pdbCrystalCreate - Revision history

Kinoshita: Created page with "'''pdbCrystalCreate''' is Eos's Command that creates the crystal structure by PDB file. == List of option == === Main option === ..."
2014-08-08T00:00:31Z
Created page with "'''pdbCrystalCreate''' is Eos's Command that creates the crystal structure by PDB file. == List of option == === Main option === <table border="1"> <tr>..."
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'''pdbCrystalCreate''' is [[Eos]]'s [[Command]] that creates the crystal structure by [[PDB]] file.

== 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>-I</td>
<td>Essential</td>
<td>Input: [[ASCII]](Crystal Information)</td>
<td>NULL</td>
</tr>
<tr>
<td>-o</td>
<td>Essential</td>
<td>Output: [[PDB]]</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>
<br>

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

===-I format===
<pre>
aAxis %15.6g %15.6g %15.6g
bAxis %15.6g %15.6g %15.6g
cAxis %15.6g %15.6g %15.6g
CellLength %15.6g %15.6g %15.6g
Origin %15.6g %15.6g %15.6g
N %15d %15d %15d
StartN %15d %15d %15d
SpaceGroup %15d
HelixInfo %10d %10d %10d
</pre>

<div>Parameter Order is important<br>
Dependent between CellLength and a|b|cAxis.<br>
Because each of aAxis, bAxis, cAxis must be a unit vector.<br>
SpaceGroup: 0: P1Symmmetry(, 1: HelicalSymmmetry(Not implemented)<br>
HelixInfo: turn unit n-strand</div>
<br>

== 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>

=== Option -I===
====Case: input data1====
<div>execute with the following.</div>
<pre>
aAxis 1 0 0
bAxis 1 0 0
cAxis 1 0 0
CellLength 1 1 1
N 2 2 2
StartN 1 1 1

</pre>
<br>

<div>Output</div>
<pre>
aAxis 1 0 0
bAxis 1 0 0
cAxis 1 0 0
CellLength 1 1 1
Origin 0 0 0
N 2 2 2
StartN 1 1 1
SpaceGroup 0
Program Start
1 1 1
3 0 0
pdbFileGoToEndPDB: 14
1 1 2
4 0 0
pdbFileGoToEndPDB: 14
1 2 1
4 0 0
pdbFileGoToEndPDB: 14

...

2 1 2
5 0 0
pdbFileGoToEndPDB: 14
2 2 1
5 0 0
pdbFileGoToEndPDB: 14
2 2 2
6 0 0
pdbFileGoToEndPDB: 14
</pre>
<br>

<div>Output file's image</div>
<table>
<tr>
<td>[[File:Outdata-pdbCrystalCreate.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">1.055301e+01 2.519590e+01 1.189075e+01<br>
3.401123e+01 <br>
26.27 23.85 28.04<br></p>
</td>
</tr>
</table>
<br>

====Case: input data2====
<div>execute with the following.</div>
<pre>
aAxis 1 0 0
bAxis 1 0 0
cAxis 1 0 0
CellLength 1 1 1
Origin 5 5 5
N 2 2 2
StartN 1 1 1

</pre>
<br>

<div>Output file's image</div>
<table>
<tr>
<td><p align="Center">[[File:Outdata1-pdbCrystalCreate.png]]<br>
White is Output file by input data1.<br></p>
</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">1.555301e+01 3.019590e+01 1.689075e+01<br>
3.401123e+01<br>
26.27 23.85 28.04<br></p>
</td>
</tr>
</table>
<br>

====Case: input data3====
<div>execute with the following.</div>
<pre>
aAxis 1 0 0
bAxis 1 0 0
cAxis 0 5 0
CellLength 1 1 1
N 2 2 2
StartN 1 1 1

</pre>
<br>

<div>Output file's image</div>
<table>
<tr>
<td><p align="Center">[[File:Outdata2-pdbCrystalCreate.png]]<br>
White is Output file by input data1.<br></p>
</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">9.053012e+00 2.669590e+01 1.189075e+01<br>
3.386472e+01<br>
25.77 24.35 28.04<br></p>
</td>
</tr>
</table>
<br>

====Case: input data4====
<div>execute with the following.</div>
<pre>
aAxis 1 0 0
bAxis 1 0 0
cAxis 1 0 0
CellLength 10 10 10
N 2 2 2
StartN 1 1 1

</pre>
<br>

<div>Output file's image</div>
<table>
<tr>
<td>[[File:Outdata3-pdbCrystalCreate.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">5.105301e+01 2.519590e+01 1.189075e+01<br>
4.525700e+01<br>
39.77 23.85 28.04<br></p>
</td>
</tr>
</table>
<br>