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Change analysis.distances.contact_matrix to use capped_distance #2102

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richardjgowers opened this Issue Oct 11, 2018 · 1 comment

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@richardjgowers
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richardjgowers commented Oct 11, 2018

So currently we have contact_matrix:
https://github.com/MDAnalysis/mdanalysis/blob/develop/package/MDAnalysis/analysis/distances.py#L59

Which finds all contacts within a certain distance and returns a sometimes sparse boolean array

This should use lib.distances.self_capped_distance so that it doesn't do the full 0.5 * N * (N-1) search

Todo:

  • verify that this is faster
  • add benchmark to benchmarks/ (will also be visible in the existing leaflet benchmark)
  • change contact_matrix to use self_capped_distance
@orbeckst

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orbeckst commented Oct 11, 2018

our leafletfinder should also use it

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