Kinoshita: Created page with "'''pdbPCA''' is Eos's Command for calculating specified axis of atom model. By using Principal Component Analysis(PCA), it calculates 3 orthogonal axis. 1st Pr..."

2014-08-08T02:37:44Z

Created page with "'''pdbPCA''' is Eos's Command for calculating specified axis of atom model. By using Principal Component Analysis(PCA), it calculates 3 orthogonal axis. 1st Pr..."

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'''pdbPCA''' is [[Eos]]'s [[Command]] for calculating specified axis of atom model. By using [[Principal Component Analysis]]([[PCA]]), it calculates 3 orthogonal axis. 1st Principal Component expresses longest direction of molecule.

== List of option ==
=== Main option ===
<table border="1">
<div align="left">
<tr>
<th>Option</th>
<th>Essential/Optional</th>
<th>Description</th>
<th>Default</th>
</tr>
<tr>
<td>-i</td>
<td>Optional</td>
<td>Input: [[PDB]]</td>
<td>stdion(Standard Input if not set)</td>
</tr>
<tr>
<td>-o</td>
<td>Optional</td>
<td>Output: calculated result outputs: [[ASCII]]</td>
<td>stdout(Standard output by default)</td>
</tr>
<tr>
<td>-oU</td>
<td>Optional</td>
<td>Output:Unit Vector: [[ASCII]](Array)</td>
<td>NULL(not output if not set)</td>
</tr>
<tr>
<td>-oM</td>
<td>Optional</td>
<td>Output:Unit Vector: [[ASCII]](Marix3D)</td>
<td>NULL(not output if not set)</td>
</tr>
<tr>
<td>-oPDB</td>
<td>Optional</td>
<td>Output: Atom model rotated by Unit : [[PDB]]<br>
　　　　　　　1st, 2nd, 3rd Principal Axis is x, y, z-axis</td>
<td>NULL(not output if not set)</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>
</div>
</table>

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

== Execution example ==
<pre>
$ pdbPCA -i 1VOM.pdb
Program Start
(0,0):=1149624.289131
(0,1):=-118627.789270
(0,2):=315483.835955
(1,0):=-118627.789270
(1,1):=2010078.268384
(1,2):=-1021173.592972
(2,0):=315483.835955
(2,1):=-1021173.592972
(2,2):=2127164.855685
nrot for PCA: 11
Result
C: covariance matrix
2 3 3
1149624.250000 -118627.789062 315483.843750
-118627.789062 2010078.250000 -1021173.562500
315483.843750 -1021173.562500 2127164.750000
u: unit vector
2 3 3
0.154886 -0.671246 0.724871 # 1st Principal ComponentのEigenvector
0.767707 0.543582 0.339330 # 2nd Principal ComponentのEigenvector
-0.621801 0.503931 0.599514 　　　　# 3rd Principal ComponentのEigenvector
lambda^2: lambda^2
1 3
3140204.500000 1205074.000000 941588.812500
　#1st Principal Component　　　#2nd Principal Component　　　# 3rd Principal Component
</pre>
<br>

===[[:Media:Input-1VOM.pdb.zip |Input file]] details===
<table>
<tr>
<td>[[File:Input-1VOM-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">6.727136e+01 3.631518e+01 -2.983928e+01<br>
5.314867e+01 <br>
40.92 41.49 48.47<br> </p>
</td>
</tr>
</table>
<br>

=== Case: Options only essential ===
<div>-o 's data</div>
<pre>
Result
C: covariance matrix
2 3 3
1149624.250000 -118627.789062 315483.843750
-118627.789062 2010078.250000 -1021173.562500
315483.843750 -1021173.562500 2127164.750000
u: unit vector
2 3 3
0.154886 -0.671246 0.724871
0.767707 0.543582 0.339330
-0.621801 0.503931 0.599514
lambda^2: lambda^2
1 3
3140204.500000 1205074.000000 941588.812500
Averege: Center Position
1 3
66.530304 36.237804 -29.722399
</pre>
<br>

<div>-oU 's data</div>
<pre>
2 3 3
0.154886 -0.671246 0.724871
0.767707 0.543582 0.339330
-0.621801 0.503931 0.599514
</pre>
<br>

<div>-oM 's data</div>
<pre>
0.154886 -0.671246 0.724871
0.767707 0.543582 0.339330
-0.621801 0.503931 0.599514
0.000000 0.000000 0.000000
</pre>
<br>

<div>-oPDB 's data</div>
<table>
<tr>
<td>[[File:Outdata-pdbPCA.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">-3.558668e+01 6.125959e+01 -4.141817e+01<br>
5.314899e+01<br>
48.12 36.21 35.41<br> </p>
</td>
</tr>
</table>
<br>

pdbPCA - Revision history

Kinoshita: Created page with "'''pdbPCA''' is Eos's Command for calculating specified axis of atom model. By using Principal Component Analysis(PCA), it calculates 3 orthogonal axis. 1st Pr..."