http://www.yasunaga-lab.bio.kyutech.ac.jp/Eos/index.php?action=history&feed=atom&title=vector2pdb
vector2pdb - Revision history
2026-05-04T20:05:40Z
Revision history for this page on the wiki
MediaWiki 1.23.6
http://www.yasunaga-lab.bio.kyutech.ac.jp/Eos/index.php?title=vector2pdb&diff=3349&oldid=prev
Kinoshita: /* List of option */
2014-08-18T05:36:42Z
<p><span dir="auto"><span class="autocomment">List of option</span></span></p>
<table class='diff diff-contentalign-left'>
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr style='vertical-align: top;'>
<td colspan='2' style="background-color: white; color:black; text-align: center;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 05:36, 18 August 2014</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 14:</td>
<td colspan="2" class="diff-lineno">Line 14:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div> <td>-o</td>  </div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div> <td>-o</td>  </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div> <td>Optional</td>  </div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div> <td>Optional</td>  </div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div> <td>Output: PDB</td>  </div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> <td>Output: <ins class="diffchange diffchange-inline">[[</ins>PDB<ins class="diffchange diffchange-inline">]]</ins></td>  </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div> <td>stdout</td>  </div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div> <td>stdout</td>  </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div> </tr>  </div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div> </tr>  </div></td></tr>
<tr><td colspan="2" class="diff-lineno">Line 101:</td>
<td colspan="2" class="diff-lineno">Line 101:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div> <td></td>  </div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div> <td></td>  </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div> </tr>  </div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div> </tr>  </div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div> </table>  </div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </table></div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div> </div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>== Execution example ==</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>== Execution example ==</div></td></tr>
</table>
Kinoshita
http://www.yasunaga-lab.bio.kyutech.ac.jp/Eos/index.php?title=vector2pdb&diff=3348&oldid=prev
Kinoshita: Created page with "'''vector2pdb''' is Eos's Command that creates PDB file by inputting parameter. == List of option == === Main option === <table border="1"> <tr> <th>O..."
2014-08-18T05:35:38Z
<p>Created page with "'''vector2pdb''' is <a href="/Eos/index.php/Eos" title="Eos">Eos</a>'s <a href="/Eos/index.php/Command" title="Command">Command</a> that creates <a href="/Eos/index.php/PDB" title="PDB">PDB</a> file by inputting parameter. == List of option == === Main option === <table border="1"> <tr> <th>O..."</p>
<p><b>New page</b></p><div>'''vector2pdb''' is [[Eos]]'s [[Command]] that creates [[PDB]] file by inputting parameter.<br />
<br />
<br />
== List of option ==<br />
=== Main option ===<br />
<table border="1"><br />
<tr> <br />
<th>Option</th> <br />
<th>Essential/Optional</th> <br />
<th>Description</th> <br />
<th>Default</th> <br />
</tr> <br />
<tr> <br />
<td>-o</td> <br />
<td>Optional</td> <br />
<td>Output: PDB</td> <br />
<td>stdout</td> <br />
</tr> <br />
<tr> <br />
<td>-v</td> <br />
<td>Optional</td> <br />
<td>Input: Vector: (vx, vy, vz)</td> <br />
<td>(1, 0, 0)</td> <br />
</tr> <br />
<tr> <br />
<td>-polar</td> <br />
<td>Optional</td> <br />
<td>Input: Vector[degree]: (phi, theta)</td> <br />
<td>(0, 0)</td> <br />
</tr> <br />
<tr> <br />
<td>-polarz</td> <br />
<td>Optional</td> <br />
<td>Input: z-axis for polar: (zx, zy, zz)</td> <br />
<td>(0, 0, 1)</td> <br />
</tr> <br />
<tr> <br />
<td>-polarx</td> <br />
<td>Optional</td> <br />
<td>Input: x-axis for polar: (xx, xy, xz)</td> <br />
<td>(1, 0, 0)</td> <br />
</tr> <br />
<tr> <br />
<td>-ori</td> <br />
<td>Optional</td> <br />
<td>Input: origin: (sx, sy, sz)</td> <br />
<td>(0, 3, 0)</td> <br />
</tr> <br />
<tr> <br />
<td>-step</td> <br />
<td>Optional</td> <br />
<td>Input: step: [A]</td> <br />
<td>1.6</td> <br />
</tr> <br />
<tr> <br />
<td>-n</td> <br />
<td>Optional</td> <br />
<td>Input: Number Of CA</td> <br />
<td>20</td> <br />
</tr> <br />
<tr> <br />
<td>-ID</td> <br />
