packing_defect.core.analyzers.radius

Classes

RadiusDefectAnalyzer(base_directory, ...[, ...])

Defect analysis based on radius-cutoff GRO filtering.
class packing_defect.core.analyzers.radius.RadiusDefectAnalyzer(base_directory, output_dir, lipid_types, frame_start, frame_end, protein_atom_count, universe=None, apply_protein_cutoff=True, cutoff_distance=1.5)[source]

Bases: BaseDefectAnalyzer

Defect analysis based on radius-cutoff GRO filtering.

Parameters:

  • universe (MDAnalysis.Universe) – Placeholder universe; used for interface consistency.

  • base_directory (str) – Root directory containing per-lipid subfolders with *_frame_N.gro.

  • output_dir (str) – Destination directory for corrected/renumbered outputs and plots.

  • lipid_types (list[str]) – List of lipid residue-name prefixes for subfolders.

  • frame_start (int) – Inclusive frame index range to process.

  • frame_end (int) – Inclusive frame index range to process.

  • protein_atom_count (int) – Number of protein atoms at the top of each GRO file.

  • apply_protein_cutoff (bool, optional) – Whether to exclude defect atoms within cutoff_distance of protein.

  • cutoff_distance (float, optional) – Distance cutoff for exclusion.

plot()[source]

Plot histograms of defect sizes.

run()[source]

Main loop: filter, renumber, analyze defects for each lipid type.

save_results(filename: str, data)

Save results to a file inside output_dir.