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