w_kinetics

WARNING: w_kinetics is being deprecated. Please use w_direct instead.

usage:

w_kinetics trace [-h] [-W WEST_H5FILE] [--first-iter N_ITER] [--last-iter N_ITER]
                       [--step-iter STEP] [-a ASSIGNMENTS] [-o OUTPUT]

Calculate state-to-state rates and transition event durations by tracing trajectories.

A bin assignment file (usually “assign.h5”) including trajectory labeling is required (see “w_assign –help” for information on generating this file).

This subcommand for w_direct is used as input for all other w_direct subcommands, which will convert the flux data in the output file into average rates/fluxes/populations with confidence intervals.

Output format

The output file (-o/–output, by default “direct.h5”) contains the following datasets:

``/conditional_fluxes`` [iteration][state][state]
  *(Floating-point)* Macrostate-to-macrostate fluxes. These are **not**
  normalized by the population of the initial macrostate.

``/conditional_arrivals`` [iteration][stateA][stateB]
  *(Integer)* Number of trajectories arriving at state *stateB* in a given
  iteration, given that they departed from *stateA*.

``/total_fluxes`` [iteration][state]
  *(Floating-point)* Total flux into a given macrostate.

``/arrivals`` [iteration][state]
  *(Integer)* Number of trajectories arriving at a given state in a given
  iteration, regardless of where they originated.

``/duration_count`` [iteration]
  *(Integer)* The number of event durations recorded in each iteration.

``/durations`` [iteration][event duration]
  *(Structured -- see below)*  Event durations for transition events ending
  during a given iteration. These are stored as follows:

    istate
      *(Integer)* Initial state of transition event.
    fstate
      *(Integer)* Final state of transition event.
    duration
      *(Floating-point)* Duration of transition, in units of tau.
    weight
      *(Floating-point)* Weight of trajectory at end of transition, **not**
      normalized by initial state population.

Because state-to-state fluxes stored in this file are not normalized by initial macrostate population, they cannot be used as rates without further processing. The w_direct kinetics command is used to perform this normalization while taking statistical fluctuation and correlation into account. See w_direct kinetics --help for more information. Target fluxes (total flux into a given state) require no such normalization.

Command-line options

optional arguments:

-h, --help            show this help message and exit

WEST input data options:

-W WEST_H5FILE, --west-data WEST_H5FILE
                      Take WEST data from WEST_H5FILE (default: read from the HDF5 file specified in
                      west.cfg).

iteration range:

--first-iter N_ITER   Begin analysis at iteration N_ITER (default: 1).
--last-iter N_ITER    Conclude analysis with N_ITER, inclusive (default: last completed iteration).
--step-iter STEP      Analyze/report in blocks of STEP iterations.

input/output options:

-a ASSIGNMENTS, --assignments ASSIGNMENTS
                      Bin assignments and macrostate definitions are in ASSIGNMENTS (default:
                      assign.h5).
-o OUTPUT, --output OUTPUT
                      Store results in OUTPUT (default: kintrace.h5).

westpa.cli.tools.w_kinetics module

class westpa.cli.tools.w_kinetics.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_kinetics.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_kinetics.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_kinetics.DKinetics(parent)

Bases: WESTKineticsBase, WKinetics

subcommand = 'init'

default_kinetics_file = 'direct.h5'

default_output_file = 'direct.h5'

