1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
| 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)
|
