Structural Analysis
Run active-site structural analysis with phase-2 edge-typing parity outputs.
This module computes local structural descriptors, neighborhood features, and site-label artifacts used by the active-sites analysis flow. It is scoped to structural characterization and table export, not event chronology detection.
Usage context
- Site typing: Classify local environments around candidate active atoms.
- Defect-aware analysis: Combine ring/defect cues with connectivity metadata.
- TrACT parity runs: Produce structural outputs aligned with TrACT conventions.
Task: ActiveSiteStructuralTask
Compute per-atom active-site structural descriptors on one frame.
Method: recommended_presentations(_result: ActiveSiteStructuralResult, payload: dict[str, Any])
Build default table/plot presentations for structural task output.
Works on
Analyzer task output payloads
Parameters
| Name | Type | Description |
|---|---|---|
_result |
ActiveSiteStructuralResult |
Analysis result object for the executed task. |
payload |
dict[str, Any] |
Serialized result payload used by presentation dispatch. |
Returns
| Type | Description |
|---|---|
list[PresentationSpec] |
Recommended renderer specs for table and d_pyr profile views. |
Examples
specs = ActiveSiteStructuralTask.recommended_presentations(result, payload)
Sample output:
A list with table and d_pyr vs atom_id plot views.
Meaning:
Structural outputs can be rendered without custom plotting metadata.
Method: run(data: ConnectivityTrajectoryData | TrajectoryData, request: ActiveSiteStructuralRequest, reporter=None)
Compute frame-level active-site structural descriptors and labels.
Builds a bond graph (BO- or distance-based), derives geometric/ring descriptors, assigns TRACT-parity labels, and returns detailed plus TRACT-compatible structural tables.
Works on
ConnectivityTrajectoryData or TrajectoryData plus structural request
Parameters
| Name | Type | Description |
|---|---|---|
data |
ConnectivityTrajectoryData \| TrajectoryData |
Input trajectory (and optional connectivity) data for selected frame. |
request |
ActiveSiteStructuralRequest |
Structural analysis configuration for frame and descriptor options. |
reporter |
Any, optional |
Optional progress callback invoked near completion. |
Returns
| Type | Description |
|---|---|
ActiveSiteStructuralResult |
Structural descriptor table, TRACT projection, summary metrics, and optional SOAP descriptors. |
Examples
req = ActiveSiteStructuralRequest(frame=0, bond_mode="bo")
result = ActiveSiteStructuralTask().run(bundle, req)
Sample output:
result.table with per-atom descriptors and labels.
Meaning:
One analyzed frame is transformed into rich structural site features.