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msmbuilder / msmbuilder-legacy

Legacy release of MSMBuilder
http://msmbuilder.org
GNU General Public License v2.0
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[WIP] Rework metrics to use mdtraj #264

Closed mpharrigan closed 10 years ago

mpharrigan commented 11 years ago

Changing metrics/ and geometry/ to use mdtraj

Sorry again about eclipse fixing all the whitespace. Use diff -w

kyleabeauchamp commented 10 years ago

Thanks for taking care of this. Looks like a good start. I guess we still need to finalize "how" drastic the changes in metrics will be for 2.8, given that Robert and Christian have giant plans for MSMB3.

schwancr commented 10 years ago

since we're deleting the entire msmbuilder.geometry module, could we add some sort of link or warning when someone tries to import it, and tell the user to use mdtraj.geometry?

schwancr commented 10 years ago

I guess we still need to finalize "how" drastic the changes in metrics will be for 2.8, given that Robert and Christian have giant plans for MSMB3.

I think we should just get things working, but not worry about making it pretty since we will be switching to features rather than metrics.

kyleabeauchamp commented 10 years ago

Agreed.

mpharrigan commented 10 years ago

I merged @schwancr 's changes into my PR.

I've started testing the changes. I've tested:

For Dihedral clustering to work, you need my PR for mdtraj as well

schwancr commented 10 years ago

since @rmcgibbo is incapacitated at the moment, why don't we divvy up the remaining files. This shouldn't be too complicated. @mpharrigan can you make a list of files that you haven't done yet and then we can split the work?

kyleabeauchamp commented 10 years ago

So is the plan for 2.8 to still essentially require the use of HDF5 trajectories?

mpharrigan commented 10 years ago

I think I've made a first pass at all the relevant files in src/. There are still some Scripts (e.g. CalculateProjectRMSD) that I haven't done

At this point, I think we should start testing all the functionality to see where things break. Just fixing Cluster.py turned up a lot of issues I thought I had taken care of

rmcgibbo commented 10 years ago

I started working on this, and cleaning up the scripts. I also added a PR for a new md.iterload on mdtraj which will make a couple things easier: https://github.com/rmcgibbo/mdtraj/pull/243.