Available reaction rules (`biomass.construction.reaction_rules`)

class biomass.construction.reaction_rules.ReactionRules(input_txt, similarity_threshold)

Create an executable biochemical model from text.

Available reaction rules
Rule	Example sentence	Parameters (optional)
`dimerize()`	A dimerizes <–> AA	\[kf, kr\]
`bind()`	A binds B <–> AB	\[kf, kr\]
`dissociate()`	AB dissociates to A and B	\[kf, kr\]
`is_phosphorylated()`	uA is phosphorylated <–> pA	\[kf, kr\]
`is_dephosphorylated()`	pA is dephosphorylated –> uA	\[V, K\]
`phosphorylate()`	B phosphorylates uA –> pA	\[V, K\]
`dephosphorylate()`	B dephosphorylates pA –> uA	\[V, K\]
`transcribe()`	B transcribes a	\[V, K, n, (KF, nF)\]
`synthesize()`	B synthesizes A	\[kf\]
`is_synthesized()`	A is synthesized	\[kf\]
`degrade()`	B degrades A	\[kf\]
`is_degraded()`	A is degraded	\[kf\]
`translocate()`	Acyt translocates from cytoplasm to nucleus (Vcyt, Vnuc) <–> Anuc	\[kf, kr, (V_{pre}, V_{post})\]
`user_defined()`	@rxn Reactant –> Product: define rate equation here	user-defined

From v0.2.2, you can specify directionality in binding-dissociation reaction via different arrows:

E + S ⇄ ES | kf=0.003, kr=0.001 | E=100, S=50  # bi-directional
ES → E + P | kf=0.002  # unidirectional

input_txt

Model description file (*.txt), e.g., Kholodenko1999.txt.

Type:: str

similarity_threshold

If all match_scores are below this value, expected_word will not be returned.

Type:: float

parameters

x : model parameters.

Type:: list of strings

species

y : model species.

Type:: list of strings

reactions

v : flux vector.

Type:: list of strings

differential_equations

dydt : right-hand side of the differential equation.

Type:: list of strings

obs_desc

Description of observables.

Type:: list of List[str]

param_info

Information about parameter values.

Type:: list of strings

init_info

Information about initial values.

Type:: list of strings

param_constraints

Information about parameter constraints.

Type:: list of strings

param_excluded

List of parameters excluded from search params because of parameter constraints.

Type:: list of strings

fixed_species

List of species which should be held fixed (never consumed) during simulation.

Type:: list of strings

sim_tspan

Interval of integration.

Type:: list of strings [‘t0’, ‘tf’]

sim_conditions

Simulation conditions with stimulation.

Type:: list of List[str]

sim_unperturbed

Untreated conditions to get steady state.

Type:: str

rule_words

Words to identify reaction rules.

Type:: dict

nothing

Available symbol for degradation/creation to/from nothing.

Type:: List[str]

fwd_arrows

Available arrows for unidirectional reactions.

Type:: List[str]

double_arrows

Available arrows for bi-directional reactions.

Type:: List[str]

_bind_and_dissociate(line_num, line)

Return type:: None

Examples

>>> 'A + B --> AB'  # bind, unidirectional
>>> 'AB --> A + B'  # dissociate, unidirectional
>>> 'A + B <--> AB' # bind and dissociate, bidirectional

dimerize(line_num, line)

Return type:: None

Examples

>>> 'A dimerizes <--> AA'
>>> 'A homodimerizes <--> AA'
>>> 'A forms a dimer <--> AA'
>>> 'A forms dimers <--> AA'

Notes

Parameters
\[kf, kr\]
Rate equation
\[v = kf * [A] * [A] - kr * [AA]\]
Differential equation
\[ \begin{align}\begin{aligned}d[A]]/dt = - 2 * v\\d[AA]/dt = + v\end{aligned}\end{align} \]

bind(line_num, line)

Return type:: None

Examples

>>> 'A binds B <--> AB'
>>> 'A forms complexes with B <--> AB'

Notes

Parameters
\[kf, kr\]
Rate equation
\[v = kf * [A] * [B] - kr * [AB]\]
Differential equation
\[ \begin{align}\begin{aligned}d[A]/dt = - v\\d[B]/dt = - v\\d[AB]/dt = + v\end{aligned}\end{align} \]

is_phosphorylated(line_num, line)

Return type:: None

Examples

>>> 'uA is phosphorylated <--> pA'

Notes

Parameters
\[kf, kr\]
Rate equation
\[v = kf * [uA] - kr * [pA]\]
Differential equation
\[ \begin{align}\begin{aligned}d[uA]/dt = - v\\d[pA]/dt = + v\end{aligned}\end{align} \]

is_dephosphorylated(line_num, line)

