Documentation status
This page was generated and edited with the assistance of an LLM and is still in development. It has not been fully vetted by the developer. Verify commands, UI labels, file paths, workflow descriptions, and scientific claims against the current code and your local workflow before relying on it.
If you notice an error, omission, or outdated guidance, please open an issue on GitHub.
Development section status
The Development section is still incomplete. Current pages are working notes for contributors rather than a fully vetted maintenance guide.
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.ymldocs/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.