Initial protein predictor

README.md

@@ -11,3 +11,6 @@ license: apache-2.0
 ---
 
 Check out the configuration reference at https://huggingface.co/docs/hub/spaces-config-reference
+
+# Protein Structure Predictor
+Predicts protein 3D structure from amino acid sequence using Facebook's ESMFold model.

app.py

@@ -0,0 +1,41 @@
+import gradio as gr
+import torch
+from transformers import EsmForProteinFolding, EsmTokenizer
+import py3Dmol
+
+# Load model
+model = EsmForProteinFolding.from_pretrained("facebook/esmfold_v1")
+tokenizer = EsmTokenizer.from_pretrained("facebook/esmfold_v1")
+
+def predict_structure(sequence):
+    # Tokenize sequence
+    inputs = tokenizer(sequence, return_tensors="pt", add_special_tokens=False)
+    
+    # Predict structure (ML happens here)
+    with torch.no_grad():
+        output = model(**inputs)
+    
+    # Extract PDB string
+    pdb_str = output["pdb"]
+
+    # Visualize structure
+    viewer = py3Dmol.view(width=400, height=400)
+    viewer.addModel(pdb_str, "pdb")
+    viewer.setStyle({"cartoon": {"color": "spectrum"}})
+    viewer.zoomTo()
+    
+    return viewer.show(), pdb_str
+
+# Gradio UI
+iface = gr.Interface(
+    fn=predict_structure,
+    inputs=gr.Textbox(label="Enter Amino Acid Sequence", placeholder="MKTAYIAKQRQISFVK..."),
+    outputs=[
+        gr.HTML(label="3D Structure"),
+        gr.Textbox(label="PDB Output")
+    ],
+    title="Protein Structure Prediction",
+    description="Enter a protein sequence to predict its 3D structure using ESMFold."
+)
+
+iface.launch()

requirements.txt

@@ -0,0 +1,4 @@
+transformers
+torch
+py3Dmol
+gradio