w_postanalysis_matrix

westpa.cli.tools.w_postanalysis_matrix module

class westpa.cli.tools.w_postanalysis_matrix.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_matrix.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_matrix.warn(message, category=None, stacklevel=1, source=None)

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

class westpa.cli.tools.w_postanalysis_matrix.RWMatrix(parent)

Bases: WESTKineticsBase, FluxMatrix

subcommand = 'init'

default_kinetics_file = 'reweight.h5'

default_output_file = 'reweight.h5'

help_text = 'create a color-labeled transition matrix from a WESTPA simulation'

description = 'Generate a colored transition matrix from a WE assignment file. The subsequent\nanalysis requires that the assignments are calculated using only the initial and\nfinal time points of each trajectory segment. This may require downsampling the\nh5file generated by a WE simulation. In the future w_assign may be enhanced to optionally\ngenerate the necessary assignment file from a h5file with intermediate time points.\nAdditionally, this analysis is currently only valid on simulations performed under\neither equilibrium or steady-state conditions without recycling target states.\n\n-----------------------------------------------------------------------------\nOutput format\n-----------------------------------------------------------------------------\n\nThe output file (-o/--output, by default "reweight.h5") contains the\nfollowing datasets:\n\n  ``/bin_populations`` [window, bin]\n     The reweighted populations of each bin based on windows. Bins contain\n     one color each, so to recover the original un-colored spatial bins,\n     one must sum over all states.\n\n  ``/iterations`` [iteration]\n    *(Structured -- see below)*  Sparse matrix data from each\n    iteration.  They are reconstructed and averaged within the\n    w_reweight {kinetics/probs} routines so that observables may\n    be calculated.  Each group contains 4 vectors of data:\n\n      flux\n        *(Floating-point)* The weight of a series of flux events\n      cols\n        *(Integer)* The bin from which a flux event began.\n      cols\n        *(Integer)* The bin into which the walker fluxed.\n      obs\n        *(Integer)* How many flux events were observed during this\n        iteration.\n\n-----------------------------------------------------------------------------\nCommand-line options\n-----------------------------------------------------------------------------\n'

add_args(parser)

Add arguments specific to this component to the given argparse parser.

process_args(args)

Take argparse-processed arguments associated with this component and deal with them appropriately (setting instance variables, etc)

go()

class westpa.cli.tools.w_postanalysis_matrix.PAMatrix(parent)

Bases: RWMatrix

subcommand = 'init'

help_text = 'averages and CIs for path-tracing kinetics analysis'

default_output_file = 'flux_matrices.h5'

class westpa.cli.tools.w_postanalysis_matrix.WReweight

Bases: WESTMasterCommand, WESTParallelTool

prog = 'w_postanalysis_matrix'

subcommands = [<class 'westpa.cli.tools.w_postanalysis_matrix.PAMatrix'>]

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

description = 'Generate a colored transition matrix from a WE assignment file. The subsequent\nanalysis requires that the assignments are calculated using only the initial and\nfinal time points of each trajectory segment. This may require downsampling the\nh5file generated by a WE simulation. In the future w_assign may be enhanced to optionally\ngenerate the necessary assignment file from a h5file with intermediate time points.\nAdditionally, this analysis is currently only valid on simulations performed under\neither equilibrium or steady-state conditions without recycling target states.\n\n-----------------------------------------------------------------------------\nOutput format\n-----------------------------------------------------------------------------\n\nThe output file (-o/--output, by default "reweight.h5") contains the\nfollowing datasets:\n\n  ``/bin_populations`` [window, bin]\n     The reweighted populations of each bin based on windows. Bins contain\n     one color each, so to recover the original un-colored spatial bins,\n     one must sum over all states.\n\n  ``/iterations`` [iteration]\n    *(Structured -- see below)*  Sparse matrix data from each\n    iteration.  They are reconstructed and averaged within the\n    w_reweight {kinetics/probs} routines so that observables may\n    be calculated.  Each group contains 4 vectors of data:\n\n      flux\n        *(Floating-point)* The weight of a series of flux events\n      cols\n        *(Integer)* The bin from which a flux event began.\n      cols\n        *(Integer)* The bin into which the walker fluxed.\n      obs\n        *(Integer)* How many flux events were observed during this\n        iteration.\n\n-----------------------------------------------------------------------------\nCommand-line options\n-----------------------------------------------------------------------------\n'

westpa.cli.tools.w_postanalysis_matrix.entry_point()