def __init__(self, coord, states, output, **kwargs):
"""
Initializes generator
**Arguments:**
:*coord*: Coordinates used to make assignments
:*output*: Tuple including path to h5 file and address
within h5 file
:*force*: Run analysis even if no new data is present
"""
from h5py import File as h5
from MDclt import parse_states
# Input
# In the long term, it is probably appropriate to have some
# settings to control how multiple molecules are handled
# Also necessary to handle multiple coordinate dimensions
# appropriately
self.coord_path, self.coord_address = coord
self.inputs = [(self.coord_path, self.coord_address)]
with h5(self.coord_path) as coord_h5:
coord_shape = coord_h5[self.coord_address].shape
self.i = 0
if len(coord_shape) > 1:
self.n_molecule_1 = coord_shape[1]
else:
self.n_molecule_1 = 1
self.j = 0
if len(coord_shape) > 2:
self.n_molecule_2 = coord_shape[2]
else:
self.n_molecule_2 = 1
# Action
self.frames_per_block = coord_shape[0] # Use whole trajectory
self.states = parse_states(states)
# Output
output[1] = output[1].rstrip("assignment")
self.outputs = [(output[0], os.path.normpath(output[1] + "//assignment"),
coord_shape)]
super(Assign_Block_Generator, self).__init__(inputs = self.inputs,
outputs = self.outputs, **kwargs)
# Does not yet support extension, must recalculate entire
# dataset
if self.preexisting_slice != self.final_slice:
self.incoming_slice = self.final_slice
if self.incoming_slice is not None:
self.current_start = self.incoming_slice.start
self.current_stop = self.incoming_slice.start + \
self.frames_per_block
self.final_stop = self.final_slice.stop
def __init__(self, pdist, states, **kwargs):
"""
Initializes
"""
from MDclt import clean_path, parse_states
# Input
pdist[1] = clean_path(pdist[1], strip = ["pdist", "blocks"])
self.pdist_path, self.pdist_address = pdist
self.inputs = [(self.pdist_path, self.pdist_address + "pdist"),
(self.pdist_path, self.pdist_address + "blocks")]
# Action
self.states = parse_states(states)
super(PDist_Analyzer, self).__init__(**kwargs)