• app.py
• boltzmann/boltz.py
• boltzmann/models.py
• boltzmann/web/apiv1.py

Related topics: Installation and Setup, API Reference, Database Models

This document outlines the architecture and key components of the Boltzmann project, focusing on the interaction between its core files.

The Boltzmann project is structured around four primary files: app.py, boltzmann/boltz.py, boltzmann/models.py, and boltzmann/web/apiv1.py. Each file plays a specific role in the application's functionality, from handling API requests to managing data models and executing core logic.

app.py serves as the entry point for the Boltzmann application. It initializes the Flask application, configures the database connection, and registers the API blueprint.

Purpose and Functionality:

• Flask app initialization
• Database configuration
• API blueprint registration

Code Snippet:

from flask import Flask
from boltzmann.web.apiv1 import bp as apiv1_bp

app = Flask(__name__)
app.config['SQLALCHEMY_DATABASE_URI'] = 'sqlite:///boltzmann.db'
app.register_blueprint(apiv1_bp, url_prefix='/api/v1')

if __name__ == '__main__':
    app.run(debug=True)

Integration:

app.py acts as the central coordinator, bringing together the other components by initializing Flask and registering the API blueprint, which makes the API endpoints accessible.

Sources: SOURCE_DISPLAY

This file contains the core business logic for the Boltzmann application, including functions for docking, scoring, and simulation management.

Purpose and Functionality:

• Docking ligands to proteins
• Implementing scoring algorithms
• Managing the simulation queue

Code Snippet:

# Example (Hypothetical) - Actual implementation may vary
def dock_ligand(ligand, protein):
    # Docking logic here
    pass

def score_docking(docking_result):
    # Scoring logic here
    pass

Integration:

boltzmann/boltz.py provides the functions that the API endpoints call to perform docking and scoring. It is a critical part of the backend processing.

Sources: SOURCE_DISPLAY

This file defines the data models used in the Boltzmann application using SQLAlchemy. These models represent the database tables and their relationships.

Purpose and Functionality:

• Defining classes for Session, Protein, and Ligand
• Setting up relationships between models
• Providing a structured way to interact with the database

Code Snippet:

from flask_sqlalchemy import SQLAlchemy

db = SQLAlchemy()

class Session(db.Model):
    id = db.Column(db.Integer, primary_key=True)
    # ... other columns

class Protein(db.Model):
    id = db.Column(db.Integer, primary_key=True)
    # ... other columns

class Ligand(db.Model):
    id = db.Column(db.Integer, primary_key=True)
    # ... other columns

Integration:

boltzmann/models.py defines the structure of the data stored and retrieved by the application. The API endpoints use these models to interact with the database.

Sources: SOURCE_DISPLAY

This file defines the API endpoints for the Boltzmann application using Flask blueprints, handling incoming requests and returning data in JSON format.

Purpose and Functionality:

• Defining routes for creating sessions, adding ligands, and retrieving results
• Handling request parsing and validation
• Serializing data into JSON format for responses

Code Snippet:

from flask import Blueprint, request, jsonify

bp = Blueprint('apiv1', __name__)

@bp.route('/enqueue/<session_id>', methods=['POST'])
def enqueue(session_id):
    # Process the request and return a JSON response
    return jsonify({'message': 'Job enqueued'}) # Example response

Integration:

boltzmann/web/apiv1.py acts as the interface between the front-end and the back-end logic. It receives requests, calls functions from boltzmann/boltz.py, and returns results.

Sources: SOURCE_DISPLAY

The following diagram illustrates the sequence of interactions between the key components of the Boltzmann application during a typical request.

sequenceDiagram
    participant User
    participant API
    participant CoreLogic
    participant Database

    User->>API: Enqueue Request
    activate API
    API->>CoreLogic: Call Docking Function
    activate CoreLogic
    CoreLogic->>Database: Retrieve Data Models
    activate Database
    Database-->>CoreLogic: Data Models
    deactivate Database
    CoreLogic->>Database: Store Results
    activate Database
    Database-->>CoreLogic: Confirmation
    deactivate Database
    CoreLogic-->>API: Results
    deactivate CoreLogic
    API-->>User: JSON Response
    deactivate API