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Output - Revision history
2024-03-28T10:39:59Z
Revision history for this page on the wiki
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Frodo at 04:01, 14 February 2014
2014-02-14T04:01:11Z
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 04:01, 14 February 2014</td>
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<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; 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><ins style="font-weight: bold; text-decoration: none;">OBSOLETE</ins></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; 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><ins style="font-weight: bold; text-decoration: none;">DOCK 6 reports several kinds of information as output which is either written to screen in interactive mode or written to file in batch mode (see Installation). All input parameters are echoed into the output. If a parameter is not needed it is not reported in the output. At the completion of each DOCK run, the number of molecules that were processed and the total time of the calculation is reported.</ins></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; 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><del style="font-weight: bold; text-decoration: none;"> DOCK reports several kinds </del>of <del style="font-weight: bold; text-decoration: none;">information as output which is either written to screen in interactive mode or written to file in batch mode (see Installation). All input parameters </del>are <del style="font-weight: bold; text-decoration: none;">echoed into the output. If a parameter is not needed it is not reported </del>in the <del style="font-weight: bold; text-decoration: none;">output</del>. <del style="font-weight: bold; text-decoration: none;">At </del>the <del style="font-weight: bold; text-decoration: none;">completion </del>of each <del style="font-weight: bold; text-decoration: none;">DOCK run</del>, the number of <del style="font-weight: bold; text-decoration: none;">molecules </del>that <del style="font-weight: bold; text-decoration: none;">were processed </del>and the <del style="font-weight: bold; text-decoration: none;">total time of </del>the <del style="font-weight: bold; text-decoration: none;">calculation is reported</del>.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; 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><ins style="font-weight: bold; text-decoration: none;">The results </ins>of <ins style="font-weight: bold; text-decoration: none;">each molecule </ins>are <ins style="font-weight: bold; text-decoration: none;">printed </ins>in the <ins style="font-weight: bold; text-decoration: none;">outfile as well</ins>. <ins style="font-weight: bold; text-decoration: none;">Depending on </ins>the <ins style="font-weight: bold; text-decoration: none;">combination </ins>of <ins style="font-weight: bold; text-decoration: none;">user parameters, </ins>each <ins style="font-weight: bold; text-decoration: none;">molecule entry will contain the number of anchors used (see Identification of Rigid Segments)</ins>, the number of <ins style="font-weight: bold; text-decoration: none;">orientations </ins>that <ins style="font-weight: bold; text-decoration: none;">passed pruning (see Orienting the Ligand), the number of fully grown conformations that passed pruning (see Pruning the Conformation Search Tree), </ins>and <ins style="font-weight: bold; text-decoration: none;">a breakdown of </ins>the <ins style="font-weight: bold; text-decoration: none;">interaction energy between </ins>the <ins style="font-weight: bold; text-decoration: none;">ligand and receptor (see Scoring)</ins>.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; 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><del style="font-weight: bold; text-decoration: none;"> The results of each molecule are printed in the outfile as well. Depending on the combination of user parameters, each molecule entry will contain the number of anchors used (see Identification of Rigid Segments), the number of orientations that passed pruning (see Orienting the Ligand), the number of fully grown conformations that passed pruning (see Pruning the Conformation Search Tree), and a breakdown of the interaction energy between the ligand and receptor (see Scoring).</del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; 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>Example Molecule Section of Output</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; 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 colspan="2" class="diff-side-added"></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; 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><del style="font-weight: bold; text-decoration: none;"> </del>Example Molecule Section of Output</div></td><td colspan="2" class="diff-side-added"></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> _______________________________________________</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> _______________________________________________</div></td></tr>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> vdw: -26.868692</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> vdw: -26.868692</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> es: -2.254913</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> es: -2.254913</div></td></tr>
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Frodo
http://wiki.docking.org/index.php?title=Output&diff=3884&oldid=prev
Therese: 1 revision
2012-10-08T20:31:13Z
<p>1 revision</p>
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<td colspan="1" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="1" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 20:31, 8 October 2012</td>
</tr><tr><td colspan="2" class="diff-notice" lang="en"><div class="mw-diff-empty">(No difference)</div>
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Therese
http://wiki.docking.org/index.php?title=Output&diff=3883&oldid=prev
JohnIrwin at 22:59, 19 September 2006
2006-09-19T22:59:55Z
<p></p>
<p><b>New page</b></p><div><br />
<br />
DOCK reports several kinds of information as output which is either written to screen in interactive mode or written to file in batch mode (see Installation). All input parameters are echoed into the output. If a parameter is not needed it is not reported in the output. At the completion of each DOCK run, the number of molecules that were processed and the total time of the calculation is reported.<br />
<br />
The results of each molecule are printed in the outfile as well. Depending on the combination of user parameters, each molecule entry will contain the number of anchors used (see Identification of Rigid Segments), the number of orientations that passed pruning (see Orienting the Ligand), the number of fully grown conformations that passed pruning (see Pruning the Conformation Search Tree), and a breakdown of the interaction energy between the ligand and receptor (see Scoring).<br />
<br />
Example Molecule Section of Output<br />
<br />
_______________________________________________<br />
Molecule: C1<br />
Anchors: 1<br />
Orientations: 1<br />
Conformations: 1<br />
<br />
Grid Score: -29.223606<br />
<br />
vdw: -26.868692<br />
es: -2.254913</div>
JohnIrwin