### Install RTMScore Dependencies

Source: https://github.com/sc8668/rtmscore/blob/main/README.md

Use conda to create an environment with specified requirements or pip to install from a requirements file.

```shell
conda create --prefix xxx --file ./requirements_conda.txt
```

```shell
pip install -r ./requirements_pip.txt
```

--------------------------------

### Predict Protein-Ligand Interactions (Pocket Input)

Source: https://github.com/sc8668/rtmscore/blob/main/README.md

Run RTMScore prediction when the protein pocket has already been extracted. Provide the pocket PDB file and ligand SDF file.

```python
python rtmscore.py -p ./1qkt_p_pocket_10.0.pdb -l ./1qkt_decoys.sdf -m ../trained_models/rtmscore_model1.pth
```

--------------------------------

### Predict Protein-Ligand Interactions (Protein Input)

Source: https://github.com/sc8668/rtmscore/blob/main/README.md

Run RTMScore prediction using a protein PDB file and ligand SDF file. The -gen_pocket flag is used when the pocket needs to be extracted from the protein.

```python
python rtmscore.py -p ./1qkt_p.pdb -l ./1qkt_decoys.sdf -rl ./1qkt_l.sdf -gen_pocket -c 10.0 -m ../trained_models/rtmscore_model1.pth
```

--------------------------------

### Calculate Atom Contributions to Score

Source: https://github.com/sc8668/rtmscore/blob/main/README.md

Use this command to calculate the contribution of each atom to the overall RTMScore. Requires pocket and ligand files.

```python
python rtmscore.py -p ./1qkt_p_pocket_10.0.pdb -l ./1qkt_decoys.sdf -ac -m ../trained_models/rtmscore_model1.pth
```

--------------------------------

### Calculate Residue Contributions to Score

Source: https://github.com/sc8668/rtmscore/blob/main/README.md

Use this command to calculate the contribution of each residue to the overall RTMScore. Requires pocket and ligand files.

```python
python rtmscore.py -p ./1qkt_p_pocket_10.0.pdb -l ./1qkt_decoys.sdf -rc -m ../trained_models/rtmscore_model1.pth
```

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