Django API for Compound Prediction

This project is a Django REST API that provides functionality for user authentication, compound data retrieval, IC50 prediction, and Google authentication.

Features

User Authentication
- Registration
- Login (JWT Authentication)
- Google OAuth Login
Compound Data Management
- Retrieve a list of compounds
- Retrieve detailed compound information
Prediction Management
- Submit SMILES strings for IC50 prediction
- Retrieve a list of user-specific predictions
- View detailed prediction data

Tech Stack

Backend: Django, Django REST Framework
Authentication: Simple JWT, Google OAuth
Database: PostgreSQL
External APIs: PubChem for compound data

Prasyarat

Sebelum memulai, pastikan Anda sudah menginstal hal-hal berikut:

Python ^3.9
pip (Python package installer)
PostgreSQL (jika menggunakan PostgreSQL sebagai database)

Instalasi

Ikuti langkah-langkah berikut untuk meng-clone dan men-setup proyek.

1. Clone repository

Clone repository proyek ke mesin lokal Anda menggunakan Git:

git clone https://github.com/DaffaNofiansyah/antimalaria-backend.git
cd antimalaria-backend

2. Membuat virtual environment

python -m venv venv
.\venv\Scripts\activate

3. Instal dependensi

pip install -r requirements.txt

File requirements.txt mencakup paket-paket berikut:

Django==5.1.4 djangorestframework psycopg2 (untuk PostgreSQL) django-environ (untuk mengelola env) djangorestframework-simplejwt (untuk JWT authentication)

4. Konfigurasi database dan .env

Pastikan database PostgreSQL sudah disiapkan sebelumnya. Buat file .env di root proyek dan tambahkan variabel lingkungan yang diperlukan (seperti pengaturan database):

DB_NAME=(nama_database)
DB_USER=(user_database)
DB_PASSWORD=(password_database)
DB_HOST=localhost
DB_PORT=5432

6. Terapkan migrasi database

Jalankan migrasi untuk menyiapkan skema database:

python manage.py migrate

7. Menjalankan server pengembangan

python manage.py runserver

API Documentation

Overview

This API provides authentication, compound prediction, and user management features. It supports user registration, login, token-based authentication, compound data retrieval, and IC50 prediction.

Base URL

https://antimalaria-backend-production.up.railway.app/

Authentication

This API uses JWT authentication.

Obtain tokens via /login/
Refresh tokens via /refresh-token/

Endpoints

1. Register a User

Endpoint:

POST /register/

Request Body:

{
  "username": "your_username",
  "email": "[email protected]",
  "password": "your_password",
  "password2": "your_password"
}

Response:

{
  "message": "User registered successfully"
}

2. Login

Endpoint:

POST /login/

Request Body:

{
  "username": "your_username",
  "password": "your_password"
}

Response:

{
  "refresh": "your_refresh_token",
  "access": "your_access_token",
  "username": "your_username",
  "email": "your_email"
}

3. Refresh Token

Endpoint:

POST /refresh-token/

Request Body:

{
  "refresh": "your_refresh_token"
}

Response:

{
  "access": "new_access_token"
}

4. Get List of Compounds Library (Not Created from Predictions)

Endpoint:

GET /compounds/base/

Response:

