packing_defect.run_radius
CLI entrypoint for radius-based GRO filtering and defect sizing.
This utility filters GRO frames by a protein-distance cutoff, optionally renumbers atoms, and measures defect cluster sizes per leaflet.
Functions
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Construct a RadiusDefectAnalyzer for filtered GRO inputs. |
- packing_defect.run_radius.build_radius_analyzer(input_dir: str, output_dir: str, lipids: list[str], start: int, end: int, protein_count: int, cutoff: float, no_cutoff: bool)[source]
Construct a RadiusDefectAnalyzer for filtered GRO inputs.
- Parameters:
input_dir (str) – Directory containing per-lipid subfolders with
*_frame_N.gro.output_dir (str) – Directory to write corrected/renumbered outputs and plots.
lipids (list[str]) – Lipid residue-name prefixes for subfolders.
start (int) – Inclusive range of frame indices to process.
end (int) – Inclusive range of frame indices to process.
protein_count (int) – Number of protein atoms at the top of each GRO file.
cutoff (float) – Distance cutoff (in same units as GRO) to exclude near-protein atoms.
no_cutoff (bool) – If True, skip the protein-distance filtering step.
- Returns:
Configured analyzer instance ready to
run().- Return type: