BioSANS2020.model.fileconvert.process_sbml¶

Functions¶

Attributes¶

BioSANS2020.model.fileconvert.process_sbml.OPERS_LIST¶

BioSANS2020.model.fileconvert.process_sbml.OPERS_LIST2¶

BioSANS2020.model.fileconvert.process_sbml.eval_exp(xvar)¶

BioSANS2020.model.fileconvert.process_sbml.get_exponent_sp(key, modk)¶

This function extract the exponent of component or species key from a given propensity expression modk. Args:

key : species/component string modk : propensity expression converted to string

example “2*0.5*A*B”

Returns:

exponent_in_formula : the power of species key

Example:

modk = (1.0)*(1.0)*S1 key = S1 exponent_in_formula = 1

BioSANS2020.model.fileconvert.process_sbml.replace_crucial_funct(trep)¶

this function converts some problematic operator/logical/function and etc. to its equivalent in SBML. Args:

trepresult of SBML formulaToString(xvar.getMath())

xvar is an object in SBML getListOfFunctionDefinitions()

BioSANS2020.model.fileconvert.process_sbml.extract_species(modk)¶

This function extracts the components or species from a given ex- pression and returns a comma concatenated string of them. Args:

modkpropensity expression converted to string

example “2*0.5*A*B”

Returns:

“,”.join(sp_comp)a string of comma concatenated components

example “A,B”

BioSANS2020.model.fileconvert.process_sbml.extract_par_num(modk)¶

This function is currently not used but it can extract the numeric values from a given expression Example:

print(extract_par_num(“(5.0)*(6.0)*S1+S2**3”)) will give {‘5.0’, ‘6.0’, ‘3’}

BioSANS2020.model.fileconvert.process_sbml.extract_var_func(ssv)¶

This function extract the variables from an expression and gives a 2D list containing a comma concatenated string of variable and a string of the expression. Args:

ssvcomma concatenated string of variables and expression.

example : “x,y,x*y”

Returns:

[“comma concatenated variables”,”expression”] :

example : [‘x,y’, ‘x*y’]

BioSANS2020.model.fileconvert.process_sbml.extract_function(pforms, rbig_params, compartments, functions, functions_str)¶

This function converts a user defined function or function call in the SBML file to actual expression. Args:

pformsfrom formulaToString(xvar.getMath()) where xvar can be

an object from getListOfRules() in libsbml. example : compartment*multiply(k1,S1)

rbig_paramsdictionary of parameter nameparameter value

from kinetic rate law expression in sbml

compartments : dictionary of compartments name : [size, units] functions : dictionary of function name : function definition functions_str : the string equivalent of functions above

example : {‘multiply’: ‘lambda x,y : x*y’}

Returns:

modkexpanded form of pforms where every function definition

is evaluated example : compartment*1*(S1*k1)

BioSANS2020.model.fileconvert.process_sbml.par_substitution(modk, parameters, index=0)¶

This function substitute parameters to modk expression by first padding the operators to ensure parameters can be distinguished from the expression. Args:

modk : math expression string parameters : dictionary of parameters name : [value, unit] index : 0 or 1. 0 will give value and 1 will give unit

Returns:

modk : expression where parameters are now numeric

BioSANS2020.model.fileconvert.process_sbml.add2_spaces_sep(modk)¶

This function adds paddings on both sides of the operators and return the expression modk with the operators padded. Args:

modk : string math expression

Returns:

modk : string math expression with the operators padded

BioSANS2020.model.fileconvert.process_sbml.sp_substitution(modk, parameters)¶

This is a redundant function to par_substitution. This function substitute parameters to modk expression by first padding the operators to ensure parameters can be distinguished fromthe expression. Args:

modk : math expression string parameters : dictionary of parameters name : [value, unit]

Intended for constant parameters

Returns:

modk : expression where parameters are now numeric

BioSANS2020.model.fileconvert.process_sbml.var_substitution(modk, rbig_params, parameters, compartments, rate_rules)¶

This function substitute variables to modk expression by first padding the operators to ensure variables can be distinguished from the expression. Args:

modk : math expression string rbig_params : dictionary of parameter name : parameter value

from kinetic rate law expression in sbml

parameters : dictionary of parameters name : [value, unit] compartments : dictionary of compartments name : [size, units] rate_rules : dictionary of variable : variable modifier function

Returns:

modk : expression where variables are substituted

BioSANS2020.model.fileconvert.process_sbml.funct_redefine_var(modk, ssv)¶

This function transform the variables in a lambda function to the actual variables needed. Args:

modk : string math lambda expression with abstract variables ssv : sympy symbols

Returns:

string definition expression with actual varaibles

BioSANS2020.model.fileconvert.process_sbml.get_sbml_units(model, sbml_units)¶

Returns units dictionary from sbml file. The model is defined by the following python syntax;

model = libsbml.SBMLReader().readSBML(sbml_file).getModel()

Args:

model : model definition like shown above sbml_units : a dictionary of sbml unit equivalence

Returns :

units_sbml : dictionary of sbml units associated to the file

BioSANS2020.model.fileconvert.process_sbml.get_compartments_details(model, molar)¶

Returns compartment dictionary from sbml file. The model is defined by the following python syntax;

model = libsbml.SBMLReader().readSBML(sbml_file).getModel()

Args:

model : model definition like shown above molar : True if conc. is in molar else False

Returns:

compartmentsdictionary of all compartments with the following

example format { ‘c1’ : [size, units]}

constant_compdictionary of constant compartments

example format { ‘c1’ : [size, units]}

non_constant_compdictionary of non constant compartments

example format { ‘c1’ : [size, units]}

orig_sizedictionary of original size of compartment

example format { ‘c1’ : size}

BioSANS2020.model.fileconvert.process_sbml.get_species_details(model)¶

Returns species dictionary from sbml file. The model is defined by the following python syntax;

model = libsbml.SBMLReader().readSBML(sbml_file).getModel()

Args:

model : model definition like shown above

Returns:

speciesdictionary of all species with the following

example format { id : species_label }

species_compdictionary of species compartments

example format { species_label : compartment }

constant_speciesdictionary of constant species

example format { species_label : True }

has_only_sunitsdictionary of species with only substance as

example format { id : True }

sp_wcfactordictionary of convertion factor

example format { id : conversion factor }

BioSANS2020.model.fileconvert.process_sbml.get_initial_conc(species)¶

Returns a dictionary of initial concentration from species

BioSANS2020.model.fileconvert.process_sbml.get_param_details(model)¶

Returns a dictionary of parameter name : [value, unit]

BioSANS2020.model.fileconvert.process_sbml.get_rule_details(model, constant_par)¶

This function returns the assignment rules, rate rules, and algebraic rules from sbml model given the disctionary of constant parameters. The constants are already substituted in the return

BioSANS2020.model.fileconvert.process_sbml.process_sbml(file, molar=False, variables=None)¶

This function read the sbml file and extracts the necessary most of the details to construct the corresponding topology file of the system described by the SBML tags. Args:

file : this is the sbml file molar : True or False, tells if the systems unit molar or not variables : None or constant compartment to show in plot