Re: [IMP-dev] define/compute interfaces between biological objects
To: List for IMP development <>
Subject: Re: [IMP-dev] define/compute interfaces between biological objects
From: Daniel Russel <>
Date: Tue, 22 Mar 2011 10:19:12 -0700
Reply-to: List for IMP development <>
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
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