# 🛠️ Installation Guide for IonNTxPred

## 🔹 PIP Installation
To install IonNTxPred via PIP, run:
```bash
pip install ionntxpred
```
To check available options, type:
```bash
ionntxpred -h
```

## 🔹 Standalone Installation
IonNTxPred is written in **Python 3** and requires the following dependencies:

### ✅ Required Libraries
```bash
python=3.10.7
pytorch
```

Additional required packages:
```bash
pip install scikit-learn==1.5.2
pip install pandas==2.2.3
pip install torch==2.6.0
pip install transformers==4.34.0
pip install joblib==1.4.2
pip install onnxruntime==1.15.1
Bio (Biopython): 1.81
tqdm: 4.64.1
```

## 🔹 Installation using environment.yml
1. Create a new Conda environment:
```bash
conda env create -f environment.yml
```
2. Activate the environment:
```bash
conda activate IonNTxPred
```

## ⚠️ Important Note-1
- Due to the large size of the model file, the model directory has been compressed and uploaded.
- Download the **zip file** from [Download Page](https://webs.iiitd.edu.in/raghava/ionntxpred/download.html).
- **Extract the file** before using the code or model.

## ⚠️ Important Note-2
- Due to the large size of the model file, the model directory has been compressed and uploaded.
- Download the **zip file** from [Download Page](https://webs.iiitd.edu.in/raghava/ionntxpred/download.html).
- **Extract the file** before using the code or model.

### 🔹 BLAST+ Dependency
IonNTxPred requires **BLAST+ version 2.17.0+** for running the Hybrid model.  
Please download the BLAST+ binary compatible with your operating system:

- **Linux (x64):** `ncbi-blast-2.17.0+-x64-linux.tar.gz`  
- **macOS (x64/arm64):** `ncbi-blast-2.17.0+-x64-macosx.tar.gz`  
- **Windows (x64):** `ncbi-blast-2.17.0+-x64-win64.tar.gz`  

🔗 [NCBI BLAST+ Download Page](https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.17.0/)  

After downloading:
```bash
# Example for Linux
tar -xvzf ncbi-blast-2.17.0+-x64-linux.tar.gz

---

🚀 **You are now ready to use IonNTxPred!**

