biocrnpyler.mechanisms.One_Step_Reversible_Conformation_Change

class biocrnpyler.mechanisms.One_Step_Reversible_Conformation_Change(name='one_step_conformation_change', mechanism_type='conformation_change')[source]

Bases: Mechanism

Reversible conformational change mechanism.

A mechanism that models the reversible conformational change of a species from one state to another. This can represent protein folding/unfolding, DNA structural changes, allosteric transitions, or any other molecular conformational switch. Additional species (cofactors, ions, etc.) can be required for the conformational change.

The reaction follows

\[{\text{S0}} + {\text{additional species}} \rightleftharpoons {\text{Sf}} + {\text{additional species}} \]

where S0 is the initial conformation and Sf is the final conformation.

Parameters:

name (str, default 'one_step_conformation_change') – Name identifier for this mechanism instance.
mechanism_type (str, default 'conformation_change') – Type classification of this mechanism.

Attributes:

name (str) – Name of the mechanism instance.
mechanism_type (str) – Type classification (‘conformation_change’).

See also

Mechanism: Base class for all mechanisms.

Notes

This mechanism is used to model conformational changes including:

Protein folding: Native \(\rightleftharpoons\) denatured states
Allosteric transitions: Inactive \(\rightleftharpoons\) active enzyme forms
DNA structural changes: B-DNA \(\rightleftharpoons\) Z-DNA transitions
Receptor activation: Closed \(\rightleftharpoons\) open channel states
Molecular switches: Any two-state molecular system

The mechanism requires two rate constants:

‘kf’: Forward rate constant (s0 \(\rightarrow\) sf)
‘kr’: Reverse rate constant (sf \(\rightarrow\) s0)

Additional species can participate in the conformational change without being modified (e.g., ATP required for a conformational switch but not consumed).

Methods

`update_reactions`	Generate reactions for conformational change.
`update_species`	Generate species for conformational change.

update_reactions(s0, sf, additional_species=None, component=None, part_id=None, **kwargs)[source]

Generate reactions for conformational change.

Creates a reversible mass-action reaction for the conformational transition between two states of a molecule.

Parameters:

s0 (Species) – The initial conformation state of the molecule.
sf (Species) – The final conformation state of the molecule.
additional_species (list of Species, optional) – Additional species required for the conformational change (e.g., cofactors, ions) but not consumed. These appear on both sides of the reaction. Default is empty list.
component (Component) – Component containing parameter values. Required for retrieving ‘kf’ and ‘kr’ rate constants.
part_id (str, optional) – Identifier for parameter lookup. If None, defaults to ‘repr(s0)-repr(sf)’.
**kwargs – Additional keyword arguments (unused).

Returns:

List containing a single reversible mass-action reaction for the conformational change.

Return type:

list of Reaction

Raises:

ValueError – If component is None (implicitly, when parameters cannot be retrieved).

Notes

The reaction equation depends on additional_species:

Without additional species: s0 \(\rightleftharpoons\) sf
With additional species: s0 + additionals \(\rightleftharpoons\) sf + additionals

The mechanism requires two parameters:

‘kf’: Forward rate constant (s0 \(\rightarrow\) sf transition)
‘kr’: Reverse rate constant (sf \(\rightarrow\) s0 transition)

Additional species are not consumed or produced; they facilitate the conformational change. This models situations where cofactors or ions must be present for the transition but are not modified.

update_species(s0, sf, additional_species=None, component=None, part_id=None, **kwargs)[source]

Generate species for conformational change.

Creates the list of species involved in the conformational change, including initial and final conformations plus any additional species required for the transition.

Parameters:

s0 (Species) – The initial conformation state of the molecule.
sf (Species) – The final conformation state of the molecule.
additional_species (list of Species, optional) – Additional species required for the conformational change (e.g., cofactors, ions) but not consumed. Default is empty list.
component (Component, optional) – Component containing this mechanism (for context, not used here).
part_id (str, optional) – Identifier for parameter lookup (not used in species generation).
**kwargs – Additional keyword arguments (unused).

Returns:

List containing [s0, sf] plus any additional species.

Return type:

list of Species

Notes

The additional species participate in the conformational change but are not modified. They appear on both sides of the reaction. This is useful for modeling:

Cofactor-dependent conformational changes
Ion-induced structural transitions
Ligand-stabilized conformations