[
  {
    "id": 1,
    "iupac_name": "ethene",
    "smiles": "C=C",
    "cid": 6325,
    "ic50": 4.262408256530762,
    "category": "Inactive",
    "molecular_formula": "C2H4",
    "molecular_weight": "28.05",
    "synonyms": "ETHYLENE, Ethene, Acetene, Elayl, Olefiant gas, 74-85-1, Athylen, Etileno, Bicarburretted hydrogen, Liquid ethylene, Ethylene, pure, Caswell No. 436, Aethylen, ...",
    "inchi": "InChI=1S/C2H4/c1-2/h1-2H2",
    "inchikey": "VGGSQFUCUMXWEO-UHFFFAOYSA-N",
    "structure_image": "https://pubchem.ncbi.nlm.nih.gov/image/imgsrv.fcgi?cid=6325&t=l",
    "description": "Ethene is an alkene and a gas molecular entity. It has a role as a refrigerant and a plant hormone."
  },
  {
    "id": 2,
    "iupac_name": "ethene",
    "smiles": "C=C",
    "cid": 6325,
    "ic50": 4.262408256530762,
    "category": "Inactive",
    "molecular_formula": "C2H4",
    "molecular_weight": "28.05",
    "synonyms": "ETHYLENE, Ethene, Acetene, Elayl, Olefiant gas, 74-85-1, Athylen, Etileno, Bicarburretted hydrogen, Liquid ethylene, Ethylene, pure, Caswell No. 436, Aethylen, ...",
    "inchi": "InChI=1S/C2H4/c1-2/h1-2H2",
    "inchikey": "VGGSQFUCUMXWEO-UHFFFAOYSA-N",
    "structure_image": "https://pubchem.ncbi.nlm.nih.gov/image/imgsrv.fcgi?cid=6325&t=l",
    "description": "Ethene is an alkene and a gas molecular entity. It has a role as a refrigerant and a plant hormone."
  }
]

5. Get List of User Predicted Compounds

Endpoint:

GET /compounds/

Headers:

Authorization: Bearer your_access_token

Response:

[
  {
    "id": 1,
    "iupac_name": "ethene",
    "smiles": "C=C",
    "cid": 6325,
    "ic50": 4.262408256530762,
    "category": "Inactive",
    "molecular_formula": "C2H4",
    "molecular_weight": "28.05",
    "synonyms": "ETHYLENE, Ethene, Acetene, Elayl, Olefiant gas, 74-85-1, Athylen, Etileno, Bicarburretted hydrogen, Liquid ethylene, Ethylene, pure, Caswell No. 436, Aethylen, ...",
    "inchi": "InChI=1S/C2H4/c1-2/h1-2H2",
    "inchikey": "VGGSQFUCUMXWEO-UHFFFAOYSA-N",
    "structure_image": "https://pubchem.ncbi.nlm.nih.gov/image/imgsrv.fcgi?cid=6325&t=l",
    "description": "Ethene is an alkene and a gas molecular entity. It has a role as a refrigerant and a plant hormone."
  },
  {
    "id": 2,
    "iupac_name": "ethene",
    "smiles": "C=C",
    "cid": 6325,
    "ic50": 4.262408256530762,
    "category": "Inactive",
    "molecular_formula": "C2H4",
    "molecular_weight": "28.05",
    "synonyms": "ETHYLENE, Ethene, Acetene, Elayl, Olefiant gas, 74-85-1, Athylen, Etileno, Bicarburretted hydrogen, Liquid ethylene, Ethylene, pure, Caswell No. 436, Aethylen, ...",
    "inchi": "InChI=1S/C2H4/c1-2/h1-2H2",
    "inchikey": "VGGSQFUCUMXWEO-UHFFFAOYSA-N",
    "structure_image": "https://pubchem.ncbi.nlm.nih.gov/image/imgsrv.fcgi?cid=6325&t=l",
    "description": "Ethene is an alkene and a gas molecular entity. It has a role as a refrigerant and a plant hormone."
  }
]

6. Get List of User Predictions

Endpoint:

GET /predictions/

Headers:

Authorization: Bearer your_access_token

Response:

[
  {
    "id": 1,
    "user": "your_username",
    "model": "model_name",
    "jenis_malaria": "default",
    "created_at": "timestamps"
  },

  {
    "id": 2,
    "user": "your_username",
    "model": "model_name",
    "jenis_malaria": "default",
    "created_at": "timestamps"
  }
]

7. Get Prediction Compounds

Endpoint:

GET /predictions/<int:prediction_id>/

Headers:

Authorization: Bearer your_access_token

Response:

