packing_defect.core.classification

classification.py

Implements the Strategy pattern for atom classification, with a default that matches your original logic and an optional JSON-driven rule set.

Classes

ClassificationStrategy()	Abstract interface for atom classification strategies.
DefaultClassification()	Default logic (mirrors your original default_classify): - For non-TRIO residues: tail atoms → 1, else → -1 - For TRIO residues: glycerol atoms → 2, else → 3
UserDictClassification(rules, label_to_code)	Load classification codes from a JSON file of the form.

class packing_defect.core.classification.ClassificationStrategy

Bases: ABC

Abstract interface for atom classification strategies.

abstractmethod classify(resname: str, atom_name: str) → int

Given a residue name and atom name, return an integer code.

class packing_defect.core.classification.DefaultClassification

Bases: ClassificationStrategy

Default logic (mirrors your original default_classify): - For non-TRIO residues: tail atoms → 1, else → -1 - For TRIO residues: glycerol atoms → 2, else → 3

classify(resname: str, atom_name: str) → int

Given a residue name and atom name, return an integer code.

class packing_defect.core.classification.UserDictClassification(rules: Dict[Tuple[str, str], int], label_to_code: Dict[str, int])

Bases: ClassificationStrategy

Load classification codes from a JSON file of the form:

{
  "RES1": {"ATOM1": "heads", "ATOM2": "tails", ...},
  "RES2": { ... }
}

Labels (“heads”, “tails”) are automatically mapped to integer codes.

classify(resname: str, atom_name: str) → int

Given a residue name and atom name, return an integer code.

classmethod from_json(json_file: str) → UserDictClassification