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from flask import Flask, render_template, request, redirect, url_for, flash
from werkzeug.utils import secure_filename
from flask_sqlalchemy import SQLAlchemy
from flask_login import LoginManager, UserMixin, login_user, login_required, logout_user, current_user
from pymatgen.io.cif import CifParser
import hashlib
import os
import uuid
app = Flask(__name__)
app.config['SECRET_KEY'] = 'MyS3cretCh3mistry4PP'
app.config['SQLALCHEMY_DATABASE_URI'] = 'sqlite:///database.db'
app.config['UPLOAD_FOLDER'] = 'uploads/'
app.config['ALLOWED_EXTENSIONS'] = {'cif'}
db = SQLAlchemy(app)
login_manager = LoginManager(app)
login_manager.login_view = 'login'
class User(UserMixin, db.Model):
id = db.Column(db.Integer, primary_key=True)
username = db.Column(db.String(150), nullable=False, unique=True)
password = db.Column(db.String(150), nullable=False)
class Structure(db.Model):
id = db.Column(db.Integer, primary_key=True)
user_id = db.Column(db.Integer, db.ForeignKey('user.id'), nullable=False)
filename = db.Column(db.String(150), nullable=False)
identifier = db.Column(db.String(100), nullable=False, unique=True)
@login_manager.user_loader
def load_user(user_id):
return User.query.get(int(user_id))
def allowed_file(filename):
return '.' in filename and filename.rsplit('.', 1)[1].lower() in app.config['ALLOWED_EXTENSIONS']
def calculate_density(structure):
atomic_mass_Si = 28.0855
num_atoms = 2
mass_unit_cell = num_atoms * atomic_mass_Si
mass_in_grams = mass_unit_cell * 1.66053906660e-24
volume_in_cm3 = structure.lattice.volume * 1e-24
density = mass_in_grams / volume_in_cm3
return density
@app.route('/')
def index():
return render_template('index.html')
@app.route('/register', methods=['GET', 'POST'])
def register():
if request.method == 'POST':
username = request.form.get('username')
password = request.form.get('password')
if User.query.filter_by(username=username).first():
flash('Username already exists.')
return redirect(url_for('register'))
hashed_password = hashlib.md5(password.encode()).hexdigest()
new_user = User(username=username, password=hashed_password)
db.session.add(new_user)
db.session.commit()
login_user(new_user)
return redirect(url_for('dashboard'))
return render_template('register.html')
@app.route('/login', methods=['GET', 'POST'])
def login():
if request.method == 'POST':
username = request.form.get('username')
password = request.form.get('password')
user = User.query.filter_by(username=username).first()
if user and user.password == hashlib.md5(password.encode()).hexdigest():
login_user(user)
return redirect(url_for('dashboard'))
flash('Invalid credentials')
return render_template('login.html')
@app.route('/logout')
@login_required
def logout():
logout_user()
return redirect(url_for('index'))
@app.route('/dashboard')
@login_required
def dashboard():
structures = Structure.query.filter_by(user_id=current_user.id).all()
return render_template('dashboard.html', structures=structures)
@app.route('/upload', methods=['POST'])
@login_required
def upload_file():
if 'file' not in request.files:
return redirect(request.url)
file = request.files['file']
if file.filename == '':
return redirect(request.url)
if file and allowed_file(file.filename):
filename = secure_filename(file.filename)
identifier = str(uuid.uuid4())
filepath = os.path.join(app.config['UPLOAD_FOLDER'], identifier + '_' + filename)
file.save(filepath)
new_structure = Structure(user_id=current_user.id, filename=filename, identifier=identifier)
db.session.add(new_structure)
db.session.commit()
return redirect(url_for('dashboard'))
return redirect(request.url)
@app.route('/structure/<identifier>')
@login_required
def show_structure(identifier):
structure_entry = Structure.query.filter_by(identifier=identifier, user_id=current_user.id).first_or_404()
filepath = os.path.join(app.config['UPLOAD_FOLDER'], structure_entry.identifier + '_' + structure_entry.filename)
parser = CifParser(filepath)
structures = parser.parse_structures()
structure_data = []
for structure in structures:
sites = [{
'label': site.species_string,
'x': site.frac_coords[0],
'y': site.frac_coords[1],
'z': site.frac_coords[2]
} for site in structure.sites]
lattice = structure.lattice
lattice_data = {
'a': lattice.a,
'b': lattice.b,
'c': lattice.c,
'alpha': lattice.alpha,
'beta': lattice.beta,
'gamma': lattice.gamma,
'volume': lattice.volume
}
density = calculate_density(structure)
structure_data.append({
'formula': structure.formula,
'lattice': lattice_data,
'density': density,
'sites': sites
})
return render_template('structure.html', structures=structure_data)
@app.route('/delete_structure/<identifier>', methods=['POST'])
@login_required
def delete_structure(identifier):
structure = Structure.query.filter_by(identifier=identifier, user_id=current_user.id).first_or_404()
filepath = os.path.join(app.config['UPLOAD_FOLDER'], structure.identifier + '_' + structure.filename)
if os.path.exists(filepath):
os.remove(filepath)
db.session.delete(structure)
db.session.commit()
return redirect(url_for('dashboard'))
if __name__ == '__main__':
with app.app_context():
db.create_all()
app.run(host='0.0.0.0', port=5000)
$
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