pdb2ucd - Revision history

Kinoshita: Created page with "'''pdb2ucd''' is Eos's Command. == List of option == === Main option ===

Option Essential/Optional ..."
2014-08-07T05:48:12Z

Created page with "'''pdb2ucd''' is Eos's Command. == List of option == === Main option === <table border="1"> <tr> <th>Option</th> <th>Essential/Optional</th> <th>..."

New page
'''pdb2ucd''' is [[Eos]]'s [[Command]].

== List of option ==
=== Main option ===
<table border="1">
<tr>
<th>Option</th>
<th>Essential/Optional</th>
<th>Description</th>
<th>Default</th>
</tr>
<tr>
<td>-i</td>
<td>Essential</td>
<td>Input: [[PDB]]</td>
<td>NULL</td>
</tr>
<tr>
<td>-o</td>
<td>Essential</td>
<td>Output</td>
<td>NULL</td>
</tr>
<tr>
<td>-c</td>
<td>Optional</td>
<td>ConfigurationFile</td>
<td>NULL</td>
</tr>
<tr>
<td>-m</td>
<td>Optional</td>
<td>Mode</td>
<td>0</td>
</tr>
<tr>
<td>-h</td>
<td>Optional</td>
<td>Help</td>
<td>　</td>
</tr>
</table>

=== -m details ===
<table border="1">
<tr>
<th>Value</th>
<th>Description</th>
</tr>
<tr>
<td>0</td>
<td></td>
</tr>
</table>

== Execution example ==
===[[:Media:Input-121P.pdb.zip|Input file]] image===
<table>
<tr>
<td>[[File:Input-121P-PDB.png]]</td>
<td><p align="left">Gravity Centre(CA)<br>
Atom far from Centre(CA)<br>
Atom far from Centre(CA, Axis)<br> </p>
</td>
<td><p align="left">6.053012e+00 2.519590e+01 1.189075e+01<br>
3.286664e+01 <br>
24.77 23.85 28.04<br></p>
</td>
</tr>
</table>
<br>

=== Example of options only essential ===
<div>Output</div>
<pre>
nNodeComponent 4nElement 1
nElement 1
nElement 1
nElement 1
0 TemperatureFactor A2
1 ChainID
2 ResNum
3 CA
</pre>
<br>

<div>-o 's data</div>
<pre>
166 165 4 0 0
0 -5.913000 31.927999 -6.676000
1 -4.759000 28.930000 -4.751000
2 -4.531000 29.674000 -1.062000
3 -2.465000 27.513000 1.336000
4 -3.586000 27.580000 4.978000

...

161 3.951000 18.742001 0.732000
162 0.404000 20.135000 0.490000
163 0.711000 20.049999 -3.346000
164 1.520000 16.308001 -3.145000
165 -1.217000 15.280000 -0.638000
0 1 line 0 1
1 1 line 1 2
2 1 line 2 3
3 1 line 3 4
4 1 line 4 5

...

160 1 line 160 161
161 1 line 161 162
162 1 line 162 163
163 1 line 163 164
164 1 line 164 165
4 1 1 1 1
TemperatureFactor, A2
ChainID,
ResNum,
CA,
0 17.270000 65.000000 1.000000 1.000000
1 16.709999 65.000000 2.000000 1.000000
2 19.320000 65.000000 3.000000 1.000000
3 15.130000 65.000000 4.000000 1.000000
4 16.799999 65.000000 5.000000 1.000000

...

161 14.550000 65.000000 162.000000 1.000000
162 15.140000 65.000000 163.000000 1.000000
163 19.200001 65.000000 164.000000 1.000000
164 26.920000 65.000000 165.000000 1.000000
165 28.840000 65.000000 166.000000 1.000000
</pre>