Return type:: None

Examples

>>> 'pA is dephosphorylated --> uA'

Notes

Parameters
\[V, K\]
Rate equation
\[v = V * [pA] / (K + [pA])\]
Differential equation
\[ \begin{align}\begin{aligned}d[uA]/dt = + v\\d[pA]/dt = - v\end{aligned}\end{align} \]

phosphorylate(line_num, line)

Return type:: None

Examples

>>> 'B phosphorylates uA --> pA'

Notes

Parameters
\[V, K\]
Rate equation
\[v = V * [B] * [uA] / (K + [uA])\]
Differential equation
\[ \begin{align}\begin{aligned}d[uA]/dt = - v\\d[pA]/dt = + v\end{aligned}\end{align} \]

dephosphorylate(line_num, line)

Return type:: None

Examples

>>> 'B dephosphorylates pA --> uA'

Notes

Parameters
\[V, K\]
Rate equation
\[v = V * [B] * [pA] / (K + [pA])\]
Differential equation
\[ \begin{align}\begin{aligned}d[uA]/dt = + v\\d[pA]/dt = - v\end{aligned}\end{align} \]

transcribe(line_num, line)

Return type:: None

Examples

>>> 'B transcribes a'
>>> 'B1 & B2 transcribe a'  # (AND-gate)
>>> 'B transcribes a, repressed by C'  # (Negative regulation)

Notes

Parameters
\[V, K, n, (KF, nF)\]
Rate equation
\[ \begin{align}\begin{aligned}v = V * [B] ^ {n} / (K ^ {n} + [B] ^ {n})\\v = V * ([B1] * [B2]) ^ {n} / (K ^ {n} + ([B1] * [B2]) ^ {n})\\v = V * [B] ^ {n} / (K ^ {n} + [B] ^ {n} + ([C] / KF) ^ {nF})\end{aligned}\end{align} \]
Differential equation
\[d[a]/dt = + v\]

synthesize(line_num, line)

Return type:: None

Examples

>>> 'B synthesizes A'

Notes

Parameters
\[kf\]
Rate equation
\[v = kf * [B]\]
Differential equation
\[d[A]/dt = + v\]

is_synthesized(line_num, line)

Return type:: None

Examples

>>> 'A is synthesized'

Notes

Parameters
\[kf\]
Rate equation
\[v = kf\]
Differential equation
\[d[A]/dt = + v\]

degrade(line_num, line)

Return type:: None

Examples

>>> 'B degrades A'

Notes

Parameters
\[kf\]
Rate equation
\[v = kf * [B] * [A]\]
Differential equation
\[d[A]/dt = - v\]

is_degraded(line_num, line)

Return type:: None

Examples

>>> 'A is degraded'

Notes

Parameters
\[kf\]
Rate equation
\[v = kf * [A]\]
Differential equation
\[d[A]/dt = - v\]

translocate(line_num, line)

Return type:: None

Examples

>>> 'A_at_cyt translocates from cytoplasm to nucleus (V_cyt, V_nuc) <--> A_at_nuc'
>>> 'A_at_cyt is translocated from cytoplasm to nucleus (V_cyt, V_nuc) <--> A_at_nuc'

Notes

Parameters
\[kf, kr, (V_{pre}, V_{post})\]
Rate equation
\[v = kf * [A\_at\_pre] - kr * (V_{post} / V_{pre}) * [A\_at\_post]\]
Differential equation
\[ \begin{align}\begin{aligned}d[A\_at\_pre]/dt = - v\\d[A\_at\_post]/dt = + v * (V_{pre} / V_{post})\end{aligned}\end{align} \]

state_transition(line_num, line)

This rule is applied only when any rule words are not detected.

Return type:: None

Examples

‘Reactant –> Product’ ‘Reactant <–> Product’ ‘E + S –> E + P’

Notes

Parameters
\[kf (, kr)\]
Rate equation
\[v = kf * [Reactant] (- kr * [Product])\]
Differential equation
\[d[Reactant]/dt = - v\]

\[d[Product]/dt = + v\]

user_defined(line_num, line)

Return type:: None

Examples

>>> '@rxn Reactant --> Product: define rate equation here'

Notes

Use p[xxx] and u[xxx] for describing parameters and species, respectively.
Use ‘0’ or ‘∅’ for degradation/creation to/from nothing.
Differential equation
\[ \begin{align}\begin{aligned}d[Reactant]/dt = - v\\d[Product]/dt = + v\end{aligned}\end{align} \]

Available reaction rules (biomass.construction.reaction_rules)

Available reaction rules (`biomass.construction.reaction_rules`)