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 -
__init__
(levels=None, n_levels=None, top_fn='', step_ps=None, ignore_fext=False)¶ Initialize self. See help(type(self)) for accurate signature.
Methods
__init__
([levels, n_levels, top_fn, …])Initialize self. parse_fn
(fn)Attributes
index