<td>Optional</td> <br />
<td>Input: Chain ID</td> <br />
<td>A</td> <br />
</tr> <br />
<tr> <br />
<td>-Res</td> <br />
<td>Optional</td> <br />
<td>Input: Chain ID</td> <br />
<td>GLY</td> <br />
</tr> <br />
<tr> <br />
<td>-c</td> <br />
<td>Optional</td> <br />
<td>ConfigurationFile</td> <br />
<td>NULL</td> <br />
</tr> <br />
<tr> <br />
<td>-m</td> <br />
<td>Optional</td> <br />
<td>Mode</td> <br />
<td>0</td> <br />
</tr> <br />
<tr> <br />
<td>-h</td> <br />
<td>Optional</td> <br />
<td>Help</td> <br />
<td> </td> <br />
</tr> <br />
</table> <br />
<br />
=== -m details ===<br />
<table border="1"><br />
<tr> <br />
<th>Value</th> <br />
<th>Description</th> <br />
</tr> <br />
<tr> <br />
<td>0</td> <br />
<td></td> <br />
</tr> <br />
</table> <br />
<br />
<br />
== Execution example ==<br />
=== Case: Options only essential ===<br />
<table> <br />
<tr> <br />
<td>[[File:Outdata-vector2pdb.png]]</td> <br />
<td><p align="left">Gravity Centre(CA)<br> <br />
Atom far from Centre(CA)<br> <br />
Atom far from Centre(CA, Axis)<br> </p><br />
</td> <br />
<td><p align="left">1.520000e+01 3.000000e+00 0.000000e+00<br> <br />
1.520000e+01 <br> <br />
15.20 0.00 0.00<br> </p><br />
</td> <br />
</tr> <br />
</table> <br />
<br />
<br />
=== Option -v===<br />
====Case: v=(1, 2, 3)==== <br />
<table> <br />
<tr> <br />
<td>[[File:Outdata-v-vector2pdb.png]]</td> <br />
<td><p align="left">Gravity Centre(CA)<br> <br />
Atom far from Centre(CA)<br> <br />
Atom far from Centre(CA, Axis)<br> </p><br />
</td> <br />
<td><p align="left">4.062400e+00 1.112470e+01 1.218715e+01<br> <br />
1.520002e+01 <br> <br />
4.06 8.12 12.19<br> </p><br />
</td> <br />
</tr> <br />
</table> <br />
<br />
<br />
=== Option -polar===<br />
====Case: polar=(30, 45), v=(1, 2, 3)==== <br />
<table> <br />
<tr> <br />
<td>[[File:Outdata-polar-vector2pdb.png]]</td> <br />
<td><p align="left">Gravity Centre(CA)<br> <br />
Atom far from Centre(CA)<br> <br />
Atom far from Centre(CA, Axis)<br> </p><br />
</td> <br />
<td><p align="left">9.308100e+00 8.374000e+00 1.074800e+01<br> <br />
1.520000e+01<br> <br />
9.31 5.37 10.75<br> </p><br />
</td> <br />
</tr> <br />
</table><br />
<br />
<br />
=== Option -polarz===<br />
====Case: polarz=(3, 2, 1), polar=(30, 45), v=(1, 2, 3)==== <br />
<table> <br />
<tr> <br />
<td>[[File:Outdata-polarz-vector2pdb.png]]</td> <br />
<td><p align="left">Gravity Centre(CA)<br> <br />
Atom far from Centre(CA)<br> <br />
Atom far from Centre(CA, Axis)<br> </p><br />
</td> <br />
<td><p align="left">1.377120e+01 9.259950e+00 -1.485850e+00<br> <br />
1.520002e+01 <br> <br />
13.77 6.26 1.49<br> </p><br />
</td> <br />
</tr> <br />
</table><br />
<br />
<br />
=== Option -polarx===<br />
====Case: polarx=(1, 2, 3), polar=(30, 45), v=(1, 2, 3)==== <br />
<table> <br />
<tr> <br />
<td>[[File:Outdata-polarx-vector2pdb.png]]</td> <br />
<td><p align="left">Gravity Centre(CA)<br> <br />
Atom far from Centre(CA)<br> <br />
Atom far from Centre(CA, Axis)<br> </p><br />
</td> <br />
<td><p align="left">-1.781550e+00 8.668600e+00 1.399045e+01<br> <br />
1.519999e+01 <br> <br />
1.78 5.67 13.99<br> </p><br />
</td> <br />
</tr> <br />
</table><br />
<br />
<br />
=== Option -ori===<br />
====Case: ori=(7, 3, 5), v=(1, 2, 3)==== <br />
<table> <br />
<tr> <br />
<td>[[File:Outdata-ori-vector2pdb.png]]</td> <br />
<td><p align="left">Gravity Centre(CA)<br> <br />
Atom far from Centre(CA)<br> <br />
Atom far from Centre(CA, Axis)<br> </p><br />
</td> <br />
<td><p align="left">1.106240e+01 1.112470e+01 1.718715e+01<br> <br />
1.520002e+01 <br> <br />
4.06 8.12 12.19<br> </p><br />
</td> <br />
</tr> <br />
</table><br />
<br />
<br />
=== Option -step===<br />
====Case: step=3.2, v=(1, 2, 3)==== <br />
<table> <br />
<tr> <br />
<td>[[File:Outdata-step-vector2pdb.png]]</td> <br />
<td><p align="left">Gravity Centre(CA)<br> <br />
Atom far from Centre(CA)<br> <br />
Atom far from Centre(CA, Axis)<br> </p><br />
</td> <br />
<td><p align="left">8.124700e+00 1.924945e+01 2.437420e+01<br> <br />
3.039995e+01<br> <br />
8.12 16.25 24.37<br> </p><br />
</td> <br />
</tr> <br />
</table><br />
<br />
<br />
=== Option -n===<br />
====Case: n=30, v=(1, 2, 3)==== <br />
<table> <br />
<tr> <br />
<td>[[File:Outdata-n-vector2pdb.png]]</td> <br />
<td><p align="left">Gravity Centre(CA)<br> <br />
Atom far from Centre(CA)<br> <br />
Atom far from Centre(CA, Axis)<br> </p><br />
</td> <br />
<td><p align="left">6.200467e+00 1.540090e+01 1.860140e+01<br> <br />
2.320029e+01<br> <br />
6.20 12.40 18.60<br> </p><br />
</td> <br />
</tr> <br />
</table></div>
Kinoshita