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moldyn/mathmech/docs/eng/help_agl.html
arcan1s 6b0a2a47db Release 1.1.0 
+ added help window
+ added help docs
+ small bug fixes
2013-09-03 06:01:23 +04:00

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<p align="center" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">agl</span></p>
<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br />Program that creates PDB file with chosen agglomerate.</p>
<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />mm_agl -a FILE -i FILE -c X,Y,Z -o FILE [ -l FILE ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-a FILE – input file with agglomerate<br />-i FILE – input trajectory file<br />-c X,Y,Z – cell size, A<br />-o FILE – output PDB file<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p>
<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p>
<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Agglomerate file (*.agl)</span></p>
<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Agglomerate title (AGL=2=1.3.4.) (1 – number of molecules in the agglomerate, 1.3.4. – agglomerate class, if verification of isomorphism is specified).</li>
<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The enumeration of molecules in the agglomerate (0000001=2,3,4,5,) (1 – number of molecule (7 characters), equal sign, the enumeration of connected molecules separated by commas).</li></ul>
<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Trajectory file (*.pdb)</span></p>
<p align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><a href="http://www.wwpdb.org/documentation/format33/sect9.html"><span style=" text-decoration: underline; color:#0000ff;">http://www.wwpdb.org/documentation/format33/sect9.html</span></a></p>
<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Operation of the application</span></p>
<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading titles of source files, setting values of initial variables.</li>
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Reading of source file.</li>
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Search for the best configuration.</li>
<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Print the result to the file.</li></ol>
<p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Working with GUI</span></p>
<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Select Menu -&gt; File creator -&gt; Agglomerate file.</li>
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the file generated by statgen. Push &quot;Select&quot;.</li>
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Select the trajectory file from the drop down list. Select the agglomerate.</li>
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output file. Create file.</li>
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Go to the tab &quot;Generate PDB&quot;. Select &quot;From agglomerate&quot; from the drop down list.</li>
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the work directory.</li>
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the input trajectory file.</li>
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the agglomerate file.</li>
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the cell size, A.</li>
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the output PDB file.</li>
<li align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Set the log file if this needed.</li>
<li align="justify" style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Run application.</li></ol></body></html>
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