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

description = 'Calculate state-to-state rates and transition event durations by tracing\ntrajectories.\n\nA bin assignment file (usually "assign.h5") including trajectory labeling\nis required (see "w_assign --help" for information on generating this file).\n\nThis subcommand for w_direct is used as input for all other w_direct\nsubcommands, which will convert the flux data in the output file into\naverage rates/fluxes/populations with confidence intervals.\n\n-----------------------------------------------------------------------------\nOutput format\n-----------------------------------------------------------------------------\n\nThe output file (-o/--output, by default "direct.h5") contains the\nfollowing datasets:\n\n  ``/conditional_fluxes`` [iteration][state][state]\n    *(Floating-point)* Macrostate-to-macrostate fluxes. These are **not**\n    normalized by the population of the initial macrostate.\n\n  ``/conditional_arrivals`` [iteration][stateA][stateB]\n    *(Integer)* Number of trajectories arriving at state *stateB* in a given\n    iteration, given that they departed from *stateA*.\n\n  ``/total_fluxes`` [iteration][state]\n    *(Floating-point)* Total flux into a given macrostate.\n\n  ``/arrivals`` [iteration][state]\n    *(Integer)* Number of trajectories arriving at a given state in a given\n    iteration, regardless of where they originated.\n\n  ``/duration_count`` [iteration]\n    *(Integer)* The number of event durations recorded in each iteration.\n\n  ``/durations`` [iteration][event duration]\n    *(Structured -- see below)*  Event durations for transition events ending\n    during a given iteration. These are stored as follows:\n\n      istate\n        *(Integer)* Initial state of transition event.\n      fstate\n        *(Integer)* Final state of transition event.\n      duration\n        *(Floating-point)* Duration of transition, in units of tau.\n      weight\n        *(Floating-point)* Weight of trajectory at end of transition, **not**\n        normalized by initial state population.\n\nBecause state-to-state fluxes stored in this file are not normalized by\ninitial macrostate population, they cannot be used as rates without further\nprocessing. The ``w_direct kinetics`` command is used to perform this normalization\nwhile taking statistical fluctuation and correlation into account. See\n``w_direct kinetics --help`` for more information.  Target fluxes (total flux\ninto a given state) require no such normalization.\n\n-----------------------------------------------------------------------------\nCommand-line options\n-----------------------------------------------------------------------------\n'

open_files()

go()

class westpa.cli.tools.w_kinetics.WKinetics(parent)

Bases: DKinetics

subcommand = 'trace'

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

default_output_file = 'kintrace.h5'

class westpa.cli.tools.w_kinetics.WDirect

Bases: WESTMasterCommand, WESTParallelTool

prog = 'w_kinetics'

subcommands = [<class 'westpa.cli.tools.w_kinetics.WKinetics'>]

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

description = 'Calculate state-to-state rates and transition event durations by tracing\ntrajectories.\n\nA bin assignment file (usually "assign.h5") including trajectory labeling\nis required (see "w_assign --help" for information on generating this file).\n\nThe output generated by this program is used as input for the ``w_kinavg``\ntool, which converts the flux data in the output file into average rates\nwith confidence intervals. See ``w_kinavg trace --help`` for more\ninformation.\n\n-----------------------------------------------------------------------------\nOutput format\n-----------------------------------------------------------------------------\n\nThe output file (-o/--output, by default "kintrace.h5") contains the\nfollowing datasets:\n\n  ``/conditional_fluxes`` [iteration][state][state]\n    *(Floating-point)* Macrostate-to-macrostate fluxes. These are **not**\n    normalized by the population of the initial macrostate.\n\n  ``/conditional_arrivals`` [iteration][stateA][stateB]\n    *(Integer)* Number of trajectories arriving at state *stateB* in a given\n    iteration, given that they departed from *stateA*.\n\n  ``/total_fluxes`` [iteration][state]\n    *(Floating-point)* Total flux into a given macrostate.\n\n  ``/arrivals`` [iteration][state]\n    *(Integer)* Number of trajectories arriving at a given state in a given\n    iteration, regardless of where they originated.\n\n  ``/duration_count`` [iteration]\n    *(Integer)* The number of event durations recorded in each iteration.\n\n  ``/durations`` [iteration][event duration]\n    *(Structured -- see below)*  Event durations for transition events ending\n    during a given iteration. These are stored as follows:\n\n      istate\n        *(Integer)* Initial state of transition event.\n      fstate\n        *(Integer)* Final state of transition event.\n      duration\n        *(Floating-point)* Duration of transition, in units of tau.\n      weight\n        *(Floating-point)* Weight of trajectory at end of transition, **not**\n        normalized by initial state population.\n\nBecause state-to-state fluxes stored in this file are not normalized by\ninitial macrostate population, they cannot be used as rates without further\nprocessing. The ``w_kinavg`` command is used to perform this normalization\nwhile taking statistical fluctuation and correlation into account. See\n``w_kinavg trace --help`` for more information.  Target fluxes (total flux\ninto a given state) require no such normalization.\n\n-----------------------------------------------------------------------------\nCommand-line options\n-----------------------------------------------------------------------------\n'

westpa.cli.tools.w_kinetics.entry_point()