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()

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_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()