Split Conformational Analysis into Explicit Serial Phases

[harryswift01]

Goal

Refactor the current serial conformational analysis into explicit phases that can later be mapped onto a chunked map-reduce workflow.

Background

The current workflow already has a two-pass structure:

identify peaks:
    collect selected-frame dihedral angles
    build histograms
    identify peaks

assign states:
    inspect selected-frame dihedral angles
    assign states using peaks
    collect state labels and flexible-dihedral counts

This sub-issue should make those phases explicit without changing execution behaviour.

Scope

• Keep execution serial.

• Refactor ConformationStateBuilder or related conformational helpers into clearer phases:

  • static dihedral/topology discovery
  • selected-frame angle collection
  • histogram/peak identification
  • state assignment from peaks
  • flexible-dihedral counting
  • final output construction

• Extract angle collection logic from peak identification.

• Extract peak construction from collected angle/histogram data.

• Extract state assignment so it can later operate on chunk-local dihedral results.

• Preserve the frame-index contract:

  • MDAnalysis Dihedral.run(...) uses active analysis-universe frame indices.
  • Dihedral.results.angles is indexed locally from zero.
  • absolute/source frame indices must not be used directly to index result arrays.

• Do not add chunking or Dask yet.