packing_defect.utils

Utility functions for packing_defect.

Functions

apply_pbc(positions, box)	Apply periodic boundary conditions to positions.
compute_pairwise_distances(positions1, ...)	Compute pairwise distances between two sets of positions.
initialize_empty_defect_universe(n_atoms, ...)	Create an empty Universe for defect trajectories.
validate_defect_thresholds(defect_types, ...)	Ensure every defect type has a corresponding threshold.
write_combined_gro(protein_atoms, ...)	Merge protein and defect atoms and write to a GRO file.

packing_defect.utils.apply_pbc(positions, box)

Apply periodic boundary conditions to positions.

packing_defect.utils.compute_pairwise_distances(positions1, positions2)

Compute pairwise distances between two sets of positions.

packing_defect.utils.initialize_empty_defect_universe(n_atoms, nframes, dims, dt)

Create an empty Universe for defect trajectories.

packing_defect.utils.validate_defect_thresholds(defect_types, defect_thresholds)

Ensure every defect type has a corresponding threshold.

packing_defect.utils.write_combined_gro(protein_atoms, defect_atoms, dimensions, filepath)

Merge protein and defect atoms and write to a GRO file.