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 entry points¶

Trajectory processing¶

saxshell.mdtrajectory.workflow.MDTrajectoryWorkflow

Cluster extraction¶

saxshell.cluster.workflow.ClusterWorkflow

Cluster dynamics¶

saxshell.clusterdynamics.workflow.ClusterDynamicsWorkflow
saxshell.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.

CLI-first note¶

Several parts of the repository are easier to discover from their CLI help than from their Python surface:

saxshell --help
saxshell saxs --help
clusters --help
mdtrajectory --help

From a source checkout, you can inspect the SAXS CLI directly with:

PYTHONPATH=src conda run --no-capture-output -n saxshell-py312 python -m saxshell.saxs --help

TODO¶

TODO: expand this section if the repository adds a stable automatic API-docs generation path later.