[
  {
    "id": 1,
    "iupac_name": "ethene",
    "smiles": "C=C",
    "cid": 6325,
    "ic50": 4.262408256530762,
    "category": "Inactive",
    "molecular_formula": "C2H4",
    "molecular_weight": "28.05",
    "synonyms": "ETHYLENE, Ethene, Acetene, Elayl, Olefiant gas, 74-85-1, Athylen, Etileno, Bicarburretted hydrogen, Liquid ethylene, Ethylene, pure, Caswell No. 436, Aethylen, ...",
    "inchi": "InChI=1S/C2H4/c1-2/h1-2H2",
    "inchikey": "VGGSQFUCUMXWEO-UHFFFAOYSA-N",
    "structure_image": "https://pubchem.ncbi.nlm.nih.gov/image/imgsrv.fcgi?cid=6325&t=l",
    "description": "Ethene is an alkene and a gas molecular entity. It has a role as a refrigerant and a plant hormone."
  },
  {
    "id": 2,
    "iupac_name": "ethene",
    "smiles": "C=C",
    "cid": 6325,
    "ic50": 4.262408256530762,
    "category": "Inactive",
    "molecular_formula": "C2H4",
    "molecular_weight": "28.05",
    "synonyms": "ETHYLENE, Ethene, Acetene, Elayl, Olefiant gas, 74-85-1, Athylen, Etileno, Bicarburretted hydrogen, Liquid ethylene, Ethylene, pure, Caswell No. 436, Aethylen, ...",
    "inchi": "InChI=1S/C2H4/c1-2/h1-2H2",
    "inchikey": "VGGSQFUCUMXWEO-UHFFFAOYSA-N",
    "structure_image": "https://pubchem.ncbi.nlm.nih.gov/image/imgsrv.fcgi?cid=6325&t=l",
    "description": "Ethene is an alkene and a gas molecular entity. It has a role as a refrigerant and a plant hormone."
  }
]

8. Get Compound Details

Endpoint:

GET /compounds/<int:compound_id>/

Headers:

Authorization: Bearer your_access_token

Response:

{
  "id": 1,
  "iupac_name": "ethene",
  "smiles": "C=C",
  "cid": 6325,
  "ic50": 4.262408256530762,
  "category": "Inactive",
  "molecular_formula": "C2H4",
  "molecular_weight": "28.05",
  "synonyms": "ETHYLENE, Ethene, Acetene, Elayl, Olefiant gas, 74-85-1, Athylen, Etileno, Bicarburretted hydrogen, Liquid ethylene, Ethylene, pure, Caswell No. 436, Aethylen, ...",
  "inchi": "InChI=1S/C2H4/c1-2/h1-2H2",
  "inchikey": "VGGSQFUCUMXWEO-UHFFFAOYSA-N",
  "structure_image": "https://pubchem.ncbi.nlm.nih.gov/image/imgsrv.fcgi?cid=6325&t=l",
  "description": "Ethene is an alkene and a gas molecular entity. It has a role as a refrigerant and a plant hormone.",
  "prediction": 1
}

9. Get Delete Prediction

Endpoint:

DELETE /predictions/<int:prediction_id>/delete

Headers:

Authorization: Bearer your_access_token

10. Get Delete Compound

Endpoint:

DELETE /compounds/<int:compound_id>/delete

Headers:

Authorization: Bearer your_access_token

11. Predict IC50 for a Compound

🔹 ECFP Models

Deep Learning, ECFP
model_ECFP_DL.h5 → model_descriptor = ecfp, model_method = dl
Random Forest, ECFP
rf_model_ecfp.pkl → model_descriptor = ecfp, model_method = rf
XGBoost, ECFP
xgb_model_ecfp.json → model_descriptor = ecfp, model_method = xgb

🔹 MACCS Models

Deep Learning, MACCS
model_MACCS_DL.h5 → model_descriptor = maccs, model_method = dl
Random Forest, MACCS
rf_model_maccs.pkl → model_descriptor = maccs, model_method = rf
XGBoost, MACCS
xgb_model_maccs.json → model_descriptor = maccs, model_method = xgb

🔹 PubchemFP Models

Deep Learning, Mordred model_PubchemFp_DL.h5 → model_descriptor = pubchemfp, model_method = dl
Random Forest, Mordred
rf_model_pubchemfp.pkl → model_descriptor = pubchemfp, model_method = rf
XGBoost, Mordred
xgb_model_pubchemfp.json → model_descriptor = pubchemfp, model_method = xgb

Endpoint:

POST /predict/

Headers:

Authorization: Bearer your_access_token

Request Body:

