packing_defect.run_defect
CLI entrypoint for packing-defect analysis.
Provides a convenience builder for a PackingDefectAnalyzer and a command-line interface that mirrors the common options used in notebooks.
Examples
Run against a topology and trajectory and write outputs to a folder:
python -m packing_defect.run_defect --top system.gro --traj traj.xtc --out results --leaflet both --start 0 --stop 100 --stride 1
Functions
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Construct a PackingDefectAnalyzer configured for a typical workflow. |
- packing_defect.run_defect.build_packing_analyzer(top_file: str, traj_file: str, out_dir: str, class_json: str | None = None, leaflet: str = 'both', start: int | None = None, stop: int | None = None, stride: int = 1)[source]
Construct a PackingDefectAnalyzer configured for a typical workflow.
- Parameters:
top_file (str) – Topology file readable by MDAnalysis (e.g., GRO, PSF, PDB).
traj_file (str) – Trajectory file (e.g., XTC, DCD) aligned with
top_file.out_dir (str) – Directory where results and artifacts will be written.
class_json (str, optional) – Path to a user JSON classification mapping. If omitted, uses
DefaultClassification.leaflet ({"both", "up", "dw"}, optional) – Which leaflet(s) to analyze.
start (int, optional) – Frame slicing parameters (as in
trajectory[start:stop:stride]).stop (int, optional) – Frame slicing parameters (as in
trajectory[start:stop:stride]).stride (int, optional) – Frame slicing parameters (as in
trajectory[start:stop:stride]).
- Returns:
Configured analyzer instance ready to
run().- Return type: