Metadata-Version: 2.1
Name: onestep-sepal-ppi
Version: 0.9.1
Summary: SEPAL-PPI inference-only one-step CLI
Requires-Python: >=3.10
Description-Content-Type: text/markdown
Requires-Dist: numpy
Requires-Dist: pandas>=2.0
Requires-Dist: torch>=2.1
Requires-Dist: scikit-learn>=1.3
Requires-Dist: pyyaml>=6.0
Requires-Dist: biopython>=1.85
Requires-Dist: tqdm>=4.66
Requires-Dist: transformers<5,>=4.46
Requires-Dist: huggingface-hub>=0.24
Requires-Dist: safetensors>=0.5
Requires-Dist: lmdb>=1.6
Requires-Dist: esm-efficient>=0.0.8
Requires-Dist: matplotlib>=3.8
Requires-Dist: seaborn>=0.13
Requires-Dist: bitsandbytes>=0.43; platform_system == "Linux" and platform_machine == "x86_64"
Provides-Extra: inference

# onestep-sepal-ppi

Inference-only one-step CLI for SEPAL-PPI.

The PyPI package name is onestep-sepal-ppi. After installation, the command name is sepal-ppi.

## Installation

Python 3.12 is recommended:

```bash
conda create -n sepal python=3.12 -y
conda activate sepal
pip install torch==2.4.1 torchvision==0.19.1 torchaudio==2.4.1 --index-url https://download.pytorch.org/whl/cu124
pip install --no-build-isolation flash-attn
pip install esm-efficient
pip install onestep-sepal-ppi
```

## Quick Start

1. Initialize the configuration:

```bash
sepal-ppi setup --ini-path /path/to/nsp3_env_config.ini
```

2. Prepare features from a FASTA file:

```bash
sepal-ppi prepare -f /path/to/input.fasta --output-dir /path/to/mutifeature
```

3. Run prediction:

```bash
sepal-ppi predict \
  --esm-precision bf16 \
  --esm-model esm2_15b \
  --length 5000 \
  --predict-batch 12800 \
  --emb-batch 1 \
  --multifeature-dir /path/to/mutifeature \
  --interaction-list /path/to/ll.csv \
  --fasta /path/to/input.fasta \
  --output-dir /path/to/output
```

## PDB Mode

```bash
sepal-ppi prepare -p /path/to/pdb_dir --output-dir /path/to/mutifeature
```

PDB mode requires dssp or mkdssp to be available in the environment.
