w_postanalysis_reweight

westpa.cli.tools.w_postanalysis_reweight module

class westpa.cli.tools.w_postanalysis_reweight.WESTMasterCommand

Bases: WESTTool

Base class for command-line tools that employ subcommands

subparsers_title = None

subcommands = None

include_help_command = True

add_args(parser): Add arguments specific to this tool to the given argparse parser.

process_args(args): Take argparse-processed arguments associated with this tool and deal with them appropriately (setting instance variables, etc)

go(): Perform the analysis associated with this tool.

class westpa.cli.tools.w_postanalysis_reweight.WESTParallelTool(wm_env=None)

Bases: WESTTool

Base class for command-line tools parallelized with wwmgr. This automatically adds and processes wwmgr command-line arguments and creates a work manager at self.work_manager.

make_parser_and_process(prog=None, usage=None, description=None, epilog=None, args=None): A convenience function to create a parser, call add_all_args(), and then call process_all_args(). The argument namespace is returned.

add_args(parser): Add arguments specific to this tool to the given argparse parser.

process_args(args): Take argparse-processed arguments associated with this tool and deal with them appropriately (setting instance variables, etc)

go(): Perform the analysis associated with this tool.

main(): A convenience function to make a parser, parse and process arguments, then run self.go() in the master process.

westpa.cli.tools.w_postanalysis_reweight.warn()

Issue a warning, or maybe ignore it or raise an exception.

message: Text of the warning message.
category: The Warning category subclass. Defaults to UserWarning.
stacklevel: How far up the call stack to make this warning appear. A value of 2 for example attributes the warning to the caller of the code calling warn().
source: If supplied, the destroyed object which emitted a ResourceWarning
skip_file_prefixes: An optional tuple of module filename prefixes indicating frames to skip during stacklevel computations for stack frame attribution.

class westpa.cli.tools.w_postanalysis_reweight.RWAverage(parent)

Bases: RWStateProbs, RWRate

subcommand = 'average'

help_text = 'Averages and returns fluxes, rates, and color/state populations.'

default_kinetics_file = 'reweight.h5'

default_output_file = 'reweight.h5'

description = 'A convenience function to run kinetics/probs. Bin assignments,\nincluding macrostate definitions, are required. (See\n"w_assign --help" for more information).\n\nFor more information on the individual subcommands this subs in for, run\nw_reweight {kinetics/probs} --help.\n\n-----------------------------------------------------------------------------\nCommand-line options\n-----------------------------------------------------------------------------\n'

go()

class westpa.cli.tools.w_postanalysis_reweight.PAAverage(parent)

Bases: RWAverage

subcommand = 'average'

help_text = ''

default_output_file = 'kinrw.h5'

default_kinetics_file = 'flux_matrices.h5'

class westpa.cli.tools.w_postanalysis_reweight.WReweight

Bases: WESTMasterCommand, WESTParallelTool

prog = 'w_postanalysis_reweight'

subcommands = [<class 'westpa.cli.tools.w_postanalysis_reweight.PAAverage'>]

subparsers_title = 'calculate state-to-state kinetics by tracing trajectories'

description = 'A convenience function to run kinetics/probs. Bin assignments,\nincluding macrostate definitions, are required. (See\n"w_assign --help" for more information).\n\nFor more information on the individual subcommands this subs in for, run\nw_reweight {kinetics/probs} --help.\n\n-----------------------------------------------------------------------------\nCommand-line options\n-----------------------------------------------------------------------------\n'

westpa.cli.tools.w_postanalysis_reweight.entry_point()