Hi,
I am trying to compute pairwise RMSD which I believe can be accomplished by running CalculatePairwiseRMSD.py script provided with the msmbuilder 2.5.1. However, the script imports HierarchicalClustering Module which is no where to be found. I was wondering if I am missing some package?
Thanks,
Gurpreet
pair wise RMSD calculation
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Robert McGibbon
- Posts: 20
- Joined: Tue Jul 19, 2011 9:25 am
Re: pair wise RMSD calculation
Thanks for the bug report!
No, you're not missing anything -- this is just a bug on our end. If you remove that line in the source code for the script (in scripts/CalculatePairwiseRMSD.py) and then reinstall the package, it should work. As you can see from grepping the source, the HierarchicalClustering module is not ever used (it was at one point, but then some of the code was restructured).
This issue has been fixed in the MSMBuilder 2.6.dev development version, which is hosted on github at https://github.com/SimTk/msmbuilder.
That site is now the main venues through which the developers are communicating and planning new features (and fixing bugs), so if you'd like to contribute to the future development of MSMBuilder either through filing bug reports, logging feature requests, or by contributing code (!), we'd love to have your input.
-Robert
No, you're not missing anything -- this is just a bug on our end. If you remove that line in the source code for the script (in scripts/CalculatePairwiseRMSD.py) and then reinstall the package, it should work. As you can see from grepping the source, the HierarchicalClustering module is not ever used (it was at one point, but then some of the code was restructured).
This issue has been fixed in the MSMBuilder 2.6.dev development version, which is hosted on github at https://github.com/SimTk/msmbuilder.
That site is now the main venues through which the developers are communicating and planning new features (and fixing bugs), so if you'd like to contribute to the future development of MSMBuilder either through filing bug reports, logging feature requests, or by contributing code (!), we'd love to have your input.
-Robert