Configuration

Controls

Configuration import/export is always available directly below the structure summary. Export JSON saves the current source metadata and settings. Import JSON reads a saved configuration; it does not occupy the Tools selector.

Restore logic

The JSON stores file names, byte sizes, available relative paths, the frame index, and display/analysis parameters. It includes camera position/direction, roll, projection and field of view, periodic display origin, cell outline colors, theme, coloring, filters, appearance overrides, slices, replication, all named vector fields, measurements, the second view, the active tool category and enabled analyses. It excludes original atom data and computed result arrays.

If the matching source is already open, restoration selects the saved frame, restores parameters and recalculates enabled analyses. Otherwise the configuration remains pending and lists the required source files. Reopening files with the matching names and sizes triggers restoration; relative paths distinguish identical names in different folders when available.

Import validates allowed fields, finite numeric ranges, source metadata and individual feature parameters before applying them. Invalid input preserves the current settings. A user edit or frame selection interrupts an in-progress restore so newer actions take priority. Older version 1 settings receive defaults for optional extensions.

External property files are recorded separately with their file metadata, ID or row-order mapping, import frame, and column names. Their numeric values are not embedded in the JSON. Files still loaded in the current session are reused. In a fresh session, reopen the source and select the requested property files under Modification tools → External properties. The panel shows which files are pending; colors and vector fields become available when their columns have been restored. Row-order imports use the original import frame to preserve the mapping when later frames reorder stable atom IDs.

Bond-length/angle distributions and Q4/Q6 are recorded in settings.extensions.bondStatistics with their enabled state and length/angle bin counts. The analysis shares settings.extensions.bonds.cutoff and its element-pair overrides; cylinder visibility and graph calculation remain independent of statistical analysis. An enabled bond-statistics recipe requires a valid saved bond cutoff even when cylinders are hidden. Voronoi parameters are recorded in settings.extensions.voronoi: enabled state, distribution bins, absolute face-area threshold and relative surface-fraction threshold. Older version 1 recipes without these optional extensions leave both analyses off.

Restoration recalculates enabled bond statistics through the saved CPU/GPU preference and Voronoi through CPU/Wasm, after restoring the physical structure and replication mode. Calculated arrays, histograms and exported CSV files are excluded from JSON. Once the analyses finish, the Statistics, Bonds, Voronoi and DXA CSV controls export the restored frame's results using the standard table schemas.

The browser cannot reopen local disk files by path without a new selection. A saved JSON is therefore a reproducible settings recipe that still needs the original files, rather than a self-contained trajectory archive.

Implementation

Configuration schema and source matching, restore sequencing, extension settings, bond/Voronoi lifecycles.