BioSANS2020.propagation.recalculate_globals

This module is the recalculate_globals module

The purpose of this module is to ensure that global variables holds True each process for multitrajectory simulation.

Module Contents

Functions

eval2(to_eval)

Evaluate a string expression using the SBML_FUNCT_DICT dictionary

rate_of(xvar)

This is to supplement the SBML rateOf function. The return is the

delay_part1(yvar, last)

Part of the delay function. See delay function for details

delay_part2(last, delt, yvar)

Part of the delay function. See delay function for details

delay(xvar, yvar)

This is to supplement the SBML delay function

none_to_list(xvar=None)

Transform a None variable into a list [] to avoid dangerous

apply_rules(conc, yconc, oras=None, spconc=None, slabels=None)

This function modifies the concentration base on the rules stated

get_globals(rfile)

This function get the global variables from BioSANS topology file

Attributes

reserve_events_words

CONCP

RATESP

ORASP

SIP

ACTUALSP

CONCP2

BioSANS2020.propagation.recalculate_globals.reserve_events_words
BioSANS2020.propagation.recalculate_globals.CONCP
BioSANS2020.propagation.recalculate_globals.RATESP
BioSANS2020.propagation.recalculate_globals.ORASP
BioSANS2020.propagation.recalculate_globals.SIP
BioSANS2020.propagation.recalculate_globals.ACTUALSP
BioSANS2020.propagation.recalculate_globals.CONCP2
BioSANS2020.propagation.recalculate_globals.eval2(to_eval)

Evaluate a string expression using the SBML_FUNCT_DICT dictionary

Args:

to_eval (str): expression

Returns:

multitype: evaluated result

BioSANS2020.propagation.recalculate_globals.rate_of(xvar)

This is to supplement the SBML rateOf function. The return is the instantaneous rate at the current state of the system

BioSANS2020.propagation.recalculate_globals.delay_part1(yvar, last)

Part of the delay function. See delay function for details

BioSANS2020.propagation.recalculate_globals.delay_part2(last, delt, yvar)

Part of the delay function. See delay function for details

BioSANS2020.propagation.recalculate_globals.delay(xvar, yvar)

This is to supplement the SBML delay function

BioSANS2020.propagation.recalculate_globals.none_to_list(xvar=None)

Transform a None variable into a list [] to avoid dangerous initial values.

BioSANS2020.propagation.recalculate_globals.apply_rules(conc, yconc, oras=None, spconc=None, slabels=None)

This function modifies the concentration base on the rules stated in BioSANS topology file.

Args:

conc (dict): dictionary of initial concentration.

For example;

{‘A’: 100.0, ‘B’: -1.0, ‘C’: 0.0} negative means unknown or for estimation

yconc (dict): dictionary of initial concentration.

For example;

{‘A’: 100.0, ‘B’: -1.0, ‘C’: 0.0} negative means unknown or for estimation

oras (float, optional): current time point. Defaults to None. spconc (list, optional): values of conc at the current time.

Defaults to None.

slabels (list, optional): names of components. Defaults to None.

BioSANS2020.propagation.recalculate_globals.get_globals(rfile)
This function get the global variables from BioSANS topology file

called rfile.

Args:

rfile (str): name of topology file