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msmbuilder / msmbuilder-legacy

Legacy release of MSMBuilder
http://msmbuilder.org
GNU General Public License v2.0
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SaveRawStructure.py into msmbuilder 2.8 #447

Open sryckbos opened 9 years ago

sryckbos commented 9 years ago

Awhile back @rmcgibbo and @schwancr wrote a script for me which saves structures from given states, but also provides the path back to the raw data for what RUN, CLONE, and frame it came from. Was called SaveRawStructure.py. It's been pretty useful for me on several occasions and I'd imagine would be for other people, but it got lost somewhere along the way as I don't see it in my latest 2.8.2 version of msmbuilder. It might need some tinkering since it doesn't seem to use mdtraj but I'd imagine it's something good to have, right?

I still have the old script so I'm fine, but do you think it should be in there or would be useful to others?

Trayder commented 9 years ago

This would be very useful. When I cluster with subset of my systems atoms (e.g. remove water for convenience/speed/memory usage) it's not possible to recover the complete system without tracing back through Assignments.h5 (which requires scripting to read).