# alphafold_integration.py

class AlphaFoldIntegration:
    def __init__(self):
        self.model = None
        self.features = None

    def setup_model(self, params):
        # Placeholder for model setup
        print(f"Setting up AlphaFold model with params: {params}")
        self.model = "AlphaFold Model Placeholder"

    def prepare_features(self, sequence):
        # Placeholder for feature preparation
        print(f"Preparing features for sequence: {sequence}")
        self.features = "Features Placeholder"

    def predict_structure(self):
        # Placeholder for structure prediction
        if self.model is None or self.features is None:
            raise ValueError("Model or features not set. Call setup_model() and prepare_features() first.")
        print("Predicting protein structure")
        return "Predicted Structure Placeholder"

    def get_plddt_scores(self):
        # Placeholder for pLDDT scores
        print("Calculating pLDDT scores")
        return [0.5] * 100  # Placeholder scores

    def get_predicted_aligned_error(self):
        # Placeholder for predicted aligned error
        print("Calculating predicted aligned error")
        return [[0.1] * 100 for _ in range(100)]  # Placeholder PAE matrix
