Core Abstractions

This page documents the three foundational abstractions of REvoDesign: the Borg-like singleton pattern, the base class for all third-party designer/scorer modules, and the central configuration-to-UI bridge.

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SingletonAbstract

SingletonAbstract is the Borg-like singleton base class. It enforces that only one instance of a class is created, supports dynamic derivation of independent singleton subclasses, provides instance re-initialization, and allows explicit instance reset. Subclasses must implement the singleton_init method for custom initialization logic.

REvoDesign.basic.abc_singleton.SingletonAbstract

Bases: ABC

A base class that enforces the Singleton design pattern. Ensures that only one instance of the class is created, with support for dynamic derivation of new singleton classes.

Attributes:

Name	Type	Description
_instance		The singleton instance of the class.

singleton_init(*args, **kwargs) abstractmethod

Abstract method to initialize the singleton instance with custom logic.

Subclasses must implement this method to initialize their specific attributes.

Parameters:

Name	Type	Description	Default
*args		Positional arguments for initialization.	()
**kwargs		Keyword arguments for initialization.	{}

initialize(*args, **kwargs) classmethod

Initializes the singleton instance if it doesn't exist yet. Updates the singleton instance with new variables if it already exists.

Parameters:

Name	Type	Description	Default
*args		Positional arguments for initialization.	()
**kwargs		Keyword arguments for initialization or updating.	{}

derive(name) classmethod

Dynamically creates a derived class with independent singleton behavior.

This method allows for the creation of new singleton classes that inherit from the current class. Each derived class has its own independent singleton instance.

Parameters:

Name	Type	Description	Default
name	str	The name of the derived class.	required

Returns:

Type	Description
type[T]	A dynamically created subclass with singleton behavior.

reset_instance() classmethod

Resets the singleton instance for the class.

After calling this method, the next instantiation will create a new singleton instance.

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ExternalDesignerAbstract

ExternalDesignerAbstract is the abstract base class for all third-party designer and scorer modules in REvoDesign. It inherits from ThirdPartyModuleAbstract and provides a framework for designing molecules, including serial and parallel scoring of mutants.

REvoDesign.basic.designer.ExternalDesignerAbstract

Bases: ThirdPartyModuleAbstract

Abstract class for external design, providing a framework for designing molecules. This class is abstract and must be inherited and implemented by concrete design classes.

Attributes:

Name	Type	Description
pdb_filename	str	Name of the PDB file, initially set to None, indicating not specified.
initialized	bool	Flag to indicate whether initialization has been performed, defaults to False.
molecule		The molecule object, storing the molecule to be designed.
reload	bool	A flag indicating whether to reload the design, defaults to False.

get_weights()

Retrieve the weights used in the design process. The implementation should define how these weights are calculated or retrieved.

initialize(*args, **kwargs) abstractmethod

Abstract method to initialize the design process. Must be implemented by subclasses to perform necessary setup steps.

Parameters:

Name	Type	Description	Default
*args, **kwargs		Flexible arguments that can be passed to perform specific initialization tasks.	required

designer(*args, **kwargs)

Abstract method to execute the design algorithm. Subclasses must provide the actual design logic.

Parameters:

Name	Type	Description	Default
*args, **kwargs		Additional parameters that can be used during the design process.	required

scorer(mutant, **kwargs)

Abstract method to evaluate or score a given sequence design. Determines the quality or fitness of the designed sequence.

Parameters:

Name	Type	Description	Default
mutant	Mutant | RosettaPyProteinSequence	The molecular sequence being evaluated.	required
*args, **kwargs		Additional parameters for scoring, if required.	required

preffer_substitutions(aa)

Method to setup amino acids that are preferred for substitution in further design.

parallel_scorer(mutants, nproc=2, **kwargs)

Parallelize the scoring of a list of mutants.

score_mutant_mapping(mutants, scores) staticmethod

Assign scores to mutants.

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ConfigBus

ConfigBus is the central configuration-to-UI bridge singleton. It inherits from both SingletonAbstract and CitableModuleAbstract, managing the bidirectional mapping between OmegaConf/Hydra YAML configuration and UI widget state. In headless mode only get_value/set_value are available; GUI methods are guarded by the @require_non_headless decorator.

See the Driver API for the full method reference.