SimTk/msmbuilder — pull request #62 by rmcgibbo (2012-09-25 23:23:01+00:00)
Title: Combine SavePDBs.py and GetRandomConfs.py

Addresses @kyleabeauchamp's issue #61

I removed the scripts SavePDBs.py and GetRandomConfs.py and wrote a script that combines the two functionalities. I'm not sure what the name of the new script should be. I called it YankConfs.py, but idk.

Here are the options that basically control how the output files are saved:

```
-f {pdb,xtc,lh5}, --format {pdb,xtc,lh5}
Format for the outputted conformations. PDB is the
standard plaintext protein databank format. XTC is the
gromacs binary trajectory format, and lh5 is the
MSMBuilder standard hdf5 based format. Default: pdb
-S {sep,tps,one}, --style {sep,tps,one}
Controls the number of conformations save per file. If
"sep" (SEPARATE), all of the conformations will be
saved in separate files, named in the format
State{i}-{j}.{ext} for the `j`th conformation sampled
from the `i`th state. If "tps" (Trajectory Per State),
each of the conformations sampled from a given state
`i` will be saved in a single file, named
State{i}.{ext}. If "one", all of the conformations
will be saved in a single file, such that the `j`th
conformation from the `states[i]`-th microstate will
be the `i+j*N`th frame in the trajectory file. The
file will be namaed Confs.{ext} . Default: sep
```