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If you notice an error, omission, or outdated guidance, please open an issue on GitHub.
API section status
The API section has not been fully created yet. Use this page as a provisional pointer to likely workflow classes, not as a complete or stable API reference.
API Overview¶
This section is intentionally lightweight. The repository does not yet include a fully automated API reference pipeline, so this page focuses on the workflow classes that are most likely to be imported directly.
Recommended Python workflow classes¶
Trajectory processing¶
saxshell.mdtrajectory.workflow.MDTrajectoryWorkflow
Cluster extraction¶
saxshell.cluster.workflow.ClusterWorkflow
Cluster dynamics¶
saxshell.clusterdynamics.workflow.ClusterDynamicsWorkflowsaxshell.clusterdynamicsml.workflow.ClusterDynamicsMLWorkflow
Bond analysis¶
saxshell.bondanalysis.workflow.BondAnalysisWorkflow
PDF calculation¶
saxshell.pdf.debyer.workflow.DebyerPDFWorkflow
XYZ to PDB conversion¶
saxshell.xyz2pdb.workflow.XYZToPDBWorkflow
SAXS prefit workflow¶
saxshell.saxs.prefit.workflow.SAXSPrefitWorkflow
Template support packages¶
The SAXS stack also includes reusable modules for:
- template loading
- template installation
- Prefit cluster geometry metadata
- DREAM runtime bundle generation and result loading
These modules are usable from Python, but their interfaces are evolving faster than the main workflow classes above.
Source-checkout launch note¶
Several tools can also be launched through their Python modules while the public Python API stabilizes. From the repository root, start the main SAXS application with:
TODO¶
TODO: expand this section if the repository adds a stable automatic API-docs generation path later.