View source for vector2pdb

'''vector2pdb''' is [[Eos]]'s [[Command]]  that creates [[PDB]] file by inputting parameter.


== 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>-o</td> 
				<td>Optional</td> 
				<td>Output: [[PDB]]</td> 
				<td>stdout</td> 
			</tr> 
			<tr> 
				<td>-v</td> 
				<td>Optional</td> 
				<td>Input: Vector: (vx, vy, vz)</td> 
				<td>(1, 0, 0)</td> 
			</tr> 
			<tr> 
				<td>-polar</td> 
				<td>Optional</td> 
				<td>Input: Vector[degree]: (phi, theta)</td> 
				<td>(0, 0)</td> 
			</tr> 
			<tr> 
				<td>-polarz</td> 
				<td>Optional</td> 
				<td>Input: z-axis for polar: (zx, zy, zz)</td> 
				<td>(0, 0, 1)</td> 
			</tr> 
			<tr> 
				<td>-polarx</td> 
				<td>Optional</td> 
				<td>Input: x-axis for polar: (xx, xy, xz)</td> 
				<td>(1, 0, 0)</td> 
			</tr> 
			<tr> 
				<td>-ori</td> 
				<td>Optional</td> 
				<td>Input: origin: (sx, sy, sz)</td> 
				<td>(0, 3, 0)</td> 
			</tr> 
			<tr> 
				<td>-step</td> 
				<td>Optional</td> 
				<td>Input: step: [A]</td> 
				<td>1.6</td> 
			</tr> 
			<tr> 
				<td>-n</td> 
				<td>Optional</td> 
				<td>Input: Number Of CA</td> 
				<td>20</td> 
			</tr> 
			<tr> 
				<td>-ID</td> 
				<td>Optional</td> 
				<td>Input: Chain ID</td> 
				<td>A</td> 
			</tr> 
			<tr> 
				<td>-Res</td> 
				<td>Optional</td> 
				<td>Input: Chain ID</td> 
				<td>GLY</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 ==
=== Case: Options only essential ===
	<table> 
		<tr> 
			<td>[[File:Outdata-vector2pdb.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">1.520000e+01    3.000000e+00    0.000000e+00<br> 
				1.520000e+01 <br> 
				15.20       0.00       0.00<br> </p>
			</td> 
		</tr> 
	</table> 


=== Option -v===
====Case: v=(1, 2, 3)==== 
	<table> 
		<tr> 
			<td>[[File:Outdata-v-vector2pdb.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">4.062400e+00    1.112470e+01    1.218715e+01<br> 
				1.520002e+01 <br> 
				4.06       8.12      12.19<br> </p>
			</td> 
		</tr> 
	</table> 


=== Option -polar===
====Case: polar=(30, 45), v=(1, 2, 3)==== 
	<table> 
		<tr> 
			<td>[[File:Outdata-polar-vector2pdb.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">9.308100e+00    8.374000e+00    1.074800e+01<br> 
				1.520000e+01<br> 
				9.31       5.37      10.75<br> </p>
			</td> 
		</tr> 
	</table>


=== Option -polarz===
====Case: polarz=(3, 2, 1), polar=(30, 45), v=(1, 2, 3)==== 
	<table> 
		<tr> 
			<td>[[File:Outdata-polarz-vector2pdb.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">1.377120e+01    9.259950e+00   -1.485850e+00<br> 
				1.520002e+01 <br> 
				13.77       6.26       1.49<br> </p>
			</td> 
		</tr> 
	</table>


=== Option -polarx===
====Case: polarx=(1, 2, 3), polar=(30, 45), v=(1, 2, 3)==== 
	<table> 
		<tr> 
			<td>[[File:Outdata-polarx-vector2pdb.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">-1.781550e+00    8.668600e+00    1.399045e+01<br> 
				1.519999e+01 <br> 
				1.78       5.67      13.99<br> </p>
			</td> 
		</tr> 
	</table>


=== Option -ori===
====Case: ori=(7, 3, 5), v=(1, 2, 3)==== 
	<table> 
		<tr> 
			<td>[[File:Outdata-ori-vector2pdb.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">1.106240e+01    1.112470e+01    1.718715e+01<br> 
				1.520002e+01 <br> 
				4.06       8.12      12.19<br> </p>
			</td> 
		</tr> 
	</table>


=== Option -step===
====Case: step=3.2, v=(1, 2, 3)==== 
	<table> 
		<tr> 
			<td>[[File:Outdata-step-vector2pdb.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">8.124700e+00    1.924945e+01    2.437420e+01<br> 
				3.039995e+01<br> 
				8.12      16.25      24.37<br> </p>
			</td> 
		</tr> 
	</table>


=== Option -n===
====Case: n=30, v=(1, 2, 3)==== 
	<table> 
		<tr> 
			<td>[[File:Outdata-n-vector2pdb.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">6.200467e+00    1.540090e+01    1.860140e+01<br> 
				2.320029e+01<br> 
				6.20      12.40      18.60<br> </p>
			</td> 
		</tr> 
	</table>