Bond Analysis¶
The Bond Analysis tool is SAXSShell's structure-analysis application for measuring bond-length and angle distributions from stoichiometry-sorted cluster folders.
Launching the application¶
Open the tool from the main SAXS UI through
Tools > Structure Analysis > Open Bond Analysis.
When the window is launched from an active SAXS project, the current project and cluster-folder reference are carried into the tool. If you change the selected clusters folder there, that reference is saved back to the project.
What the tool does¶
The current UI supports:
- choosing one sorted clusters directory as the analysis source
- saving results into a separate output directory
- limiting the run to checked stoichiometry labels
- defining bond-pair cutoffs directly in a table
- defining angle triplets directly in a table
- loading built-in presets and saving custom presets for later reuse
- reopening an existing bond-analysis output folder and browsing its saved distributions
The right side of the window focuses on the computed distributions. You can refresh a results directory, select one or more saved bond-pair or angle entries, and open them in a dedicated plot window. Matching items from multiple cluster types can be overlaid together for comparison.
Typical workflow¶
- Start from the project's sorted clusters folder.
- Confirm or choose the bond-analysis output directory.
- Refresh the detected cluster types and clear any stoichiometries you do not want to include.
- Load a preset or define the bond pairs and angle triplets manually.
- Run the calculation and inspect the saved distributions from the results browser.