Update app.py

app.py

@@ -1,77 +1,104 @@
 import streamlit as st
-import random
-import hashlib
+from stmol import showmol
 import py3Dmol
 import requests
-import io
-from Bio import PDB
+import biotite.structure.io as bsio
+import random
+import hashlib
+import urllib3
+
+urllib3.disable_warnings(urllib3.exceptions.InsecureRequestWarning)
+
+st.set_page_config(layout='wide')
+st.sidebar.title('🎈 ESMFold Protein Structure Predictor')
+st.sidebar.write('[*ESMFold*](https://esmatlas.com/about) is an end-to-end single sequence protein structure predictor based on the ESM-2 language model. For more information, read the [research article](https://www.biorxiv.org/content/10.1101/2022.07.20.500902v2) and the [news article](https://www.nature.com/articles/d41586-022-03539-1) published in *Nature*.')
 
+# Function to generate protein sequence from words
 def generate_sequence_from_words(words, length):
     seed = ' '.join(words).encode('utf-8')
     random.seed(hashlib.md5(seed).hexdigest())
     amino_acids = "ACDEFGHIKLMNPQRSTVWY"
     return ''.join(random.choice(amino_acids) for _ in range(length))
 
-def predict_structure(sequence):
-    url = "https://api.esmatlas.com/foldSequence/v1/pdb/"
-    headers = {"Content-Type": "application/x-www-form-urlencoded"}
-    data = {"sequence": sequence}
-    
-    response = requests.post(url, headers=headers, data=data, timeout=300)
-    if response.status_code == 200:
-        return response.text
-    else:
-        st.error(f"Error in structure prediction: {response.status_code} - {response.text}")
-        return None
-
-def visualize_protein(pdb_string):
-    view = py3Dmol.view(width=800, height=400)
-    view.addModel(pdb_string, 'pdb')
-    view.setStyle({'cartoon': {'color': 'spectrum'}})
-    view.zoomTo()
-    return view
+# stmol
+def render_mol(pdb):
+    pdbview = py3Dmol.view()
+    pdbview.addModel(pdb,'pdb')
+    pdbview.setStyle({'cartoon':{'color':'spectrum'}})
+    pdbview.setBackgroundColor('white')
+    pdbview.zoomTo()
+    pdbview.zoom(2, 800)
+    pdbview.spin(True)
+    showmol(pdbview, height = 500,width=800)
 
-st.title("Protein Sequence Generator and Structure Predictor")
+# ESMfold
+def update(sequence, word1, word2, word3, sequence_length):
+    headers = {
+        'Content-Type': 'application/x-www-form-urlencoded',
+    }
+    try:
+        response = requests.post('https://api.esmatlas.com/foldSequence/v1/pdb/', 
+                                 headers=headers, 
+                                 data=sequence, 
+                                 verify=False,  # Disable SSL verification
+                                 timeout=300)  # Set a longer timeout
+        response.raise_for_status()  # Raise an exception for bad status codes
+        pdb_string = response.content.decode('utf-8')
+        
+        with open('predicted.pdb', 'w') as f:
+            f.write(pdb_string)
+        
+        struct = bsio.load_structure('predicted.pdb', extra_fields=["b_factor"])
+        b_value = round(struct.b_factor.mean(), 2)
+        
+        # Display protein structure
+        st.subheader(f'Predicted protein structure using seed: {word1}, {word2}, and {word3} + length ({sequence_length})')
+        render_mol(pdb_string)
+        
+        # plDDT value is stored in the B-factor field
+        st.subheader('plDDT Score')
+        st.write('plDDT is a per-residue estimate of the confidence in prediction on a scale from 0-100.')
+        st.info(f'Average plDDT: {b_value}%')
+        
+        st.download_button(
+            label="Download PDB",
+            data=pdb_string,
+            file_name='predicted.pdb',
+            mime='text/plain',
+        )
+    except requests.exceptions.RequestException as e:
+        st.error(f"An error occurred while calling the API: {str(e)}")
+        st.write("Please try again later or contact support if the issue persists.")
 
-st.write("Enter three random words to seed your protein sequence:")
-word1 = st.text_input("Word 1")
-word2 = st.text_input("Word 2")
-word3 = st.text_input("Word 3")
+# Streamlit app
+st.title("Word-Seeded Protein Sequence Generator and Structure Predictor")
 
-sequence_length = st.number_input("Enter desired sequence length", 
-                                  min_value=50, 
-                                  max_value=400, 
-                                  value=100, 
-                                  step=10)
+# Input for word-seeded sequence generation
+st.sidebar.subheader("Generate Sequence from Words")
+word1 = st.sidebar.text_input("Word 1")
+word2 = st.sidebar.text_input("Word 2")
+word3 = st.sidebar.text_input("Word 3")
+sequence_length = st.sidebar.number_input("Sequence Length", min_value=50, max_value=400, value=100, step=10)
 
-if st.button("Generate Sequence and Predict Structure"):
+# Generate and predict button
+if st.sidebar.button('Generate and Predict'):
     if word1 and word2 and word3:
-        words = [word1, word2, word3]
-        sequence = generate_sequence_from_words(words, sequence_length)
-        st.write(f"Generated sequence inspired by '{word1}', '{word2}', and '{word3}' with length '{sequence_length}':")
-        st.code(sequence)
-
-        st.header("Protein Structure Prediction")
+        sequence = generate_sequence_from_words([word1, word2, word3], sequence_length)
+        st.sidebar.text_area("Generated Sequence", sequence, height=100)
+        st.sidebar.info("Note: The same words and length will always produce the same sequence.")
+        
         with st.spinner("Predicting protein structure... This may take a few minutes."):
-            pdb_string = predict_structure(sequence)
-            if pdb_string:
-                view = visualize_protein(pdb_string)
-                
-                st_py3dmol = py3Dmol.show3d(view, width=800, height=400)
-                st.components.v1.html(st_py3dmol.startjs, height=400)
-
-                st.success("Structure prediction complete!")
-                st.write("Note: This is a computational prediction and may not represent the actual biological structure.")
-            else:
-                st.error("Failed to predict structure. Please try again.")
+            update(sequence, word1, word2, word3, sequence_length)
     else:
-        st.error("Please enter all three words.")
+        st.sidebar.warning("Please enter all three words to generate a sequence.")
 
-st.markdown("""
+# Information display
+st.sidebar.markdown("""
 ## What to do next:
-1. Experiment with different seed words and sequence lengths.
-2. Learn about how protein sequences relate to their predicted structures.
-3. Remember that these are computational predictions and may not represent the actual biological structure.
-4. For real protein structures, visit the [Protein Data Bank (PDB)](https://www.rcsb.org/).
-Enjoy exploring the world of protein sequences and predicted structures!
+1. Enter three words and a sequence length.
+2. Click 'Generate and Predict' to generate the sequence, visualize the protein, and get its plDDT score.
+3. Explore the 3D structure and download the PDB file if desired.
+4. Experiment with different words or sequence lengths to see how they affect the predicted structure.
+
+Remember, these predictions are based on AI models and should be interpreted with caution.
 """)