Update README.md

README.md

@@ -11,4 +11,30 @@ license: mit
 short_description: AllMetal3D
 ---
 
-Check out the configuration reference at https://huggingface.co/docs/hub/spaces-config-reference
+# AllMetal3D
+
+
+![Inference app](https://github.com/lcbc-epfl/allmetal3d/raw/main/inference_app.png)
+
+
+AllMetal3D is an improvement of the Metal3D model trained using a wider amount of ions (NA, K, MG, CA, ZN, FE, FE2, CU, CO, MN). 
+The model will predict location, identity and geometry for each site. 
+
+Location is very accurate and can be evaluated using the predicted probability. 
+Identity also works well with the ion being classed into majority labels (Alkali, MG, CA, ZN, Non zinc transition metal and NoMetal). NoMetal are likely false positive location predictions. 
+Geometry prediction works well to differentiate between octahedral and tetrahedral but not so well for the other classes. 
+
+
+## How to run
+
+In webbrowser for single structures and visual processing use the gradio app. 
+```
+python app.py
+```
+
+
+For running in batch mode use the commandline tool:
+
+```
+python run_metalsitepred.py --pdb 2cba.pdb --cubefile test.cube --probefile 2cba_probe.pdb --batch_size 30
+```