pdbTrans - Revision history

Kinoshita: Created page with "'''pdbTrans''' is Eos's Command that that performs Affine Transform of PDB file. == List of option == === Main option ===
..."
2014-08-18T01:33:53Z

Created page with "'''pdbTrans''' is Eos's Command that that performs Affine Transform of PDB file. == List of option == === Main option === <table border="1"> <div align="left">..."

New page
'''pdbTrans''' is [[Eos]]'s [[Command]] that that performs Affine Transform of [[PDB]] file.

== 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>Essential</td>
<td>Input: [[PDB]]</td>
<td>NULL</td>
</tr>
<tr>
<td>-o</td>
<td>Essential</td>
<td>Output: [[PDB]]</td>
<td>NULL</td>
</tr>
<tr>
<td>-M</td>
<td>Optional</td>
<td>Matrixfile: [[ASCII]](4x4 Matrix)</td>
<td>NULL</td>
</tr>
<tr>
<td>-EA</td>
<td>Optional</td>
<td>[[Euler Angle]]</td>
<td>Mode　0.0　0.0　0.0</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">
<tr>
<th>Value</th>
<th>Description</th>
</tr>
<tr>
<td>0</td>
<td></td>
</tr>
</table>

===-M format===
<pre>
data(0, 0) data(0, 1) data(0, 2) data(0, 3)
data(1, 0) data(1, 1) data(1, 2) data(1, 3)
data(2, 0) data(2, 1) data(2, 2) data(2, 3)
data(3, 0) data(3, 1) data(3, 2) data(3, 3)
</pre>
<div>You can create by using [[matrix3DFromEulerAngle]].</div>

=== [[Euler Angle|Rotation Order]] details ===
<pre>
1st digit: Setting the rotation axis of the first
2nd digit: Setting the order-1 of the rotation axis
O: Order Z -> Y-> X
E: Order Z -> X-> Y
3rd digit: Setting the order-2 of the rotation axis
Y: Keep the order
N: Reverse the order
4th digit: Setting rotation method
S: Rotate the object
N: Move the coordinates
</pre>
<br>
<div>If both -M and -EA are set, -M is run at first, and -EA is run at next.</div>

== Execution example ==
===[[:Media:Input-121P.pdb.zip|Input file]] image===
[[File:121p.png]]<br>
<br>
====Input file details by [[pdbInfo]]====
[[File:121p-Info.png]]<br>
<div>There isn't difference between input and output by default.</div>
<br>

=== Option -M===
====Example1: coordinate transformation by Shear at x-axis====
<table>
<tr>
Matrix file data<br>
<pre>
1.000000 1.000000 1.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 0.000000 0.000000 1.000000
</pre>
</tr>
<tr>
Output image<br>
[[File:Outdata-M-pdbTrans.png]]
</tr>
</table>
<br>

====Example2: coordinate transformation by Reflecting at XY-plane====
<table>
<tr>
Matrix file data<br>
<pre>
1.000000 0.000000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 -1.000000 0.000000
0.000000 0.000000 0.000000 1.000000
</pre>
</tr>
<tr>
Output image<br>
[[File:Outdata-M1-pdbTrans.png]]
</tr>
</table>
<br>

====Example3: coordinate transformation by Rotation at x-axis====
<table>
<tr>
Matrix file data<br>
<pre>
1.000000 0.000000 0.000000 0.000000
0.000000 0.707107 -0.707107 0.000000
0.000000 0.707107 0.707107 0.000000
0.000000 0.000000 0.000000 1.000000
</pre>
</tr>
<tr>
Output image<br>
[[File:Outdata-M2-pdbTrans.png]]
</tr>
</table>
<br>

====Example4: coordinate transform by parallel transformation along x-axis====
<table>
<tr>
Matrix file data<br>
<pre>
1.000000 0.000000 0.000000 1.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 0.000000 0.000000 1.000000
</pre>
</tr>
<tr>
Output image<br>
[[File:Outdata-M3-pdbTrans.png]]
</tr>
</table>
<br>

=== Option -EA===
==== Option -EA ZONS 30 30 30 ====
[[File:121p.ea-pdbTrans.png]]<br>
<br>
<div>*White…Input image, Pink…Output image</div>
<br>