choderalab/msm-tis — pull request #45 by dwhswenson (2014-10-28 15:32:38+00:00)
Title: Calculations & Factories

Added `Calculation` class, with `Bootstrapping` as the first example of it. The `ala_dipeptide_example.py` example file runs the bootstrapping in a simple way. Added a cheap `ala_dipeptide_analysis.py` script to check the max value of the order parameter for each trajectory (note: this doesn't distinguish between accepted and rejected).

Also added factories and factory methods for a few conveniences: `TISEnsembleSet`, `VolumeSet` (needed for `TISEnsembleSet`), and `OneWayShootingSet`. These generate a list of objects of the specified type, making is really easy to set up all your TISEnsembles and OneWayShooters from a list of minima/maxima that define your volumes. (Look at lines [197-206 of `ala_dipeptide_example`](https://github.com/dwhswenson/msm-tis/compare/calculation?expand=1#diff-55af4a266c6175ee78ac8a5e69ade559R197) to see how easy it is.)

More calculation objects to come (in particular, TIS), but issuing PR now because we're hitting a point where we can actually play with some of these things.