Repo Structure

This page is a short orientation guide for contributors.

Top-level layout

src/saxshell/
  bondanalysis/
  cluster/
  clusterdynamics/
  fullrmc/
  mdtrajectory/
  saxs/
  xyz2pdb/
tests/
requirements/
docs/
.github/workflows/

Main application packages

src/saxshell/mdtrajectory

Trajectory inspection, cutoff selection, frame export, and the matching Qt UI.

src/saxshell/xyz2pdb

Residue-aware XYZ-to-PDB conversion, reference-library helpers, and UI code.

src/saxshell/cluster

Cluster extraction workflows and UI.

src/saxshell/clusterdynamics

Time-binned cluster-distribution analysis, lifetime/rate summaries, dataset save/load helpers, and the matching UI.

src/saxshell/bondanalysis

Bond-pair and angle-analysis workflows and UI.

src/saxshell/saxs

SAXS-specific project management, templates, Debye profile generation, Prefit, DREAM runtime support, the contrast-mode supporting workflow, and the main SAXS UI.

src/saxshell/fullrmc

Downstream helpers and UI for preparing fullrmc-oriented artifacts from a SAXS project.

Tests

The repository keeps targeted tests in tests/, with separate files for SAXS, UI, template-installation, fullrmc, xyz2pdb, and other workflows.

Docs

The docs site is now a MkDocs project rooted at:

• mkdocs.yml
• docs/
• requirements/docs.txt

Legacy and deprecated code

The repository still contains some _deprecated directories. These should not be treated as the primary implementation path when adding new behavior.