{
  "smiles": "C=C, CHO, H2O, ..",
  "model_descriptor": "model_descriptor",
  "model_method": "model_method"
}
OR
{
  "file": ".csv/.json",
  "model_descriptor": "model_descriptor",
  "model_method": "model_method"
}

Response:

[
  {
    "id": 1,
    "iupac_name": "ethene",
    "smiles": "C=C",
    "cid": 6325,
    "ic50": 4.262408256530762,
    "category": "Inactive",
    "molecular_formula": "C2H4",
    "molecular_weight": "28.05",
    "synonyms": "ETHYLENE, Ethene, Acetene, Elayl, Olefiant gas, 74-85-1, Athylen, Etileno, Bicarburretted hydrogen, Liquid ethylene, Ethylene, pure, Caswell No. 436, Aethylen, ...",
    "inchi": "InChI=1S/C2H4/c1-2/h1-2H2",
    "inchikey": "VGGSQFUCUMXWEO-UHFFFAOYSA-N",
    "structure_image": "https://pubchem.ncbi.nlm.nih.gov/image/imgsrv.fcgi?cid=6325&t=l",
    "description": "Ethene is an alkene and a gas molecular entity. It has a role as a refrigerant and a plant hormone."
  },
  {
    "id": 1,
    "iupac_name": "ethene",
    "smiles": "C=C",
    "cid": 6325,
    "ic50": 4.262408256530762,
    "category": "Inactive",
    "molecular_formula": "C2H4",
    "molecular_weight": "28.05",
    "synonyms": "ETHYLENE, Ethene, Acetene, Elayl, Olefiant gas, 74-85-1, Athylen, Etileno, Bicarburretted hydrogen, Liquid ethylene, Ethylene, pure, Caswell No. 436, Aethylen, ...",
    "inchi": "InChI=1S/C2H4/c1-2/h1-2H2",
    "inchikey": "VGGSQFUCUMXWEO-UHFFFAOYSA-N",
    "structure_image": "https://pubchem.ncbi.nlm.nih.gov/image/imgsrv.fcgi?cid=6325&t=l",
    "description": "Ethene is an alkene and a gas molecular entity. It has a role as a refrigerant and a plant hormone."
  },
]

Name		Name	Last commit message	Last commit date
Latest commit History 55 Commits
antimalaria_backend		antimalaria_backend
api		api
.gcloudignore		.gcloudignore
.gitattributes		.gitattributes
.gitignore		.gitignore
Dockerfile		Dockerfile
Pipfile		Pipfile
README.md		README.md
manage.py		manage.py
requirements.txt		requirements.txt
test.txt		test.txt
vercel.json		vercel.json
vercel_app.py		vercel_app.py

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Django API for Compound Prediction

Features

Tech Stack

Prasyarat

Instalasi

1. Clone repository

2. Membuat virtual environment

3. Instal dependensi

4. Konfigurasi database dan .env

6. Terapkan migrasi database

7. Menjalankan server pengembangan

API Documentation

Overview

Base URL

Authentication

Endpoints

1. Register a User

2. Login

3. Refresh Token

4. Get List of Compounds Library (Not Created from Predictions)

5. Get List of User Predicted Compounds

6. Get List of User Predictions

7. Get Prediction Compounds

8. Get Compound Details

9. Get Delete Prediction

10. Get Delete Compound

11. Predict IC50 for a Compound

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DaffaNofiansyah/antimalaria-backend

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Repository files navigation

Django API for Compound Prediction

Features

Tech Stack

Prasyarat

Instalasi

1. Clone repository

2. Membuat virtual environment

3. Instal dependensi

4. Konfigurasi database dan .env

6. Terapkan migrasi database

7. Menjalankan server pengembangan

API Documentation

Overview

Base URL

Authentication

Endpoints

1. Register a User

2. Login

3. Refresh Token

4. Get List of Compounds Library (Not Created from Predictions)

5. Get List of User Predicted Compounds

6. Get List of User Predictions

7. Get Prediction Compounds

8. Get Compound Details

9. Get Delete Prediction

10. Get Delete Compound

11. Predict IC50 for a Compound

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