MDAnalysis Extension-Layer API

polyzymd.analyses.mda is the public MDAnalysis extension-layer API for analyses that run as MDAnalysis-compatible jobs and persist PolyzyMD artifacts. The primary contributor surface is the job, frame-selection, collector, artifact, and artifact-store API. Use these pages for lookup. For the contributor workflow, see Extend PolyzyMD with MDAnalysis-native analyses.

The package is import-light: importing polyzymd.analyses.mda should not import MDAnalysis or other heavy simulation dependencies. Individual jobs and helpers perform heavy imports lazily when they actually build or run an analysis.

API overview

Area	Public objects	Details
Public facade	Re-exported public MDAnalysis-layer symbols	Public facade
Jobs	MDAAnalysisJob, MDAFunctionAdapter, MDAJobResult, MDABackendPolicy, MDAUniversePolicy	Job execution
Frame selection	FrameSelection	Frame selection
Plugin lifecycle	MDAReplicateJobContext, MDACollectorContext, MDAArtifactCollector, StrictJSONMDAResultCollector	Plugin lifecycle and collectors
Artifacts	ReplicateArtifact, ConditionArtifact, ComparisonArtifact, ArtifactManifest, ArtifactSidecarRef	Artifact envelopes and store
Storage	ArtifactStore, ArtifactStoreError	Artifact envelopes and store
Aggregation	aggregate_replicate_artifacts, aggregate_replicate_artifacts_from_disk, ExplicitReplicateMetricPolicy	Aggregation and comparison
Comparison	compare_condition_artifacts, MDAComparisonContext	Aggregation and comparison
Universe provenance	UniverseProvider, UniverseProvenance, FileIdentity	Universe provenance and shared MDAnalysis primitives
Shared primitives	AnalysisBaseLike, MDARunKwargs, PairDistanceSpec, build_pair_distance_analysis	Universe provenance and shared MDAnalysis primitives