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.
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
First focus on minimize Logfile.
Perhaps also distinguish minimize, run, and replay.
Steps: