I&#39;d look at one of the general graph libraries (eg networkx in python or boost.graph in c++) for the graph data management and than map things to connectivity restraints as appropriate. <div><br></div><div>      Daniel<span></span><br>
<br>On Friday, November 1, 2013, Hongzhu Cui  wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi, Daniel,<div><br></div><div>Many Thanks.</div>
<div><br></div><div>We would like to input a network, which means a set of binary proteins with interaction, and hope IMP could produce a graph of the network. Also, we want to represent some biological restraints on the protein-protein interaction we generalized in IMP, reduce some interactions and optimize the network. </div>

<div><br></div><div>So, could you give me some more advice?</div><div><br></div><div>Thank,again,</div><div>Hongzhu</div></div><div class="gmail_extra"><br clear="all"><div><div dir="ltr"><div>--<br></div><div>Hongzhu Cui, PhD Student<br>

</div><div><br></div><div>University of Missouri</div><div>Informatics Institute</div><div>246 Engineering Building West</div><div>Columbia, MO 65211</div><div>phone: +1(573)239-1592</div><div>e-mail: <a href="javascript:_e({}, &#39;cvml&#39;, &#39;cuihzh@gmail.com&#39;);" target="_blank">cuihzh@gmail.com</a>;</div>

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<br><br><div class="gmail_quote">2013/11/1 Daniel Russel <span dir="ltr">&lt;<a href="javascript:_e({}, &#39;cvml&#39;, &#39;drussel@gmail.com&#39;);" target="_blank">drussel@gmail.com</a>&gt;</span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">

<div dir="ltr">Can you provide a bit more information about what you want to do with the network? Are you looking to find a structure? Or produce a graph of the network at the end?<div><br></div><div>The connectivity restraints may be something you want to look at core::ConnectivityRestraint and core::MSConnectivityRestraint and atom::create_connectivity_restraint().</div>


</div><div class="gmail_extra"><br><br><div class="gmail_quote"><div><div>On Thu, Oct 31, 2013 at 10:13 PM, Hongzhu Cui <span dir="ltr">&lt;<a href="javascript:_e({}, &#39;cvml&#39;, &#39;cuihzh@gmail.com&#39;);" target="_blank">cuihzh@gmail.com</a>&gt;</span> wrote:<br>


</div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div><div dir="ltr"><br clear="all"><div><div>Hi, all, </div></div><div><br></div><div>Recently, I have a project with IMP. Basically, we need to represent a protein-protein interaction network in IMP, and then we add some restraints to see how we could optimize this network. But I stuck on this problem, and I did not find any similar example in the Manual documentation.</div>



<div><br></div><div>Thanks &amp; Regards,</div><div>Hongzhu</div>
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