prolint.analysis.base¶

Analysis base module.

This module provides the base classes and registry for ProLint analyses.

Classes¶

`AnalysisResult`	Container for analysis results.
`BaseAnalysis`	Abstract base class for all ProLint analyses.
`AnalysisRegistry`	Registry for analysis types.

Module Contents¶

class prolint.analysis.base.AnalysisResult[source]¶

Container for analysis results.

The data attribute holds primary analysis data (varies by analysis type). The metadata attribute holds metadata about the analysis (parameters, timestamps, etc.).

data: Dict[str, Any][source]¶: Primary analysis data (varies by analysis type).

metadata: Dict[str, Any][source]¶: Metadata about the analysis (parameters, timestamps, etc.).

class prolint.analysis.base.BaseAnalysis(universe, contacts: prolint.core.contact_provider.ComputedContacts)[source]¶

Bases: abc.ABC

Abstract base class for all ProLint analyses.

Provides common functionality for filtering contacts, building residue mappings, and generating frame ranges.

Parameters:

universe (Universe) – ProLint Universe instance.
contacts (ComputedContacts) – Computed contact data to analyze.

See also

AnalysisRegistry: Registry for creating analyses by name
ComputedContacts.analyze: High-level interface to run analyses

name: str = 'base_analysis'[source]¶: Analysis name for registry.

description: str = 'Base analysis class'[source]¶: Human-readable description.

universe[source]¶

contacts[source]¶

abstractmethod run(**kwargs) → AnalysisResult[source]¶

Run the analysis and return results.

Parameters:: **kwargs (dict) – Analysis-specific parameters.
Returns:: Container with analysis data and metadata.
Return type:: AnalysisResult

class prolint.analysis.base.AnalysisRegistry[source]¶

Registry for analysis types.

Manages registration and creation of analysis classes. All built-in analyses are registered automatically on import.

Examples

List available analyses:

>>> from prolint.analysis import AnalysisRegistry
>>> AnalysisRegistry.available()
['timeseries', 'database_contacts', 'kinetics', ...]

Create an analysis:

>>> analysis = AnalysisRegistry.create("timeseries", universe, contacts)
>>> result = analysis.run(database_type="CHOL")

classmethod register(name: str, analysis_class: Type[BaseAnalysis])[source]¶

Parameters:

name (str) – Name to register under.
analysis_class (type) – Analysis class (must inherit from BaseAnalysis).

classmethod create(name: str, universe, contacts: prolint.core.contact_provider.ComputedContacts, **kwargs) → BaseAnalysis[source]¶

Create an analysis instance.

Parameters:

name (str) – Analysis type name.
universe (Universe) – ProLint Universe instance.
contacts (ComputedContacts) – Computed contact data.
**kwargs (dict) – Additional arguments for the analysis.

Returns:

Initialized analysis instance.

Return type:

BaseAnalysis

classmethod available() → List[str][source]¶

List available analysis types.

Returns:: Registered analysis names.
Return type:: list of str

classmethod get_class(name: str) → Type[BaseAnalysis][source]¶

Get an analysis class by name.

Parameters:: name (str) – Analysis name.
Returns:: Analysis class.
Return type:: type