def parse_ijk(path, columns, include_frame=False):
"""
Generic parser for pos, for, and vel files.
Args:
path (str): File path
columns (list): Header
include_frame (bool): Include the frame index (default: false)
Returns:
df (:pandas:`~pandas.DataFrame`): Atom-like dataframe
"""
fcol = columns[0]
lcol = columns[-1]
df = pd.read_csv(path, delim_whitespace=True, names=columns)
step = df[df[lcol].isnull()]
starts = step.drop_duplicates(fcol, keep='last').index.values + 1
nframes = len(step)
nat = np.min(starts[1:] - starts[:-1]) - 1
frame, label, indices = starts_count(starts, nat)
frame = pd.Series(frame, dtype='category')
df = df[df.index.isin(indices)].reset_index(drop=True)
if include_frame:
df['frame'] = frame
return df
def parse_cel(path):
"""
Parse cell dimensions.
"""
df = pd.read_csv(path, delim_whitespace=True, names=('i', 'j', 'k'))
starts = df[::4].drop_duplicates(df.columns[0], keep='last').index.values + 1
frame, label, indices = starts_count(starts, 3)
df = df[df.index.isin(indices)].reset_index(drop=True)
df['frame'] = pd.Series(frame, dtype='category')
df['label'] = pd.Series(label, dtype='category')
df = df.pivot('frame', 'label')
df.columns = ['xi', 'xj', 'xk', 'yi', 'yj', 'yk', 'zi', 'zj', 'zk']
df['ox'] = 0.0
df['oy'] = 0.0
df['oz'] = 0.0
df.index.names = [None]
return df
