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(message, category=None, stacklevel=1, source=None)

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

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()