msmbuilder-legacy

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Change `reduce` to `reduction`?

1

Not sure if people have issues with overwriting standard function names with our modules

kyleabeauchamp

Anyone find the positional script arguments confusing?

2

So my one beef with the current scripts is how the meaning of various flags _changes_ as you move from left to right. I know we're short on characters, but...

kyleabeauchamp

So right now, we have a MinLength validator. However, there is one slight problem in that it requires us to load the trajectory to determine if the length is sufficient....

kyleabeauchamp

Use Pandas for Assignments?

39

kyleabeauchamp

Better sanity checks in ConvertProjectToHDF.py

3

We have the machinery set up to do this (validators), but I don't think the script actually uses any of it! This would have prevented issue #309

schwancr

CalculateImpliedTimescales.py crashes using assignments given by AssignHierarchical.py

5

Following on from the issue I raised earlier (#295), I'm having troubles with the CalculateImpliedTimescales.py script when working with assignments generated by AssignHierarchical.py. This does not seem to occur when...

s-gordon

Unit tests for various Project Builder failure modes

2

So there are a lot of edge cases in the project building. It might be good to create a wider variety of tests to see how these edge cases are...

kyleabeauchamp

Include an option in ConvertDataToHDF to convert trajectories when all trajectories are in a single folder instead of a directory tree.

1

diwakarshukla

Reorganize docs slightly

2

Re #271 So I think the current "main" tutorial is pretty good. Maybe for the second tutorial, we should _just_ do Ward / alternative clustering / RMSD choices. Then, we...

kyleabeauchamp

Continuous contact pairs read indexed from 0

1

I'm using the ContinuousContact metric, and noticed that my residue pairs, when passed in as indexed from 1 as ResidueID is were off. Passing an array with Residue ID indexed...

mlawrenz