adesomics.io.gsmm

 1from pathlib import Path
 2import cobra
 3
 4# Force GLPK: an expired Gurobi/CPLEX license on this machine otherwise gets
 5# picked up as cobra's default solver and breaks validation/optimization.
 6cobra.Configuration().solver = "glpk"
 7
 8_XML_SUFFIXES = {".xml"}
 9
10class Model:
11    """
12    Represents a metabolic model.
13
14    Attributes
15    ----------
16    model : cobra.Model
17        The metabolic model data.
18    source_path : Path or None
19        The path to the source file from which the model was loaded.
20    """
21
22    def __init__(self, model: cobra.Model, source_path: Path | None = None, objective: str | None = None):
23        self.model = model
24        self.source_path = source_path
25        self.objective = objective
26
27    @classmethod
28    def from_file(cls, path: str | Path, objective: str | None = None) -> "Model":
29        """
30        Load a metabolic model from a file.
31
32        Parameters
33        ----------
34        path : str or Path
35            The path to the metabolic model file (.xml).
36
37        Raises
38        ------
39        FileNotFoundError
40            If the specified file does not exist.
41        ValueError
42            If the file extension is not recognized or if there is a parse failure.
43        Returns
44        -------
45        Model
46            An instance of Model containing the loaded cobra.Model.
47        """
48
49        path = Path(path)
50
51        if not path.exists():
52            raise FileNotFoundError(f"Metabolic model file not found: {path}")
53
54        suffix = path.suffix.lower()
55
56        if suffix in _XML_SUFFIXES:
57            try:
58                model = cobra.io.read_sbml_model(str(path))
59                return cls(model=model, source_path=path)
60            except Exception as e:
61                raise ValueError(f"Could not parse SBML model file '{path}': {e}") from e
62        else:
63            raise ValueError(f"Unrecognized file extension for metabolic model: {suffix}")
64
65    def summary(self) -> str:
66        return (
67            f"Metabolic model summary:\n"
68            f"  Genes: {len(self.model.genes)}\n"
69            f"  Reactions: {len(self.model.reactions)}\n"
70            f"  Metabolites: {len(self.model.metabolites)}"
71        )
72    
73    def optimize(self):
74        """
75        Optimize the metabolic model using the default solver.
76
77        Returns
78        -------
79        cobra.Solution
80            The solution object containing optimization results.
81        """
82        self.objective = self.model.optimize()
83        return self.objective
84    
85
86    """
87    def __repr__(self) -> str:
88        src = self.source_path.name if self.source_path else "in-memory"
89        return f"<Model {len(self.model.reactions)}r x {len(self.model.metabolites)}m from '{src}'>"
90    """