sbmlutils.reaction_equation

Module for parsing reaction equation strings.

Various string formats are allowed which are subsequently brought into an internal standard format.

Equations are of the form

‘1.0 S1 + 2 S2 => 2.0 P1 + 2 P2 [M1, M2]’

The equation consists of - substrates concatenated via ‘+’ on the left side

(with optional stoichiometric coefficients)

• separation characters separating the left and right equation sides: ‘<=>’ or ‘<->’ for reversible reactions, ‘=>’ or ‘->’ for irreversible reactions (irreversible reactions are written from left to right)

• products concatenated via ‘+’ on the right side (with optional stoichiometric coefficients)

• optional list of modifiers within brackets [] separated by ‘,’

Examples of valid equations are:

‘1.0 S1 + 2 S2 => 2.0 P1 + 2 P2 [M1, M2]’, ‘c__gal1p => c__gal + c__phos’, ‘e__h2oM <-> c__h2oM’, ‘3 atp + 2.0 phos + ki <-> 16.98 tet’, ‘c__gal1p => c__gal + c__phos [c__udp, c__utp]’, ‘A_ext => A []’, ‘=> cit’, ‘acoa =>’,

In addition, variable stoichiometries can be used, by providing sids as stoichiometries. Examples of valid equations with variable stoichiometries are:

‘fS1 S1 + 2 S2 => 2.0 P1 + 2 P2 [M1, M2]’, ‘f1 c__gal1p => f1 c__gal + f1 c__phos’, ‘f1 * e__h2oM <-> f1 * c__h2oM’, ‘3 atp + 2.0 phos + ki <-> stet tet’, ‘f * c__gal1p => f * c__gal + f * c__phos [c__udp, c__utp]’, ‘A_ext => f * A []’, ‘=> f * cit’, ‘f * acoa =>’,

Module Contents

Classes

EquationPart	EquationPart.
ReactionEquation	Representation of stoichiometric equations with modifiers.

Attributes

REVERSIBILITY_PATTERN
IRREVERSIBILITY_PATTERN
MODIFIER_PATTERN
REVERSIBILITY_SEPARATOR
IRREVERSIBILITY_SEPARATOR
examples

class sbmlutils.reaction_equation.EquationPart

EquationPart.

# FIXME: this must be a SpeciesReference, but circular imports!

An equation consists of parts which define species with their respective stoichiometries. The stoichiometries could be constant or vary over time.

The sid may be target of an InitialAssignment, EventAssignment or Rule.

Two main cases exists: 1. stoichiometry=float, constant=True

The EquationPart has a constant stoichiometry and does not change in the simulation. It could be set via an InitialAssignment if an sid is provided.

2. stoichiometry=None, constant=False, sid=str

species :str

stoichiometry :Optional[float]

sid :Optional[str]

constant :bool = True

metaId :Optional[str]

sboTerm :Optional[str]

name :Optional[str]

annotations :Optional[List]

notes :Optional[str]

keyValuePairs :Optional[List[Any]]

sbmlutils.reaction_equation.REVERSIBILITY_PATTERN :Final = <[-=]>

sbmlutils.reaction_equation.IRREVERSIBILITY_PATTERN :Final = [-=]>

sbmlutils.reaction_equation.MODIFIER_PATTERN :Final = \[.*\]

sbmlutils.reaction_equation.REVERSIBILITY_SEPARATOR :Final = <=>

sbmlutils.reaction_equation.IRREVERSIBILITY_SEPARATOR :Final = =>

class sbmlutils.reaction_equation.ReactionEquation(reactants=None, products=None, modifiers=None, reversible=True)

Representation of stoichiometric equations with modifiers.

Parameters

• reactants (Optional[List[EquationPart]]) –

• products (Optional[List[EquationPart]]) –

• modifiers (Optional[List[str]]) –

• reversible (bool) –

static from_str(equation_str)

Parse components of equation string.

Parameters

equation_str (str) –

Return type

ReactionEquation

_parse_equation(equation_str)

Parameters

equation_str (str) –

Return type

None

_parse_modifiers(s)

Parameters

s (str) –

Return type

None

_parse_half_equation(string)

Parse half-equation.

Only ‘+ supported in equation !, do not use negative stoichiometries.

Parameters

string (str) –

Return type

List[EquationPart]

static _parse_reactant(item)

Parse stoichiometry, species, sid information.

Parameters

item (str) –

Return type

EquationPart

static _to_string_side(items)

Parameters

items (Iterable[EquationPart]) –

Return type

str

_to_string_modifiers()

Return type

str

to_string(modifiers=False)

Get string representation of equation.

Parameters

modifiers (bool) –

Return type

str

info()

Print overview of parsed equation.

Return type

None

static help()

Get help information string.

Return type

str

sbmlutils.reaction_equation.examples = ['1.0 S1 + 2 S2 => 2.0 P1 + 2 P2 [M1, M2]', 'c__gal1p => c__gal + c__phos', 'e__h2oM <->...