biocrnpyler.mechanisms.conformation

Classes

One_Step_Reversible_Conformation_Change([...])

Reversible conformational change mechanism.

class biocrnpyler.mechanisms.conformation.One_Step_Reversible_Conformation_Change(name='one_step_conformation_change', mechanism_type='conformation_change')

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:

s0 [+ additional species] <–> sf [+ additional species]

where s0 is the initial conformation and sf is the final conformation.

Parameters:

namestr, default=’one_step_conformation_change’

Name identifier for this mechanism instance.

mechanism_typestr, default=’conformation_change’

Type classification of this mechanism.

Attributes:

namestr

Name of the mechanism instance.

mechanism_typestr

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 <–> denatured states

• Allosteric transitions: Inactive <–> active enzyme forms

• DNA structural changes: B-DNA <–> Z-DNA transitions

• Receptor activation: Closed <–> open channel states

• Molecular switches: Any two-state molecular system

The mechanism requires two rate constants:

• ‘kf’: Forward rate constant (s0 -> sf)

• ‘kr’: Reverse rate constant (sf -> s0)

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

update_reactions(s0, sf, additional_species=None, component=None, part_id=None, **kwargs)

Generate reactions for conformational change.

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

Parameters:

s0Species

The initial conformation state of the molecule.

sfSpecies

The final conformation state of the molecule.

additional_specieslist 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.

componentComponent

Component containing parameter values. Required for retrieving ‘kf’ and ‘kr’ rate constants.

part_idstr, optional

Identifier for parameter lookup. If None, defaults to ‘repr(s0)-repr(sf)’.

**kwargs

Additional keyword arguments (unused).

Returns:

list of Reaction

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

Raises:

ValueError

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

Notes

The reaction equation depends on additional_species:

• Without additional species: s0 <–> sf

• With additional species: s0 + additionals <–> sf + additionals

The mechanism requires two parameters:

• ‘kf’: Forward rate constant (s0 -> sf transition)

• ‘kr’: Reverse rate constant (sf -> 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)

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:

s0Species

The initial conformation state of the molecule.

sfSpecies

The final conformation state of the molecule.

additional_specieslist of Species, optional

Additional species required for the conformational change (e.g., cofactors, ions) but not consumed. Default is empty list.

componentComponent, optional

Component containing this mechanism (for context, not used here).

part_idstr, optional

Identifier for parameter lookup (not used in species generation).

**kwargs

Additional keyword arguments (unused).

Returns:

list of Species

List containing [s0, sf] plus any additional 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