Given a PDB file, I am interested in getting the list of (pairs of) chains that do interact. Is there already something in IMP to do such things ?
--Ben.S
Not as one command (and it depends what you mean by interact), but for most meanings it isn't hard.
If you want interaction to mean that some leaf particles touch, you can use the core.KClosePairsPairScore eg let ps=core.KClosePairsPairScore(core.SphereDistancePairScore(1), core.LeavesRefiner()), that is score each pair of leaves based on the sphere distance then for each pair of chains if ps(chaina, chainb)<=.01: they interact
If you want more efficiency, you can compute bounding volumes for the chains and use a close pairs container instead of testing all pairs.
On Mar 22, 2011, at 9:10 AM, Benjamin SCHWARZ wrote:
> Given a PDB file, I am interested in getting the list of (pairs of) chains that do interact. Is there already something in IMP to do such things ? > > --Ben.S > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev
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Benjamin SCHWARZ -
Daniel Russel