rmcgibbo/mixtape — pull request #15 by rmcgibbo (2014-02-16 02:56:40+00:00)
Title: [WIP] New command line interface

Based on subcommands. cc @gkiss

```
$ hmsm -h
usage: hmsm [-h] {fit-em,atomindices} ...

Hidden Markov Models of Biomolecular Dynamics

positional arguments:
{fit-em,atomindices}
fit-em Fit a gaussian fusion hidden Markov models with EM
atomindices Create index file for atoms or distance pairs

optional arguments:
-h, --help show this help message and exit
```

```
$ hmsm atomindices -h
usage: hmsm atomindices [-h] -p PDB (-d | -a)
(--minimal | --heavy | --alpha | --all) -o OUT

Create index file for atoms or distance pairs

optional arguments:
-h, --help show this help message and exit
-p PDB, --pdb PDB Path to PDB file
-o OUT, --out OUT Path to output file

Mode: Choose One

-d, --distance-pairs Create a 2-dimensional index file with (N choose 2)
rows and 2 columns, where each row specifies a pair of
indices. All (N choose 2) pairs of the selected atoms
will be written.
-a, --atoms Create a 1-dimensional index file containing the
indices of the selected atoms.

Selection Criteria: Choose One

--minimal Keep the atoms in protein residues with names CA, CB,
C, N, O, (recommended).
--heavy All non-hydrogen atoms that are not symmetry
equivalent. By symmetry equivalent, we mean atoms
identical under an exchange of labels. For example,
heavy will exclude the two pairs of equivalent carbons
(CD, CE) in a PHE ring.
--alpha Only alpha carbons.
--all Selection includes every atom.
```