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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] Change ContinuousContact to use the new mdtraj contact code #352

Closed schwancr closed 10 years ago

schwancr commented 10 years ago

I fixed this bug for the closest-heavy/closest scheme, but it was also present in the calpha scheme and I didn't realize.

rmcgibbo commented 10 years ago

Aren't we about to remove this code anyways?

schwancr commented 10 years ago

Yea, I'll use this PR to use the new wrapper when it's done

On Wed, Feb 12, 2014 at 12:35 PM, Robert McGibbon notifications@github.comwrote:

Aren't we about to remove this code anyways?

Reply to this email directly or view it on GitHubhttps://github.com/SimTk/msmbuilder/pull/352#issuecomment-34914306 .

kyleabeauchamp commented 10 years ago

Yes I suppose there could be value in fixing bugs first to have a reference. On Feb 12, 2014 3:35 PM, "Robert McGibbon" notifications@github.com wrote:

Aren't we about to remove this code anyways?

Reply to this email directly or view it on GitHubhttps://github.com/SimTk/msmbuilder/pull/352#issuecomment-34914306 .

schwancr commented 10 years ago

The -1's were actually buggy. The indices that mdtraj used are already 0-indexed.

kyleabeauchamp commented 10 years ago

Yeah that sounds right, it seemed to double-subtract them.

schwancr commented 10 years ago

Now that rmcgibbo/mdtraj#304 is pulled in, we can use that code

rmcgibbo commented 10 years ago

Yeah. As I mentioned at https://github.com/rmcgibbo/mdtraj/issues/312, we should do an mdtraj release first. Then we can put in an install_requires flag during msmbuilder setup.py to ensure the proper version.

rmcgibbo commented 10 years ago

Okay. I've made the mdtraj-0.7.0 release on pypi/github/binstar.

rmcgibbo commented 10 years ago

I'm closing this. I've fixed this in master now.

rmcgibbo commented 10 years ago

Or atleast in #375