msmbuilder.io.HierarchyParser

class msmbuilder.io.HierarchyParser(levels=None, n_levels=None, top_fn='', step_ps=None, ignore_fext=False)

Parse a hierarchical index from files nested in directories

A trajectory with path:

PROJ9704.new/RUN4/CLONE10.xtc

will be given an index of

(‘PROJ9704.new’, ‘RUN4’, ‘CLONE10.xtc’)

If you set the flag ignore_fext=True, it will be given an index of

(‘PROJ9704’, ‘RUN4’, ‘CLONE10’)

Parameters:

levels : list of str

Level names

n_levels : int

Number of levels. Either this or levels must be provided (but not both). The levels will be named i0, i1, ... i(n-1)

top_fn : str

Topology filename

step_ps : int

Number of picoseconds per frame

ignore_fext : bool

Ignore file extensions. If set to true, this will fail if there is more than one ”.” per file/directory name. Anything after a ”.” is considered a file extension and will be ignored; including in directory names

Attributes

index

Methods

parse_fn(fn)

__init__(levels=None, n_levels=None, top_fn='', step_ps=None, ignore_fext=False)

Methods

__init__([levels, n_levels, top_fn, ...])
parse_fn(fn)

Attributes

index