Read namd minimisation output

[ferchault]

Steps:

1. Generate sample output and add it to the repository.
2. Write Reader class to extract and convert data.

[ferchault]

Reading namd2 input files: Read all configuration lines and create a python dict with option name as key and value as value. While doing so replace variable in namd input.

[sharonJXY]

1. Generalize the code to support parsing all namd options in config files. Using notstartwith '#' and using strip to remove whitespaces
2. stop reading with first run/minimize line

[sharonJXY]

Reading namd2 logfile:

1. Define all interested information
2. Each frame is a dictionary. Parse all per-frame entry to the dictionary. If one entry is missing at a frame, leave this entry missing in dictionary. def _parse_output_file(lines): frames = [] for frame in logfile: data = {} data['totalenergy'] = ... data['framenum'] = ... data['otherproperty'] = ... frames.append(data) return frames
3. First focus on minimize Logfile.
4. Perhaps also distinguish minimize, run, and replay.