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[WIP] Tpt2.8: same commits as before but ontop of the newest master. #429
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…rycecr used in msmexplorer as suggested in Frank Noe's paper on TPT. Additionally I re-wrote the dijkstra code so that it's a bit more readable and added a lot of comments. Conflicts: scripts/FindPaths.py I'll have to re-edit this script.
Conflicts: MSMBuilder/tpt.py
… FindPaths test since it was written for the old code. I don't think it's necessary to have a test other than knowing if it actually runs since it just has two lines: tpt.calculate_net_fluxes and tpt.get_paths Conflicts: tests/test_tpt.py
… since the other test is an example where I know the answer. It would be nice, however to have a transition matrix with a known flux. This also shouldn't be difficult to generate, just have to think it up.
schwancr
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see PR #257