rmcgibbo/mixtape — pull request #53 by rmcgibbo (2014-02-25 08:44:06+00:00)
Title: New command for structures

Example

```
$ head structures.csv
# command: /home/rmcgibbo/miniconda/bin/hmsm sample-ghmm -i hmms.jsonlines --featurizer atoms.pkl --n-states 5 --lag-time 1 --dir ~/local/msmbuilder/Tutorial/XTC/RUN* --ext xtc --top /home/rmcgibbo/local/msmbuilder/Tutorial/native.pdb --n-per-state 100
,filename,index,state
0,/home/rmcgibbo/local/msmbuilder/Tutorial/XTC/RUN85/frame0.xtc,338,0
1,/home/rmcgibbo/local/msmbuilder/Tutorial/XTC/RUN91/frame0.xtc,344,0
2,/home/rmcgibbo/local/msmbuilder/Tutorial/XTC/RUN51/frame0.xtc,198,0
3,/home/rmcgibbo/local/msmbuilder/Tutorial/XTC/RUN52/frame0.xtc,220,0
4,/home/rmcgibbo/local/msmbuilder/Tutorial/XTC/RUN62/frame0.xtc,356,0
5,/home/rmcgibbo/local/msmbuilder/Tutorial/XTC/RUN13/frame0.xtc,428,0
6,/home/rmcgibbo/local/msmbuilder/Tutorial/XTC/RUN96/frame0.xtc,319,0
7,/home/rmcgibbo/local/msmbuilder/Tutorial/XTC/RUN05/frame0.xtc,86,0
rmcgibbo@vspm9 ~/projects/mixtape ‹structures›
$ hmsm structures structures.csv --top ~/local/msmbuilder/Tutorial/native.pdb --ext xtc --prefix samples
saving samples-0.xtc...
saving samples-1.xtc...
saving samples-2.xtc...
saving samples-3.xtc...
saving samples-4.xtc...
done
```