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Robust #28

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Description

Fixed two "TODOs" from last time:

  1. Made chain identification more robust by it's relative position in the chain list (the actual order by which MDtraj reads in the coordinates) instead of translating letters into integers.
  2. Enabled using MDTraj DSL for atom selection
  3. Cleaned up features so it totally matches the Dunbrack paper.

Todos

Notable points that this PR has either accomplished or will accomplish.

  • TODO 1

Questions

  • Question1

Status

  • Ready to go

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@jiayeguo