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README.md

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# Source code for Geometric Transformers for Protein Interface Contact Prediction (ICLR 2022)
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[![Paper](http://img.shields.io/badge/paper-arxiv.2110.02423-B31B1B.svg)](https://openreview.net/forum?id=CS4463zx6Hi) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.6299835.svg)](https://doi.org/10.5281/zenodo.6299835)
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[![Paper](http://img.shields.io/badge/paper-arxiv.2110.02423-B31B1B.svg)](https://openreview.net/forum?id=CS4463zx6Hi) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.6671582.svg)](https://doi.org/10.5281/zenodo.6671582)
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[<img src="https://twixes.gallerycdn.vsassets.io/extensions/twixes/pypi-assistant/1.0.3/1589834023190/Microsoft.VisualStudio.Services.Icons.Default" width="50"/>](https://pypi.org/project/DeepInteract/)
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```bash
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mkdir -p project/checkpoints
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wget -P project/checkpoints https://zenodo.org/record/6299835/files/LitGINI-GeoTran-DilResNet.ckpt
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wget -P project/checkpoints https://zenodo.org/record/6299835/files/LitGINI-GeoTran-DilResNet-DB5-Fine-Tuned.ckpt
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wget -P project/checkpoints https://zenodo.org/record/6671582/files/LitGINI-GeoTran-DilResNet.ckpt
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wget -P project/checkpoints https://zenodo.org/record/6671582/files/LitGINI-GeoTran-DilResNet-DB5-Fine-Tuned.ckpt
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```
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3. Build the Docker image (Warning: Requires ~13GB of Space):
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# Download CASP-CAPRI
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mkdir -p project/datasets/CASP_CAPRI/final
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cd project/datasets/CASP_CAPRI/final
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wget https://zenodo.org/record/6299835/files/final_raw_casp_capri.tar.gz
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wget https://zenodo.org/record/6299835/files/final_processed_casp_capri.tar.gz
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wget https://zenodo.org/record/6671582/files/final_raw_casp_capri.tar.gz
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wget https://zenodo.org/record/6671582/files/final_processed_casp_capri.tar.gz
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# Extract CASP-CAPRI
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tar -xzf final_raw_casp_capri.tar.gz
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# Download DB5-Plus
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mkdir -p ../../DB5/final
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cd ../../DB5/final
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wget https://zenodo.org/record/6299835/files/final_raw_db5.tar.gz
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wget https://zenodo.org/record/6299835/files/final_processed_db5.tar.gz
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wget https://zenodo.org/record/6671582/files/final_raw_db5.tar.gz
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wget https://zenodo.org/record/6671582/files/final_processed_db5.tar.gz
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# Extract DB5-Plus
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tar -xzf final_raw_db5.tar.gz
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# Download DIPS-Plus
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mkdir -p ../../DIPS/final
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cd ../../DIPS/final
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wget https://zenodo.org/record/6299835/files/final_raw_dips.tar.gz
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wget https://zenodo.org/record/6299835/files/final_processed_dips.tar.gz.partaa
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wget https://zenodo.org/record/6299835/files/final_processed_dips.tar.gz.partab
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wget https://zenodo.org/record/6671582/files/final_raw_dips.tar.gz
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wget https://zenodo.org/record/6671582/files/final_processed_dips.tar.gz.partaa
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wget https://zenodo.org/record/6671582/files/final_processed_dips.tar.gz.partab
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# First, reassemble all processed DGLGraphs
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# We split the (tar.gz) archive into two separate parts with
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# Download our trained model checkpoints
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mkdir -p project/checkpoints
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wget -P project/checkpoints https://zenodo.org/record/6299835/files/LitGINI-GeoTran-DilResNet.ckpt
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wget -P project/checkpoints https://zenodo.org/record/6299835/files/LitGINI-GeoTran-DilResNet-DB5-Fine-Tuned.ckpt
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wget -P project/checkpoints https://zenodo.org/record/6671582/files/LitGINI-GeoTran-DilResNet.ckpt
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wget -P project/checkpoints https://zenodo.org/record/6671582/files/LitGINI-GeoTran-DilResNet-DB5-Fine-Tuned.ckpt
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```
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### Predict interface contact probability maps

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