def __init__(self, coord, frames_per_block, output, **kwargs):
"""
Initializes generator
**Arguments:**
:*log*: Simulation log
:*coord*: Coordinates used to generate pmf
:*output*: Tuple including path to h5 file and address
within h5 file
:*force*: Run analysis even if no new data is present
"""
from MDclt import clean_path
# Input
self.coord_path, self.coord_address = coord
self.inputs = [(self.coord_path, self.coord_address)]
# Action
self.frames_per_block = frames_per_block
# Output
output[1] = clean_path(output[1], strip = ["pdist", "blocks"])
self.outputs = [(output[0], os.path.normpath(output[1] + "/pdist")),
(output[0], os.path.normpath(output[1] + "/blocks"))]
super(PDist_Block_Generator, self).__init__(**kwargs)
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, assign, output, **kwargs):
"""
Initializes generator
**Arguments:**
:*output*: List including path to output h5 file and
address of output within h5 file
"""
from MDclt import clean_path
# Input
assign[1] = clean_path(assign[1], strip = "assignment")
self.assign_path, self.assign_address = assign
self.inputs = [(self.assign_path, self.assign_address + "assignment")]
# Output
output[1] = clean_path(output[1], strip = "assignment")
self.outputs = [(output[0], output[1] + "assignment")]
super(Assign_Analyzer, self).__init__(**kwargs)
def __init__(self, assign, **kwargs):
"""
Initializes
"""
from MDclt import clean_path
# Input
assign[1] = clean_path(assign[1], strip = "assignment")
self.assign_path, self.assign_address = assign
self.inputs = [(self.assign_path, self.assign_address + "assignment")]
super(Assign_Analyzer, self).__init__(**kwargs)
def __init__(self, output, **kwargs):
"""
Initializes generator
**Arguments:**
:*output*: List including path to output h5 file and
address of output within h5 file
"""
from MDclt import clean_path
# Output
output[1] = clean_path(output[1], strip = "stateprobs")
self.outputs = [(output[0], output[1] + "stateprobs")]
super(StateProb_Analyzer, self).__init__(**kwargs)
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)
