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pdbMolecularInterfaceFind - Revision history
2026-05-04T15:26:14Z
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Kinoshita: Created page with "'''pdbMolecularInterfaceFind''' is Eos's Command. == List of option == === Main option === <table border="1"> <tr> <th>Option</th> <th>Essential/Optio..."
2014-08-08T01:13:02Z
<p>Created page with "'''pdbMolecularInterfaceFind''' is <a href="/Eos/index.php/Eos" title="Eos">Eos</a>'s <a href="/Eos/index.php/Command" title="Command">Command</a>. == List of option == === Main option === <table border="1"> <tr> <th>Option</th> <th>Essential/Optio..."</p>
<p><b>New page</b></p><div>'''pdbMolecularInterfaceFind''' is [[Eos]]'s [[Command]].<br />
<br />
<br />
== List of option ==<br />
=== Main option ===<br />
<table border="1"><br />
<tr> <br />
<th>Option</th> <br />
<th>Essential/Optional</th> <br />
<th>Description</th> <br />
<th>Default</th> <br />
</tr> <br />
<tr> <br />
<td>-i</td> <br />
<td>Essential</td> <br />
<td>Input: [[PDB]]</td> <br />
<td>NULL</td> <br />
</tr> <br />
<tr> <br />
<td>-o</td> <br />
<td>Optional</td> <br />
<td>Output(Not implemented)</td> <br />
<td>NULL</td> <br />
</tr> <br />
<tr> <br />
<td>-id1</td> <br />
<td>Optional</td> <br />
<td>Chain ID1</td> <br />
<td>A</td> <br />
</tr> <br />
<tr> <br />
<td>-id2</td> <br />
<td>Optional</td> <br />
<td>Chain ID2</td> <br />
<td>B</td> <br />
</tr> <br />
<tr> <br />
<td>-d</td> <br />
<td>Optional</td> <br />
<td>Threshold distance</td> <br />
<td>1</td> <br />
</tr> <br />
<tr> <br />
<td>-c</td> <br />
<td>Optional</td> <br />
<td>ConfigurationFile</td> <br />
<td>NULL</td> <br />
</tr> <br />
<tr> <br />
<td>-m</td> <br />
<td>Optional</td> <br />
<td>Mode</td> <br />
<td>0</td> <br />
</tr> <br />
<tr> <br />
<td>-h</td> <br />
<td>Optional</td> <br />
<td>Help</td> <br />
<td> </td> <br />
</tr> <br />
</table> <br />
<div>Currently, Result Output is Standard Output.</div><br />
<br><br />
<br />
=== -m details ===<br />
<table border="1"><br />
<tr> <br />
<th>Value</th> <br />
<th>Description</th> <br />
</tr> <br />
<tr> <br />
<td>0</td> <br />
<td></td> <br />
</tr> <br />
</table> <br />
<br><br />
<br />
== Execution example ==<br />
===[[:Media:Input-121P-Two.pdb.zip|Input file]] image===<br />
<table> <br />
<tr> <br />
<td>[[File:Input-121P-Two.png]]</td> <br />
<td><p align="left">Gravity Centre(CA)<br> <br />
Atom far from Centre(CA)<br> <br />
Atom far from Centre(CA, Axis)<br> </p><br />
</td> <br />
<td><p align="left">3.281389e+00 2.225817e+01 -4.999687e-04<br> <br />
3.798185e+01<br> <br />
27.38 27.08 34.08<br></p><br />
</td> <br />
</tr> <br />
</table> <br />
<br><br />
<br />
=== Case: Options only essential ===<br />
<div>Output</div><br />
<pre><br />
2A <br />
3A <br />
3A <br />
3A <br />
3A <br />
4A <br />
<br />
...<br />
<br />
177A <br />
193A <br />
194A <br />
215A <br />
255A <br />
2B <br />
3B <br />
3B <br />
3B <br />
3B <br />
4B <br />
<br />
...<br />
<br />
177B <br />
193B <br />
194B <br />
215B <br />
255B <br />
</pre><br />
<br><br />
<br />
=== Option -id1, -id2===<br />
====Case: id1=B, id2=A==== <br />
<div>Output</div><br />
<pre><br />
2B <br />
3B <br />
3B <br />
3B <br />
3B <br />
4B <br />
<br />
...<br />
<br />
177B <br />
193B <br />
194B <br />
215B <br />
255B <br />
2A <br />
3A <br />
3A <br />
3A <br />
3A <br />
4A <br />
<br />
...<br />
<br />
177A <br />
193A <br />
194A <br />
215A <br />
255A <br />
<br />
</pre><br />
<br><br />
<br />
=== Option -d===<br />
====Case: d=0.5==== <br />
<div>Output</div><br />
<pre><br />
5A <br />
47A <br />
47A <br />
52A <br />
109A <br />
109A <br />
157A <br />
161A <br />
162A <br />
162A <br />
177A <br />
255A <br />
5B <br />
47B <br />
47B <br />
52B <br />
109B <br />
109B <br />
157B <br />
161B <br />
162B <br />
162B <br />
177B <br />
255B <br />
</pre><br />
<br></div>
Kinoshita