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README.md

@@ -1,8 +1,22 @@
-#### Quick Commands
+---
+title: AbMelt Benchmark
+emoji: 🧬
+colorFrom: blue
+colorTo: purple
+sdk: docker
+pinned: false
+---
 
-1. quick test - `python quick_test.py`
-2. Run inference
-    - Using pdb file - `python infer.py --pdb "/workspace/antibody-developability-abmelt/AbMelt/public_tm/train_pdbs/alemtuzumab.pdb" --name "alemtuzumab" --config configs/testing_config.yaml`
-    - Using chains - `python infer.py --h [] --l [] --name [] --config configs/testing_config.yaml`
+# AbMelt Inference Pipeline Benchmark
 
-    `python infer.py --h "QVQLQESGPGLVRPSQTLSLTCTVSGFTFTDFYMNWVRQPPGRGLEWIGFIRDKAKGYTTEYNPSVKGRVTMLVDTSKNQFSLRLSSVTAADTAVYYCAREGHTAAPFDYWGQGSLVTVSS" --l "DIQMTQSPSSLSASVGDRVTITCKASQNIDKYLNWYQQKPGKAPKLLIYNTNNLQTGVPSRFSGSGSGTDFTFTISSLQPEDIATYYCLQHISRPRTFGQGTKVEIK" --name "alemtuzumab" --config configs/testing_config.yaml`
+This Space contains the Docker environment for running AbMelt antibody thermostability predictions with GROMACS and CUDA support.
+
+## Usage
+
+This Space is used as a Docker image for HF Jobs:
+
+```bash
+hf jobs run --namespace hugging-science --flavor a100-large \
+  hf.co/spaces/hugging-science/abmelt-benchmark \
+  bash -c "source /usr/local/gromacs/bin/GMXRC && conda activate abmelt-3-11-env && cd /opt/antibody-developability-abmelt/abmelt_infer_pipeline && python infer.py --h '...' --l '...' --config configs/paper_config.yaml --timing-report timing.json"
+```