("all")<br />
</pyton></source></div>
Inchoate