def __init__(self):
super(WEDDist, self).__init__()
# Parallel processing by default (this is not actually necessary, but it is
# informative!)
self.wm_env.default_work_manager = self.wm_env.default_parallel_work_manager
# These are used throughout
self.progress = ProgressIndicatorComponent()
self.default_kinetics_file = 'kintrace.h5'
self.kinetics_filename = None
self.kinetics_file = None #Kinavg file
self.istate = None
self.fstate = None
##Duration and weight dsspecs
self.duration_dsspec = None
self.wt_dsspec = None
self.binspec = None
self.output_filename = None
self.output_file = None
# These are used during histogram generation only
self.iter_start = None
self.iter_stop = None
self.ndim = None
#self.ntimepoints = None
self.dset_dtype = None
self.binbounds = None # bin boundaries for each dimension
self.midpoints = None # bin midpoints for each dimension
self.data_range = None # data range for each dimension, as the pairs (min,max)
self.ignore_out_of_range = False
self.compress_output = False
def __init__(self):
super(WPDist, self).__init__()
# Parallel processing by default (this is not actually necessary, but it is
# informative!)
self.wm_env.default_work_manager = self.wm_env.default_parallel_work_manager
# These are used throughout
self.progress = ProgressIndicatorComponent()
self.data_reader = WESTDataReader()
self.input_dssynth = WESTDSSynthesizer(default_dsname='pcoord')
self.iter_range = IterRangeSelection(self.data_reader)
self.iter_range.include_args['iter_step'] = False
self.binspec = None
self.output_filename = None
self.output_file = None
self.dsspec = None
self.wt_dsspec = None # dsspec for weights
# These are used during histogram generation only
self.iter_start = None
self.iter_stop = None
self.ndim = None
self.ntimepoints = None
self.dset_dtype = None
self.binbounds = None # bin boundaries for each dimension
self.midpoints = None # bin midpoints for each dimension
self.data_range = None # data range for each dimension, as the pairs (min,max)
self.ignore_out_of_range = False
self.compress_output = False
def __init__(self, parent):
super(KineticsSubcommands, self).__init__(parent)
self.progress = ProgressIndicatorComponent()
self.data_reader = WESTDataReader()
self.iter_range = IterRangeSelection()
self.output_file = None
self.assignments_file = None
self.do_compression = True
def __init__(self):
super(WNetworker, self).__init__()
self.data_reader = WESTDataReader()
self.iter_range = IterRangeSelection()
self.progress = ProgressIndicatorComponent()
self.output_filename = None
self.tm_filename = None
self.postprocess_function = None
def __init__(self):
super(WESTTool,self).__init__()
self.progress = ProgressIndicatorComponent()
# We no longer care about a lot of this.
self.ntrials = 0
self.nstates = 0
self.kin_trial = {}
self.west = {}
self.niters = 0
def __init__(self):
super(WCrawl,self).__init__()
# These are used throughout
self.progress = ProgressIndicatorComponent()
self.data_reader = WESTDataReader()
self.iter_range = IterRangeSelection(self.data_reader)
self.crawler = None
self.task_callable = None
def __init__(self):
super(WSelectTool, self).__init__()
self.data_reader = WESTDataReader()
self.iter_range = IterRangeSelection()
self.progress = ProgressIndicatorComponent()
self.output_file = None
self.output_filename = None
self.predicate = None
self.invert = False
self.include_ancestors = False
def __init__(self):
super(WNTopTool, self).__init__()
self.data_reader = WESTDataReader()
self.iter_range = IterRangeSelection()
self.progress = ProgressIndicatorComponent()
self.output_file = None
self.assignments_filename = None
self.output_filename = None
self.what = None
self.timepoint = None
self.count = None
def __init__(self, parent):
super(CommonPloterrs, self).__init__(parent)
self.progress = ProgressIndicatorComponent()
self.xscale = None
self.yscale = None
self.xrange = None
self.yrange = None
self.xlabel = None
self.ylabel = None
self.title = None
self.plot_options_group = None
def __init__(self):
super(WIPI,self).__init__()
self.data_reader = WESTDataReader()
self.wm_env.default_work_manager = self.wm_env.default_parallel_work_manager
self.progress = ProgressIndicatorComponent()
self._iter = 1
self.config_required = True
self.version = "1.0B"
# Set to matplotlib if you want that. But why would you?
# Well, whatever, we'll just set it to that for now.
self.interface = 'matplotlib'
self._scheme = None
global iteration
def __init__(self):
super(WAssign, self).__init__()
# Parallel processing by default (this is not actually necessary, but it is
# informative!)
self.wm_env.default_work_manager = self.wm_env.default_parallel_work_manager
self.data_reader = WESTDataReader()
self.dssynth = WESTDSSynthesizer(default_dsname='pcoord')
self.binning = BinMappingComponent()
self.progress = ProgressIndicatorComponent()
self.output_file = None
self.output_filename = None
self.states = []
def __init__(self):
super(WPostAnalysisReweightTool, self).__init__()
self.data_reader = WESTDataReader()
self.iter_range = IterRangeSelection()
self.progress = ProgressIndicatorComponent()
self.output_filename = None
self.kinetics_filename = None
self.assignment_filename = None
self.output_file = None
self.assignments_file = None
self.kinetics_file = None
self.evolution_mode = None
def __init__(self):
super(StateProbTool, self).__init__()
self.data_reader = WESTDataReader()
self.iter_range = IterRangeSelection()
self.progress = ProgressIndicatorComponent()
self.output_filename = None
self.kinetics_filename = None
self.output_file = None
self.assignments_file = None
self.evolution_mode = None
self.mcbs_alpha = None
self.mcbs_acalpha = None
self.mcbs_nsets = None
def __init__(self, parent):
super(WESTKineticsBase,self).__init__(parent)
self.data_reader = WESTDataReader()
self.iter_range = IterRangeSelection()
self.progress = ProgressIndicatorComponent()
self.output_filename = None
# This is actually applicable to both.
self.assignment_filename = None
self.output_file = None
self.assignments_file = None
self.evolution_mode = None
self.mcbs_alpha = None
self.mcbs_acalpha = None
self.mcbs_nsets = None
# Now we're adding in things that come from the old w_kinetics
self.do_compression = True
